NIH Director's New Innovator (NIA)
NIH Director's New Innovator (NIA)
Program Publications
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The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date | PubMedLink |
|---|---|---|---|---|---|---|
| Exploring Antibiotic Resistance in Diverse Homologs of the Dihydrofolate Reductase Protein Family through Broad Mutational Scanning. | Romanowicz KJ, Resnick C, Hinton SR, Plesa C | bioRxiv : the preprint server for biology | 39896582 | bioRxiv | 2025 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/39896582 |
| Potent in vivo lung cancer Wnt signaling inhibition via cyclodextrin-LGK974 inclusion complexes. | Guimaraes PPG, Tan M, Tammela T, Wu K, Chung A, Oberli M, Wang K, Spektor R, Riley RS, Viana CTR, Jacks T, Langer R, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 30290244 | J Control Release | 2018 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/30290244 |
| Delivery technologies for cancer immunotherapy. | Riley RS, June CH, Langer R, Mitchell MJ | Nature reviews. Drug discovery | 30622344 | Nat Rev Drug Discov | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30622344 |
| Biomaterials for vaccine-based cancer immunotherapy. | Zhang R, Billingsley MM, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 30312721 | J Control Release | 2018 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/30312721 |
| Nanotechnology-based strategies against SARS-CoV-2 variants. | Huang X, Kon E, Han X, Zhang X, Kong N, Mitchell MJ, Peer D, Tao W | Nature nanotechnology | 35982317 | Nat Nanotechnol | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35982317 |
| Hydroxycholesterol substitution in ionizable lipid nanoparticles for mRNA delivery to T cells. | Patel SK, Billingsley MM, Frazee C, Han X, Swingle KL, Qin J, Alameh MG, Wang K, Weissman D, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 35569584 | J Control Release | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35569584 |
| Nanomaterial Interactions with Human Neutrophils. | Bisso PW, Gaglione S, Guimarães PPG, Mitchell MJ, Langer R | ACS biomaterials science & engineering | 31497639 | ACS Biomater Sci Eng | 2018 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/31497639 |
| Ionizable lipid nanoparticles encapsulating barcoded mRNA for accelerated in vivo delivery screening. | Guimaraes PPG, Zhang R, Spektor R, Tan M, Chung A, Billingsley MM, El-Mayta R, Riley RS, Wang L, Wilson JM, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 31678653 | J Control Release | 2019 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/31678653 |
| Nanoparticles for nucleic acid delivery: Applications in cancer immunotherapy. | Mukalel AJ, Riley RS, Zhang R, Mitchell MJ | Cancer letters | 31100411 | Cancer Lett | 2019 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/31100411 |
| Predictive High-Throughput Platform for Dual Screening of mRNA Lipid Nanoparticle Blood-Brain Barrier Transfection and Crossing. | Han EL, Padilla MS, Palanki R, Kim D, Mrksich K, Li JJ, Tang S, Yoon IC, Mitchell MJ | Nano letters | 38259198 | Nano Lett | 2024 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/38259198 |
| Throughput-scalable manufacturing of SARS-CoV-2 mRNA lipid nanoparticle vaccines. | Shepherd SJ, Han X, Mukalel AJ, El-Mayta R, Thatte AS, Wu J, Padilla MS, Alameh MG, Srikumar N, Lee D, Weissman D, Issadore D, Mitchell MJ | Proceedings of the National Academy of Sciences of the United States of America | 37556502 | Proc Natl Acad Sci U S A | 2023 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/37556502 |
| Antigen Presenting Cell Mimetic Lipid Nanoparticles for Rapid mRNA CAR T Cell Cancer Immunotherapy. | Metzloff AE, Padilla MS, Gong N, Billingsley MM, Han X, Merolle M, Mai D, Figueroa-Espada CG, Thatte AS, Haley RM, Mukalel AJ, Hamilton AG, Alameh MG, Weissman D, Sheppard NC, June CH, Mitchell MJ | Advanced materials (Deerfield Beach, Fla.) | 38419362 | Adv Mater | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38419362 |
| Oxidized mRNA Lipid Nanoparticles for In Situ Chimeric Antigen Receptor Monocyte Engineering. | Mukalel AJ, Hamilton AG, Billingsley MM, Li J, Thatte AS, Han X, Safford HC, Padilla MS, Papp T, Parhiz H, Weissman D, Mitchell MJ | Advanced functional materials | 39628840 | Adv Funct Mater | 2024 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/39628840 |
| Bioengineered Nanomaterials for siRNA Therapy of Chemoresistant Cancers. | Sanati M, Figueroa-Espada CG, Han EL, Mitchell MJ, Yavari SA | ACS nano | 39666006 | ACS Nano | 2024 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/39666006 |
| Multiarm-Assisted Design of Dendron-like Degradable Ionizable Lipids Facilitates Systemic mRNA Delivery to the Spleen. | Xue L, Xiong X, Zhao G, Molina-Arocho W, Palanki R, Xiao Z, Han X, Yoon IC, Figueroa-Espada CG, Xu J, Gong N, Shi Q, Chen Q, Alameh MG, Vaughan AE, Haldar M, Wang K, Weissman D, Mitchell MJ | Journal of the American Chemical Society | 39742515 | J Am Chem Soc | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39742515 |
| Emerging strategies for nanomedicine in autoimmunity. | Thatte AS, Billingsley MM, Weissman D, Melamed JR, Mitchell MJ | Advanced drug delivery reviews | 38342243 | Adv Drug Deliv Rev | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38342243 |
| Upregulation of exosome secretion from tumor-associated macrophages plays a key role in the suppression of anti-tumor immunity. | Zhong W, Lu Y, Han X, Yang J, Qin Z, Zhang W, Yu Z, Wu B, Liu S, Xu W, Zheng C, Schuchter LM, Karakousis GC, Mitchell TC, Amaravadi R, Flowers AJ, Gimotty PA, Xiao M, Mills G, Herlyn M, Dong H, Mitchell MJ, Kim J, Xu X, Guo W | Cell reports | 37805922 | Cell Rep | 2023 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/37805922 |
| Adjuvant lipidoid-substituted lipid nanoparticles augment the immunogenicity of SARS-CoV-2 mRNA vaccines. | Han X, Alameh MG, Butowska K, Knox JJ, Lundgreen K, Ghattas M, Gong N, Xue L, Xu Y, Lavertu M, Bates P, Xu J, Nie G, Zhong Y, Weissman D, Mitchell MJ | Nature nanotechnology | 37365276 | Nat Nanotechnol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37365276 |
| Bile acid-containing lipid nanoparticles enhance extrahepatic mRNA delivery. | Patel SK, Billingsley MM, Mukalel AJ, Thatte AS, Hamilton AG, Gong N, El-Mayta R, Safford HC, Merolle M, Mitchell MJ | Theranostics | 38164140 | Theranostics | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38164140 |
| Ionizable Lipid Nanoparticle-Mediated mRNA Delivery for Human CAR T Cell Engineering. | Billingsley MM, Singh N, Ravikumar P, Zhang R, June CH, Mitchell MJ | Nano letters | 31951421 | Nano Lett | 2020 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/31951421 |
| Nanoparticle protein corona: from structure and function to therapeutic targeting. | Bashiri G, Padilla MS, Swingle KL, Shepherd SJ, Mitchell MJ, Wang K | Lab on a chip | 36655824 | Lab Chip | 2023 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/36655824 |
| An ionizable lipid toolbox for RNA delivery. | Han X, Zhang H, Butowska K, Swingle KL, Alameh MG, Weissman D, Mitchell MJ | Nature communications | 34903741 | Nat Commun | 2021 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/34903741 |
| Amniotic fluid stabilized lipid nanoparticles for in utero intra-amniotic mRNA delivery. | Swingle KL, Billingsley MM, Bose SK, White B, Palanki R, Dave A, Patel SK, Gong N, Hamilton AG, Alameh MG, Weissman D, Peranteau WH, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 34742747 | J Control Release | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34742747 |
| Helper lipid structure influences protein adsorption and delivery of lipid nanoparticles to spleen and liver. | Zhang R , El-Mayta R , Murdoch TJ , Warzecha CC , Billingsley MM , Shepherd SJ , Gong N , Wang L , Wilson JM , Lee D , Mitchell MJ | Biomaterials science | 33404020 | Biomater Sci | 2021 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/33404020 |
| Probing the Role of Lipid Nanoparticle Elasticity on mRNA Delivery to the Placenta. | Safford HC, Shuler CF, Geisler HC, Thatte AS, Swingle KL, Han EL, Murray AM, Hamilton AG, Yamagata HM, Mitchell MJ | Nano letters | 40084657 | Nano Lett | 2025 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/40084657 |
| Branched endosomal disruptor (BEND) lipids mediate delivery of mRNA and CRISPR-Cas9 ribonucleoprotein complex for hepatic gene editing and T cell engineering. | Padilla MS, Mrksich K, Wang Y, Haley RM, Li JJ, Han EL, El-Mayta R, Kim EH, Dias S, Gong N, Teerdhala SV, Han X, Chowdhary V, Xue L, Siddiqui Z, Yamagata HM, Kim D, Yoon IC, Wilson JM, Radhakrishnan R, Mitchell MJ | Nature communications | 39856035 | Nat Commun | 2025 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/39856035 |
| Peptide-functionalized nanoparticles for brain-targeted therapeutics. | Tang S, Han EL, Mitchell MJ | Drug delivery and translational research | 40164912 | Drug Deliv Transl Res | 2025 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/40164912 |
| Influence of ionizable lipid tail length on lipid nanoparticle delivery of mRNA of varying length. | Mrksich K, Padilla MS, Joseph RA, Han EL, Kim D, Palanki R, Xu J, Mitchell MJ | Journal of biomedical materials research. Part A | 38487970 | J Biomed Mater Res A | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38487970 |
| High-throughput barcoding of nanoparticles identifies cationic, degradable lipid-like materials for mRNA delivery to the lungs in female preclinical models. | Xue L, Hamilton AG, Zhao G, Xiao Z, El-Mayta R, Han X, Gong N, Xiong X, Xu J, Figueroa-Espada CG, Shepherd SJ, Mukalel AJ, Alameh MG, Cui J, Wang K, Vaughan AE, Weissman D, Mitchell MJ | Nature communications | 38424061 | Nat Commun | 2024 Feb 29 | https://www.ncbi.nlm.nih.gov/pubmed/38424061 |
| Tumour-derived small extracellular vesicles act as a barrier to therapeutic nanoparticle delivery. | Gong N, Zhong W, Alameh MG, Han X, Xue L, El-Mayta R, Zhao G, Vaughan AE, Qin Z, Xu F, Hamilton AG, Kim D, Xu J, Kim J, Teng X, Li J, Liang XJ, Weissman D, Guo W, Mitchell MJ | Nature materials | 39223270 | Nat Mater | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39223270 |
| Breaking the final barrier: Evolution of cationic and ionizable lipid structure in lipid nanoparticles to escape the endosome. | Mrksich K, Padilla MS, Mitchell MJ | Advanced drug delivery reviews | 39293650 | Adv Drug Deliv Rev | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39293650 |
| Ionizable lipid nanoparticles for RAS protease delivery to inhibit cancer cell proliferation. | Atsavapranee E, Haley RM, Billingsley MM, Chan A, Ruan B, Figueroa-Espada CG, Gong N, Mukalel AJ, Bryan PN, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 38729436 | J Control Release | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38729436 |
| Enhancing in situ cancer vaccines using delivery technologies. | Gong N, Alameh MG, El-Mayta R, Xue L, Weissman D, Mitchell MJ | Nature reviews. Drug discovery | 38951662 | Nat Rev Drug Discov | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38951662 |
| Cyclodextrins in drug delivery: applications in gene and combination therapy. | Haley RM, Gottardi R, Langer R, Mitchell MJ | Drug delivery and translational research | 32077052 | Drug Deliv Transl Res | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32077052 |
| Lipid Nanoparticle Delivery of Small Proteins for Potent In Vivo RAS Inhibition. | Haley RM, Chan A, Billingsley MM, Gong N, Padilla MS, Kim EH, Wang H, Yin D, Wangensteen KJ, Tsourkas A, Mitchell MJ | ACS applied materials & interfaces | 37115558 | ACS Appl Mater Interfaces | 2023 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/37115558 |
| Rational Design of Nanomedicine for Placental Disorders: Birthing a New Era in Women's Reproductive Health. | Geisler HC, Safford HC, Mitchell MJ | Small (Weinheim an der Bergstrasse, Germany) | 37191231 | Small | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37191231 |
| Flow cytometric analysis of the murine placenta to evaluate nanoparticle platforms during pregnancy. | Swingle KL, Hamilton AG, Mitchell MJ | Placenta | 39181830 | Placenta | 2025 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/39181830 |
| Combinatorial design of siloxane-incorporated lipid nanoparticles augments intracellular processing for tissue-specific mRNA therapeutic delivery. | Xue L, Zhao G, Gong N, Han X, Shepherd SJ, Xiong X, Xiao Z, Palanki R, Xu J, Swingle KL, Warzecha CC, El-Mayta R, Chowdhary V, Yoon IC, Xu J, Cui J, Shi Y, Alameh MG, Wang K, Wang L, Pochan DJ, Weissman D, Vaughan AE, Wilson JM, Mitchell MJ | Nature nanotechnology | 39354147 | Nat Nanotechnol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39354147 |
| TGF-βR2 signaling coordinates pulmonary vascular repair after viral injury in mice and human tissue. | Zhao G, Xue L, Weiner AI, Gong N, Adams-Tzivelekidis S, Wong J, Gentile ME, Nottingham AN, Basil MC, Lin SM, Niethamer TK, Diamond JM, Bermudez CA, Cantu E, Han X, Cao Y, Alameh MG, Weissman D, Morrisey EE, Mitchell MJ, Vaughan AE | Science translational medicine | 38295183 | Sci Transl Med | 2024 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/38295183 |
| Precision treatment of viral pneumonia through macrophage-targeted lipid nanoparticle delivery. | Zhao G, Xue L, Geisler HC, Xu J, Li X, Mitchell MJ, Vaughan AE | Proceedings of the National Academy of Sciences of the United States of America | 38315853 | Proc Natl Acad Sci U S A | 2024 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/38315853 |
| High-Throughput In Vivo Screening Identifies Differential Influences on mRNA Lipid Nanoparticle Immune Cell Delivery by Administration Route. | Hamilton AG, Swingle KL, Thatte AS, Mukalel AJ, Safford HC, Billingsley MM, El-Mayta RD, Han X, Nachod BE, Joseph RA, Metzloff AE, Mitchell MJ | ACS nano | 38861479 | ACS Nano | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38861479 |
| Rational design of anti-inflammatory lipid nanoparticles for mRNA delivery. | Zhang H, Han X, Alameh MG, Shepherd SJ, Padilla MS, Xue L, Butowska K, Weissman D, Mitchell MJ | Journal of biomedical materials research. Part A | 35076171 | J Biomed Mater Res A | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35076171 |
| Targeted Nanocarriers Co-Opting Pulmonary Intravascular Leukocytes for Drug Delivery to the Injured Brain. | Nong J, Glassman PM, Myerson JW, Zuluaga-Ramirez V, Rodriguez-Garcia A, Mukalel A, Omo-Lamai S, Walsh LR, Zamora ME, Gong X, Wang Z, Bhamidipati K, Kiseleva RY, Villa CH, Greineder CF, Kasner SE, Weissman D, Mitchell MJ, Muro S, Persidsky Y, Brenner JS, Muzykantov VR, Marcos-Contreras OA | ACS nano | 37432926 | ACS Nano | 2023 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/37432926 |
| In utero delivery of targeted ionizable lipid nanoparticles facilitates in vivo gene editing of hematopoietic stem cells. | Palanki R, Riley JS, Bose SK, Luks V, Dave A, Kus N, White BM, Ricciardi AS, Swingle KL, Xue L, Sung D, Thatte AS, Safford HC, Chaluvadi VS, Carpenter M, Han EL, Maganti R, Hamilton AG, Mrksich K, Billingsley MB, Zoltick PW, Alameh MG, Weissman D, Mitchell MJ, Peranteau WH | Proceedings of the National Academy of Sciences of the United States of America | 39078677 | Proc Natl Acad Sci U S A | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39078677 |
| Ionizable lipid nanoparticles for in utero mRNA delivery. | Riley RS, Kashyap MV, Billingsley MM, White B, Alameh MG, Bose SK, Zoltick PW, Li H, Zhang R, Cheng AY, Weissman D, Peranteau WH, Mitchell MJ | Science advances | 33523869 | Sci Adv | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33523869 |
| Nanomaterials for T-cell cancer immunotherapy. | Gong N, Sheppard NC, Billingsley MM, June CH, Mitchell MJ | Nature nanotechnology | 33437036 | Nat Nanotechnol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33437036 |
| Microfluidic formulation of nanoparticles for biomedical applications. | Shepherd SJ, Issadore D, Mitchell MJ | Biomaterials | 33965797 | Biomaterials | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33965797 |
| Scalable mRNA and siRNA Lipid Nanoparticle Production Using a Parallelized Microfluidic Device. | Shepherd SJ, Warzecha CC, Yadavali S, El-Mayta R, Alameh MG, Wang L, Weissman D, Wilson JM, Issadore D, Mitchell MJ | Nano letters | 34189917 | Nano Lett | 2021 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/34189917 |
| siRNA Lipid-Polymer Nanoparticles Targeting E-Selectin and Cyclophilin A in Bone Marrow for Combination Multiple Myeloma Therapy. | Figueroa-Espada CG, Guimarães PPG, Riley RS, Xue L, Wang K, Mitchell MJ | Cellular and molecular bioengineering | 37810998 | Cell Mol Bioeng | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37810998 |
| Ionizable Lipid Nanoparticles for Therapeutic Base Editing of Congenital Brain Disease. | Palanki R, Bose SK, Dave A, White BM, Berkowitz C, Luks V, Yaqoob F, Han E, Swingle KL, Menon P, Hodgson E, Biswas A, Billingsley MM, Li L, Yiping F, Carpenter M, Trokhan A, Yeo J, Johana N, Wan TY, Alameh MG, Bennett FC, Storm PB, Jain R, Chan J, Weissman D, Mitchell MJ, Peranteau WH | ACS nano | 37458484 | ACS Nano | 2023 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/37458484 |
| A (Controlled) Spill of IL2 for Localized Treatment of Mesothelioma. | Palanki R, Swingle KL, Mitchell MJ | Clinical cancer research : an official journal of the American Association for Cancer Research | 36190329 | Clin Cancer Res | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36190329 |
| Testing the In Vitro and In Vivo Efficiency of mRNA-Lipid Nanoparticles Formulated by Microfluidic Mixing. | El-Mayta R, Padilla MS, Billingsley MM, Han X, Mitchell MJ | Journal of visualized experiments : JoVE | 36744791 | J Vis Exp | 2023 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/36744791 |
| Ionizable Lipid Nanoparticles for In Vivo mRNA Delivery to the Placenta during Pregnancy. | Swingle KL, Safford HC, Geisler HC, Hamilton AG, Thatte AS, Billingsley MM, Joseph RA, Mrksich K, Padilla MS, Ghalsasi AA, Alameh MG, Weissman D, Mitchell MJ | Journal of the American Chemical Society | 36789893 | J Am Chem Soc | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36789893 |
| Plug-and-play assembly of biodegradable ionizable lipids for potent mRNA delivery and gene editing in vivo. | Han X, Xu Y, Ricciardi A, Xu J, Palanki R, Chowdhary V, Xue L, Gong N, Alameh MG, Peranteau WH, Wilson JM, Weissman D, Mitchell MJ | bioRxiv : the preprint server for biology | 40060499 | bioRxiv | 2025 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/40060499 |
| Lipid Nanoparticles for In Vivo Lung Delivery of CRISPR-Cas9 Ribonucleoproteins Allow Gene Editing of Clinical Targets. | Haley RM, Padilla MS, El-Mayta RD, Joseph RA, Weber JA, Figueroa-Espada CG, Mukalel AJ, Ricciardi AS, Palanki R, Geisler HC, Jester MT, Davidson BL, Mitchell MJ | ACS nano | 40183470 | ACS Nano | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/40183470 |
| Chiral Supraparticles for Controllable Nanomedicine. | Yeom J, Guimaraes PPG, Ahn HM, Jung BK, Hu Q, McHugh K, Mitchell MJ, Yun CO, Langer R, Jaklenec A | Advanced materials (Deerfield Beach, Fla.) | 31686433 | Adv Mater | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31686433 |
| Endothelial plasticity drives aberrant vascularization and impedes cardiac repair after myocardial infarction. | Huang M, Yang F, Zhang D, Lin M, Duan H, El-Mayta R, Zhang L, Qin L, Shewale SV, Pei L, Mitchell MJ, Rader DJ, Fan Y, Gong Y | Nature cardiovascular research | 35571674 | Nat Cardiovasc Res | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35571674 |
| One-Component Multifunctional Sequence-Defined Ionizable Amphiphilic Janus Dendrimer Delivery Systems for mRNA. | Zhang D, Atochina-Vasserman EN, Maurya DS, Huang N, Xiao Q, Ona N, Liu M, Shahnawaz H, Ni H, Kim K, Billingsley MM, Pochan DJ, Mitchell MJ, Weissman D, Percec V | Journal of the American Chemical Society | 34324336 | J Am Chem Soc | 2021 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/34324336 |
| Delivery technologies for in utero gene therapy. | Palanki R, Peranteau WH, Mitchell MJ | Advanced drug delivery reviews | 33181188 | Adv Drug Deliv Rev | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33181188 |
| Peptide functionalized liposomes for receptor targeted cancer therapy. | Aronson MR, Medina SH, Mitchell MJ | APL bioengineering | 33532673 | APL Bioeng | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33532673 |
| Engineering precision nanoparticles for drug delivery. | Mitchell MJ, Billingsley MM, Haley RM, Wechsler ME, Peppas NA, Langer R | Nature reviews. Drug discovery | 33277608 | Nat Rev Drug Discov | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33277608 |
| Cytosolic Delivery of Small Protein Scaffolds Enables Efficient Inhibition of Ras and Myc. | Chan A, Wang HH, Haley RM, Song C, Gonzalez-Martinez D, Bugaj L, Mitchell MJ, Tsourkas A | Molecular pharmaceutics | 35225618 | Mol Pharm | 2022 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/35225618 |
| Small-molecule-mediated control of the anti-tumour activity and off-tumour toxicity of a supramolecular bispecific T cell engager. | Gong N, Han X, Xue L, Billingsley MM, Huang X, El-Mayta R, Qin J, Sheppard NC, June CH, Mitchell MJ | Nature biomedical engineering | 38378820 | Nat Biomed Eng | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38378820 |
| Ionizable Lipid Nanoparticles with Integrated Immune Checkpoint Inhibition for mRNA CAR T Cell Engineering. | Hamilton AG, Swingle KL, Joseph RA, Mai D, Gong N, Billingsley MM, Alameh MG, Weissman D, Sheppard NC, June CH, Mitchell MJ | Advanced healthcare materials | 37602495 | Adv Healthc Mater | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37602495 |
| Orthogonal Design of Experiments for Engineering of Lipid Nanoparticles for mRNA Delivery to the Placenta. | Safford HC, Swingle KL, Geisler HC, Hamilton AG, Thatte AS, Ghalsasi AA, Billingsley MM, Alameh MG, Weissman D, Mitchell MJ | Small (Weinheim an der Bergstrasse, Germany) | 37537704 | Small | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37537704 |
| In Vivo mRNA CAR T Cell Engineering via Targeted Ionizable Lipid Nanoparticles with Extrahepatic Tropism. | Billingsley MM, Gong N, Mukalel AJ, Thatte AS, El-Mayta R, Patel SK, Metzloff AE, Swingle KL, Han X, Xue L, Hamilton AG, Safford HC, Alameh MG, Papp TE, Parhiz H, Weissman D, Mitchell MJ | Small (Weinheim an der Bergstrasse, Germany) | 38072809 | Small | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38072809 |
| Placenta-tropic VEGF mRNA lipid nanoparticles ameliorate murine pre-eclampsia. | Swingle KL, Hamilton AG, Safford HC, Geisler HC, Thatte AS, Palanki R, Murray AM, Han EL, Mukalel AJ, Han X, Joseph RA, Ghalsasi AA, Alameh MG, Weissman D, Mitchell MJ | Nature | 39663452 | Nature | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39663452 |
| Solution biophysics identifies lipid nanoparticle non-sphericity, polydispersity, and dependence on internal ordering for efficacious mRNA delivery. | Padilla MS, Shepherd SJ, Hanna AR, Kurnik M, Zhang X, Chen M, Byrnes J, Joseph RA, Yamagata HM, Ricciardi AS, Mrksich K, Issadore D, Gupta K, Mitchell MJ | bioRxiv : the preprint server for biology | 39763759 | bioRxiv | 2025 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/39763759 |
| Lipid nanoparticle-mediated RNA delivery for immune cell modulation. | Kim EH, Teerdhala SV, Padilla MS, Joseph RA, Li JJ, Haley RM, Mitchell MJ | European journal of immunology | 39279550 | Eur J Immunol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39279550 |
| Piperazine-Derived Bisphosphonate-Based Ionizable Lipid Nanoparticles Enhance mRNA Delivery to the Bone Microenvironment. | Yoon IC, Xue L, Chen Q, Liu J, Xu J, Siddiqui Z, Kim D, Chen B, Shi Q, Laura Han E, Cherry Ruiz M, Vining KH, Mitchell MJ | Angewandte Chemie (International ed. in English) | 39379320 | Angew Chem Int Ed Engl | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39379320 |
| EGFR-targeted ionizable lipid nanoparticles enhance in vivo mRNA delivery to the placenta. | Geisler HC, Ghalsasi AA, Safford HC, Swingle KL, Thatte AS, Mukalel AJ, Gong N, Hamilton AG, Han EL, Nachod BE, Padilla MS, Mitchell MJ | Journal of controlled release : official journal of the Controlled Release Society | 38789090 | J Control Release | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38789090 |
| Fast and facile synthesis of amidine-incorporated degradable lipids for versatile mRNA delivery in vivo. | Han X, Alameh MG, Gong N, Xue L, Ghattas M, Bojja G, Xu J, Zhao G, Warzecha CC, Padilla MS, El-Mayta R, Dwivedi G, Xu Y, Vaughan AE, Wilson JM, Weissman D, Mitchell MJ | Nature chemistry | 38982196 | Nat Chem | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38982196 |
| Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins. | Chan A, Haley RM, Najar MA, Gonzalez-Martinez D, Bugaj LJ, Burslem GM, Mitchell MJ, Tsourkas A | Nature communications | 38987546 | Nat Commun | 2024 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/38987546 |
| Optimized microfluidic formulation and organic excipients for improved lipid nanoparticle mediated genome editing. | Palanki R, Han EL, Murray AM, Maganti R, Tang S, Swingle KL, Kim D, Yamagata H, Safford HC, Mrksich K, Peranteau WH, Mitchell MJ | Lab on a chip | 39037068 | Lab Chip | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39037068 |
| In vivo bone marrow microenvironment siRNA delivery using lipid-polymer nanoparticles for multiple myeloma therapy. | Guimarães PPG, Figueroa-Espada CG, Riley RS, Gong N, Xue L, Sewastianik T, Dennis PS, Loebel C, Chung A, Shepherd SJ, Haley RM, Hamilton AG, El-Mayta R, Wang K, Langer R, Anderson DG, Carrasco RD, Mitchell MJ | Proceedings of the National Academy of Sciences of the United States of America | 37310997 | Proc Natl Acad Sci U S A | 2023 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/37310997 |
| Automated and parallelized microfluidic generation of large and precisely-defined lipid nanoparticle libraries. | Hanna AR, Shepherd SJ, Datto GA, Navarro IB, Ricciardi AS, Padilla MS, Srikumar N, Zhang S, Yamagata HM, Meng NY, Buser JR, Mitchell MJ, Issadore DA | bioRxiv : the preprint server for biology | 40501993 | bioRxiv | 2025 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/40501993 |
| Methicillin-resistant Staphylococcus aureus causes sustained collecting lymphatic vessel dysfunction. | Jones D, Meijer EFJ, Blatter C, Liao S, Pereira ER, Bouta EM, Jung K, Chin SM, Huang P, Munn LL, Vakoc BJ, Otto M, Padera TP | Science translational medicine | 29343625 | Sci Transl Med | 2018 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/29343625 |
| Reply to Davis: Nitric oxide regulates lymphatic contractions. | Kunert C, Baish JW, Liao S, Padera TP, Munn LL | Proceedings of the National Academy of Sciences of the United States of America | 26719425 | Proc Natl Acad Sci U S A | 2016 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/26719425 |
| Vascular endothelial growth factor-C enhances radiosensitivity of lymphatic endothelial cells. | Kesler CT, Kuo AH, Wong HK, Masuck DJ, Shah JL, Kozak KR, Held KD, Padera TP | Angiogenesis | 24201897 | Angiogenesis | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24201897 |
| The lymph node microenvironment and its role in the progression of metastatic cancer. | Pereira ER, Jones D, Jung K, Padera TP | Seminars in cell & developmental biology | 25620792 | Semin Cell Dev Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25620792 |
| Solid stress impairs lymphocyte infiltration into lymph-node metastases. | Jones D, Wang Z, Chen IX, Zhang S, Banerji R, Lei PJ, Zhou H, Xiao V, Kwong C, van Wijnbergen JWM, Pereira ER, Vakoc BJ, Huang P, Nia HT, Padera TP | Nature biomedical engineering | 34282290 | Nat Biomed Eng | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34282290 |
| Inducible Nitric Oxide Synthase and CD11b(+)Gr1(+) Cells Impair Lymphatic Contraction of Tumor-Draining Lymphatic Vessels. | Liao S, Bouta EM, Morris LM, Jones D, Jain RK, Padera TP | Lymphatic research and biology | 30358484 | Lymphat Res Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30358484 |
| A retrospective analysis of commonly prescribed medications and the risk of developing breast cancer related lymphedema. | Meijer EF, Bouta EM, Mendonca C, Skolny MN, Salama LW, Taghian AG, Padera TP | Clinical research and trials | 32864167 | Clin Res Trials | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32864167 |
| In vivo label-free measurement of lymph flow velocity and volumetric flow rates using Doppler optical coherence tomography. | Blatter C, Meijer EF, Nam AS, Jones D, Bouma BE, Padera TP, Vakoc BJ | Scientific reports | 27377852 | Sci Rep | 2016 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/27377852 |
| Investigation of the Lack of Angiogenesis in the Formation of Lymph Node Metastases. | Jeong HS, Jones D, Liao S, Wattson DA, Cui CH, Duda DG, Willett CG, Jain RK, Padera TP | Journal of the National Cancer Institute | 26063793 | J Natl Cancer Inst | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26063793 |
| Effects of vascular-endothelial protein tyrosine phosphatase inhibition on breast cancer vasculature and metastatic progression. | Goel S, Gupta N, Walcott BP, Snuderl M, Kesler CT, Kirkpatrick ND, Heishi T, Huang Y, Martin JD, Ager E, Samuel R, Wang S, Yazbek J, Vakoc BJ, Peterson RT, Padera TP, Duda DG, Fukumura D, Jain RK | Journal of the National Cancer Institute | 23899555 | J Natl Cancer Inst | 2013 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/23899555 |
| Lymphatic vessels in health and disease. | Kesler CT, Liao S, Munn LL, Padera TP | Wiley interdisciplinary reviews. Systems biology and medicine | 23209022 | Wiley Interdiscip Rev Syst Biol Med | 2013 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/23209022 |
| Angiopoietin-4 increases permeability of blood vessels and promotes lymphatic dilation. | Kesler CT, Pereira ER, Cui CH, Nelson GM, Masuck DJ, Baish JW, Padera TP | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 25977256 | FASEB J | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25977256 |
| Mechanobiological oscillators control lymph flow. | Kunert C, Baish JW, Liao S, Padera TP, Munn LL | Proceedings of the National Academy of Sciences of the United States of America | 26283382 | Proc Natl Acad Sci U S A | 2015 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/26283382 |
| The Lymphatic System in Disease Processes and Cancer Progression. | Padera TP, Meijer EF, Munn LL | Annual review of biomedical engineering | 26863922 | Annu Rev Biomed Eng | 2016 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/26863922 |
| Method for the quantitative measurement of collecting lymphatic vessel contraction in mice. | Liao S, Jones D, Cheng G, Padera TP | Journal of biological methods | 25512945 | J Biol Methods | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25512945 |
| Measuring Vascular Permeability In Vivo. | Meijer EF, Baish JW, Padera TP, Fukumura D | Methods in molecular biology (Clifton, N.J.) | 27581015 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27581015 |
| Targeting CXCR4-dependent immunosuppressive Ly6C(low) monocytes improves antiangiogenic therapy in colorectal cancer. | Jung K, Heishi T, Incio J, Huang Y, Beech EY, Pinter M, Ho WW, Kawaguchi K, Rahbari NN, Chung E, Kim JK, Clark JW, Willett CG, Yun SH, Luster AD, Padera TP, Jain RK, Fukumura D | Proceedings of the National Academy of Sciences of the United States of America | 28900008 | Proc Natl Acad Sci U S A | 2017 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/28900008 |
| Murine chronic lymph node window for longitudinal intravital lymph node imaging. | Meijer EFJ, Jeong HS, Pereira ER, Ruggieri TA, Blatter C, Vakoc BJ, Padera TP | Nature protocols | 28683064 | Nat Protoc | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28683064 |
| Video-rate resonant scanning multiphoton microscopy: An emerging technique for intravital imaging of the tumor microenvironment. | Kirkpatrick ND, Chung E, Cook DC, Han X, Gruionu G, Liao S, Munn LL, Padera TP, Fukumura D, Jain RK | Intravital | 24353926 | Intravital | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/24353926 |
| Novel molecular pathways in Gorham disease: implications for treatment. | Hagendoorn J, Yock TI, Borel Rinkes IH, Padera TP, Ebb DH | Pediatric blood & cancer | 24214028 | Pediatr Blood Cancer | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24214028 |
| Lymphatic function and immune regulation in health and disease. | Liao S, Padera TP | Lymphatic research and biology | 24024577 | Lymphat Res Biol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24024577 |
| Synchronization and Random Triggering of Lymphatic Vessel Contractions. | Baish JW, Kunert C, Padera TP, Munn LL | PLoS computational biology | 27935958 | PLoS Comput Biol | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27935958 |
| Solid stress and elastic energy as measures of tumour mechanopathology. | Nia HT, Liu H, Seano G, Datta M, Jones D, Rahbari N, Incio J, Chauhan VP, Jung K, Martin JD, Askoxylakis V, Padera TP, Fukumura D, Boucher Y, Hornicek FJ, Grodzinsky AJ, Baish JW, Munn LL, Jain RK | Nature biomedical engineering | 28966873 | Nat Biomed Eng | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28966873 |
| Lymph node effective vascular permeability and chemotherapy uptake. | Meijer EFJ, Blatter C, Chen IX, Bouta E, Jones D, Pereira ER, Jung K, Vakoc BJ, Baish JW, Padera TP | Microcirculation (New York, N.Y. : 1994) | 28510992 | Microcirculation | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28510992 |
| Imaging the lymphatic system. | Munn LL, Padera TP | Microvascular research | 24956510 | Microvasc Res | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24956510 |
| Growth and Immune Evasion of Lymph Node Metastasis. | Jones D, Pereira ER, Padera TP | Frontiers in oncology | 29527513 | Front Oncol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29527513 |
| Solid stress in brain tumours causes neuronal loss and neurological dysfunction and can be reversed by lithium. | Seano G, Nia HT, Emblem KE, Datta M, Ren J, Krishnan S, Kloepper J, Pinho MC, Ho WW, Ghosh M, Askoxylakis V, Ferraro GB, Riedemann L, Gerstner ER, Batchelor TT, Wen PY, Lin NU, Grodzinsky AJ, Fukumura D, Huang P, Baish JW, Padera TP, Munn LL, Jain RK | Nature biomedical engineering | 30948807 | Nat Biomed Eng | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30948807 |
| Fate Mapping of Cancer Cells in Metastatic Lymph Nodes Using Photoconvertible Proteins. | Pereira ER, Kedrin D, Padera TP | Methods in molecular biology (Clifton, N.J.) | 33704727 | Methods Mol Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33704727 |
| Lymphatic function measurements influenced by contrast agent volume and body position. | Bouta EM, Blatter C, Ruggieri TA, Meijer EF, Munn LL, Vakoc BJ, Padera TP | JCI insight | 29367467 | JCI Insight | 2018 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/29367467 |
| Compression of pancreatic tumor blood vessels by hyaluronan is caused by solid stress and not interstitial fluid pressure. | Chauhan VP, Boucher Y, Ferrone CR, Roberge S, Martin JD, Stylianopoulos T, Bardeesy N, DePinho RA, Padera TP, Munn LL, Jain RK | Cancer cell | 25026209 | Cancer Cell | 2014 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/25026209 |
| Lymph node metastases can invade local blood vessels, exit the node, and colonize distant organs in mice. | Pereira ER, Kedrin D, Seano G, Gautier O, Meijer EFJ, Jones D, Chin SM, Kitahara S, Bouta EM, Chang J, Beech E, Jeong HS, Carroll MC, Taghian AG, Padera TP | Science (New York, N.Y.) | 29567713 | Science | 2018 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/29567713 |
| Ly6Clo monocytes drive immunosuppression and confer resistance to anti-VEGFR2 cancer therapy. | Jung K, Heishi T, Khan OF, Kowalski PS, Incio J, Rahbari NN, Chung E, Clark JW, Willett CG, Luster AD, Yun SH, Langer R, Anderson DG, Padera TP, Jain RK, Fukumura D | The Journal of clinical investigation | 28691930 | J Clin Invest | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28691930 |
| Local failure in parameningeal rhabdomyosarcoma correlates with poor response to induction chemotherapy. | Ladra MM, Mandeville HC, Niemierko A, Padera TP, Friedmann AM, MacDonald SM, Ebb D, Chen YL, Tarbell NJ, Yock TI | International journal of radiation oncology, biology, physics | 25864172 | Int J Radiat Oncol Biol Phys | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/25864172 |
| Significance of lymph node metastasis in cancer dissemination of head and neck cancer. | Cho JK, Hyun SH, Choi N, Kim MJ, Padera TP, Choi JY, Jeong HS | Translational oncology | 25926078 | Transl Oncol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25926078 |
| Editorial: rapid growth in the field of lymphatic biology. | Padera TP | Seminars in cell & developmental biology | 25868083 | Semin Cell Dev Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25868083 |
| Simultaneous measurements of lymphatic vessel contraction, flow and valve dynamics in multiple lymphangions using optical coherence tomography. | Blatter C, Meijer EFJ, Padera TP, Vakoc BJ | Journal of biophotonics | 28700145 | J Biophotonics | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28700145 |
| Cardiac and inflammatory biomarkers do not correlate with volume of heart or lung receiving radiation. | Kuo AH, Ancukiewicz M, Kozak KR, Yock TI, Padera TP | Radiation oncology (London, England) | 25573181 | Radiat Oncol | 2015 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/25573181 |
| Microtubule Dynamics Scale with Cell Size to Set Spindle Length and Assembly Timing. | Lacroix B, Letort G, Pitayu L, Sallé J, Stefanutti M, Maton G, Ladouceur AM, Canman JC, Maddox PS, Maddox AS, Minc N, Nédélec F, Dumont J | Developmental cell | 29787710 | Dev Cell | 2018 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/29787710 |
| period-Regulated Feeding Behavior and TOR Signaling Modulate Survival of Infection. | Allen VW, O'Connor RM, Ulgherait M, Zhou CG, Stone EF, Hill VM, Murphy KR, Canman JC, Ja WW, Shirasu-Hiza MM | Current biology : CB | 26748856 | Curr Biol | 2016 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/26748856 |
| Stuck in the middle: Rac, adhesion, and cytokinesis. | Davies T, Canman JC | The Journal of cell biology | 22945931 | J Cell Biol | 2012 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/22945931 |
| High-resolution temporal analysis reveals a functional timeline for the molecular regulation of cytokinesis. | Davies T, Jordan SN, Chand V, Sees JA, Laband K, Carvalho AX, Shirasu-Hiza M, Kovar DR, Dumont J, Canman JC | Developmental cell | 25073157 | Dev Cell | 2014 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/25073157 |
| Cell-intrinsic and -extrinsic mechanisms promote cell-type-specific cytokinetic diversity. | Davies T, Kim HX, Romano Spica N, Lesea-Pringle BJ, Dumont J, Shirasu-Hiza M, Canman JC | eLife | 30028292 | Elife | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/30028292 |
| Low Efficiency Upconversion Nanoparticles for High-Resolution Coalignment of Near-Infrared and Visible Light Paths on a Light Microscope. | Sundaramoorthy S, Garcia Badaracco A, Hirsch SM, Park JH, Davies T, Dumont J, Shirasu-Hiza M, Kummel AC, Canman JC | ACS applied materials & interfaces | 28221018 | ACS Appl Mater Interfaces | 2017 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/28221018 |
| A Drosophila model of Fragile X syndrome exhibits defects in phagocytosis by innate immune cells. | O'Connor RM, Stone EF, Wayne CR, Marcinkevicius EV, Ulgherait M, Delventhal R, Pantalia MM, Hill VM, Zhou CG, McAllister S, Chen A, Ziegenfuss JS, Grueber WB, Canman JC, Shirasu-Hiza MM | The Journal of cell biology | 28223318 | J Cell Biol | 2017 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/28223318 |
| CYK-4 regulates Rac, but not Rho, during cytokinesis. | Zhuravlev Y, Hirsch SM, Jordan SN, Dumont J, Shirasu-Hiza M, Canman JC | Molecular biology of the cell | 28298491 | Mol Biol Cell | 2017 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/28298491 |
| Kinetochore components are required for central spindle assembly. | Maton G, Edwards F, Lacroix B, Stefanutti M, Laband K, Lieury T, Kim T, Espeut J, Canman JC, Dumont J | Nature cell biology | 26123112 | Nat Cell Biol | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26123112 |
| FLIRT: fast local infrared thermogenetics for subcellular control of protein function. | Hirsch SM, Sundaramoorthy S, Davies T, Zhuravlev Y, Waters JC, Shirasu-Hiza M, Dumont J, Canman JC | Nature methods | 30377360 | Nat Methods | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30377360 |
| Using fast-acting temperature-sensitive mutants to study cell division in Caenorhabditis elegans. | Davies T, Sundaramoorthy S, Jordan SN, Shirasu-Hiza M, Dumont J, Canman JC | Methods in cell biology | 28065312 | Methods Cell Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28065312 |
| Dietary Restriction Extends the Lifespan of Circadian Mutants tim and per. | Ulgherait M, Chen A, Oliva MK, Kim HX, Canman JC, Ja WW, Shirasu-Hiza M | Cell metabolism | 27916531 | Cell Metab | 2016 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/27916531 |
| Rho GTPases in animal cell cytokinesis: an occupation by the one percent. | Jordan SN, Canman JC | Cytoskeleton (Hoboken, N.J.) | 23047851 | Cytoskeleton (Hoboken) | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23047851 |
| period-Regulated Feeding Behavior and TOR Signaling Modulate Survival of Infection. | Allen VW, O'Connor RM, Ulgherait M, Zhou CG, Stone EF, Hill VM, Murphy KR, Canman JC, Ja WW, Shirasu-Hiza MM | Current biology : CB | 27218838 | Curr Biol | 2016 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/27218838 |
| Inhibition of ectopic microtubule assembly by the kinesin-13 KLP-7 prevents chromosome segregation and cytokinesis defects in oocytes. | Gigant E, Stefanutti M, Laband K, Gluszek-Kustusz A, Edwards F, Lacroix B, Maton G, Canman JC, Welburn JPI, Dumont J | Development (Cambridge, England) | 28289130 | Development | 2017 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/28289130 |
| Cortical PAR polarity proteins promote robust cytokinesis during asymmetric cell division. | Jordan SN, Davies T, Zhuravlev Y, Dumont J, Shirasu-Hiza M, Canman JC | The Journal of cell biology | 26728855 | J Cell Biol | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26728855 |
| Kinetochore components are required for central spindle assembly. | Maton G, Edwards F, Lacroix B, Stefanutti M, Laband K, Lieury T, Kim T, Espeut J, Canman JC, Dumont J | Nature cell biology | 25866924 | Nat Cell Biol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25866924 |
| Ammonium chloride alters neuronal excitability and synaptic vesicle release. | Lazarenko RM, DelBove CE, Strothman CE, Zhang Q | Scientific reports | 28698583 | Sci Rep | 2017 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/28698583 |
| Effect of Competitive Surface Functionalization on Dual-Modality Fluorescence and Magnetic Resonance Imaging of Single-Walled Carbon Nanotubes. | Hong T, Lazarenko RM, Colvin DC, Flores RL, Zhang Q, Xu YQ | The journal of physical chemistry. C, Nanomaterials and interfaces | 26644813 | J Phys Chem C Nanomater Interfaces | 2012 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/26644813 |
| Reciprocal modulation between amyloid precursor protein and synaptic membrane cholesterol revealed by live cell imaging. | DelBove CE, Strothman CE, Lazarenko RM, Huang H, Sanders CR, Zhang Q | Neurobiology of disease | 30885793 | Neurobiol Dis | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30885793 |
| A Stem Cell-Derived Platform for Studying Single Synaptic Vesicles in Dopaminergic Synapses. | Gu H, Lazarenko RM, Koktysh D, Iacovitti L, Zhang Q | Stem cells translational medicine | 26025981 | Stem Cells Transl Med | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26025981 |
| Fluorescent Measurement of Synaptic Activity Using FM Dyes in Dissociated Hippocampal Cultured Neurons. | Lazarenko RM, DelBove CE, Zhang Q | Bio-protocol | 29552593 | Bio Protoc | 2018 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/29552593 |
| Classic Ulcerative Pyoderma Gangrenosum Is a T Cell-Mediated Disease Targeting Follicular Adnexal Structures: A Hypothesis Based on Molecular and Clinicopathologic Studies. | Wang EA, Steel A, Luxardi G, Mitra A, Patel F, Cheng MY, Wilken R, Kao J, de Ga K, Sultani H, Merleev AA, Marusina AI, Brassard A, Fung MA, Konia T, Shimoda M, Maverakis E | Frontiers in immunology | 29379508 | Front Immunol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29379508 |
| A site-specific map of the human plasma glycome and its age and gender-associated alterations. | Merleev AA, Park D, Xie Y, Kailemia MJ, Xu G, Ruhaak LR, Kim K, Hong Q, Li Q, Patel F, Wan YY, Marusina AI, Adamopoulos IE, Lal NN, Mitra A, Le ST, Shimoda M, Luxardi G, Lebrilla CB, Maverakis E | Scientific reports | 33060657 | Sci Rep | 2020 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/33060657 |
| Persistence of Autoreactive IgA-Secreting B Cells Despite Multiple Immunosuppressive Medications Including Rituximab. | He Y, Shimoda M, Ono Y, Villalobos IB, Mitra A, Konia T, Grando SA, Zone JJ, Maverakis E | JAMA dermatology | 25901938 | JAMA Dermatol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25901938 |
| Characteristic Changes in Cell Surface Glycosylation Accompany Intestinal Epithelial Cell (IEC) Differentiation: High Mannose Structures Dominate the Cell Surface Glycome of Undifferentiated Enterocytes. | Park D, Brune KA, Mitra A, Marusina AI, Maverakis E, Lebrilla CB | Molecular & cellular proteomics : MCP | 26355101 | Mol Cell Proteomics | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26355101 |
| Membrane glycomics reveal heterogeneity and quantitative distribution of cell surface sialylation. | Park DD, Xu G, Wong M, Phoomak C, Liu M, Haigh NE, Wongkham S, Yang P, Maverakis E, Lebrilla CB | Chemical science | 30123482 | Chem Sci | 2018 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/30123482 |
| Meta-analysis of RNA sequencing datasets reveals an association between TRAJ23, psoriasis, and IL-17A. | Merleev AA, Marusina AI, Ma C, Elder JT, Tsoi LC, Raychaudhuri SP, Weidinger S, Wang EA, Adamopoulos IE, Luxardi G, Gudjonsson JE, Shimoda M, Maverakis E | JCI insight | 29997305 | JCI Insight | 2018 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/29997305 |
| Metastasis of cholangiocarcinoma is promoted by extended high-mannose glycans. | Park DD, Phoomak C, Xu G, Olney LP, Tran KA, Park SS, Haigh NE, Luxardi G, Lert-Itthiporn W, Shimoda M, Li Q, Matoba N, Fierro F, Wongkham S, Maverakis E, Lebrilla CB | Proceedings of the National Academy of Sciences of the United States of America | 32213588 | Proc Natl Acad Sci U S A | 2020 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/32213588 |
| NKG2C, HLA-E and their association with psoriasis. | Patel F, Marusina AI, Duong C, Adamopoulos IE, Maverakis E | Experimental dermatology | 24279916 | Exp Dermatol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24279916 |
| International consensus criteria for the diagnosis of Raynaud's phenomenon. | Maverakis E, Patel F, Kronenberg DG, Chung L, Fiorentino D, Allanore Y, Guiducci S, Hesselstrand R, Hummers LK, Duong C, Kahaleh B, Macgregor A, Matucci-Cerinic M, Wollheim FA, Mayes MD, Gershwin ME | Journal of autoimmunity | 24491823 | J Autoimmun | 2014 Feb-Mar | https://www.ncbi.nlm.nih.gov/pubmed/24491823 |
| Salmonella Typhimurium Enzymatically Landscapes the Host Intestinal Epithelial Cell (IEC) Surface Glycome to Increase Invasion. | Park D, Arabyan N, Williams CC, Song T, Mitra A, Weimer BC, Maverakis E, Lebrilla CB | Molecular & cellular proteomics : MCP | 27754876 | Mol Cell Proteomics | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27754876 |
| A Phase I Study of the Combination of Rituximab and Ipilimumab in Patients with Relapsed/Refractory B-Cell Lymphoma. | Tuscano JM, Maverakis E, Groshen S, Tsao-Wei D, Luxardi G, Merleev AA, Beaven A, DiPersio JF, Popplewell L, Chen R, Kirschbaum M, Schroeder MA, Newman EM | Clinical cancer research : an official journal of the American Association for Cancer Research | 31481504 | Clin Cancer Res | 2019 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31481504 |
| Trends in National Institutes of Health Funding of Principal Investigators in Dermatology Research by Academic Degree and Sex. | Cheng MY, Sukhov A, Sultani H, Kim K, Maverakis E | JAMA dermatology | 27191545 | JAMA Dermatol | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27191545 |
| Interactions of the Immune System with Skin and Bone Tissue in Psoriatic Arthritis: A Comprehensive Review. | Sukhov A, Adamopoulos IE, Maverakis E | Clinical reviews in allergy & immunology | 26780035 | Clin Rev Allergy Immunol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26780035 |
| Glycans in the immune system and The Altered Glycan Theory of Autoimmunity: a critical review. | Maverakis E, Kim K, Shimoda M, Gershwin ME, Patel F, Wilken R, Raychaudhuri S, Ruhaak LR, Lebrilla CB | Journal of autoimmunity | 25578468 | J Autoimmun | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25578468 |
| Clonal Vγ6(+)Vδ4(+) T cells promote IL-17-mediated immunity against Staphylococcus aureus skin infection. | Marchitto MC, Dillen CA, Liu H, Miller RJ, Archer NK, Ortines RV, Alphonse MP, Marusina AI, Merleev AA, Wang Y, Pinsker BL, Byrd AS, Brown ID, Ravipati A, Zhang E, Cai SS, Limjunyawong N, Dong X, Yeaman MR, Simon SI, Shen W, Durum SK, O'Brien RL, Maverakis E, Miller LS | Proceedings of the National Academy of Sciences of the United States of America | 31088972 | Proc Natl Acad Sci U S A | 2019 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/31088972 |
| Biogeographic and disease-specific alterations in epidermal lipid composition and single-cell analysis of acral keratinocytes. | Merleev AA, Le ST, Alexanian C, Toussi A, Xie Y, Marusina AI, Watkins SM, Patel F, Billi AC, Wiedemann J, Izumiya Y, Kumar A, Uppala R, Kahlenberg JM, Liu FT, Adamopoulos IE, Wang EA, Ma C, Cheng MY, Xiong H, Kirane A, Luxardi G, Andersen B, Tsoi LC, Lebrilla CB, Gudjonsson JE, Maverakis E | JCI insight | 35900871 | JCI Insight | 2022 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/35900871 |
| Glycan biomarkers of autoimmunity and bile acid-associated alterations of the human glycome: Primary biliary cirrhosis and primary sclerosing cholangitis-specific glycans. | Maverakis E, Merleev AA, Park D, Kailemia MJ, Xu G, Ruhaak LR, Kim K, Hong Q, Li Q, Leung P, Liakos W, Wan YY, Bowlus CL, Marusina AI, Lal NN, Xie Y, Luxardi G, Lebrilla CB | Clinical immunology (Orlando, Fla.) | 34403816 | Clin Immunol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34403816 |
| Dual mTOR Inhibition Is Required to Prevent TGF-β-Mediated Fibrosis: Implications for Scleroderma. | Mitra A, Luna JI, Marusina AI, Merleev A, Kundu-Raychaudhuri S, Fiorentino D, Raychaudhuri SP, Maverakis E | The Journal of investigative dermatology | 26134944 | J Invest Dermatol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26134944 |
| ITK inhibition for the targeted treatment of CTCL. | Bustos-Villalobos I, Bergstrom JW, Haigh NE, Luna JI, Mitra A, Marusina AI, Merleev AA, Wang EA, Sukhov A, Sultani H, Liu R, Bhardwaj G, Guo W, Kung HJ, Lam KS, Maverakis E | Journal of dermatological science | 28434812 | J Dermatol Sci | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28434812 |
| Clonally expanded γδ T cells protect against Staphylococcus aureus skin reinfection. | Dillen CA, Pinsker BL, Marusina AI, Merleev AA, Farber ON, Liu H, Archer NK, Lee DB, Wang Y, Ortines RV, Lee SK, Marchitto MC, Cai SS, Ashbaugh AG, May LS, Holland SM, Freeman AF, Miller LG, Yeaman MR, Simon SI, Milner JD, Maverakis E, Miller LS | The Journal of clinical investigation | 29400698 | J Clin Invest | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29400698 |
| Controlling the Release of Small, Bioactive Proteins via Dual Mechanisms with Therapeutic Potential. | Kharkar PM, Scott RA, Olney LP, LeValley PJ, Maverakis E, Kiick KL, Kloxin AM | Advanced healthcare materials | 29024487 | Adv Healthc Mater | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29024487 |
| γδ T cells in rheumatic diseases: from fundamental mechanisms to autoimmunity. | Nguyen CT, Maverakis E, Eberl M, Adamopoulos IE | Seminars in immunopathology | 31506867 | Semin Immunopathol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31506867 |
| Serum levels of innate immunity cytokines are elevated in dogs with metaphyseal osteopathy (hypertrophic osteodytrophy) during active disease and remission. | Safra N, Hitchens PL, Maverakis E, Mitra A, Korff C, Johnson E, Kol A, Bannasch MJ, Pedersen NC, Bannasch DL | Veterinary immunology and immunopathology | 27590423 | Vet Immunol Immunopathol | 2016 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/27590423 |
| Infection-generated electric field in gut epithelium drives bidirectional migration of macrophages. | Sun Y, Reid B, Ferreira F, Luxardi G, Ma L, Lokken KL, Zhu K, Xu G, Sun Y, Ryzhuk V, Guo BP, Lebrilla CB, Maverakis E, Mogilner A, Zhao M | PLoS biology | 30964858 | PLoS Biol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30964858 |
| T cell clonal expansions detected in patients with primary biliary cirrhosis express CX3CR1. | Zhang W, Ono Y, Miyamura Y, Bowlus CL, Gershwin ME, Maverakis E | Journal of autoimmunity | 21636249 | J Autoimmun | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21636249 |
| CD4(+) virtual memory: Antigen-inexperienced T cells reside in the naïve, regulatory, and memory T cell compartments at similar frequencies, implications for autoimmunity. | Marusina AI, Ono Y, Merleev AA, Shimoda M, Ogawa H, Wang EA, Kondo K, Olney L, Luxardi G, Miyamura Y, Yilma TD, Villalobos IB, Bergstrom JW, Kronenberg DG, Soulika AM, Adamopoulos IE, Maverakis E | Journal of autoimmunity | 27894837 | J Autoimmun | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27894837 |
| Oncolytic Reactivation of KSHV as a Therapeutic Approach for Primary Effusion Lymphoma. | Zhou F, Shimoda M, Olney L, Lyu Y, Tran K, Jiang G, Nakano K, Davis RR, Tepper CG, Maverakis E, Campbell M, Li Y, Dandekar S, Izumiya Y | Molecular cancer therapeutics | 28847988 | Mol Cancer Ther | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28847988 |
| HDL Glycoprotein Composition and Site-Specific Glycosylation Differentiates Between Clinical Groups and Affects IL-6 Secretion in Lipopolysaccharide-Stimulated Monocytes. | Krishnan S, Shimoda M, Sacchi R, Kailemia MJ, Luxardi G, Kaysen GA, Parikh AN, Ngassam VN, Johansen K, Chertow GM, Grimes B, Smilowitz JT, Maverakis E, Lebrilla CB, Zivkovic AM | Scientific reports | 28287093 | Sci Rep | 2017 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/28287093 |
| Peristomal pyoderma gangrenosum: An exceedingly rare and overdiagnosed entity? | Le ST, Wang JZ, Alexanian C, Ellis S, Martinez-Alvarado YC, Johng S, Sood A, Maverakis E | Journal of the American Academy of Dermatology | 30772334 | J Am Acad Dermatol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30772334 |
| Surface Glycans Regulate Salmonella Infection-Dependent Directional Switch in Macrophage Galvanotaxis Independent of NanH. | Sun YH, Luxardi G, Xu G, Zhu K, Reid B, Guo BP, Lebrilla CB, Maverakis E, Zhao M | Infection and immunity | 34662214 | Infect Immun | 2022 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/34662214 |
| A Method for Comprehensive Glycosite-Mapping and Direct Quantitation of Serum Glycoproteins. | Hong Q, Ruhaak LR, Stroble C, Parker E, Huang J, Maverakis E, Lebrilla CB | Journal of proteome research | 26510530 | J Proteome Res | 2015 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/26510530 |
| Perfusion Decellularization of Discarded Human Kidneys: A Valuable Platform for Organ Regeneration. | Ott HC | Transplantation | 26203856 | Transplantation | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26203856 |
| Regeneration and experimental orthotopic transplantation of a bioengineered kidney. | Song JJ, Guyette JP, Gilpin SE, Gonzalez G, Vacanti JP, Ott HC | Nature medicine | 23584091 | Nat Med | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23584091 |
| Bioengineering Human Myocardium on Native Extracellular Matrix. | Guyette JP, Charest JM, Mills RW, Jank BJ, Moser PT, Gilpin SE, Gershlak JR, Okamoto T, Gonzalez G, Milan DJ, Gaudette GR, Ott HC | Circulation research | 26503464 | Circ Res | 2016 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/26503464 |
| Enhanced lung epithelial specification of human induced pluripotent stem cells on decellularized lung matrix. | Gilpin SE, Ren X, Okamoto T, Guyette JP, Mou H, Rajagopal J, Mathisen DJ, Vacanti JP, Ott HC | The Annals of thoracic surgery | 25149047 | Ann Thorac Surg | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25149047 |
| Engineering pulmonary vasculature in decellularized rat and human lungs. | Ren X, Moser PT, Gilpin SE, Okamoto T, Wu T, Tapias LF, Mercier FE, Xiong L, Ghawi R, Scadden DT, Mathisen DJ, Ott HC | Nature biotechnology | 26368048 | Nat Biotechnol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26368048 |
| Perfusion decellularization of human and porcine lungs: bringing the matrix to clinical scale. | Gilpin SE, Guyette JP, Gonzalez G, Ren X, Asara JM, Mathisen DJ, Vacanti JP, Ott HC | The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation | 24365767 | J Heart Lung Transplant | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24365767 |
| Decellularized scaffolds as a platform for bioengineered organs. | Tapias LF, Ott HC | Current opinion in organ transplantation | 24480969 | Curr Opin Organ Transplant | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24480969 |
| Regenerative potential of human airway stem cells in lung epithelial engineering. | Gilpin SE, Charest JM, Ren X, Tapias LF, Wu T, Evangelista-Leite D, Mathisen DJ, Ott HC | Biomaterials | 27622532 | Biomaterials | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27622532 |
| Bioengineering kidneys for transplantation. | Madariaga ML, Ott HC | Seminars in nephrology | 25217267 | Semin Nephrol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25217267 |
| Bioengineering of functional human induced pluripotent stem cell-derived intestinal grafts. | Kitano K, Schwartz DM, Zhou H, Gilpin SE, Wojtkiewicz GR, Ren X, Sommer CA, Capilla AV, Mathisen DJ, Goldstein AM, Mostoslavsky G, Ott HC | Nature communications | 29018244 | Nat Commun | 2017 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/29018244 |
| Design and validation of a clinical-scale bioreactor for long-term isolated lung culture. | Charest JM, Okamoto T, Kitano K, Yasuda A, Gilpin SE, Mathisen DJ, Ott HC | Biomaterials | 25818415 | Biomaterials | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25818415 |
| Ex vivo non-invasive assessment of cell viability and proliferation in bio-engineered whole organ constructs. | Ren X, Tapias LF, Jank BJ, Mathisen DJ, Lanuti M, Ott HC | Biomaterials | 25818417 | Biomaterials | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25818417 |
| Engineered composite tissue as a bioartificial limb graft. | Jank BJ, Xiong L, Moser PT, Guyette JP, Ren X, Cetrulo CL, Leonard DA, Fernandez L, Fagan SP, Ott HC | Biomaterials | 26004237 | Biomaterials | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26004237 |
| Metabolic glycan labeling and chemoselective functionalization of native biomaterials. | Ren X, Evangelista-Leite D, Wu T, Rajab TK, Moser PT, Kitano K, Economopoulos KP, Gorman DE, Bloom JP, Tan JJ, Gilpin SE, Zhou H, Mathisen DJ, Ott HC | Biomaterials | 30118980 | Biomaterials | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30118980 |
| Creation of a Bioengineered Skin Flap Scaffold with a Perfusable Vascular Pedicle. | Jank BJ, Goverman J, Guyette JP, Charest JM, Randolph M, Gaudette GR, Gershlak JR, Purschke M, Javorsky E, Nazarian RM, Leonard DA, Cetrulo CL, Austen WG, Ott HC | Tissue engineering. Part A | 28323545 | Tissue Eng Part A | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28323545 |
| Physicochemical regulation of biofilm formation. | Renner LD, Weibel DB | MRS bulletin | 22125358 | MRS Bull | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/22125358 |
| Small Molecule Chelators Reveal That Iron Starvation Inhibits Late Stages of Bacterial Cytokinesis. | Santos TMA, Lammers MG, Zhou M, Sparks IL, Rajendran M, Fang D, De Jesus CLY, Carneiro GFR, Cui Q, Weibel DB | ACS chemical biology | 29227619 | ACS Chem Biol | 2018 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/29227619 |
| Bacterial Cell Mechanics. | Auer GK, Weibel DB | Biochemistry | 28666084 | Biochemistry | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28666084 |
| Bacterial growth and adaptation in microdroplet chemostats. | Jakiela S, Kaminski TS, Cybulski O, Weibel DB, Garstecki P | Angewandte Chemie (International ed. in English) | 23832572 | Angew Chem Int Ed Engl | 2013 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/23832572 |
| Bacteria-surface interactions. | Tuson HH, Weibel DB | Soft matter | 23930134 | Soft Matter | 2013 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/23930134 |
| Mechanical Genomic Studies Reveal the Role of d-Alanine Metabolism in Pseudomonas aeruginosa Cell Stiffness. | Trivedi RR, Crooks JA, Auer GK, Pendry J, Foik IP, Siryaporn A, Abbott NL, Gitai Z, Weibel DB | mBio | 30206169 | mBio | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30206169 |
| Mechanical Genomics Identifies Diverse Modulators of Bacterial Cell Stiffness. | Auer GK, Lee TK, Rajendram M, Cesar S, Miguel A, Huang KC, Weibel DB | Cell systems | 27321372 | Cell Syst | 2016 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/27321372 |
| DCAP: a broad-spectrum antibiotic that targets the cytoplasmic membrane of bacteria. | Eun YJ, Foss MH, Kiekebusch D, Pauw DA, Westler WM, Thanbichler M, Weibel DB | Journal of the American Chemical Society | 22741745 | J Am Chem Soc | 2012 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/22741745 |
| Using liquid crystals to reveal how mechanical anisotropy changes interfacial behaviors of motile bacteria. | Mushenheim PC, Trivedi RR, Weibel DB, Abbott NL | Biophysical journal | 24988359 | Biophys J | 2014 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24988359 |
| Gyramides prevent bacterial growth by inhibiting DNA gyrase and altering chromosome topology. | Rajendram M, Hurley KA, Foss MH, Thornton KM, Moore JT, Shaw JT, Weibel DB | ACS chemical biology | 24712739 | ACS Chem Biol | 2014 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/24712739 |
| Polar localization of Escherichia coli chemoreceptors requires an intact Tol-Pal complex. | Santos TM, Lin TY, Rajendran M, Anderson SM, Weibel DB | Molecular microbiology | 24720726 | Mol Microbiol | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24720726 |
| Dynamic self-assembly of motile bacteria in liquid crystals. | Mushenheim PC, Trivedi RR, Tuson HH, Weibel DB, Abbott NL | Soft matter | 24652584 | Soft Matter | 2014 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/24652584 |
| Targeting quinolone- and aminocoumarin-resistant bacteria with new gyramide analogs that inhibit DNA gyrase. | Hurley KA, Santos TMA, Fensterwald MR, Rajendran M, Moore JT, Balmond EI, Blahnik BJ, Faulkner KC, Foss MH, Heinrich VA, Lammers MG, Moore LC, Reynolds GD, Shearn-Nance GP, Stearns BA, Yao ZW, Shaw JT, Weibel DB | MedChemComm | 30034678 | Medchemcomm | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/30034678 |
| A chemist building paths to cell biology. | Weibel DB | Molecular biology of the cell | 24174456 | Mol Biol Cell | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24174456 |
| Divin: a small molecule inhibitor of bacterial divisome assembly. | Eun YJ, Zhou M, Kiekebusch D, Schlimpert S, Trivedi RR, Bakshi S, Zhong Z, Wahlig TA, Thanbichler M, Weibel DB | Journal of the American Chemical Society | 23738839 | J Am Chem Soc | 2013 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/23738839 |
| From swimming to swarming: Escherichia coli cell motility in two-dimensions. | Swiecicki JM, Sliusarenko O, Weibel DB | Integrative biology : quantitative biosciences from nano to macro | 24145500 | Integr Biol (Camb) | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24145500 |
| The outer membrane is an essential load-bearing element in Gram-negative bacteria. | Rojas ER, Billings G, Odermatt PD, Auer GK, Zhu L, Miguel A, Chang F, Weibel DB, Theriot JA, Huang KC | Nature | 30022160 | Nature | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30022160 |
| A Cardiolipin-Deficient Mutant of Rhodobacter sphaeroides Has an Altered Cell Shape and Is Impaired in Biofilm Formation. | Lin TY, Santos TM, Kontur WS, Donohue TJ, Weibel DB | Journal of bacteriology | 26283770 | J Bacteriol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26283770 |
| Anionic Phospholipids Stabilize RecA Filament Bundles in Escherichia coli. | Rajendram M, Zhang L, Reynolds BJ, Auer GK, Tuson HH, Ngo KV, Cox MM, Yethiraj A, Cui Q, Weibel DB | Molecular cell | 26481664 | Mol Cell | 2015 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/26481664 |
| 5-Alkyloxytryptamines are membrane-targeting, broad-spectrum antibiotics. | Faulkner KC, Hurley KA, Weibel DB | Bioorganic & medicinal chemistry letters | 27765507 | Bioorg Med Chem Lett | 2016 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/27765507 |
| Measuring the stiffness of bacterial cells from growth rates in hydrogels of tunable elasticity. | Tuson HH, Auer GK, Renner LD, Hasebe M, Tropini C, Salick M, Crone WC, Gopinathan A, Huang KC, Weibel DB | Molecular microbiology | 22548341 | Mol Microbiol | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22548341 |
| Inhibitors of bacterial tubulin target bacterial membranes in vivo. | Foss MH, Eun YJ, Grove CI, Pauw DA, Sorto NA, Rensvold JW, Pagliarini DJ, Shaw JT, Weibel DB | MedChemComm | 23539337 | Medchemcomm | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23539337 |
| Draft Genome Sequences of Two Pairs of Human Intestinal Bifidobacterium longum subsp. longum Strains, 44B and 1-6B and 35B and 2-2B, Consecutively Isolated from Two Children after a 5-Year Time Period. | Shkoporov AN, Efimov BA, Khokhlova EV, Chaplin AV, Kafarskaya LI, Durkin AS, McCorrison J, Torralba M, Gillis M, Sutton G, Weibel DB, Nelson KE, Smeianov VV | Genome announcements | 23682142 | Genome Announc | 2013 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/23682142 |
| Flagellum density regulates Proteus mirabilis swarmer cell motility in viscous environments. | Tuson HH, Copeland MF, Carey S, Sacotte R, Weibel DB | Journal of bacteriology | 23144253 | J Bacteriol | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23144253 |
| Studying biomolecule localization by engineering bacterial cell wall curvature. | Renner LD, Eswaramoorthy P, Ramamurthi KS, Weibel DB | PloS one | 24391905 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24391905 |
| Structure-activity studies of divin: an inhibitor of bacterial cell division. | Zhou M, Eun YJ, Guzei IA, Weibel DB | ACS medicinal chemistry letters | 24044050 | ACS Med Chem Lett | 2013 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/24044050 |
| Maspin binds to cardiolipin in mitochondria and triggers apoptosis. | Mahajan N, Hoover B, Rajendram M, Shi HY, Kawasaki K, Weibel DB, Zhang M | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 30786218 | FASEB J | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30786218 |
| Membrane-Targeting DCAP Analogues with Broad-Spectrum Antibiotic Activity against Pathogenic Bacteria. | Hurley KA, Heinrich VA, Hershfield JR, Demons ST, Weibel DB | ACS medicinal chemistry letters | 25941556 | ACS Med Chem Lett | 2015 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/25941556 |
| Decoding the Chemical Language of Motile Bacteria by Using High-Throughput Microfluidic Assays. | Crooks JA, Stilwell MD, Oliver PM, Zhong Z, Weibel DB | Chembiochem : a European journal of chemical biology | 26285783 | Chembiochem | 2015 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/26285783 |
| Bacterial Swarming Reduces Proteus mirabilis and Vibrio parahaemolyticus Cell Stiffness and Increases β-Lactam Susceptibility. | Auer GK, Oliver PM, Rajendram M, Lin TY, Yao Q, Jensen GJ, Weibel DB | mBio | 31594808 | mBio | 2019 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/31594808 |
| Bacterial cellulose as a substrate for microbial cell culture. | Yin N, Santos TM, Auer GK, Crooks JA, Oliver PM, Weibel DB | Applied and environmental microbiology | 24441155 | Appl Environ Microbiol | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24441155 |
| Microfluidics for High School Chemistry Students. | Hemling M, Crooks JA, Oliver PM, Brenner K, Gilbertson J, Lisensky GC, Weibel DB | Journal of chemical education | 25584013 | J Chem Educ | 2014 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/25584013 |
| Localization of anionic phospholipids in Escherichia coli cells. | Oliver PM, Crooks JA, Leidl M, Yoon EJ, Saghatelian A, Weibel DB | Journal of bacteriology | 25002539 | J Bacteriol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25002539 |
| Nuclease-resistant DNA via high-density packing in polymeric micellar nanoparticle coronas. | Rush AM, Thompson MP, Tatro ET, Gianneschi NC | ACS nano | 23379679 | ACS Nano | 2013 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/23379679 |
| Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. | Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC | Journal of the American Chemical Society | 25314576 | J Am Chem Soc | 2014 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/25314576 |
| Polymerization of Protecting-Group-Free Peptides via ROMP. | Kammeyer JK, Blum AP, Adamiak L, Hahn ME, Gianneschi NC | Polymer chemistry | 24015154 | Polym Chem | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24015154 |
| Fluorogenic Enzyme-Responsive Micellar Nanoparticles. | Chien MP, Thompson MP, Lin EC, Gianneschi NC | Chemical science | 23585924 | Chem Sci | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23585924 |
| Cellular Delivery of Nanoparticles Revealed with Combined Optical and Isotopic Nanoscopy. | Proetto MT, Anderton CR, Hu D, Szymanski CJ, Zhu Z, Patterson JP, Kammeyer JK, Nilewski LG, Rush AM, Bell NC, Evans JE, Orr G, Howell SB, Gianneschi NC | ACS nano | 27022832 | ACS Nano | 2016 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/27022832 |
| Stimuli-responsive nanomaterials for biomedical applications. | Blum AP, Kammeyer JK, Rush AM, Callmann CE, Hahn ME, Gianneschi NC | Journal of the American Chemical Society | 25474531 | J Am Chem Soc | 2015 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/25474531 |
| Polymeric Gd-DOTA amphiphiles form spherical and fibril-shaped nanoparticle MRI contrast agents. | Randolph LM, LeGuyader CLM, Hahn ME, Andolina CM, Patterson JP, Mattrey RF, Millstone JE, Botta M, Scadeng M, Gianneschi NC | Chemical science | 30155069 | Chem Sci | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/30155069 |
| Polycatechol Nanoparticle MRI Contrast Agents. | Li Y, Huang Y, Wang Z, Carniato F, Xie Y, Patterson JP, Thompson MP, Andolina CM, Ditri TB, Millstone JE, Figueroa JS, Rinehart JD, Scadeng M, Botta M, Gianneschi NC | Small (Weinheim an der Bergstrasse, Germany) | 26681255 | Small | 2016 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/26681255 |
| Polymerization of a peptide-based enzyme substrate. | Hahn ME, Randolph LM, Adamiak L, Thompson MP, Gianneschi NC | Chemical communications (Cambridge, England) | 23450132 | Chem Commun (Camb) | 2013 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/23450132 |
| Enzyme-directed assembly of a nanoparticle probe in tumor tissue. | Chien MP, Thompson MP, Barback CV, Ku TH, Hall DJ, Gianneschi NC | Advanced materials (Deerfield Beach, Fla.) | 23712821 | Adv Mater | 2013 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/23712821 |
| Dynamics of soft nanomaterials captured by transmission electron microscopy in liquid water. | Proetto MT, Rush AM, Chien MP, Abellan Baeza P, Patterson JP, Thompson MP, Olson NH, Moore CE, Rheingold AL, Andolina C, Millstone J, Howell SB, Browning ND, Evans JE, Gianneschi NC | Journal of the American Chemical Society | 24422495 | J Am Chem Soc | 2014 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/24422495 |
| Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles. | Rush AM, Nelles DA, Blum AP, Barnhill SA, Tatro ET, Yeo GW, Gianneschi NC | Journal of the American Chemical Society | 24827740 | J Am Chem Soc | 2014 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/24827740 |
| Blending block copolymer micelles in solution; Obstacles of blending. | Wright DB, Patterson JP, Gianneschi NC, Chassenieux C, Colombani O, O'Reilly RK | Polymer chemistry | 26918033 | Polym Chem | 2016 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/26918033 |
| Activating Peptides for Cellular Uptake via Polymerization into High Density Brushes. | Blum AP, Kammeyer JK, Gianneschi NC | Chemical science | 26925209 | Chem Sci | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26925209 |
| Biosynthetic Polymers as Functional Materials. | Carlini AS, Adamiak L, Gianneschi NC | Macromolecules | 27375299 | Macromolecules | 2016 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/27375299 |
| Enzyme-directed assembly of nanoparticles in tumors monitored by in vivo whole animal imaging and ex vivo super-resolution fluorescence imaging. | Chien MP, Carlini AS, Hu D, Barback CV, Rush AM, Hall DJ, Orr G, Gianneschi NC | Journal of the American Chemical Society | 24308273 | J Am Chem Soc | 2013 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/24308273 |
| Biological stimuli and biomolecules in the assembly and manipulation of nanoscale polymeric particles. | Randolph LM, Chien MP, Gianneschi NC | Chemical science | 24353895 | Chem Sci | 2012 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24353895 |
| Labelling Polymers and Micellar Nanoparticles via Initiation, Propagation and Termination with ROMP. | Thompson MP, Randolph LM, James CR, Davalos AN, Hahn ME, Gianneschi NC | Polymer chemistry | 24855496 | Polym Chem | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/24855496 |
| A beginning of the end: new insights into the functional organization of telomeres. | Wood AM, Laster K, Rice EL, Kosak ST | Nucleus (Austin, Tex.) | 25961132 | Nucleus | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25961132 |
| Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. | Yang R, Kerschner JL, Gosalia N, Neems D, Gorsic LK, Safi A, Crawford GE, Kosak ST, Leir SH, Harris A | Nucleic acids research | 26673704 | Nucleic Acids Res | 2016 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/26673704 |
| Topologically associated domains enriched for lineage-specific genes reveal expression-dependent nuclear topologies during myogenesis. | Neems DS, Garza-Gongora AG, Smith ED, Kosak ST | Proceedings of the National Academy of Sciences of the United States of America | 26957603 | Proc Natl Acad Sci U S A | 2016 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/26957603 |
| Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus. | Gosalia N, Neems D, Kerschner JL, Kosak ST, Harris A | Nucleic acids research | 25081205 | Nucleic Acids Res | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25081205 |
| Clinical Epigenetic Therapies Disrupt Sex Chromosome Dosage Compensation in Human Female Cells. | Laskowski AI, Fanslow DA, Smith ED, Kosak ST | Gender and the genome | 30899898 | Gend Genome | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30899898 |
| Interstitial telomeric loops and implications of the interaction between TRF2 and lamin A/C. | Smith ED, Garza-Gongora AG, MacQuarrie KL, Kosak ST | Differentiation; research in biological diversity | 29979997 | Differentiation | 2018 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/29979997 |
| TRF2 and lamin A/C interact to facilitate the functional organization of chromosome ends. | Wood AM, Rendtlew Danielsen JM, Lucas CA, Rice EL, Scalzo D, Shimi T, Goldman RD, Smith ED, Le Beau MM, Kosak ST | Nature communications | 25399868 | Nat Commun | 2014 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/25399868 |
| Characterization of a large human transgene following invasin-mediated delivery in a bacterial artificial chromosome. | Gillen AE, Lucas CA, Haussecker PL, Kosak ST, Harris A | Chromosoma | 23749207 | Chromosoma | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23749207 |
| Varying levels of X chromosome coalescence in female somatic cells alters the balance of X-linked dosage compensation and is implicated in female-dominant systemic lupus erythematosus. | Laskowski AI, Neems DS, Laster K, Strojny-Okyere C, Rice EL, Konieczna IM, Voss JH, Mathew JM, Leventhal JR, Ramsey-Goldman R, Smith ED, Kosak ST | Scientific reports | 31142749 | Sci Rep | 2019 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/31142749 |
| A Crowdsourced nucleus: understanding nuclear organization in terms of dynamically networked protein function. | Wood AM, Garza-Gongora AG, Kosak ST | Biochimica et biophysica acta | 24412853 | Biochim Biophys Acta | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24412853 |
| Syndecan-1 in mechanosensing of nanotopological cues in engineered materials. | Le V, Lee J, Chaterji S, Spencer A, Liu YL, Kim P, Yeh HC, Kim DH, Baker AB | Biomaterials | 29156422 | Biomaterials | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29156422 |
| Murine model of femoral artery wire injury with implantation of a perivascular drug delivery patch. | Le V, Johnson CG, Lee JD, Baker AB | Journal of visualized experiments : JoVE | 25742368 | J Vis Exp | 2015 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/25742368 |
| A novel system for studying mechanical strain waveform-dependent responses in vascular smooth muscle cells. | Lee J, Wong M, Smith Q, Baker AB | Lab on a chip | 24096612 | Lab Chip | 2013 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/24096612 |
| Overcoming disease-induced growth factor resistance in therapeutic angiogenesis using recombinant co-receptors delivered by a liposomal system. | Das S, Singh G, Baker AB | Biomaterials | 24138828 | Biomaterials | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24138828 |
| Synergistic effects of matrix nanotopography and stiffness on vascular smooth muscle cell function. | Chaterji S, Kim P, Choe SH, Tsui JH, Lam CH, Ho DS, Baker AB, Kim DH | Tissue engineering. Part A | 24694244 | Tissue Eng Part A | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24694244 |
| Glypican-1 nanoliposomes for potentiating growth factor activity in therapeutic angiogenesis. | Monteforte AJ, Lam B, Das S, Mukhopadhyay S, Wright CS, Martin PE, Dunn AK, Baker AB | Biomaterials | 27101205 | Biomaterials | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27101205 |
| Biomaterials and Nanotherapeutics for Enhancing Skin Wound Healing. | Das S, Baker AB | Frontiers in bioengineering and biotechnology | 27843895 | Front Bioeng Biotechnol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27843895 |
| Syndecan-4 proteoliposomes enhance fibroblast growth factor-2 (FGF-2)-induced proliferation, migration, and neovascularization of ischemic muscle. | Jang E, Albadawi H, Watkins MT, Edelman ER, Baker AB | Proceedings of the National Academy of Sciences of the United States of America | 22307630 | Proc Natl Acad Sci U S A | 2012 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/22307630 |
| Analysis of a high-throughput cone-and-plate apparatus for the application of defined spatiotemporal flow to cultured cells. | Spruell C, Baker AB | Biotechnology and bioengineering | 23280552 | Biotechnol Bioeng | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23280552 |
| Heparanase regulates thrombosis in vascular injury and stent-induced flow disturbance. | Baker AB, Gibson WJ, Kolachalama VB, Golomb M, Indolfi L, Spruell C, Zcharia E, Vlodavsky I, Edelman ER | Journal of the American College of Cardiology | 22516446 | J Am Coll Cardiol | 2012 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/22516446 |
| Computational analysis of fluid flow within a device for applying biaxial strain to cultured cells. | Lee J, Baker AB | Journal of biomechanical engineering | 25611013 | J Biomech Eng | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25611013 |
| Syndecan-1 regulates vascular smooth muscle cell phenotype. | Chaterji S, Lam CH, Ho DS, Proske DC, Baker AB | PloS one | 24587062 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24587062 |
| High Throughput Label Free Measurement of Cancer Cell Adhesion Kinetics Under Hemodynamic Flow. | Spencer A, Baker AB | Scientific reports | 26816215 | Sci Rep | 2016 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/26816215 |
| Loss of syndecan-1 induces a pro-inflammatory phenotype in endothelial cells with a dysregulated response to atheroprotective flow. | Voyvodic PL, Min D, Liu R, Williams E, Chitalia V, Dunn AK, Baker AB | The Journal of biological chemistry | 24554698 | J Biol Chem | 2014 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/24554698 |
| Synergistic effect of local endothelial shear stress and systemic hypercholesterolemia on coronary atherosclerotic plaque progression and composition in pigs. | Koskinas KC, Chatzizisis YS, Papafaklis MI, Coskun AU, Baker AB, Jarolim P, Antoniadis A, Edelman ER, Stone PH, Feldman CL | International journal of cardiology | 24148915 | Int J Cardiol | 2013 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/24148915 |
| The role of scaffold microarchitecture in engineering endothelial cell immunomodulation. | Indolfi L, Baker AB, Edelman ER | Biomaterials | 22796162 | Biomaterials | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22796162 |
| Syndesome Therapeutics for Enhancing Diabetic Wound Healing. | Das S, Singh G, Majid M, Sherman MB, Mukhopadhyay S, Wright CS, Martin PE, Dunn AK, Baker AB | Advanced healthcare materials | 27385307 | Adv Healthc Mater | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27385307 |
| (*) Glioblastoma Exosomes for Therapeutic Angiogenesis in Peripheral Ischemia. | Monteforte A, Lam B, Sherman MB, Henderson K, Sligar AD, Spencer A, Tang B, Dunn AK, Baker AB | Tissue engineering. Part A | 28699397 | Tissue Eng Part A | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28699397 |
| A high-throughput mechanofluidic screening platform for investigating tumor cell adhesion during metastasis. | Spencer A, Spruell C, Nandi S, Wong M, Creixell M, Baker AB | Lab on a chip | 26584160 | Lab Chip | 2016 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/26584160 |
| Optimized design of a hyperflexible sieve electrode to enhance neurovascular regeneration for a peripheral neural interface. | Veith A, Li X, Modi H, Abbaspour A, Luan L, Xie C, Baker AB | Biomaterials | 34147716 | Biomaterials | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34147716 |
| A multichannel dampened flow system for studies on shear stress-mediated mechanotransduction. | Voyvodic PL, Min D, Baker AB | Lab on a chip | 22836694 | Lab Chip | 2012 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22836694 |
| Thin-capped atheromata with reduced collagen content in pigs develop in coronary arterial regions exposed to persistently low endothelial shear stress. | Koskinas KC, Sukhova GK, Baker AB, Papafaklis MI, Chatzizisis YS, Coskun AU, Quillard T, Jonas M, Maynard C, Antoniadis AP, Shi GP, Libby P, Edelman ER, Feldman CL, Stone PH | Arteriosclerosis, thrombosis, and vascular biology | 23640495 | Arterioscler Thromb Vasc Biol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23640495 |
| Syndecan-4 enhances PDGF-BB activity in diabetic wound healing. | Das S, Majid M, Baker AB | Acta biomaterialia | 27381525 | Acta Biomater | 2016 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/27381525 |
| Syndecan-4 Enhances Therapeutic Angiogenesis after Hind Limb Ischemia in Mice with Type 2 Diabetes. | Das S, Monteforte AJ, Singh G, Majid M, Sherman MB, Dunn AK, Baker AB | Advanced healthcare materials | 26891081 | Adv Healthc Mater | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26891081 |
| Overhauser Dynamic Nuclear Polarization-Enhanced NMR Relaxometry. | Franck JM, Kausik R, Han S | Microporous and mesoporous materials : the official journal of the International Zeolite Association | 23837010 | Microporous Mesoporous Mater | 2013 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/23837010 |
| Quantitative analysis of molecular transport across liposomal bilayer by J-mediated 13C Overhauser dynamic nuclear polarization. | Cheng CY, Goor OJ, Han S | Analytical chemistry | 23072518 | Anal Chem | 2012 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/23072518 |
| Dynamic nuclear polarization methods in solids and solutions to explore membrane proteins and membrane systems. | Cheng CY, Han S | Annual review of physical chemistry | 23331309 | Annu Rev Phys Chem | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23331309 |
| Nonlinear scaling of surface water diffusion with bulk water viscosity of crowded solutions. | Franck JM, Scott JA, Han S | Journal of the American Chemical Society | 23347324 | J Am Chem Soc | 2013 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/23347324 |
| Specific ions modulate diffusion dynamics of hydration water on lipid membrane surfaces. | Song J, Franck J, Pincus P, Kim MW, Han S | Journal of the American Chemical Society | 24456096 | J Am Chem Soc | 2014 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/24456096 |
| Cholesterol enhances surface water diffusion of phospholipid bilayers. | Cheng CY, Olijve LL, Kausik R, Han S | The Journal of chemical physics | 25494784 | J Chem Phys | 2014 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/25494784 |
| Nanometer-scale water- and proton-diffusion heterogeneities across water channels in polymer electrolyte membranes. | Song J, Han OH, Han S | Angewandte Chemie (International ed. in English) | 25630609 | Angew Chem Int Ed Engl | 2015 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/25630609 |
| Correlating steric hydration forces with water dynamics through surface force and diffusion NMR measurements in a lipid-DMSO-H2O system. | Schrader AM, Donaldson SH Jr, Song J, Cheng CY, Lee DW, Han S, Israelachvili JN | Proceedings of the National Academy of Sciences of the United States of America | 26261313 | Proc Natl Acad Sci U S A | 2015 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/26261313 |
| DMSO induces dehydration near lipid membrane surfaces. | Cheng CY, Song J, Pas J, Meijer LH, Han S | Biophysical journal | 26200868 | Biophys J | 2015 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/26200868 |
| Tau Aggregation Propensity Engrained in Its Solution State. | Eschmann NA, Do TD, LaPointe NE, Shea JE, Feinstein SC, Bowers MT, Han S | The journal of physical chemistry. B | 26484390 | J Phys Chem B | 2015 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/26484390 |
| Intrinsic surface-drying properties of bioadhesive proteins. | Akdogan Y, Wei W, Huang KY, Kageyama Y, Danner EW, Miller DR, Martinez Rodriguez NR, Waite JH, Han S | Angewandte Chemie (International ed. in English) | 25168789 | Angew Chem Int Ed Engl | 2014 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/25168789 |
| Functional consequences of the oligomeric assembly of proteorhodopsin. | Hussain S, Kinnebrew M, Schonenbach NS, Aye E, Han S | Journal of molecular biology | 25597999 | J Mol Biol | 2015 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/25597999 |
| Probing water density and dynamics in the chaperonin GroEL cavity. | Franck JM, Sokolovski M, Kessler N, Matalon E, Gordon-Grossman M, Han SI, Goldfarb D, Horovitz A | Journal of the American Chemical Society | 24888581 | J Am Chem Soc | 2014 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/24888581 |
| Asymmetric collapse in biomimetic complex coacervates revealed by local polymer and water dynamics. | Ortony JH, Hwang DS, Franck JM, Waite JH, Han S | Biomacromolecules | 23540713 | Biomacromolecules | 2013 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/23540713 |
| Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces. | Franck JM, Ding Y, Stone K, Qin PZ, Han S | Journal of the American Chemical Society | 26256693 | J Am Chem Soc | 2015 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/26256693 |
| Hydration dynamics as an intrinsic ruler for refining protein structure at lipid membrane interfaces. | Cheng CY, Varkey J, Ambroso MR, Langen R, Han S | Proceedings of the National Academy of Sciences of the United States of America | 24082088 | Proc Natl Acad Sci U S A | 2013 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/24082088 |
| Quantitative cw Overhauser effect dynamic nuclear polarization for the analysis of local water dynamics. | Franck JM, Pavlova A, Scott JA, Han S | Progress in nuclear magnetic resonance spectroscopy | 24083461 | Prog Nucl Magn Reson Spectrosc | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24083461 |
| Ion specific effects: decoupling ion-ion and ion-water interactions. | Song J, Kang TH, Kim MW, Han S | Physical chemistry chemical physics : PCCP | 25761273 | Phys Chem Chem Phys | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25761273 |
| Structural and biochemical studies of a fluoroacetyl-CoA-specific thioesterase reveal a molecular basis for fluorine selectivity. | Weeks AM, Coyle SM, Jinek M, Doudna JA, Chang MC | Biochemistry | 20836570 | Biochemistry | 2010 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20836570 |
| Catalytic control of enzymatic fluorine specificity. | Weeks AM, Chang MC | Proceedings of the National Academy of Sciences of the United States of America | 23150553 | Proc Natl Acad Sci U S A | 2012 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/23150553 |
| Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. | Weeks AM, Chang MC | Biochemistry | 21591680 | Biochemistry | 2011 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/21591680 |
| Molecular recognition of fluorine impacts substrate selectivity in the fluoroacetyl-CoA thioesterase FlK. | Weeks AM, Keddie NS, Wadoux RD, O'Hagan D, Chang MC | Biochemistry | 24635371 | Biochemistry | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24635371 |
| Synthetic biology approaches to fluorinated polyketides. | Thuronyi BW, Chang MC | Accounts of chemical research | 25719427 | Acc Chem Res | 2015 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/25719427 |
| Natural and engineered biosynthesis of fluorinated natural products. | Walker MC, Chang MC | Chemical Society reviews | 24776946 | Chem Soc Rev | 2014 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/24776946 |
| Elucidating the mechanism of fluorinated extender unit loading for improved production of fluorine-containing polyketides. | Ad O, Thuronyi BW, Chang MC | Proceedings of the National Academy of Sciences of the United States of America | 28096394 | Proc Natl Acad Sci U S A | 2017 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/28096394 |
| Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. | Walker MC, Thuronyi BW, Charkoudian LK, Lowry B, Khosla C, Chang MC | Science (New York, N.Y.) | 24009388 | Science | 2013 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/24009388 |
| Temporal and fluoride control of secondary metabolism regulates cellular organofluorine biosynthesis. | Walker MC, Wen M, Weeks AM, Chang MC | ACS chemical biology | 22769062 | ACS Chem Biol | 2012 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22769062 |
| Editorial overview: Opportunities and challenges in synthetic biology. | Chang MC, Zhao H | Current opinion in chemical biology | 26456417 | Curr Opin Chem Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26456417 |
| Mechanisms of carbon nanotube aggregation and the reversion of carbon nanotube aggregates in aqueous medium. | Koh B, Cheng W | Langmuir : the ACS journal of surfaces and colloids | 25144606 | Langmuir | 2014 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/25144606 |
| The Density Code for the Development of a Vaccine? | Cheng W | Journal of pharmaceutical sciences | 27649885 | J Pharm Sci | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27649885 |
| Optimized Infectivity of the Cell-Free Single-Cycle Human Immunodeficiency Viruses Type 1 (HIV-1) and Its Restriction by Host Cells. | Kim JH, Song H, Austin JL, Cheng W | PloS one | 23825637 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23825637 |
| Using optical trap to measure the refractive index of a single animal virus in culture fluid with high precision. | Pang Y, Song H, Cheng W | Biomedical optics express | 27231613 | Biomed Opt Express | 2016 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/27231613 |
| Mechanisms of HCV NS3 helicase monitored by optical tweezers. | Cheng W | Methods in molecular biology (Clifton, N.J.) | 25579590 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25579590 |
| Quantitation and Stability of Protein Conjugation on Liposomes for Controlled Density of Surface Epitopes. | Chen Z, Moon JJ, Cheng W | Bioconjugate chemistry | 29528624 | Bioconjug Chem | 2018 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/29528624 |
| Probability of Immobilization on Host Cell Surface Regulates Viral Infectivity. | DeSantis MC, Tian C, Kim JH, Austin JL, Cheng W | Physical review letters | 33016741 | Phys Rev Lett | 2020 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/33016741 |
| Step detection in single-molecule real time trajectories embedded in correlated noise. | Arunajadai SG, Cheng W | PloS one | 23533612 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23533612 |
| Microfluidic-based high-throughput optical trapping of nanoparticles. | Kotnala A, Zheng Y, Fu J, Cheng W | Lab on a chip | 28561826 | Lab Chip | 2017 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/28561826 |
| The Single-Molecule Centroid Localization Algorithm Improves the Accuracy of Fluorescence Binding Assays. | Hua B, Wang Y, Park S, Han KY, Singh D, Kim JH, Cheng W, Ha T | Biochemistry | 29457977 | Biochemistry | 2018 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/29457977 |
| Reversible aggregation of HIV-1 Gag proteins mediated by nucleic acids. | Chen Z, Cheng W | Biochemical and biophysical research communications | 27965093 | Biochem Biophys Res Commun | 2017 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/27965093 |
| Dynasore inhibition on productive infection of HIV-1 in commonly used cell lines is independent of transferrin endocytosis. | Song H, DeSantis M, Tian C, Cheng W | Matters | 31058179 | Matters (Zur) | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/31058179 |
| Fluorophore and dye-assisted dispersion of carbon nanotubes in aqueous solution. | Koh B, Kim G, Yoon HK, Park JB, Kopelman R, Cheng W | Langmuir : the ACS journal of surfaces and colloids | 22812904 | Langmuir | 2012 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/22812904 |
| Detection of single fluorescent proteins inside eukaryotic cells using two-photon fluorescence. | Hou X, Cheng W | Biomedical optics express | 22312586 | Biomed Opt Express | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22312586 |
| Quantitative Correlation between Infectivity and Gp120 Density on HIV-1 Virions Revealed by Optical Trapping Virometry. | DeSantis MC, Kim JH, Song H, Klasse PJ, Cheng W | The Journal of biological chemistry | 27129237 | J Biol Chem | 2016 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/27129237 |
| Optical manipulation of a single human virus for study of viral-cell interactions. | Hou X, DeSantis MC, Tian C, Cheng W | Proceedings of SPIE--the International Society for Optical Engineering | 27746582 | Proc SPIE Int Soc Opt Eng | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27746582 |
| Label-free detection and manipulation of single biological nanoparticles. | DeSantis MC, Cheng W | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 26846164 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26846164 |
| Optical trapping of individual human immunodeficiency viruses in culture fluid reveals heterogeneity with single-molecule resolution. | Pang Y, Song H, Kim JH, Hou X, Cheng W | Nature nanotechnology | 25038779 | Nat Nanotechnol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25038779 |
| Recovering degraded quasi-solid-state dye-sensitized solar cells by applying electrical pulses. | Zhang X, Huang X, Jiang H | Physical chemistry chemical physics : PCCP | 23545782 | Phys Chem Chem Phys | 2013 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/23545782 |
| Liquid Tunable Microlenses based on MEMS techniques. | Zeng X, Jiang H | Journal of physics D: Applied physics | 24163480 | J Phys D Appl Phys | 2013 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/24163480 |
| Tunable dielectric liquid lens on flexible substrate. | Lu YS, Tu H, Xu Y, Jiang H | Applied physics letters | 24493877 | Appl Phys Lett | 2013 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/24493877 |
| Double Sided-Design of Electrodes Driving Tunable Dielectrophoretic Miniature Lens. | Almoallem Y, Jiang H | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 29606846 | J Microelectromech Syst | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29606846 |
| Energy Storage via Polyvinylidene Fluoride Dielectric on the Counterelectrode of Dye-Sensitized Solar Cells. | Huang X, Zhang X, Jiang H | Journal of power sources | 24327797 | J Power Sources | 2014 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/24327797 |
| Design and fabrication of an electrohydrodynamically actuated microlens with areal density modulated electrodes. | Ashtiani AO, Jiang H | Journal of micromechanics and microengineering : structures, devices, and systems | 32773966 | J Micromech Microeng | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32773966 |
| Lateral dye-sensitized microscale solar cells via femtosecond laser patterning. | Zhang X, Huang Y, Hao B, Hewei L, Huang X, Jiang H | Advanced materials technologies | 31341947 | Adv Mater Technol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31341947 |
| High Performance All-Solid-State Flexible Micro-Pseudocapacitor Based on Hierarchically Nanostructured Tungsten Trioxide Composite. | Huang X, Liu H, Zhang X, Jiang H | ACS applied materials & interfaces | 26618406 | ACS Appl Mater Interfaces | 2015 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/26618406 |
| Photovoltaically Self-Charging Cells with WO(3)·H(2)O/CNTs/PVDF Composite. | Huang X, Zhang X, Jiang H | RSC advances | 27774146 | RSC Adv | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27774146 |
| Actuators based on liquid crystalline elastomer materials. | Jiang H, Li C, Huang X | Nanoscale | 23648966 | Nanoscale | 2013 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/23648966 |
| Dye-sensitized solar cell with energy storage function through PVDF/ZnO nanocomposite counter electrode. | Zhang X, Huang X, Li C, Jiang H | Advanced materials (Deerfield Beach, Fla.) | 23740719 | Adv Mater | 2013 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/23740719 |
| Electrowetting-driven variable-focus microlens on flexible surfaces. | Li C, Jiang H | Applied physics letters | 22904571 | Appl Phys Lett | 2012 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/22904571 |
| Artificial eye for scotopic vision with bioinspired all-optical photosensitivity enhancer. | Liu H, Huang Y, Jiang H | Proceedings of the National Academy of Sciences of the United States of America | 26976565 | Proc Natl Acad Sci U S A | 2016 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/26976565 |
| A Liquid Optical Phase Shifter with an Embedded Electrowetting Actuator. | Ashtiani AO, Jiang H | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 29038640 | J Microelectromech Syst | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29038640 |
| Remote Axial Tuning in Microscopy Utilizing Hydrogel-Driven Tunable Liquid Lens. | Kanhere A, Lin G, Jiang H | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 31983867 | J Microelectromech Syst | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31983867 |
| Scattering-layer-induced energy storage function in polymer-based quasi-solid-state dye-sensitized solar cells. | Zhang X, Jiang H | Applied physics letters | 25829547 | Appl Phys Lett | 2015 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/25829547 |
| One-step femtosecond laser patterning of light-trapping structure on dye-sensitized solar cell photoelectrodes†. | Zhang X, Liu H, Huang X, Jiang H | Journal of materials chemistry. C | 26113977 | J Mater Chem C Mater | 2015 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/26113977 |
| Fabrication and Characterization of Flexible Electrowetting on Dielectrics (EWOD) Microlens. | Li C, Jiang H | Micromachines | 25360324 | Micromachines (Basel) | 2014 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/25360324 |
| Chemiluminescent Biosensors for Detection of Second Messenger Cyclic di-GMP. | Dippel AB, Anderson WA, Evans RS, Deutsch S, Hammond MC | ACS chemical biology | 29466657 | ACS Chem Biol | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/29466657 |
| In Vitro and In Vivo Enzyme Activity Screening via RNA-Based Fluorescent Biosensors for S-Adenosyl-l-homocysteine (SAH). | Su Y, Hickey SF, Keyser SG, Hammond MC | Journal of the American Chemical Society | 27191512 | J Am Chem Soc | 2016 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/27191512 |
| RNA-based fluorescent biosensors for live cell imaging of second messengers cyclic di-GMP and cyclic AMP-GMP. | Kellenberger CA, Wilson SC, Sales-Lee J, Hammond MC | Journal of the American Chemical Society | 23488798 | J Am Chem Soc | 2013 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/23488798 |
| An RNA-Based Fluorescent Biosensor for High-Throughput Analysis of the cGAS-cGAMP-STING Pathway. | Bose D, Su Y, Marcus A, Raulet DH, Hammond MC | Cell chemical biology | 27889408 | Cell Chem Biol | 2016 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/27889408 |
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| De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. | Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL | Science (New York, N.Y.) | 28336562 | Science | 2017 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/28336562 |
| High-resolution antibody dynamics of vaccine-induced immune responses. | Laserson U, Vigneault F, Gadala-Maria D, Yaari G, Uduman M, Vander Heiden JA, Kelton W, Taek Jung S, Liu Y, Laserson J, Chari R, Lee JH, Bachelet I, Hickey B, Lieberman-Aiden E, Hanczaruk B, Simen BB, Egholm M, Koller D, Georgiou G, Kleinstein SH, Church GM | Proceedings of the National Academy of Sciences of the United States of America | 24639495 | Proc Natl Acad Sci U S A | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24639495 |
| De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. | Di Pierro M, Cheng RR, Lieberman Aiden E, Wolynes PG, Onuchic JN | Proceedings of the National Academy of Sciences of the United States of America | 29087948 | Proc Natl Acad Sci U S A | 2017 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/29087948 |
| Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function. | Lawlor N, Márquez EJ, Orchard P, Narisu N, Shamim MS, Thibodeau A, Varshney A, Kursawe R, Erdos MR, Kanke M, Gu H, Pak E, Dutra A, Russell S, Li X, Piecuch E, Luo O, Chines PS, Fuchbserger C, NIH Intramural Sequencing Center, Sethupathy P, Aiden AP, Ruan Y, Aiden EL, Collins FS, Ucar D, Parker SCJ, Stitzel ML | Cell reports | 30650367 | Cell Rep | 2019 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/30650367 |
| An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening. | MacConnell AB, Price AK, Paegel BM | ACS combinatorial science | 28199790 | ACS Comb Sci | 2017 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/28199790 |
| DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis. | MacConnell AB, McEnaney PJ, Cavett VJ, Paegel BM | ACS combinatorial science | 26290177 | ACS Comb Sci | 2015 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/26290177 |
| hνSABR: Photochemical Dose-Response Bead Screening in Droplets. | Price AK, MacConnell AB, Paegel BM | Analytical chemistry | 26815064 | Anal Chem | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26815064 |
| Evolution of a mass spectrometry-grade protease with PTM-directed specificity. | Tran DT, Cavett VJ, Dang VQ, Torres HL, Paegel BM | Proceedings of the National Academy of Sciences of the United States of America | 27940920 | Proc Natl Acad Sci U S A | 2016 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/27940920 |
| Chemoselective Coupling Preserves the Substrate Integrity of Surface-Immobilized Oligonucleotides for Emulsion PCR-Based Gene Library Construction. | Malone ML, Cavett VJ, Paegel BM | ACS combinatorial science | 28064476 | ACS Comb Sci | 2017 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/28064476 |
| What is a "DNA-Compatible" Reaction? | Malone ML, Paegel BM | ACS combinatorial science | 26971959 | ACS Comb Sci | 2016 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/26971959 |
| Microfluidic bead suspension hopper. | Price AK, MacConnell AB, Paegel BM | Analytical chemistry | 24761972 | Anal Chem | 2014 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/24761972 |
| High-throughput Identification of DNA-Encoded IgG Ligands that Distinguish Active and Latent Mycobacterium tuberculosis Infections. | Mendes KR, Malone ML, Ndungu JM, Suponitsky-Kroyter I, Cavett VJ, McEnaney PJ, MacConnell AB, Doran TM, Ronacher K, Stanley K, Utset O, Walzl G, Paegel BM, Kodadek T | ACS chemical biology | 27957856 | ACS Chem Biol | 2017 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/27957856 |
| Discovery in Droplets. | Price AK, Paegel BM | Analytical chemistry | 26558892 | Anal Chem | 2016 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/26558892 |
| Shape-Changing Photodegradable Hydrogels for Dynamic 3D Cell Culture. | Käpylä E, Delgado SM, Kasko AM | ACS applied materials & interfaces | 27322508 | ACS Appl Mater Interfaces | 2016 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/27322508 |
| Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. | Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM | ACS applied materials & interfaces | 29851335 | ACS Appl Mater Interfaces | 2018 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/29851335 |
| Engineering persister-specific antibiotics with synergistic antimicrobial functions. | Schmidt NW, Deshayes S, Hawker S, Blacker A, Kasko AM, Wong GC | ACS nano | 25130648 | ACS Nano | 2014 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/25130648 |
| Pentobra: A Potent Antibiotic with Multiple Layers of Selective Antimicrobial Mechanisms against Propionibacterium Acnes. | Schmidt NW, Agak GW, Deshayes S, Yu Y, Blacker A, Champer J, Xian W, Kasko AM, Kim J, Wong GCL | The Journal of investigative dermatology | 25668237 | J Invest Dermatol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25668237 |
| Small-Molecule Patterning via Prefunctionalized Alkanethiols. | Cao HH, Nakatsuka N, Deshayes S, Abendroth JM, Yang H, Weiss PS, Kasko AM, Andrews AM | Chemistry of materials : a publication of the American Chemical Society | 30828130 | Chem Mater | 2018 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/30828130 |
| Complex dynamic substrate control: dual-tone hydrogel photoresists allow double-dissociation of topography and modulus. | Xue C, Wong DY, Kasko AM | Advanced materials (Deerfield Beach, Fla.) | 24339260 | Adv Mater | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24339260 |
| Magnetic field activated drug delivery using thermodegradable azo-functionalised PEG-coated core-shell mesoporous silica nanoparticles. | Saint-Cricq P, Deshayes S, Zink JI, Kasko AM | Nanoscale | 26181577 | Nanoscale | 2015 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/26181577 |
| Steric effects in peptide and protein exchange with activated disulfides. | Kerr J, Schlosser JL, Griffin DR, Wong DY, Kasko AM | Biomacromolecules | 23865598 | Biomacromolecules | 2013 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/23865598 |
| Low-Dose, Long-Wave UV Light Does Not Affect Gene Expression of Human Mesenchymal Stem Cells. | Wong DY, Ranganath T, Kasko AM | PloS one | 26418040 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26418040 |
| Photo-selective delivery of model therapeutics from hydrogels. | Griffin DR, Kasko AM | ACS macro letters | 25285242 | ACS Macro Lett | 2012 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/25285242 |
| Synthesis of photodegradable macromers for conjugation and release of bioactive molecules. | Griffin DR, Schlosser JL, Lam SF, Nguyen TH, Maynard HD, Kasko AM | Biomacromolecules | 23506440 | Biomacromolecules | 2013 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/23506440 |
| Photodegradable macromers and hydrogels for live cell encapsulation and release. | Griffin DR, Kasko AM | Journal of the American Chemical Society | 22765384 | J Am Chem Soc | 2012 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/22765384 |
| Turning single cells into microarrays by super-resolution barcoding. | Cai L | Briefings in functional genomics | 23178478 | Brief Funct Genomics | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23178478 |
| In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus. | Shah S, Lubeck E, Zhou W, Cai L | Neuron | 27764670 | Neuron | 2016 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/27764670 |
| Identification of a neural crest stem cell niche by Spatial Genomic Analysis. | Lignell A, Kerosuo L, Streichan SJ, Cai L, Bronner ME | Nature communications | 29184067 | Nat Commun | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/29184067 |
| Single-cell systems biology by super-resolution imaging and combinatorial labeling. | Lubeck E, Cai L | Nature methods | 22660740 | Nat Methods | 2012 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/22660740 |
| Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing. | Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, Lignell A, Choi HM, Gradinaru V, Pierce NA, Cai L | Development (Cambridge, England) | 27342713 | Development | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27342713 |
| Quantitative assessment of ratiometric bimolecular beacons as a tool for imaging single engineered RNA transcripts and measuring gene expression in living cells. | Zhang X, Song Y, Shah AY, Lekova V, Raj A, Huang L, Behlke MA, Tsourkas A | Nucleic acids research | 23814183 | Nucleic Acids Res | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23814183 |
| Gene transcription is coordinated with, but not dependent on, cell divisions during C. elegans embryonic fate specification. | Nair G, Walton T, Murray JI, Raj A | Development (Cambridge, England) | 23863485 | Development | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23863485 |
| Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation. | Levesque MJ, Raj A | Nature methods | 23416756 | Nat Methods | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23416756 |
| Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. | Mirouze N, Desai Y, Raj A, Dubnau D | PLoS genetics | 22412392 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22412392 |
| Nanoscale imaging of RNA with expansion microscopy. | Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES | Nature methods | 27376770 | Nat Methods | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27376770 |
| Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. | Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A | Nature | 28607484 | Nature | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/28607484 |
| Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. | Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J | Immunity | 28930659 | Immunity | 2017 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/28930659 |
| Rare Cell Detection by Single-Cell RNA Sequencing as Guided by Single-Molecule RNA FISH. | Torre E, Dueck H, Shaffer S, Gospocic J, Gupte R, Bonasio R, Kim J, Murray J, Raj A | Cell systems | 29454938 | Cell Syst | 2018 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/29454938 |
| Amendments: Author Correction: ClampFISH detects individual nucleic acid molecules using click chemistry-based amplification. | Rouhanifard SH, Mellis IA, Dunagin M, Bayatpour S, Jiang CL, Dardani I, Symmons O, Emert B, Torre E, Cote A, Sullivan A, Stamatoyannopoulos JA, Raj A | Nature biotechnology | 30605160 | Nat Biotechnol | 2019 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/30605160 |
| Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. | Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A | Genome biology | 25630241 | Genome Biol | 2015 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/25630241 |
| Dynamic enhancer-gene body contacts during transcription elongation. | Lee K, Hsiung CC, Huang P, Raj A, Blobel GA | Genes & development | 26443845 | Genes Dev | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26443845 |
| Enhancer Regulation of Transcriptional Bursting Parameters Revealed by Forced Chromatin Looping. | Bartman CR, Hsu SC, Hsiung CC, Raj A, Blobel GA | Molecular cell | 27067601 | Mol Cell | 2016 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/27067601 |
| Turbo FISH: a method for rapid single molecule RNA FISH. | Shaffer SM, Wu MT, Levesque MJ, Raj A | PloS one | 24066168 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24066168 |
| Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another? | Mellis IA, Raj A | Genome research | 26430156 | Genome Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26430156 |
| LincRNA-p21 activates p21 in cis to promote Polycomb target gene expression and to enforce the G1/S checkpoint. | Dimitrova N, Zamudio JR, Jong RM, Soukup D, Resnick R, Sarma K, Ward AJ, Raj A, Lee JT, Sharp PA, Jacks T | Molecular cell | 24857549 | Mol Cell | 2014 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/24857549 |
| Visualization of lncRNA by single-molecule fluorescence in situ hybridization. | Dunagin M, Cabili MN, Rinn J, Raj A | Methods in molecular biology (Clifton, N.J.) | 25555572 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25555572 |
| Tumor endothelial marker 1-specific DNA vaccination targets tumor vasculature. | Facciponte JG, Ugel S, De Sanctis F, Li C, Wang L, Nair G, Sehgal S, Raj A, Matthaiou E, Coukos G, Facciabene A | The Journal of clinical investigation | 24642465 | J Clin Invest | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24642465 |
| Targeting tumor vasculature: expanding the potential of DNA cancer vaccines. | Ugel S, Facciponte JG, De Sanctis F, Facciabene A | Cancer immunology, immunotherapy : CII | 26267042 | Cancer Immunol Immunother | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26267042 |
| Heterogeneous lineage marker expression in naive embryonic stem cells is mostly due to spontaneous differentiation. | Nair G, Abranches E, Guedes AM, Henrique D, Raj A | Scientific reports | 26292941 | Sci Rep | 2015 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/26292941 |
| Robust hematopoietic progenitor cell commitment in the presence of a conflicting cue. | Shah NA, Levesque MJ, Raj A, Sarkar CA | Journal of cell science | 26159733 | J Cell Sci | 2015 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/26159733 |
| SAVER: gene expression recovery for single-cell RNA sequencing. | Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, Zhang NR | Nature methods | 29941873 | Nat Methods | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29941873 |
| A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition. | Hsiung CC, Bartman CR, Huang P, Ginart P, Stonestrom AJ, Keller CA, Face C, Jahn KS, Evans P, Sankaranarayanan L, Giardine B, Hardison RC, Raj A, Blobel GA | Genes & development | 27340175 | Genes Dev | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27340175 |
| Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms. | Padovan-Merhar O, Nair GP, Biaesch AG, Mayer A, Scarfone S, Foley SW, Wu AR, Churchman LS, Singh A, Raj A | Molecular cell | 25866248 | Mol Cell | 2015 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/25866248 |
| Multiplexed detection of viral infections using rapid in situ RNA analysis on a chip. | Shaffer SM, Joshi RP, Chambers BS, Sterken D, Biaesch AG, Gabrieli DJ, Li Y, Feemster KA, Hensley SE, Issadore D, Raj A | Lab on a chip | 26113495 | Lab Chip | 2015 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/26113495 |
| The Bicoid class homeodomain factors ceh-36/OTX and unc-30/PITX cooperate in C. elegans embryonic progenitor cells to regulate robust development. | Walton T, Preston E, Nair G, Zacharias AL, Raj A, Murray JI | PLoS genetics | 25738873 | PLoS Genet | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25738873 |
| The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries. | Hsu SC, Gilgenast TG, Bartman CR, Edwards CR, Stonestrom AJ, Huang P, Emerson DJ, Evans P, Werner MT, Keller CA, Giardine B, Hardison RC, Raj A, Phillips-Cremins JE, Blobel GA | Molecular cell | 28388437 | Mol Cell | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28388437 |
| Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. | Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL | Nature structural & molecular biology | 24463464 | Nat Struct Mol Biol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24463464 |
| linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. | Maamar H, Cabili MN, Rinn J, Raj A | Genes & development | 23723417 | Genes Dev | 2013 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/23723417 |
| Nup98 promotes antiviral gene expression to restrict RNA viral infection in Drosophila. | Panda D, Pascual-Garcia P, Dunagin M, Tudor M, Hopkins KC, Xu J, Gold B, Raj A, Capelson M, Cherry S | Proceedings of the National Academy of Sciences of the United States of America | 25197089 | Proc Natl Acad Sci U S A | 2014 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/25197089 |
| Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant. | Ginart P, Kalish JM, Jiang CL, Yu AC, Bartolomei MS, Raj A | Genes & development | 26944681 | Genes Dev | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26944681 |
| Identification of a Natural Viral RNA Motif That Optimizes Sensing of Viral RNA by RIG-I. | Xu J, Mercado-López X, Grier JT, Kim WK, Chun LF, Irvine EB, Del Toro Duany Y, Kell A, Hur S, Gale M Jr, Raj A, López CB | mBio | 26443454 | mBio | 2015 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/26443454 |
| What's Luck Got to Do with It: Single Cells, Multiple Fates, and Biological Nondeterminism. | Symmons O, Raj A | Molecular cell | 27259209 | Mol Cell | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27259209 |
| The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. | Kotzin JJ, Spencer SP, McCright SJ, Kumar DBU, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CCD, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J | Nature | 27525555 | Nature | 2016 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/27525555 |
| Control of somatic tissue differentiation by the long non-coding RNA TINCR. | Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA | Nature | 23201690 | Nature | 2013 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/23201690 |
| Visualizing SNVs to quantify allele-specific expression in single cells. | Levesque MJ, Ginart P, Wei Y, Raj A | Nature methods | 23913259 | Nat Methods | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23913259 |
| Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency. | Abranches E, Guedes AM, Moravec M, Maamar H, Svoboda P, Raj A, Henrique D | Development (Cambridge, England) | 25005472 | Development | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25005472 |
| Transcriptional Bursting Explains the Noise-Versus-Mean Relationship in mRNA and Protein Levels. | Dar RD, Shaffer SM, Singh A, Razooky BS, Simpson ML, Raj A, Weinberger LS | PloS one | 27467384 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27467384 |
| Using variability in gene expression as a tool for studying gene regulation. | Padovan-Merhar O, Raj A | Wiley interdisciplinary reviews. Systems biology and medicine | 23996796 | Wiley Interdiscip Rev Syst Biol Med | 2013 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/23996796 |
| Visualizing adenosine-to-inosine RNA editing in single mammalian cells. | Mellis IA, Gupte R, Raj A, Rouhanifard SH | Nature methods | 28604724 | Nat Methods | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28604724 |
| Single-cell differences in matrix gene expression do not predict matrix deposition. | Cote AJ, McLeod CM, Farrell MJ, McClanahan PD, Dunagin MC, Raj A, Mauck RL | Nature communications | 26936319 | Nat Commun | 2016 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/26936319 |
| Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting. | Symmons O, Chang M, Mellis IA, Kalish JM, Park J, Suszták K, Bartolomei MS, Raj A | PLoS genetics | 30625149 | PLoS Genet | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30625149 |
| Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development. | Paralkar VR, Mishra T, Luan J, Yao Y, Kossenkov AV, Anderson SM, Dunagin M, Pimkin M, Gore M, Sun D, Konuthula N, Raj A, An X, Mohandas N, Bodine DM, Hardison RC, Weiss MJ | Blood | 24497530 | Blood | 2014 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/24497530 |
| Inhibition of intestinal tumor formation by deletion of the DNA methyltransferase 3a. | Weis B, Schmidt J, Maamar H, Raj A, Lin H, Tóth C, Riedmann K, Raddatz G, Seitz HK, Ho AD, Lyko F, Linhart HG | Oncogene | 24837369 | Oncogene | 2015 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/24837369 |
| Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells. | Haimovich G, Ecker CM, Dunagin MC, Eggan E, Raj A, Gerst JE, Singer RH | Proceedings of the National Academy of Sciences of the United States of America | 29078295 | Proc Natl Acad Sci U S A | 2017 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/29078295 |
| Specialized ribosomes: a new frontier in gene regulation and organismal biology. | Xue S, Barna M | Nature reviews. Molecular cell biology | 22617470 | Nat Rev Mol Cell Biol | 2012 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/22617470 |
| Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. | Kondrashov N, Pusic A, Stumpf CR, Shimizu K, Hsieh AC, Ishijima J, Shiroishi T, Barna M | Cell | 21529712 | Cell | 2011 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/21529712 |
| Translating the genome in time and space: specialized ribosomes, RNA regulons, and RNA-binding proteins. | Shi Z, Barna M | Annual review of cell and developmental biology | 26443190 | Annu Rev Cell Dev Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26443190 |
| The Mammalian Ribo-interactome Reveals Ribosome Functional Diversity and Heterogeneity. | Simsek D, Tiu GC, Flynn RA, Byeon GW, Leppek K, Xu AF, Chang HY, Barna M | Cell | 28575669 | Cell | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28575669 |
| Cis-regulatory RNA elements that regulate specialized ribosome activity. | Xue S, Barna M | RNA biology | 26327194 | RNA Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26327194 |
| RNA regulons in Hox 5' UTRs confer ribosome specificity to gene regulation. | Xue S, Tian S, Fujii K, Kladwang W, Das R, Barna M | Nature | 25409156 | Nature | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25409156 |
| Heterogeneous Ribosomes Preferentially Translate Distinct Subpools of mRNAs Genome-wide. | Shi Z, Fujii K, Kovary KM, Genuth NR, Röst HL, Teruel MN, Barna M | Molecular cell | 28625553 | Mol Cell | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28625553 |
| Differential Requirements for eIF4E Dose in Normal Development and Cancer. | Truitt ML, Conn CS, Shi Z, Pang X, Tokuyasu T, Coady AM, Seo Y, Barna M, Ruggero D | Cell | 26095252 | Cell | 2015 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/26095252 |
| Ribosomes take control. | Barna M | Proceedings of the National Academy of Sciences of the United States of America | 23243144 | Proc Natl Acad Sci U S A | 2013 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/23243144 |
| Tailor made protein synthesis for HSCs. | Barna M, Ruggero D | Cell stem cell | 24702992 | Cell Stem Cell | 2014 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/24702992 |
| Covalent Protein Labeling by SpyTag-SpyCatcher in Fixed Cells for Super-Resolution Microscopy. | Pessino V, Citron YR, Feng S, Huang B | Chembiochem : a European journal of chemical biology | 28514494 | Chembiochem | 2017 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/28514494 |
| EGF and NRG induce phosphorylation of HER3/ERBB3 by EGFR using distinct oligomeric mechanisms. | van Lengerich B, Agnew C, Puchner EM, Huang B, Jura N | Proceedings of the National Academy of Sciences of the United States of America | 28320942 | Proc Natl Acad Sci U S A | 2017 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/28320942 |
| 2-Hydroxyglutarate-Mediated Autophagy of the Endoplasmic Reticulum Leads to an Unusual Downregulation of Phospholipid Biosynthesis in Mutant IDH1 Gliomas. | Viswanath P, Radoul M, Izquierdo-Garcia JL, Ong WQ, Luchman HA, Cairncross JG, Huang B, Pieper RO, Phillips JJ, Ronen SM | Cancer research | 29358170 | Cancer Res | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29358170 |
| The centrosomin CM2 domain is a multi-functional binding domain with distinct cell cycle roles. | Citron YR, Fagerstrom CJ, Keszthelyi B, Huang B, Rusan NM, Kelly MJS, Agard DA | PloS one | 29315319 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29315319 |
| Correction of depth-dependent aberrations in 3D single-molecule localization and super-resolution microscopy. | McGorty R, Schnitzbauer J, Zhang W, Huang B | Optics letters | 24562125 | Opt Lett | 2014 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/24562125 |
| Little fish, big catch: zebrafish as a model for kidney disease. | Poureetezadi SJ, Wingert RA | Kidney international | 27165832 | Kidney Int | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27165832 |
| Zebrafish nephrogenesis is regulated by interactions between retinoic acid, mecom, and Notch signaling. | Li Y, Cheng CN, Verdun VA, Wingert RA | Developmental biology | 24309209 | Dev Biol | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24309209 |
| Zebrafish pronephros tubulogenesis and epithelial identity maintenance are reliant on the polarity proteins Prkc iota and zeta. | Gerlach GF, Wingert RA | Developmental biology | 25446529 | Dev Biol | 2014 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/25446529 |
| Microbead Implantation in the Zebrafish Embryo. | Gerlach GF, Morales EE, Wingert RA | Journal of visualized experiments : JoVE | 26274386 | J Vis Exp | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26274386 |
| Cutting edge: Asymmetric memory T cell division in response to rechallenge. | Ciocca ML, Barnett BE, Burkhardt JK, Chang JT, Reiner SL | Journal of immunology (Baltimore, Md. : 1950) | 22467651 | J Immunol | 2012 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/22467651 |
| Downregulation of 26S proteasome catalytic activity promotes epithelial-mesenchymal transition. | Banno A, Garcia DA, van Baarsel ED, Metz PJ, Fisch K, Widjaja CE, Kim SH, Lopez J, Chang AN, Geurink PP, Florea BI, Overkleeft HS, Ovaa H, Bui JD, Yang J, Chang JT | Oncotarget | 26930717 | Oncotarget | 2016 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/26930717 |
| Integrin Activation Controls Regulatory T Cell-Mediated Peripheral Tolerance. | Klann JE, Kim SH, Remedios KA, He Z, Metz PJ, Lopez J, Tysl T, Olvera JG, Ablack JN, Cantor JM, Boland BS, Yeo G, Zheng Y, Lu LF, Bui JD, Ginsberg MH, Petrich BG, Chang JT | Journal of immunology (Baltimore, Md. : 1950) | 29703862 | J Immunol | 2018 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/29703862 |
| USP11 Enhances TGFβ-Induced Epithelial-Mesenchymal Plasticity and Human Breast Cancer Metastasis. | Garcia DA, Baek C, Estrada MV, Tysl T, Bennett EJ, Yang J, Chang JT | Molecular cancer research : MCR | 29724812 | Mol Cancer Res | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29724812 |
| Validation of gene expression biomarker analysis for biopsy-based clinical trials in Crohn's disease. | Boland BS, Boyle DL, Sandborn WJ, Firestein GS, Levesque BG, Hillman J, Zhang B, Proudfoot J, Eckmann L, Ernst PB, Rivera-Nieves J, Pola S, Copur-Dahi N, Zou G, Chang JT | Inflammatory bowel diseases | 25545378 | Inflamm Bowel Dis | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25545378 |
| Tamoxifen augments the innate immune function of neutrophils through modulation of intracellular ceramide. | Corriden R, Hollands A, Olson J, Derieux J, Lopez J, Chang JT, Gonzalez DJ, Nizet V | Nature communications | 26458291 | Nat Commun | 2015 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/26458291 |
| Ubiquitylation of CD98 limits cell proliferation and clonal expansion. | Ablack JN, Metz PJ, Chang JT, Cantor JM, Ginsberg MH | Journal of cell science | 26493331 | J Cell Sci | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26493331 |
| Reply to: "CD8(+) T cell diversification by asymmetric cell division". | Arsenio J, Kakaradov B, Metz PJ, Yeo GW, Chang JT | Nature immunology | 26287585 | Nat Immunol | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26287585 |
| Proteasome activity regulates CD8+ T lymphocyte metabolism and fate specification. | Widjaja CE, Olvera JG, Metz PJ, Phan AT, Savas JN, de Bruin G, Leestemaker Y, Berkers CR, de Jong A, Florea BI, Fisch K, Lopez J, Kim SH, Garcia DA, Searles S, Bui JD, Chang AN, Yates JR 3rd, Goldrath AW, Overkleeft HS, Ovaa H, Chang JT | The Journal of clinical investigation | 28846070 | J Clin Invest | 2017 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/28846070 |
| Geometrically controlled asymmetric division of CD4+ T cells studied by immunological synapse arrays. | Jung HR, Song KH, Chang JT, Doh J | PloS one | 24632942 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24632942 |
| Asymmetric Cell Division in T Lymphocyte Fate Diversification. | Arsenio J, Metz PJ, Chang JT | Trends in immunology | 26474675 | Trends Immunol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26474675 |
| A gp130-Src-YAP module links inflammation to epithelial regeneration. | Taniguchi K, Wu LW, Grivennikov SI, de Jong PR, Lian I, Yu FX, Wang K, Ho SB, Boland BS, Chang JT, Sandborn WJ, Hardiman G, Raz E, Maehara Y, Yoshimura A, Zucman-Rossi J, Guan KL, Karin M | Nature | 25731159 | Nature | 2015 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/25731159 |
| Molecular regulation of effector and memory T cell differentiation. | Chang JT, Wherry EJ, Goldrath AW | Nature immunology | 25396352 | Nat Immunol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25396352 |
| Regulation of Asymmetric Division by Atypical Protein Kinase C Influences Early Specification of CD8(+) T Lymphocyte Fates. | Metz PJ, Lopez J, Kim SH, Akimoto K, Ohno S, Chang JT | Scientific reports | 26765121 | Sci Rep | 2016 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/26765121 |
| Regulation of asymmetric division and CD8+ T lymphocyte fate specification by protein kinase Cζ and protein kinase Cλ/ι. | Metz PJ, Arsenio J, Kakaradov B, Kim SH, Remedios KA, Oakley K, Akimoto K, Ohno S, Yeo GW, Chang JT | Journal of immunology (Baltimore, Md. : 1950) | 25617472 | J Immunol | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/25617472 |
| The Microtubule-Associated Protein Lis1 Regulates T Lymphocyte Homeostasis and Differentiation. | Ngoi SM, Lopez JM, Chang JT | Journal of immunology (Baltimore, Md. : 1950) | 27029586 | J Immunol | 2016 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/27029586 |
| Early transcriptional and epigenetic regulation of CD8(+) T cell differentiation revealed by single-cell RNA sequencing. | Kakaradov B, Arsenio J, Widjaja CE, He Z, Aigner S, Metz PJ, Yu B, Wehrens EJ, Lopez J, Kim SH, Zuniga EI, Goldrath AW, Chang JT, Yeo GW | Nature immunology | 28218746 | Nat Immunol | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28218746 |
| Talin Plays a Critical Role in the Maintenance of the Regulatory T Cell Pool. | Klann JE, Remedios KA, Kim SH, Metz PJ, Lopez J, Mack LA, Zheng Y, Ginsberg MH, Petrich BG, Chang JT | Journal of immunology (Baltimore, Md. : 1950) | 28515282 | J Immunol | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/28515282 |
| Early specification of CD8+ T lymphocyte fates during adaptive immunity revealed by single-cell gene-expression analyses. | Arsenio J, Kakaradov B, Metz PJ, Kim SH, Yeo GW, Chang JT | Nature immunology | 24584088 | Nat Immunol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24584088 |
| Immunodeficiency and autoimmune enterocolopathy linked to NFAT5 haploinsufficiency. | Boland BS, Widjaja CE, Banno A, Zhang B, Kim SH, Stoven S, Peterson MR, Jones MC, Su HI, Crowe SE, Bui JD, Ho SB, Okugawa Y, Goel A, Marietta EV, Khosroheidari M, Jepsen K, Aramburu J, López-Rodríguez C, Sandborn WJ, Murray JA, Harismendy O, Chang JT | Journal of immunology (Baltimore, Md. : 1950) | 25667416 | J Immunol | 2015 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/25667416 |
| Polarity and lymphocyte fate determination. | Chang JT | Current opinion in cell biology | 22658837 | Curr Opin Cell Biol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22658837 |
| Update on Janus kinase antagonists in inflammatory bowel disease. | Boland BS, Sandborn WJ, Chang JT | Gastroenterology clinics of North America | 25110261 | Gastroenterol Clin North Am | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25110261 |
| Validated gene expression biomarker analysis for biopsy-based clinical trials in ulcerative colitis. | Boland BS, Boyle DL, Sandborn WJ, Firestein GS, Levesque BG, Hillman J, Zhang B, Proudfoot J, Eckmann L, Ernst PB, Rivera-Nieves J, Pola S, Copur-Dahi N, Chang JT | Alimentary pharmacology & therapeutics | 25041724 | Aliment Pharmacol Ther | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25041724 |
| A multiparametric computational algorithm for comprehensive assessment of genetic mutations in mucopolysaccharidosis type IIIA (Sanfilippo syndrome). | Ugrinov KG, Freed SD, Thomas CL, Lee SW | PloS one | 25807448 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25807448 |
| The wide world of ribosomally encoded bacterial peptides. | Flaherty RA, Freed SD, Lee SW | PLoS pathogens | 25079075 | PLoS Pathog | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25079075 |
| CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants. | Bao YJ, Liang Z, Mayfield JA, Lee SW, Ploplis VA, Castellino FJ | Journal of bacteriology | 26216843 | J Bacteriol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26216843 |
| Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains. | Fields FR, Freed SD, Carothers KE, Hamid MN, Hammers DE, Ross JN, Kalwajtys VR, Gonzalez AJ, Hildreth AD, Friedberg I, Lee SW | Drug development research | 31483516 | Drug Dev Res | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31483516 |
| Synthesis, biological evaluation, and in silico study of novel library sulfonates containing quinazolin-4(3H)-one derivatives as potential aldose reductase inhibitors. | Tokalı FS, Demir Y, Demircioğlu İH, Türkeş C, Kalay E, Şendil K, Beydemir Ş | Drug development research | 34585414 | Drug Dev Res | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/34585414 |
| Using bacterial genomes and essential genes for the development of new antibiotics. | Fields FR, Lee SW, McConnell MJ | Biochemical pharmacology | 27940263 | Biochem Pharmacol | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27940263 |
| HIV protease inhibitors block streptolysin S production. | Maxson T, Deane CD, Molloy EM, Cox CL, Markley AL, Lee SW, Mitchell DA | ACS chemical biology | 25668590 | ACS Chem Biol | 2015 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/25668590 |
| Rationally Designed Minimal Bioactive Domains of AS-48 Bacteriocin Homologs Possess Potent Antileishmanial Properties. | Corman HN, Ross JN, Fields FR, Shoue DA, McDowell MA, Lee SW | Microbiology spectrum | 36342284 | Microbiol Spectr | 2022 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/36342284 |
| Implementation of a Permeable Membrane Insert-based Infection System to Study the Effects of Secreted Bacterial Toxins on Mammalian Host Cells. | Flaherty RA, Lee SW | Journal of visualized experiments : JoVE | 27585035 | J Vis Exp | 2016 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/27585035 |
| Virulence Factor Targeting of the Bacterial Pathogen Staphylococcus aureus for Vaccine and Therapeutics. | Kane TL, Carothers KE, Lee SW | Current drug targets | 27894236 | Curr Drug Targets | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/27894236 |
| A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. | Morton JT, Freed SD, Lee SW, Friedberg I | BMC bioinformatics | 26558535 | BMC Bioinformatics | 2015 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/26558535 |
| Design and evaluation of a peptide-based immunotoxin for breast cancer therapeutics. | Weigel KJ, Shen L, Thomas CL, Alber D, Drapalik L, Schafer ZT, Lee SW | FEBS open bio | 25853036 | FEBS Open Bio | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25853036 |
| Synthetic Peptide Libraries Designed From a Minimal Alpha-Helical Domain of AS-48-Bacteriocin Homologs Exhibit Potent Antibacterial Activity. | Ross JN, Fields FR, Kalwajtys VR, Gonzalez AJ, O'Connor S, Zhang A, Moran TE, Hammers DE, Carothers KE, Lee SW | Frontiers in microbiology | 33281785 | Front Microbiol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33281785 |
| Rational design of syn-safencin, a novel linear antimicrobial peptide derived from the circular bacteriocin safencin AS-48. | Fields FR, Carothers KE, Balsara RD, Ploplis VA, Castellino FJ, Lee SW | The Journal of antibiotics | 29463889 | J Antibiot (Tokyo) | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29463889 |
| Neutralization of Streptolysin S-Dependent and Independent Inflammatory Cytokine IL-1β Activity Reduces Pathology During Early Group A Streptococcal Skin Infection. | Flaherty RA, Donahue DL, Carothers KE, Ross JN, Ploplis VA, Castellino FJ, Lee SW | Frontiers in cellular and infection microbiology | 30018884 | Front Cell Infect Microbiol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30018884 |
| Knowing is half the battle: targeting virulence factors of group A Streptococcus for vaccine and therapeutics. | Thomas CL, Lee SW | Current drug targets | 22206254 | Curr Drug Targets | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22206254 |
| Streptolysin S Promotes Programmed Cell Death and Enhances Inflammatory Signaling in Epithelial Keratinocytes during Group A Streptococcus Infection. | Flaherty RA, Puricelli JM, Higashi DL, Park CJ, Lee SW | Infection and immunity | 26238711 | Infect Immun | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26238711 |
| Group A Streptococcus-Induced Activation of Human Plasminogen Is Required for Keratinocyte Wound Retraction and Rapid Clot Dissolution. | Vu HM, Hammers DE, Liang Z, Nguyen GL, Benz ME, Moran TE, Higashi DL, Park CJ, Ayinuola YA, Donahue DL, Flores-Mireles AL, Ploplis VA, Castellino FJ, Lee SW | Frontiers in cardiovascular medicine | 34179133 | Front Cardiovasc Med | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34179133 |
| In Vivo Rescue of the Hematopoietic Niche By Pluripotent Stem Cell Complementation of Defective Osteoblast Compartments. | Chubb R, Oh J, Riley AK, Kimura T, Wu SM, Wu JY | Stem cells (Dayton, Ohio) | 28741855 | Stem Cells | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28741855 |
| Comparative effects of teriparatide, denosumab, and combination therapy on peripheral compartmental bone density, microarchitecture, and estimated strength: the DATA-HRpQCT Study. | Tsai JN, Uihlein AV, Burnett-Bowie SA, Neer RM, Zhu Y, Derrico N, Lee H, Bouxsein ML, Leder BZ | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 25043459 | J Bone Miner Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25043459 |
| PTH Signaling in Osteoprogenitors Is Essential for B-Lymphocyte Differentiation and Mobilization. | Panaroni C, Fulzele K, Saini V, Chubb R, Pajevic PD, Wu JY | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 26191777 | J Bone Miner Res | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26191777 |
| Direct Reprogramming of Mouse Fibroblasts into Functional Osteoblasts. | Zhu H, Swami S, Yang P, Shapiro F, Wu JY | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 31793059 | J Bone Miner Res | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31793059 |
| Teriparatide (PTH 1-34) treatment increases peripheral hematopoietic stem cells in postmenopausal women. | Yu EW, Kumbhani R, Siwila-Sackman E, DeLelys M, Preffer FI, Leder BZ, Wu JY | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 24420643 | J Bone Miner Res | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24420643 |
| Engineering genetic circuits that compute and remember. | Siuti P, Yazbek J, Lu TK | Nature protocols | 24810038 | Nat Protoc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24810038 |
| Complete Genome Sequence of Pseudomonas aeruginosa Phage vB_PaeM_CEB_DP1. | Pires DP, Sillankorva S, Kropinski AM, Lu TK, Azeredo J | Genome announcements | 26404589 | Genome Announc | 2015 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/26404589 |
| Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. | Farzadfard F, Lu TK | Science (New York, N.Y.) | 25395541 | Science | 2014 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/25395541 |
| Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases. | Citorik RJ, Mimee M, Lu TK | Nature biotechnology | 25240928 | Nat Biotechnol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25240928 |
| DNA nanotechnology: new adventures for an old warhorse. | Zakeri B, Lu TK | Current opinion in chemical biology | 26056949 | Curr Opin Chem Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26056949 |
| Advancing bacteriophage-based microbial diagnostics with synthetic biology. | Lu TK, Bowers J, Koeris MS | Trends in biotechnology | 23608522 | Trends Biotechnol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23608522 |
| Foundations and Emerging Paradigms for Computing in Living Cells. | Ma KC, Perli SD, Lu TK | Journal of molecular biology | 26908220 | J Mol Biol | 2016 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/26908220 |
| Strong underwater adhesives made by self-assembling multi-protein nanofibres. | Zhong C, Gurry T, Cheng AA, Downey J, Deng Z, Stultz CM, Lu TK | Nature nanotechnology | 25240674 | Nat Nanotechnol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25240674 |
| Enhancing phage therapy through synthetic biology and genome engineering. | Lenneman BR, Fernbach J, Loessner MJ, Lu TK, Kilcher S | Current opinion in biotechnology | 33310655 | Curr Opin Biotechnol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33310655 |
| Engineering Phage Host-Range and Suppressing Bacterial Resistance through Phage Tail Fiber Mutagenesis. | Yehl K, Lemire S, Yang AC, Ando H, Mimee M, Torres MT, de la Fuente-Nunez C, Lu TK | Cell | 31585083 | Cell | 2019 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/31585083 |
| A synthetic biology framework for programming eukaryotic transcription functions. | Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ | Cell | 22863014 | Cell | 2012 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/22863014 |
| Surface charge-switching polymeric nanoparticles for bacterial cell wall-targeted delivery of antibiotics. | Radovic-Moreno AF, Lu TK, Puscasu VA, Yoon CJ, Langer R, Farokhzad OC | ACS nano | 22471841 | ACS Nano | 2012 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/22471841 |
| Enhanced killing of antibiotic-resistant bacteria enabled by massively parallel combinatorial genetics. | Cheng AA, Ding H, Lu TK | Proceedings of the National Academy of Sciences of the United States of America | 25114216 | Proc Natl Acad Sci U S A | 2014 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/25114216 |
| Bacteriophage-based synthetic biology for the study of infectious diseases. | Citorik RJ, Mimee M, Lu TK | Current opinion in microbiology | 24997401 | Curr Opin Microbiol | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24997401 |
| Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity. | Seker UO, Chen AY, Citorik RJ, Lu TK | ACS synthetic biology | 27794590 | ACS Synth Biol | 2017 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/27794590 |
| Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM. | Wong AS, Choi GC, Cui CH, Pregernig G, Milani P, Adam M, Perli SD, Kazer SW, Gaillard A, Hermann M, Shalek AK, Fraenkel E, Lu TK | Proceedings of the National Academy of Sciences of the United States of America | 26864203 | Proc Natl Acad Sci U S A | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26864203 |
| Rule-based design of synthetic transcription factors in eukaryotes. | Purcell O, Peccoud J, Lu TK | ACS synthetic biology | 24933274 | ACS Synth Biol | 2014 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/24933274 |
| Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. | Farzadfard F, Perli SD, Lu TK | ACS synthetic biology | 23977949 | ACS Synth Biol | 2013 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/23977949 |
| Natural combinatorial genetics and prolific polyamine production enable siderophore diversification in Serratia plymuthica. | Cleto S, Haslinger K, Prather KLJ, Lu TK | BMC biology | 33722216 | BMC Biol | 2021 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/33722216 |
| Multiplexed Sequence Encoding: A Framework for DNA Communication. | Zakeri B, Carr PA, Lu TK | PloS one | 27050646 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27050646 |
| Towards a whole-cell modeling approach for synthetic biology. | Purcell O, Jain B, Karr JR, Covert MW, Lu TK | Chaos (Woodbury, N.Y.) | 23822510 | Chaos | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23822510 |
| Synthetic biology: an emerging engineering discipline. | Cheng AA, Lu TK | Annual review of biomedical engineering | 22577777 | Annu Rev Biomed Eng | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22577777 |
| Synthetic biology of antimicrobial discovery. | Zakeri B, Lu TK | ACS synthetic biology | 23654251 | ACS Synth Biol | 2013 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/23654251 |
| Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. | Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK | Molecular cell | 24837679 | Mol Cell | 2014 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/24837679 |
| Massively parallel high-order combinatorial genetics in human cells. | Wong AS, Choi GC, Cheng AA, Purcell O, Lu TK | Nature biotechnology | 26280411 | Nat Biotechnol | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26280411 |
| Gene networks that compensate for crosstalk with crosstalk. | Müller IE, Rubens JR, Jun T, Graham D, Xavier R, Lu TK | Nature communications | 31492904 | Nat Commun | 2019 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/31492904 |
| A model for coordinating nuclear mechanics and membrane remodeling to support nuclear integrity. | King MC, Lusk CP | Current opinion in cell biology | 27031045 | Curr Opin Cell Biol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27031045 |
| A role for nuclear envelope-bridging complexes in homology-directed repair. | Swartz RK, Rodriguez EC, King MC | Molecular biology of the cell | 24943839 | Mol Biol Cell | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/24943839 |
| A quality control mechanism linking meiotic success to release of ascospores. | Guo H, King MC | PloS one | 24312672 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24312672 |
| Forces, fluctuations, and self-organization in the nucleus. | Pederson T, King MC, Marko JF | Molecular biology of the cell | 26543199 | Mol Biol Cell | 2015 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/26543199 |
| TeloPCR-seq: a high-throughput sequencing approach for telomeres. | Bennett HW, Liu N, Hu Y, King MC | FEBS letters | 27714790 | FEBS Lett | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27714790 |
| RNA-DNA Hybrids Support Recombination-Based Telomere Maintenance in Fission Yeast. | Hu Y, Bennett HW, Liu N, Moravec M, Williams JF, Azzalin CM, King MC | Genetics | 31405990 | Genetics | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31405990 |
| The KASH protein Kms2 coordinates mitotic remodeling of the spindle pole body. | Wälde S, King MC | Journal of cell science | 24963130 | J Cell Sci | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/24963130 |
| Rev7 and 53BP1/Crb2 prevent RecQ helicase-dependent hyper-resection of DNA double-strand breaks. | Leland BA, Chen AC, Zhao AY, Wharton RC, King MC | eLife | 29697047 | Elife | 2018 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/29697047 |
| Improved Determination of Subnuclear Position Enabled by Three-Dimensional Membrane Reconstruction. | Zhao Y, Schreiner SM, Koo PK, Colombi P, King MC, Mochrie SG | Biophysical journal | 27410730 | Biophys J | 2016 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/27410730 |
| TERRA promotes telomerase-mediated telomere elongation in Schizosaccharomyces pombe. | Moravec M, Wischnewski H, Bah A, Hu Y, Liu N, Lafranchi L, King MC, Azzalin CM | EMBO reports | 27154402 | EMBO Rep | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27154402 |
| A comprehensive thalamocortical projection map at the mesoscopic level. | Hunnicutt BJ, Long BR, Kusefoglu D, Gertz KJ, Zhong H, Mao T | Nature neuroscience | 25086607 | Nat Neurosci | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25086607 |
| Applying superresolution localization-based microscopy to neurons. | Zhong H | Synapse (New York, N.Y.) | 25648102 | Synapse | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25648102 |
| Subdiffractive microscopy: techniques, applications, and challenges. | Long BR, Robinson DC, Zhong H | Wiley interdisciplinary reviews. Systems biology and medicine | 24443323 | Wiley Interdiscip Rev Syst Biol Med | 2014 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/24443323 |
| Live imaging of endogenous PSD-95 using ENABLED: a conditional strategy to fluorescently label endogenous proteins. | Fortin DA, Tillo SE, Yang G, Rah JC, Melander JB, Bai S, Soler-Cedeño O, Qin M, Zemelman BV, Guo C, Mao T, Zhong H | The Journal of neuroscience : the official journal of the Society for Neuroscience | 25505322 | J Neurosci | 2014 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/25505322 |
| A comprehensive excitatory input map of the striatum reveals novel functional organization. | Hunnicutt BJ, Jongbloets BC, Birdsong WT, Gertz KJ, Zhong H, Mao T | eLife | 27892854 | Elife | 2016 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/27892854 |
| Liberated PKA Catalytic Subunits Associate with the Membrane via Myristoylation to Preferentially Phosphorylate Membrane Substrates. | Tillo SE, Xiong WH, Takahashi M, Miao S, Andrade AL, Fortin DA, Yang G, Qin M, Smoody BF, Stork PJS, Zhong H | Cell reports | 28423323 | Cell Rep | 2017 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/28423323 |
| Measuring Caenorhabditis elegans life span in 96 well microtiter plates. | Solis GM, Petrascheck M | Journal of visualized experiments : JoVE | 21445049 | J Vis Exp | 2011 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/21445049 |
| Suppression of transcriptional drift extends C. elegans lifespan by postponing the onset of mortality. | Rangaraju S, Solis GM, Thompson RC, Gomez-Amaro RL, Kurian L, Encalada SE, Niculescu AB 3rd, Salomon DR, Petrascheck M | eLife | 26623667 | Elife | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26623667 |
| Translation attenuation by minocycline enhances longevity and proteostasis in old post-stress-responsive organisms. | Solis GM, Kardakaris R, Valentine ER, Bar-Peled L, Chen AL, Blewett MM, McCormick MA, Williamson JR, Kennedy B, Cravatt BF, Petrascheck M | eLife | 30479271 | Elife | 2018 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/30479271 |
| A pharmacological network for lifespan extension in Caenorhabditis elegans. | Ye X, Linton JM, Schork NJ, Buck LB, Petrascheck M | Aging cell | 24134630 | Aging Cell | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24134630 |
| Pharmacological classes that extend lifespan of Caenorhabditis elegans. | Carretero M, Gomez-Amaro RL, Petrascheck M | Frontiers in genetics | 25784926 | Front Genet | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25784926 |
| Proteostasis is differentially modulated by inhibition of translation initiation or elongation. | Clay KJ, Yang Y, Clark C, Petrascheck M | eLife | 37795690 | Elife | 2023 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/37795690 |
| Mood, stress and longevity: convergence on ANK3. | Rangaraju S, Levey DF, Nho K, Jain N, Andrews KD, Le-Niculescu H, Salomon DR, Saykin AJ, Petrascheck M, Niculescu AB | Molecular psychiatry | 27217151 | Mol Psychiatry | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27217151 |
| Measuring Food Intake and Nutrient Absorption in Caenorhabditis elegans. | Gomez-Amaro RL, Valentine ER, Carretero M, LeBoeuf SE, Rangaraju S, Broaddus CD, Solis GM, Williamson JR, Petrascheck M | Genetics | 25903497 | Genetics | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25903497 |
| Computational Analysis of Lifespan Experiment Reproducibility. | Petrascheck M, Miller DL | Frontiers in genetics | 28713422 | Front Genet | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28713422 |
| The metabolite α-ketoglutarate extends lifespan by inhibiting ATP synthase and TOR. | Chin RM, Fu X, Pai MY, Vergnes L, Hwang H, Deng G, Diep S, Lomenick B, Meli VS, Monsalve GC, Hu E, Whelan SA, Wang JX, Jung G, Solis GM, Fazlollahi F, Kaweeteerawat C, Quach A, Nili M, Krall AS, Godwin HA, Chang HR, Faull KF, Guo F, Jiang M, Trauger SA, Saghatelian A, Braas D, Christofk HR, Clarke CF, Teitell MA, Petrascheck M, Reue K, Jung ME, Frand AR, Huang J | Nature | 24828042 | Nature | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24828042 |
| High-throughput small-molecule screening in Caenorhabditis elegans. | Rangaraju S, Solis GM, Petrascheck M | Methods in molecular biology (Clifton, N.J.) | 25618342 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25618342 |
| The aging transcriptome: read between the lines. | Perez-Gomez A, Buxbaum JN, Petrascheck M | Current opinion in neurobiology | 32563038 | Curr Opin Neurobiol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32563038 |
| A phenotypic Caenorhabditis elegans screen identifies a selective suppressor of antipsychotic-induced hyperphagia. | Perez-Gomez A, Carretero M, Weber N, Peterka V, To A, Titova V, Solis G, Osborn O, Petrascheck M | Nature communications | 30532051 | Nat Commun | 2018 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/30532051 |
| Atypical antidepressants extend lifespan of Caenorhabditis elegans by activation of a non-cell-autonomous stress response. | Rangaraju S, Solis GM, Andersson SI, Gomez-Amaro RL, Kardakaris R, Broaddus CD, Niculescu AB 3rd, Petrascheck M | Aging cell | 26255886 | Aging Cell | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26255886 |
| Efficient mammalian germline transgenesis by cis-enhanced Sleeping Beauty transposition. | Carlson DF, Geurts AM, Garbe JR, Park CW, Rangel-Filho A, O'Grady SM, Jacob HJ, Steer CJ, Largaespada DA, Fahrenkrug SC | Transgenic research | 20352328 | Transgenic Res | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20352328 |
| Zinc-finger nuclease knockout of dual-specificity protein phosphatase-5 enhances the myogenic response and autoregulation of cerebral blood flow in FHH.1BN rats. | Fan F, Geurts AM, Pabbidi MR, Smith SV, Harder DR, Jacob H, Roman RJ | PloS one | 25397684 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25397684 |
| Chronic central serotonin depletion attenuates ventilation and body temperature in young but not adult Tph2 knockout rats. | Kaplan K, Echert AE, Massat B, Puissant MM, Palygin O, Geurts AM, Hodges MR | Journal of applied physiology (Bethesda, Md. : 1985) | 26869713 | J Appl Physiol (1985) | 2016 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/26869713 |
| Essential role of Kir5.1 channels in renal salt handling and blood pressure control. | Palygin O, Levchenko V, Ilatovskaya DV, Pavlov TS, Pochynyuk OM, Jacob HJ, Geurts AM, Hodges MR, Staruschenko A | JCI insight | 28931751 | JCI Insight | 2017 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/28931751 |
| Efficient Precision Genome Editing in iPSCs via Genetic Co-targeting with Selection. | Mitzelfelt KA, McDermott-Roe C, Grzybowski MN, Marquez M, Kuo CT, Riedel M, Lai S, Choi MJ, Kolander KD, Helbling D, Dimmock DP, Battle MA, Jou CJ, Tristani-Firouzi M, Verbsky JW, Benjamin IJ, Geurts AM | Stem cell reports | 28238794 | Stem Cell Reports | 2017 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/28238794 |
| Nitric oxide production by glomerular podocytes. | Palygin O, Ilatovskaya DV, Levchenko V, Endres BT, Geurts AM, Staruschenko A | Nitric oxide : biology and chemistry | 29128399 | Nitric Oxide | 2018 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/29128399 |
| Maternal diet during gestation and lactation modifies the severity of salt-induced hypertension and renal injury in Dahl salt-sensitive rats. | Geurts AM, Mattson DL, Liu P, Cabacungan E, Skelton MM, Kurth TM, Yang C, Endres BT, Klotz J, Liang M, Cowley AW Jr | Hypertension (Dallas, Tex. : 1979) | 25452472 | Hypertension | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25452472 |
| Transposon-mediated transgenesis, transgenic rescue, and tissue-specific gene expression in rodents and rabbits. | Katter K, Geurts AM, Hoffmann O, Mátés L, Landa V, Hiripi L, Moreno C, Lazar J, Bashir S, Zidek V, Popova E, Jerchow B, Becker K, Devaraj A, Walter I, Grzybowksi M, Corbett M, Filho AR, Hodges MR, Bader M, Ivics Z, Jacob HJ, Pravenec M, Bosze Z, Rülicke T, Izsvák Z | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23195032 | FASEB J | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23195032 |
| Early development of podocyte injury independently of hyperglycemia and elevations in arterial pressure in nondiabetic obese Dahl SS leptin receptor mutant rats. | McPherson KC, Taylor L, Johnson AC, Didion SP, Geurts AM, Garrett MR, Williams JM | American journal of physiology. Renal physiology | 27465994 | Am J Physiol Renal Physiol | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27465994 |
| 2015 Guidelines for Establishing Genetically Modified Rat Models for Cardiovascular Research. | Flister MJ, Prokop JW, Lazar J, Shimoyama M, Dwinell M, Geurts A, International Committee on Standardized Genetic Nomenclature for Mice, Rat Genome and Nomenclature Committee | Journal of cardiovascular translational research | 25920443 | J Cardiovasc Transl Res | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25920443 |
| Characterization of Dahl salt-sensitive rats with genetic disruption of the A2B adenosine receptor gene: implications for A2B adenosine receptor signaling during hypertension. | Nayak S, Khan MA, Wan TC, Pei H, Linden J, Dwinell MR, Geurts AM, Imig JD, Auchampach JA | Purinergic signalling | 26385692 | Purinergic Signal | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26385692 |
| Rab38 modulates proteinuria in model of hypertension-associated renal disease. | Rangel-Filho A, Lazar J, Moreno C, Geurts A, Jacob HJ | Journal of the American Society of Nephrology : JASN | 23291471 | J Am Soc Nephrol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23291471 |
| p66Shc regulates renal vascular tone in hypertension-induced nephropathy. | Miller B, Palygin O, Rufanova VA, Chong A, Lazar J, Jacob HJ, Mattson D, Roman RJ, Williams JM, Cowley AW Jr, Geurts AM, Staruschenko A, Imig JD, Sorokin A | The Journal of clinical investigation | 27270176 | J Clin Invest | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/27270176 |
| Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease. | Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M | Journal of the American Heart Association | 26888427 | J Am Heart Assoc | 2016 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/26888427 |
| Intravital imaging of the kidney in a rat model of salt-sensitive hypertension. | Endres BT, Sandoval RM, Rhodes GJ, Campos-Bilderback SB, Kamocka MM, McDermott-Roe C, Staruschenko A, Molitoris BA, Geurts AM, Palygin O | American journal of physiology. Renal physiology | 28404591 | Am J Physiol Renal Physiol | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28404591 |
| Germline transgenesis in rodents by pronuclear microinjection of Sleeping Beauty transposons. | Ivics Z, Mátés L, Yau TY, Landa V, Zidek V, Bashir S, Hoffmann OI, Hiripi L, Garrels W, Kues WA, Bösze Z, Geurts A, Pravenec M, Rülicke T, Izsvák Z | Nature protocols | 24625778 | Nat Protoc | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24625778 |
| Impaired myogenic response and autoregulation of cerebral blood flow is rescued in CYP4A1 transgenic Dahl salt-sensitive rat. | Fan F, Geurts AM, Murphy SR, Pabbidi MR, Jacob HJ, Roman RJ | American journal of physiology. Regulatory, integrative and comparative physiology | 25540098 | Am J Physiol Regul Integr Comp Physiol | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/25540098 |
| The Human 343delT HSPB5 Chaperone Associated with Early-onset Skeletal Myopathy Causes Defects in Protein Solubility. | Mitzelfelt KA, Limphong P, Choi MJ, Kondrat FD, Lai S, Kolander KD, Kwok WM, Dai Q, Grzybowski MN, Zhang H, Taylor GM, Lui Q, Thao MT, Hudson JA, Barresi R, Bushby K, Jungbluth H, Wraige E, Geurts AM, Benesch JL, Riedel M, Christians ES, Minella AC, Benjamin IJ | The Journal of biological chemistry | 27226619 | J Biol Chem | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27226619 |
| Generation and characterization of rat liver stem cell lines and their engraftment in a rat model of liver failure. | Kuijk EW, Rasmussen S, Blokzijl F, Huch M, Gehart H, Toonen P, Begthel H, Clevers H, Geurts AM, Cuppen E | Scientific reports | 26915950 | Sci Rep | 2016 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/26915950 |
| The NRF2 knockout rat: a new animal model to study endothelial dysfunction, oxidant stress, and microvascular rarefaction. | Priestley JR, Kautenburg KE, Casati MC, Endres BT, Geurts AM, Lombard JH | American journal of physiology. Heart and circulatory physiology | 26637559 | Am J Physiol Heart Circ Physiol | 2016 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/26637559 |
| CXM: a new tool for mapping breast cancer risk in the tumor microenvironment. | Flister MJ, Endres BT, Rudemiller N, Sarkis AB, Santarriaga S, Roy I, Lemke A, Geurts AM, Moreno C, Ran S, Tsaih SW, De Pons J, Carlson DF, Tan W, Fahrenkrug SC, Lazarova Z, Lazar J, North PE, LaViolette PS, Dwinell MB, Shull JD, Jacob HJ | Cancer research | 25172839 | Cancer Res | 2014 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/25172839 |
| Mutation of Plekha7 attenuates salt-sensitive hypertension in the rat. | Endres BT, Priestley JR, Palygin O, Flister MJ, Hoffman MJ, Weinberg BD, Grzybowski M, Lombard JH, Staruschenko A, Moreno C, Jacob HJ, Geurts AM | Proceedings of the National Academy of Sciences of the United States of America | 25136115 | Proc Natl Acad Sci U S A | 2014 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/25136115 |
| Myosin Id is required for planar cell polarity in ciliated tracheal and ependymal epithelial cells. | Hegan PS, Ostertag E, Geurts AM, Mooseker MS | Cytoskeleton (Hoboken, N.J.) | 26446290 | Cytoskeleton (Hoboken) | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26446290 |
| A NOX4/TRPC6 Pathway in Podocyte Calcium Regulation and Renal Damage in Diabetic Kidney Disease. | Ilatovskaya DV, Blass G, Palygin O, Levchenko V, Pavlov TS, Grzybowski MN, Winsor K, Shuyskiy LS, Geurts AM, Cowley AW Jr, Birnbaumer L, Staruschenko A | Journal of the American Society of Nephrology : JASN | 29793963 | J Am Soc Nephrol | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29793963 |
| Rats are the smart choice: Rationale for a renewed focus on rats in behavioral genetics. | Parker CC, Chen H, Flagel SB, Geurts AM, Richards JB, Robinson TE, Solberg Woods LC, Palmer AA | Neuropharmacology | 23791960 | Neuropharmacology | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23791960 |
| Identifying multiple causative genes at a single GWAS locus. | Flister MJ, Tsaih SW, O'Meara CC, Endres B, Hoffman MJ, Geurts AM, Dwinell MR, Lazar J, Jacob HJ, Moreno C | Genome research | 24006081 | Genome Res | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24006081 |
| Two-photon Imaging of Intracellular Ca2+ Handling and Nitric Oxide Production in Endothelial and Smooth Muscle Cells of an Isolated Rat Aorta. | Endres BT, Staruschenko A, Schulte M, Geurts AM, Palygin O | Journal of visualized experiments : JoVE | 26132549 | J Vis Exp | 2015 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/26132549 |
| Structural analyses of Ca²⁺/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation. | Wang C, Chung BC, Yan H, Wang HG, Lee SY, Pitt GS | Nature communications | 25232683 | Nat Commun | 2014 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/25232683 |
| Crystal structure of the ternary complex of a NaV C-terminal domain, a fibroblast growth factor homologous factor, and calmodulin. | Wang C, Chung BC, Yan H, Lee SY, Pitt GS | Structure (London, England : 1993) | 22705208 | Structure | 2012 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/22705208 |
| Current view on regulation of voltage-gated sodium channels by calcium and auxiliary proteins. | Pitt GS, Lee SY | Protein science : a publication of the Protein Society | 27262167 | Protein Sci | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27262167 |
| Cryo-electron microscopy structure of the TRPV2 ion channel. | Zubcevic L, Herzik MA Jr, Chung BC, Liu Z, Lander GC, Lee SY | Nature structural & molecular biology | 26779611 | Nat Struct Mol Biol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26779611 |
| Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å. | Johnson ZL, Cheong CG, Lee SY | Nature | 22407322 | Nature | 2012 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/22407322 |
| A monoclonal antibody that targets a NaV1.7 channel voltage sensor for pain and itch relief. | Lee JH, Park CK, Chen G, Han Q, Xie RG, Liu T, Ji RR, Lee SY | Cell | 24856969 | Cell | 2014 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/24856969 |
| Molecular mechanisms of robustness in plants. | Lempe J, Lachowiec J, Sullivan AM, Queitsch C | Current opinion in plant biology | 23279801 | Curr Opin Plant Biol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23279801 |
| Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. | Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C | Genome research | 26240161 | Genome Res | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26240161 |
| Variability in a Short Tandem Repeat Mediates Complex Epistatic Interactions in Arabidopsis thaliana. | Press MO, Queitsch C | Genetics | 27866166 | Genetics | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27866166 |
| Massive variation of short tandem repeats with functional consequences across strains of Arabidopsis thaliana. | Press MO, McCoy RC, Hall AN, Akey JM, Queitsch C | Genome research | 29970452 | Genome Res | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29970452 |
| Redundancy, Feedback, and Robustness in the Arabidopsis thaliana BZR/BEH Gene Family. | Lachowiec J, Mason GA, Schultz K, Queitsch C | Frontiers in genetics | 30542366 | Front Genet | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30542366 |
| HSP90 Contributes to Entrainment of the Arabidopsis Circadian Clock via the Morning Loop. | Davis AM, Ronald J, Ma Z, Wilkinson AJ, Philippou K, Shindo T, Queitsch C, Davis SJ | Genetics | 30337341 | Genetics | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30337341 |
| PIF4 and ELF3 Act Independently in Arabidopsis thaliana Thermoresponsive Flowering. | Press MO, Lanctot A, Queitsch C | PloS one | 27564448 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27564448 |
| The protein chaperone HSP90 can facilitate the divergence of gene duplicates. | Lachowiec J, Lemus T, Thomas JH, Murphy PJ, Nemhauser JL, Queitsch C | Genetics | 23410833 | Genetics | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23410833 |
| Molecular mechanisms governing differential robustness of development and environmental responses in plants. | Lachowiec J, Queitsch C, Kliebenstein DJ | Annals of botany | 26473020 | Ann Bot | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26473020 |
| Medicine. Combating evolution to fight disease. | Rosenberg SM, Queitsch C | Science (New York, N.Y.) | 24604189 | Science | 2014 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/24604189 |
| Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage. | Xia J, Chiu LY, Nehring RB, Bravo Núñez MA, Mei Q, Perez M, Zhai Y, Fitzgerald DM, Pribis JP, Wang Y, Hu CW, Powell RT, LaBonte SA, Jalali A, Matadamas Guzmán ML, Lentzsch AM, Szafran AT, Joshi MC, Richters M, Gibson JL, Frisch RL, Hastings PJ, Bates D, Queitsch C, Hilsenbeck SG, Coarfa C, Hu JC, Siegele DA, Scott KL, Liang H, Mancini MA, Herman C, Miller KM, Rosenberg SM | Cell | 30633903 | Cell | 2019 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/30633903 |
| It's not magic - Hsp90 and its effects on genetic and epigenetic variation. | Zabinsky RA, Mason GA, Queitsch C, Jarosz DF | Seminars in cell & developmental biology | 29807130 | Semin Cell Dev Biol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29807130 |
| AGO1 and HSP90 buffer different genetic variants in Arabidopsis thaliana. | Lemus T, Mason GA, Bubb KL, Alexandre CM, Queitsch C, Cuperus JT | Genetics | 36303325 | Genetics | 2023 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/36303325 |
| Lessons from model organisms: phenotypic robustness and missing heritability in complex disease. | Queitsch C, Carlson KD, Girirajan S | PLoS genetics | 23166511 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23166511 |
| Evolutionary assembly patterns of prokaryotic genomes. | Press MO, Queitsch C, Borenstein E | Genome research | 27197212 | Genome Res | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27197212 |
| MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals. | Carlson KD, Sudmant PH, Press MO, Eichler EE, Shendure J, Queitsch C | Genome research | 25659649 | Genome Res | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25659649 |
| The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana. | Rival P, Press MO, Bale J, Grancharova T, Undurraga SF, Queitsch C | Genetics | 25116137 | Genetics | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25116137 |
| The overdue promise of short tandem repeat variation for heritability. | Press MO, Carlson KD, Queitsch C | Trends in genetics : TIG | 25182195 | Trends Genet | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25182195 |
| A Genome-Wide Association Analysis Reveals Epistatic Cancellation of Additive Genetic Variance for Root Length in Arabidopsis thaliana. | Lachowiec J, Shen X, Queitsch C, Carlborg Ö | PLoS genetics | 26397943 | PLoS Genet | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26397943 |
| Hsp90 promotes kinase evolution. | Lachowiec J, Lemus T, Borenstein E, Queitsch C | Molecular biology and evolution | 25246701 | Mol Biol Evol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25246701 |
| The Mechanistic Underpinnings of an ago1-Mediated, Environmentally Dependent, and Stochastic Phenotype. | Mason GA, Lemus T, Queitsch C | Plant physiology | 26872948 | Plant Physiol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26872948 |
| Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90. | Press MO, Li H, Creanza N, Kramer G, Queitsch C, Sourjik V, Borenstein E | PLoS genetics | 23874229 | PLoS Genet | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23874229 |
| Background-dependent effects of polyglutamine variation in the Arabidopsis thaliana gene ELF3. | Undurraga SF, Press MO, Legendre M, Bujdoso N, Bale J, Wang H, Davis SJ, Verstrepen KJ, Queitsch C | Proceedings of the National Academy of Sciences of the United States of America | 23129635 | Proc Natl Acad Sci U S A | 2012 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/23129635 |
| GC-rich DNA elements enable replication origin activity in the methylotrophic yeast Pichia pastoris. | Liachko I, Youngblood RA, Tsui K, Bubb KL, Queitsch C, Raghuraman MK, Nislow C, Brewer BJ, Dunham MJ | PLoS genetics | 24603708 | PLoS Genet | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24603708 |
| Bacterial cell wall composition and the influence of antibiotics by cell-wall and whole-cell NMR. | Romaniuk JA, Cegelski L | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 26370936 | Philos Trans R Soc Lond B Biol Sci | 2015 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/26370936 |
| Spectral snapshots of bacterial cell-wall composition and the influence of antibiotics by whole-cell NMR. | Nygaard R, Romaniuk JAH, Rice DM, Cegelski L | Biophysical journal | 25809251 | Biophys J | 2015 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/25809251 |
| Molecular determinants of mechanical properties of V. cholerae biofilms at the air-liquid interface. | Hollenbeck EC, Fong JC, Lim JY, Yildiz FH, Fuller GG, Cegelski L | Biophysical journal | 25418293 | Biophys J | 2014 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/25418293 |
| Bottom-up and top-down solid-state NMR approaches for bacterial biofilm matrix composition. | Cegelski L | Journal of magnetic resonance (San Diego, Calif. : 1997) | 25797008 | J Magn Reson | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25797008 |
| Toward a biorelevant structure of protein kinase C bound modulators: design, synthesis, and evaluation of labeled bryostatin analogues for analysis with rotational echo double resonance NMR spectroscopy. | Loy BA, Lesser AB, Staveness D, Billingsley KL, Cegelski L, Wender PA | Journal of the American Chemical Society | 25710634 | J Am Chem Soc | 2015 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/25710634 |
| Analysis of the Aspergillus fumigatus Biofilm Extracellular Matrix by Solid-State Nuclear Magnetic Resonance Spectroscopy. | Reichhardt C, Ferreira JA, Joubert LM, Clemons KV, Stevens DA, Cegelski L | Eukaryotic cell | 26163318 | Eukaryot Cell | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26163318 |
| Curcumin as an amyloid-indicator dye in E. coli. | McCrate OA, Zhou X, Cegelski L | Chemical communications (Cambridge, England) | 23287899 | Chem Commun (Camb) | 2013 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/23287899 |
| Dimethyl sulfoxide and ethanol elicit increased amyloid biogenesis and amyloid-integrated biofilm formation in Escherichia coli. | Lim JY, May JM, Cegelski L | Applied and environmental microbiology | 22389366 | Appl Environ Microbiol | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22389366 |
| Nutrient-dependent structural changes in S. aureus peptidoglycan revealed by solid-state NMR spectroscopy. | Zhou X, Cegelski L | Biochemistry | 22974326 | Biochemistry | 2012 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/22974326 |
| Quantitative analysis of amyloid-integrated biofilms formed by uropathogenic Escherichia coli at the air-liquid interface. | Wu C, Lim JY, Fuller GG, Cegelski L | Biophysical journal | 22947862 | Biophys J | 2012 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/22947862 |
| REDOR NMR for drug discovery. | Cegelski L | Bioorganic & medicinal chemistry letters | 24035486 | Bioorg Med Chem Lett | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24035486 |
| Sum of the parts: composition and architecture of the bacterial extracellular matrix. | McCrate OA, Zhou X, Reichhardt C, Cegelski L | Journal of molecular biology | 23827139 | J Mol Biol | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23827139 |
| Disruption of Escherichia coli amyloid-integrated biofilm formation at the air-liquid interface by a polysorbate surfactant. | Wu C, Lim JY, Fuller GG, Cegelski L | Langmuir : the ACS journal of surfaces and colloids | 23259693 | Langmuir | 2013 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/23259693 |
| Solid-State NMR for Bacterial Biofilms. | Reichhardt C, Cegelski L | Molecular physics | 24976646 | Mol Phys | 2014 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/24976646 |
| Characterization of the Vibrio cholerae extracellular matrix: a top-down solid-state NMR approach. | Reichhardt C, Fong JC, Yildiz F, Cegelski L | Biochimica et biophysica acta | 24911407 | Biochim Biophys Acta | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24911407 |
| Cell-Based High-Throughput Screening Identifies Rifapentine as an Inhibitor of Amyloid and Biofilm Formation in Escherichia coli. | Maher MC, Lim JY, Gunawan C, Cegelski L | ACS infectious diseases | 27623312 | ACS Infect Dis | 2015 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/27623312 |
| Putative hydrogen bond to tyrosine M208 in photosynthetic reaction centers from Rhodobacter capsulatus significantly slows primary charge separation. | Saggu M, Carter B, Zhou X, Faries K, Cegelski L, Holten D, Boxer SG, Kirmaier C | The journal of physical chemistry. B | 24902471 | J Phys Chem B | 2014 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/24902471 |
| Frequency-selective REDOR and spin-diffusion relays in uniformly labeled whole cells. | Rice DM, Romaniuk JA, Cegelski L | Solid state nuclear magnetic resonance | 26493462 | Solid State Nucl Magn Reson | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26493462 |
| Community behavior and amyloid-associated phenotypes among a panel of uropathogenic E. coli. | Lim JY, Pinkner JS, Cegelski L | Biochemical and biophysical research communications | 24239885 | Biochem Biophys Res Commun | 2014 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/24239885 |
| Non-exomic and synonymous variants in ABCA4 are an important cause of Stargardt disease. | Braun TA, Mullins RF, Wagner AH, Andorf JL, Johnston RM, Bakall BB, Deluca AP, Fishman GA, Lam BL, Weleber RG, Cideciyan AV, Jacobson SG, Sheffield VC, Tucker BA, Stone EM | Human molecular genetics | 23918662 | Hum Mol Genet | 2013 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/23918662 |
| Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis. | Drivas TG, Wojno AP, Tucker BA, Stone EM, Bennett J | Science translational medicine | 26062849 | Sci Transl Med | 2015 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/26062849 |
| Intravesical and alternative bladder-preservation therapies in the management of non-muscle-invasive bladder cancer unresponsive to bacillus Calmette-Guérin. | Steinberg RL, Thomas LJ, Nepple KG | Urologic oncology | 26777259 | Urol Oncol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26777259 |
| Perception of patient appearance following various methods of reconstruction after orbital exenteration. | Kuiper JJ, Zimmerman MB, Pagedar NA, Carter KD, Allen RC, Shriver EM | Orbit (Amsterdam, Netherlands) | 27341072 | Orbit | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27341072 |
| SIRT3 deacetylates and increases pyruvate dehydrogenase activity in cancer cells. | Ozden O, Park SH, Wagner BA, Song HY, Zhu Y, Vassilopoulos A, Jung B, Buettner GR, Gius D | Free radical biology & medicine | 25152236 | Free Radic Biol Med | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25152236 |
| Duplication of TBK1 Stimulates Autophagy in iPSC-derived Retinal Cells from a Patient with Normal Tension Glaucoma. | Tucker BA, Solivan-Timpe F, Roos BR, Anfinson KR, Robin AL, Wiley LA, Mullins RF, Fingert JH | Journal of stem cell research & therapy | 24883232 | J Stem Cell Res Ther | 2014 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/24883232 |
| ABCB5 is a limbal stem cell gene required for corneal development and repair. | Ksander BR, Kolovou PE, Wilson BJ, Saab KR, Guo Q, Ma J, McGuire SP, Gregory MS, Vincent WJ, Perez VL, Cruz-Guilloty F, Kao WW, Call MK, Tucker BA, Zhan Q, Murphy GF, Lathrop KL, Alt C, Mortensen LJ, Lin CP, Zieske JD, Frank MH, Frank NY | Nature | 25030174 | Nature | 2014 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/25030174 |
| Loss of CD34 expression in aging human choriocapillaris endothelial cells. | Sohn EH, Flamme-Wiese MJ, Whitmore SS, Wang K, Tucker BA, Mullins RF | PloS one | 24466138 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24466138 |
| Complement activation and choriocapillaris loss in early AMD: implications for pathophysiology and therapy. | Whitmore SS, Sohn EH, Chirco KR, Drack AV, Stone EM, Tucker BA, Mullins RF | Progress in retinal and eye research | 25486088 | Prog Retin Eye Res | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25486088 |
| Use of the Teres Major Muscle in Chimeric Subscapular System Free Flaps for Head and Neck Reconstruction. | Tomlinson AR, Jameson MJ, Pagedar NA, Schoeff SS, Shearer AE, Boyd NH | JAMA otolaryngology-- head & neck surgery | 26312435 | JAMA Otolaryngol Head Neck Surg | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26312435 |
| Molecular response of chorioretinal endothelial cells to complement injury: implications for macular degeneration. | Zeng S, Whitmore SS, Sohn EH, Riker MJ, Wiley LA, Scheetz TE, Stone EM, Tucker BA, Mullins RF | The Journal of pathology | 26564985 | J Pathol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26564985 |
| Patient-specific iPSC-derived photoreceptor precursor cells as a means to investigate retinitis pigmentosa. | Tucker BA, Mullins RF, Streb LM, Anfinson K, Eyestone ME, Kaalberg E, Riker MJ, Drack AV, Braun TA, Stone EM | eLife | 23991284 | Elife | 2013 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/23991284 |
| Allogenic iPSC-derived RPE cell transplants induce immune response in pigs: a pilot study. | Sohn EH, Jiao C, Kaalberg E, Cranston C, Mullins RF, Stone EM, Tucker BA | Scientific reports | 26138532 | Sci Rep | 2015 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/26138532 |
| Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa. | Tucker BA, Scheetz TE, Mullins RF, DeLuca AP, Hoffmann JM, Johnston RM, Jacobson SG, Sheffield VC, Stone EM | Proceedings of the National Academy of Sciences of the United States of America | 21825139 | Proc Natl Acad Sci U S A | 2011 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/21825139 |
| Weight loss after head and neck cancer: A dynamic relationship with depressive symptoms. | Van Liew JR, Brock RL, Christensen AJ, Karnell LH, Pagedar NA, Funk GF | Head & neck | 27704695 | Head Neck | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27704695 |
| Sources of bias in peoples' social-comparative estimates of food consumption. | Scherer AM, Bruchmann K, Windschitl PD, Rose JP, Smith AR, Koestner B, Snetselaar L, Suls J | Journal of experimental psychology. Applied | 27054551 | J Exp Psychol Appl | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27054551 |
| Prognostic factors for survival in patients with high-grade osteosarcoma using the Surveillance, Epidemiology, and End Results (SEER) Program database. | Duchman KR, Gao Y, Miller BJ | Cancer epidemiology | 26002013 | Cancer Epidemiol | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26002013 |
| A Method for Sectioning and Immunohistochemical Analysis of Stem Cell-Derived 3-D Organoids. | Wiley LA, Beebe DC, Mullins RF, Stone EM, Tucker BA | Current protocols in stem cell biology | 27171793 | Curr Protoc Stem Cell Biol | 2016 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/27171793 |
| Photoreceptor cells with profound structural deficits can support useful vision in mice. | Thompson S, Blodi FR, Lee S, Welder CR, Mullins RF, Tucker BA, Stasheff SF, Stone EM | Investigative ophthalmology & visual science | 24569582 | Invest Ophthalmol Vis Sci | 2014 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/24569582 |
| Stem cells as tools for studying the genetics of inherited retinal degenerations. | Wiley LA, Burnight ER, Mullins RF, Stone EM, Tucker BA | Cold Spring Harbor perspectives in medicine | 25502747 | Cold Spring Harb Perspect Med | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25502747 |
| CEP290 gene transfer rescues Leber congenital amaurosis cellular phenotype. | Burnight ER, Wiley LA, Drack AV, Braun TA, Anfinson KR, Kaalberg EE, Halder JA, Affatigato LM, Mullins RF, Stone EM, Tucker BA | Gene therapy | 24807808 | Gene Ther | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24807808 |
| Prevascularized silicon membranes for the enhancement of transport to implanted medical devices. | Worthington KS, Wiley LA, Mullins RF, Tucker BA, Nuxoll E | Journal of biomedical materials research. Part B, Applied biomaterials | 26316050 | J Biomed Mater Res B Appl Biomater | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26316050 |
| Treatment and Survival Trends in Glottic Carcinoma in Situ and Stage I Cancer From 1988 to 2012. | Khaja SF, Hoffman HT, Pagedar NA | The Annals of otology, rhinology, and laryngology | 26481178 | Ann Otol Rhinol Laryngol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26481178 |
| Hypomorphic mutations in TRNT1 cause retinitis pigmentosa with erythrocytic microcytosis. | DeLuca AP, Whitmore SS, Barnes J, Sharma TP, Westfall TA, Scott CA, Weed MC, Wiley JS, Wiley LA, Johnston RM, Schnieders MJ, Lentz SR, Tucker BA, Mullins RF, Scheetz TE, Stone EM, Slusarski DC | Human molecular genetics | 26494905 | Hum Mol Genet | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26494905 |
| Influence of a loop electrosurgical excision procedure (LEEP) on levels of cytokines in cervical secretions. | Saftlas AF, Spracklen CN, Ryckman KK, Stockdale CK, Penrose K, Ault K, Rubenstein LM, Pinto LA | Journal of reproductive immunology | 25721621 | J Reprod Immunol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25721621 |
| Concise Review: Patient-Specific Stem Cells to Interrogate Inherited Eye Disease. | Giacalone JC, Wiley LA, Burnight ER, Songstad AE, Mullins RF, Stone EM, Tucker BA | Stem cells translational medicine | 26683869 | Stem Cells Transl Med | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26683869 |
| Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq. | Whitmore SS, Wagner AH, DeLuca AP, Drack AV, Stone EM, Tucker BA, Zeng S, Braun TA, Mullins RF, Scheetz TE | Experimental eye research | 25446321 | Exp Eye Res | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25446321 |
| The membrane attack complex in aging human choriocapillaris: relationship to macular degeneration and choroidal thinning. | Mullins RF, Schoo DP, Sohn EH, Flamme-Wiese MJ, Workamelahu G, Johnston RM, Wang K, Tucker BA, Stone EM | The American journal of pathology | 25204844 | Am J Pathol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25204844 |
| Gene therapy using stem cells. | Burnight ER, Wiley LA, Mullins RF, Stone EM, Tucker BA | Cold Spring Harbor perspectives in medicine | 25395375 | Cold Spring Harb Perspect Med | 2014 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/25395375 |
| Using patient-specific induced pluripotent stem cells to interrogate the pathogenicity of a novel retinal pigment epithelium-specific 65 kDa cryptic splice site mutation and confirm eligibility for enrollment into a clinical gene augmentation trial. | Tucker BA, Cranston CM, Anfinson KA, Shrestha S, Streb LM, Leon A, Mullins RF, Stone EM | Translational research : the journal of laboratory and clinical medicine | 26364624 | Transl Res | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26364624 |
| Generating iPSC-Derived Choroidal Endothelial Cells to Study Age-Related Macular Degeneration. | Songstad AE, Wiley LA, Duong K, Kaalberg E, Flamme-Wiese MJ, Cranston CM, Riker MJ, Levasseur D, Stone EM, Mullins RF, Tucker BA | Investigative ophthalmology & visual science | 26720480 | Invest Ophthalmol Vis Sci | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26720480 |
| Differentiation of Induced Pluripotent Stem Cells to Neural Retinal Precursor Cells on Porous Poly-Lactic-co-Glycolic Acid Scaffolds. | Worthington KS, Wiley LA, Guymon CA, Salem AK, Tucker BA | Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics | 26692377 | J Ocul Pharmacol Ther | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26692377 |
| cGMP production of patient-specific iPSCs and photoreceptor precursor cells to treat retinal degenerative blindness. | Wiley LA, Burnight ER, DeLuca AP, Anfinson KR, Cranston CM, Kaalberg EE, Penticoff JA, Affatigato LM, Mullins RF, Stone EM, Tucker BA | Scientific reports | 27471043 | Sci Rep | 2016 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/27471043 |
| Risk of recurrent preterm birth among women according to change in partner. | Baer RJ, Yang J, Chambers CD, Ryckman KK, Saftlas AF, Berghella V, Schetter CD, Shaw GM, Stevenson DK, Jelliffe-Pawlowski LL | Journal of perinatal medicine | 27718495 | J Perinat Med | 2017 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/27718495 |
| Use of a synthetic xeno-free culture substrate for induced pluripotent stem cell induction and retinal differentiation. | Tucker BA, Anfinson KR, Mullins RF, Stone EM, Young MJ | Stem cells translational medicine | 23283489 | Stem Cells Transl Med | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23283489 |
| Is age-related macular degeneration a microvascular disease? | Mullins RF, Khanna A, Schoo DP, Tucker BA, Sohn EH, Drack AV, Stone EM | Advances in experimental medicine and biology | 24664709 | Adv Exp Med Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24664709 |
| Natural history of cone disease in the murine model of Leber congenital amaurosis due to CEP290 mutation: determining the timing and expectation of therapy. | Boye SE, Huang WC, Roman AJ, Sumaroka A, Boye SL, Ryals RC, Olivares MB, Ruan Q, Tucker BA, Stone EM, Swaroop A, Cideciyan AV, Hauswirth WW, Jacobson SG | PloS one | 24671090 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24671090 |
| Stem cells for investigation and treatment of inherited retinal disease. | Tucker BA, Mullins RF, Stone EM | Human molecular genetics | 24647603 | Hum Mol Genet | 2014 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/24647603 |
| Low-oxygen culture conditions extend the multipotent properties of human retinal progenitor cells. | Baranov PY, Tucker BA, Young MJ | Tissue engineering. Part A | 24320879 | Tissue Eng Part A | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24320879 |
| Controlled drug delivery from 3D printed two-photon polymerized poly(ethylene glycol) dimethacrylate devices. | Do AV, Worthington KS, Tucker BA, Salem AK | International journal of pharmaceutics | 30268853 | Int J Pharm | 2018 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/30268853 |
| Structural and biochemical analyses of choroidal thickness in human donor eyes. | Sohn EH, Khanna A, Tucker BA, Abràmoff MD, Stone EM, Mullins RF | Investigative ophthalmology & visual science | 24519422 | Invest Ophthalmol Vis Sci | 2014 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/24519422 |
| Patient-specific induced pluripotent stem cells (iPSCs) for the study and treatment of retinal degenerative diseases. | Wiley LA, Burnight ER, Songstad AE, Drack AV, Mullins RF, Stone EM, Tucker BA | Progress in retinal and eye research | 25448922 | Prog Retin Eye Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25448922 |
| Mechanical properties of murine and porcine ocular tissues in compression. | Worthington KS, Wiley LA, Bartlett AM, Stone EM, Mullins RF, Salem AK, Guymon CA, Tucker BA | Experimental eye research | 24613781 | Exp Eye Res | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24613781 |
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| Tailored Polymeric Membranes for Mycobacterium Smegmatis Porin A (MspA) Based Biosensors. | Morton D, Mortezaei S, Yemenicioglu S, Isaacman MJ, Nova IC, Gundlach JH, Theogarajan L | Journal of materials chemistry. B | 26413301 | J Mater Chem B | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26413301 |
| Rapid Metal -free Macromolecular Coupling via in situ Nitrile Oxide-Activated Alkene Cycloaddition. | Isaacman MJ, Cui W, Theogarajan LS | Journal of polymer science. Part A, Polymer chemistry | 26811566 | J Polym Sci A Polym Chem | 2014 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/26811566 |
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| Wearable multi-channel microelectrode membranes for elucidating electrophysiological phenotypes of injured myocardium. | Cao H, Yu F, Zhao Y, Zhang X, Tai J, Lee J, Darehzereshki A, Bersohn M, Lien CL, Chi NC, Tai YC, Hsiai TK | Integrative biology : quantitative biosciences from nano to macro | 24945366 | Integr Biol (Camb) | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24945366 |
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| Polo-like kinase 2 regulates angiogenic sprouting and blood vessel development. | Yang H, Fang L, Zhan R, Hegarty JM, Ren J, Hsiai TK, Gleeson JG, Miller YI, Trejo J, Chi NC | Developmental biology | 26004360 | Dev Biol | 2015 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/26004360 |
| Craniofacial and dental development in cardio-facio-cutaneous syndrome: the importance of Ras signaling homeostasis. | Goodwin AF, Oberoi S, Landan M, Charles C, Groth J, Martinez A, Fairley C, Weiss LA, Tidyman WE, Klein OD, Rauen KA | Clinical genetics | 22946697 | Clin Genet | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22946697 |
| Autism traits in the RASopathies. | Adviento B, Corbin IL, Widjaja F, Desachy G, Enrique N, Rosser T, Risi S, Marco EJ, Hendren RL, Bearden CE, Rauen KA, Weiss LA | Journal of medical genetics | 24101678 | J Med Genet | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24101678 |
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| RASopathies are associated with a distinct personality profile. | Bizaoui V, Gage J, Brar R, Rauen KA, Weiss LA | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 29659143 | Am J Med Genet B Neuropsychiatr Genet | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29659143 |
| Autonomous and Non-autonomous Defects Underlie Hypertrophic Cardiomyopathy in BRAF-Mutant hiPSC-Derived Cardiomyocytes. | Josowitz R, Mulero-Navarro S, Rodriguez NA, Falce C, Cohen N, Ullian EM, Weiss LA, Rauen KA, Sobie EA, Gelb BD | Stem cell reports | 27569062 | Stem Cell Reports | 2016 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/27569062 |
| Human iPS Cell-Derived Neurons Uncover the Impact of Increased Ras Signaling in Costello Syndrome. | Rooney GE, Goodwin AF, Depeille P, Sharir A, Schofield CM, Yeh E, Roose JP, Klein OD, Rauen KA, Weiss LA, Ullian EM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26740656 | J Neurosci | 2016 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/26740656 |
| Disease Burden and Symptom Structure of Autism in Neurofibromatosis Type 1: A Study of the International NF1-ASD Consortium Team (INFACT). | Morris SM, Acosta MT, Garg S, Green J, Huson S, Legius E, North KN, Payne JM, Plasschaert E, Frazier TW, Weiss LA, Zhang Y, Gutmann DH, Constantino JN | JAMA psychiatry | 27760236 | JAMA Psychiatry | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27760236 |
| Reverse Pathway Genetic Approach Identifies Epistasis in Autism Spectrum Disorders. | Mitra I, Lavillaureix A, Yeh E, Traglia M, Tsang K, Bearden CE, Rauen KA, Weiss LA | PLoS genetics | 28076348 | PLoS Genet | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28076348 |
| Cellular Phenotypes in Human iPSC-Derived Neurons from a Genetic Model of Autism Spectrum Disorder. | Deshpande A, Yadav S, Dao DQ, Wu ZY, Hokanson KC, Cahill MK, Wiita AP, Jan YN, Ullian EM, Weiss LA | Cell reports | 29212016 | Cell Rep | 2017 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/29212016 |
| Dysregulation of astrocyte extracellular signaling in Costello syndrome. | Krencik R, Hokanson KC, Narayan AR, Dvornik J, Rooney GE, Rauen KA, Weiss LA, Rowitch DH, Ullian EM | Science translational medicine | 25947161 | Sci Transl Med | 2015 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/25947161 |
| Patient-derived iPSCs show premature neural differentiation and neuron type-specific phenotypes relevant to neurodevelopment. | Yeh E, Dao DQ, Wu ZY, Kandalam SM, Camacho FM, Tom C, Zhang W, Krencik R, Rauen KA, Ullian EM, Weiss LA | Molecular psychiatry | 29158583 | Mol Psychiatry | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29158583 |
| Origins and formation of histone methylation across the human cell cycle. | Zee BM, Britton LM, Wolle D, Haberman DM, Garcia BA | Molecular and cellular biology | 22547680 | Mol Cell Biol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22547680 |
| Large-scale global identification of protein lysine methylation in vivo. | Cao XJ, Arnaudo AM, Garcia BA | Epigenetics | 23644510 | Epigenetics | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23644510 |
| Combining genomic and proteomic approaches for epigenetics research. | Han Y, Garcia BA | Epigenomics | 23895656 | Epigenomics | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23895656 |
| Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. | Sridharan R, Gonzales-Cope M, Chronis C, Bonora G, McKee R, Huang C, Patel S, Lopez D, Mishra N, Pellegrini M, Carey M, Garcia BA, Plath K | Nature cell biology | 23748610 | Nat Cell Biol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23748610 |
| Comprehending dynamic protein methylation with mass spectrometry. | Afjehi-Sadat L, Garcia BA | Current opinion in chemical biology | 23333572 | Curr Opin Chem Biol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23333572 |
| Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. | Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI | Nature structural & molecular biology | 23295261 | Nat Struct Mol Biol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23295261 |
| Examining histone posttranslational modification patterns by high-resolution mass spectrometry. | Lin S, Garcia BA | Methods in enzymology | 22910200 | Methods Enzymol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22910200 |
| Asymmetrically modified nucleosomes. | Voigt P, LeRoy G, Drury WJ 3rd, Zee BM, Son J, Beck DB, Young NL, Garcia BA, Reinberg D | Cell | 23021224 | Cell | 2012 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/23021224 |
| Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. | Rothbart SB, Lin S, Britton LM, Krajewski K, Keogh MC, Garcia BA, Strahl BD | Scientific reports | 22761995 | Sci Rep | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22761995 |
| Global turnover of histone post-translational modifications and variants in human cells. | Zee BM, Levin RS, DiMaggio PA, Garcia BA | Epigenetics & chromatin | 21134274 | Epigenetics Chromatin | 2010 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/21134274 |
| Revealing histone variant induced changes via quantitative proteomics. | Arnaudo AM, Molden RC, Garcia BA | Critical reviews in biochemistry and molecular biology | 21526979 | Crit Rev Biochem Mol Biol | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21526979 |
| Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation. | Van Aller GS, Reynoird N, Barbash O, Huddleston M, Liu S, Zmoos AF, McDevitt P, Sinnamon R, Le B, Mas G, Annan R, Sage J, Garcia BA, Tummino PJ, Gozani O, Kruger RG | Epigenetics | 22419068 | Epigenetics | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22419068 |
| Proteomic interrogation of human chromatin. | Torrente MP, Zee BM, Young NL, Baliban RC, LeRoy G, Floudas CA, Hake SB, Garcia BA | PloS one | 21935452 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21935452 |
| Low Resolution Data-Independent Acquisition in an LTQ-Orbitrap Allows for Simplified and Fully Untargeted Analysis of Histone Modifications. | Sidoli S, Simithy J, Karch KR, Kulej K, Garcia BA | Analytical chemistry | 26505526 | Anal Chem | 2015 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/26505526 |
| The histone lysine methyltransferase KMT2D sustains a gene expression program that represses B cell lymphoma development. | Ortega-Molina A, Boss IW, Canela A, Pan H, Jiang Y, Zhao C, Jiang M, Hu D, Agirre X, Niesvizky I, Lee JE, Chen HT, Ennishi D, Scott DW, Mottok A, Hother C, Liu S, Cao XJ, Tam W, Shaknovich R, Garcia BA, Gascoyne RD, Ge K, Shilatifard A, Elemento O, Nussenzweig A, Melnick AM, Wendel HG | Nature medicine | 26366710 | Nat Med | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26366710 |
| Selective inhibition of EZH2 and EZH1 enzymatic activity by a small molecule suppresses MLL-rearranged leukemia. | Xu B, On DM, Ma A, Parton T, Konze KD, Pattenden SG, Allison DF, Cai L, Rockowitz S, Liu S, Liu Y, Li F, Vedadi M, Frye SV, Garcia BA, Zheng D, Jin J, Wang GG | Blood | 25395428 | Blood | 2015 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/25395428 |
| Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. | Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW | Science (New York, N.Y.) | 27174990 | Science | 2016 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/27174990 |
| Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis. | Sidoli S, Bhanu NV, Karch KR, Wang X, Garcia BA | Journal of visualized experiments : JoVE | 27286567 | J Vis Exp | 2016 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/27286567 |
| PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism. | Jain SU, Do TJ, Lund PJ, Rashoff AQ, Diehl KL, Cieslik M, Bajic A, Juretic N, Deshmukh S, Venneti S, Muir TW, Garcia BA, Jabado N, Lewis PW | Nature communications | 31086175 | Nat Commun | 2019 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/31086175 |
| High resolution is not a strict requirement for characterization and quantification of histone post-translational modifications. | Karch KR, Zee BM, Garcia BA | Journal of proteome research | 25325711 | J Proteome Res | 2014 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/25325711 |
| Stable-isotope-labeled histone peptide library for histone post-translational modification and variant quantification by mass spectrometry. | Lin S, Wein S, Gonzales-Cope M, Otte GL, Yuan ZF, Afjehi-Sadat L, Maile T, Berger SL, Rush J, Lill JR, Arnott D, Garcia BA | Molecular & cellular proteomics : MCP | 25000943 | Mol Cell Proteomics | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25000943 |
| Multi-faceted quantitative proteomics analysis of histone H2B isoforms and their modifications. | Molden RC, Bhanu NV, LeRoy G, Arnaudo AM, Garcia BA | Epigenetics & chromatin | 25922622 | Epigenetics Chromatin | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25922622 |
| Defining heterochromatin in C. elegans through genome-wide analysis of the heterochromatin protein 1 homolog HPL-2. | Garrigues JM, Sidoli S, Garcia BA, Strome S | Genome research | 25467431 | Genome Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25467431 |
| Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis. | Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED | Nature cell biology | 25503565 | Nat Cell Biol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25503565 |
| Quantitative proteomic analysis of histone modifications. | Huang H, Lin S, Garcia BA, Zhao Y | Chemical reviews | 25688442 | Chem Rev | 2015 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/25688442 |
| SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. | Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF | Nature | 22722849 | Nature | 2012 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/22722849 |
| H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. | Chicas A, Kapoor A, Wang X, Aksoy O, Evertts AG, Zhang MQ, Garcia BA, Bernstein E, Lowe SW | Proceedings of the National Academy of Sciences of the United States of America | 22615382 | Proc Natl Acad Sci U S A | 2012 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/22615382 |
| Global secretome analysis identifies novel mediators of bone metastasis. | Blanco MA, LeRoy G, Khan Z, Alečković M, Zee BM, Garcia BA, Kang Y | Cell research | 22688892 | Cell Res | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22688892 |
| A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics. | Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA | Molecular & cellular proteomics : MCP | 27114449 | Mol Cell Proteomics | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27114449 |
| Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation. | Cao XJ, Zee BM, Garcia BA | Methods in molecular biology (Clifton, N.J.) | 23436372 | Methods Mol Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23436372 |
| MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. | Gaspar-Maia A, Qadeer ZA, Hasson D, Ratnakumar K, Leu NA, Leroy G, Liu S, Costanzi C, Valle-Garcia D, Schaniel C, Lemischka I, Garcia B, Pehrson JR, Bernstein E | Nature communications | 23463008 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23463008 |
| Proteogenomic characterization and mapping of nucleosomes decoded by Brd and HP1 proteins. | LeRoy G, Chepelev I, DiMaggio PA, Blanco MA, Zee BM, Zhao K, Garcia BA | Genome biology | 22897906 | Genome Biol | 2012 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/22897906 |
| Memory acquisition and retrieval impact different epigenetic processes that regulate gene expression. | Peixoto LL, Wimmer ME, Poplawski SG, Tudor JC, Kenworthy CA, Liu S, Mizuno K, Garcia BA, Zhang NR, Giese K, Abel T | BMC genomics | 26040834 | BMC Genomics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26040834 |
| H3R42me2a is a histone modification with positive transcriptional effects. | Casadio F, Lu X, Pollock SB, LeRoy G, Garcia BA, Muir TW, Roeder RG, Allis CD | Proceedings of the National Academy of Sciences of the United States of America | 23980157 | Proc Natl Acad Sci U S A | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/23980157 |
| SnapShot: histone modifications. | Huang H, Sabari BR, Garcia BA, Allis CD, Zhao Y | Cell | 25303536 | Cell | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25303536 |
| Middle-Down and Top-Down Mass Spectrometric Analysis of Co-occurring Histone Modifications. | Molden RC, Garcia BA | Current protocols in protein science | 25081742 | Curr Protoc Protein Sci | 2014 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/25081742 |
| A proteomic glimpse into the initial global epigenetic changes during HIV infection. | Britton LM, Sova P, Belisle S, Liu S, Chan EY, Katze MG, Garcia BA | Proteomics | 25116026 | Proteomics | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25116026 |
| Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression. | Jain SU, Khazaei S, Marchione DM, Lundgren SM, Wang X, Weinberg DN, Deshmukh S, Juretic N, Lu C, Allis CD, Garcia BA, Jabado N, Lewis PW | Proceedings of the National Academy of Sciences of the United States of America | 33067396 | Proc Natl Acad Sci U S A | 2020 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/33067396 |
| SMYD3 links lysine methylation of MAP3K2 to Ras-driven cancer. | Mazur PK, Reynoird N, Khatri P, Jansen PW, Wilkinson AW, Liu S, Barbash O, Van Aller GS, Huddleston M, Dhanak D, Tummino PJ, Kruger RG, Garcia BA, Butte AJ, Vermeulen M, Sage J, Gozani O | Nature | 24847881 | Nature | 2014 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/24847881 |
| Quantitative proteomic discovery of dynamic epigenome changes that control human cytomegalovirus (HCMV) infection. | O'Connor CM, DiMaggio PA Jr, Shenk T, Garcia BA | Molecular & cellular proteomics : MCP | 24987098 | Mol Cell Proteomics | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24987098 |
| In vivo proximity labeling for the detection of protein-protein and protein-RNA interactions. | Beck DB, Narendra V, Drury WJ 3rd, Casey R, Jansen PW, Yuan ZF, Garcia BA, Vermeulen M, Bonasio R | Journal of proteome research | 25311790 | J Proteome Res | 2014 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/25311790 |
| Evaluation of proteomic search engines for the analysis of histone modifications. | Yuan ZF, Lin S, Molden RC, Garcia BA | Journal of proteome research | 25167464 | J Proteome Res | 2014 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/25167464 |
| Quantitative dynamics of the link between cellular metabolism and histone acetylation. | Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA | The Journal of biological chemistry | 23482559 | J Biol Chem | 2013 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/23482559 |
| Validation of protein acetylation by mass spectrometry. | Zee BM, Garcia BA | Methods in molecular biology (Clifton, N.J.) | 23381849 | Methods Mol Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23381849 |
| SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. | Binda O, Sevilla A, LeRoy G, Lemischka IR, Garcia BA, Richard S | Epigenetics | 23324626 | Epigenetics | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23324626 |
| Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. | Wu Y, DiMaggio PA Jr, Perlman DH, Zakian VA, Garcia BA | Journal of proteome research | 23181431 | J Proteome Res | 2013 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/23181431 |
| Inhibition of PRC2 activity by a gain-of-function H3 mutation found in pediatric glioblastoma. | Lewis PW, Müller MM, Koletsky MS, Cordero F, Lin S, Banaszynski LA, Garcia BA, Muir TW, Becher OJ, Allis CD | Science (New York, N.Y.) | 23539183 | Science | 2013 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/23539183 |
| Discovery of lysine post-translational modifications through mass spectrometric detection. | Zee BM, Garcia BA | Essays in biochemistry | 22708569 | Essays Biochem | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22708569 |
| Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses. | Green EM, Mas G, Young NL, Garcia BA, Gozani O | Nature structural & molecular biology | 22343720 | Nat Struct Mol Biol | 2012 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/22343720 |
| Quantitative proteomic approaches to studying histone modifications. | Zee BM, Young NL, Garcia BA | Current chemical genomics | 21966350 | Curr Chem Genomics | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21966350 |
| H4K20 methylation regulates quiescence and chromatin compaction. | Evertts AG, Manning AL, Wang X, Dyson NJ, Garcia BA, Coller HA | Molecular biology of the cell | 23924899 | Mol Biol Cell | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23924899 |
| Initial characterization of histone H3 serine 10 O-acetylation. | Britton LM, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, Janicki SM, Garcia BA | Epigenetics | 23949383 | Epigenetics | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23949383 |
| Nitric Oxide Regulates Gene Expression in Cancers by Controlling Histone Posttranslational Modifications. | Vasudevan D, Hickok JR, Bovee RC, Pham V, Mantell LL, Bahroos N, Kanabar P, Cao XJ, Maienschein-Cline M, Garcia BA, Thomas DD | Cancer research | 26542213 | Cancer Res | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26542213 |
| Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation. | Lee JV, Carrer A, Shah S, Snyder NW, Wei S, Venneti S, Worth AJ, Yuan ZF, Lim HW, Liu S, Jackson E, Aiello NM, Haas NB, Rebbeck TR, Judkins A, Won KJ, Chodosh LA, Garcia BA, Stanger BZ, Feldman MD, Blair IA, Wellen KE | Cell metabolism | 24998913 | Cell Metab | 2014 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/24998913 |
| EpiProfile Quantifies Histone Peptides With Modifications by Extracting Retention Time and Intensity in High-resolution Mass Spectra. | Yuan ZF, Lin S, Molden RC, Cao XJ, Bhanu NV, Wang X, Sidoli S, Liu S, Garcia BA | Molecular & cellular proteomics : MCP | 25805797 | Mol Cell Proteomics | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25805797 |
| The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation. | Wu L, Zee BM, Wang Y, Garcia BA, Dou Y | Molecular cell | 21726816 | Mol Cell | 2011 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/21726816 |
| Breaking the histone code with quantitative mass spectrometry. | Britton LM, Gonzales-Cope M, Zee BM, Garcia BA | Expert review of proteomics | 21999833 | Expert Rev Proteomics | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21999833 |
| Post-Translational Modification Profiling--a High-Content Assay for Identifying Protein Modifications in Mammalian Cellular Systems. | Merbl Y, Kirschner MW | Current protocols in protein science | 25081743 | Curr Protoc Protein Sci | 2014 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/25081743 |
| Proteomic characterization of novel histone post-translational modifications. | Arnaudo AM, Garcia BA | Epigenetics & chromatin | 23916056 | Epigenetics Chromatin | 2013 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/23916056 |
| Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. | Gonzales-Cope M, Sidoli S, Bhanu NV, Won KJ, Garcia BA | BMC genomics | 26847871 | BMC Genomics | 2016 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/26847871 |
| Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. | Önder Ö, Sidoli S, Carroll M, Garcia BA | Expert review of proteomics | 26400466 | Expert Rev Proteomics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26400466 |
| NSD2 links dimethylation of histone H3 at lysine 36 to oncogenic programming. | Kuo AJ, Cheung P, Chen K, Zee BM, Kioi M, Lauring J, Xi Y, Park BH, Shi X, Garcia BA, Li W, Gozani O | Molecular cell | 22099308 | Mol Cell | 2011 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/22099308 |
| BRD4 assists elongation of both coding and enhancer RNAs by interacting with acetylated histones. | Kanno T, Kanno Y, LeRoy G, Campos E, Sun HW, Brooks SR, Vahedi G, Heightman TD, Garcia BA, Reinberg D, Siebenlist U, O'Shea JJ, Ozato K | Nature structural & molecular biology | 25383670 | Nat Struct Mol Biol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25383670 |
| Mass spectrometric analysis of histone proteoforms. | Yuan ZF, Arnaudo AM, Garcia BA | Annual review of analytical chemistry (Palo Alto, Calif.) | 24896311 | Annu Rev Anal Chem (Palo Alto Calif) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24896311 |
| Drawbacks in the use of unconventional hydrophobic anhydrides for histone derivatization in bottom-up proteomics PTM analysis. | Sidoli S, Yuan ZF, Lin S, Karch K, Wang X, Bhanu N, Arnaudo AM, Britton LM, Cao XJ, Gonzales-Cope M, Han Y, Liu S, Molden RC, Wein S, Afjehi-Sadat L, Garcia BA | Proteomics | 25641854 | Proteomics | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25641854 |
| Characterization of BRD4 during mammalian postmeiotic sperm development. | Bryant JM, Donahue G, Wang X, Meyer-Ficca M, Luense LJ, Weller AH, Bartolomei MS, Blobel GA, Meyer RG, Garcia BA, Berger SL | Molecular and cellular biology | 25691659 | Mol Cell Biol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25691659 |
| De novo peptide design and experimental validation of histone methyltransferase inhibitors. | Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA | PloS one | 24587223 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24587223 |
| An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions. | Sevilla A, Papatsenko D, Mazloom AR, Xu H, Vasileva A, Unwin RD, LeRoy G, Chen EY, Garrett-Bakelman FE, Lee DF, Trinite B, Webb RL, Wang Z, Su J, Gingold J, Melnick A, Garcia BA, Whetton AD, MacArthur BD, Ma'ayan A, Lemischka IR | Frontiers in cell and developmental biology | 33816475 | Front Cell Dev Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33816475 |
| ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression. | Ratnakumar K, Duarte LF, LeRoy G, Hasson D, Smeets D, Vardabasso C, Bönisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E | Genes & development | 22391447 | Genes Dev | 2012 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/22391447 |
| Neutron-encoded mass signatures for quantitative top-down proteomics. | Rhoads TW, Rose CM, Bailey DJ, Riley NM, Molden RC, Nestler AJ, Merrill AE, Smith LM, Hebert AS, Westphall MS, Pagliarini DJ, Garcia BA, Coon JJ | Analytical chemistry | 24475910 | Anal Chem | 2014 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/24475910 |
| A chemical probe selectively inhibits G9a and GLP methyltransferase activity in cells. | Vedadi M, Barsyte-Lovejoy D, Liu F, Rival-Gervier S, Allali-Hassani A, Labrie V, Wigle TJ, Dimaggio PA, Wasney GA, Siarheyeva A, Dong A, Tempel W, Wang SC, Chen X, Chau I, Mangano TJ, Huang XP, Simpson CD, Pattenden SG, Norris JL, Kireev DB, Tripathy A, Edwards A, Roth BL, Janzen WP, Garcia BA, Petronis A, Ellis J, Brown PJ, Frye SV, Arrowsmith CH, Jin J | Nature chemical biology | 21743462 | Nat Chem Biol | 2011 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/21743462 |
| LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2. | Nguyen H, Allali-Hassani A, Antonysamy S, Chang S, Chen LH, Curtis C, Emtage S, Fan L, Gheyi T, Li F, Liu S, Martin JR, Mendel D, Olsen JB, Pelletier L, Shatseva T, Wu S, Zhang FF, Arrowsmith CH, Brown PJ, Campbell RM, Garcia BA, Barsyte-Lovejoy D, Mader M, Vedadi M | The Journal of biological chemistry | 25825497 | J Biol Chem | 2015 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/25825497 |
| Bottom-up and middle-down proteomics have comparable accuracies in defining histone post-translational modification relative abundance and stoichiometry. | Sidoli S, Lin S, Karch KR, Garcia BA | Analytical chemistry | 25719549 | Anal Chem | 2015 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/25719549 |
| Transient inability to manage proteobacteria promotes chronic gut inflammation in TLR5-deficient mice. | Carvalho FA, Koren O, Goodrich JK, Johansson ME, Nalbantoglu I, Aitken JD, Su Y, Chassaing B, Walters WA, González A, Clemente JC, Cullender TC, Barnich N, Darfeuille-Michaud A, Vijay-Kumar M, Knight R, Ley RE, Gewirtz AT | Cell host & microbe | 22863420 | Cell Host Microbe | 2012 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/22863420 |
| Gut microbial diversity is associated with lower arterial stiffness in women. | Menni C, Lin C, Cecelja M, Mangino M, Matey-Hernandez ML, Keehn L, Mohney RP, Steves CJ, Spector TD, Kuo CF, Chowienczyk P, Valdes AM | European heart journal | 29750272 | Eur Heart J | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29750272 |
| An Investigation Into Physical Frailty as a Link Between the Gut Microbiome and Cognitive Health. | Verdi S, Jackson MA, Beaumont M, Bowyer RCE, Bell JT, Spector TD, Steves CJ | Frontiers in aging neuroscience | 30564113 | Front Aging Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30564113 |
| Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids. | Di Rienzi SC, Jacobson J, Kennedy EA, Bell ME, Shi Q, Waters JL, Lawrence P, Brenna JT, Britton RA, Walter J, Ley RE | eLife | 29580380 | Elife | 2018 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/29580380 |
| Human genetics shape the gut microbiome. | Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, Beaumont M, Van Treuren W, Knight R, Bell JT, Spector TD, Clark AG, Ley RE | Cell | 25417156 | Cell | 2014 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/25417156 |
| Interleukin-1β (IL-1β) promotes susceptibility of Toll-like receptor 5 (TLR5) deficient mice to colitis. | Carvalho FA, Nalbantoglu I, Ortega-Fernandez S, Aitken JD, Su Y, Koren O, Walters WA, Knight R, Ley RE, Vijay-Kumar M, Gewirtz AT | Gut | 21646247 | Gut | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21646247 |
| A heritability-based comparison of methods used to cluster 16S rRNA gene sequences into operational taxonomic units. | Jackson MA, Bell JT, Spector TD, Steves CJ | PeerJ | 27635321 | PeerJ | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27635321 |
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| Synthesis of purine-scaffold fluorescent probes for heat shock protein 90 with use in flow cytometry and fluorescence microscopy. | Taldone T, Gomes-DaGama EM, Zong H, Sen S, Alpaugh ML, Zatorska D, Alonso-Sabadell R, Guzman ML, Chiosis G | Bioorganic & medicinal chemistry letters | 21802945 | Bioorg Med Chem Lett | 2011 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/21802945 |
| Multiscale photoacoustic microscopy of single-walled carbon nanotube-incorporated tissue engineering scaffolds. | Cai X, Paratala BS, Hu S, Sitharaman B, Wang LV | Tissue engineering. Part C, Methods | 22082018 | Tissue Eng Part C Methods | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22082018 |
| Cell specific cytotoxicity and uptake of graphene nanoribbons. | Mullick Chowdhury S, Lalwani G, Zhang K, Yang JY, Neville K, Sitharaman B | Biomaterials | 23072942 | Biomaterials | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23072942 |
| Physicochemical characterization, and relaxometry studies of micro-graphite oxide, graphene nanoplatelets, and nanoribbons. | Paratala BS, Jacobson BD, Kanakia S, Francis LD, Sitharaman B | PloS one | 22685555 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22685555 |
| Fabrication and cytocompatibility of in situ crosslinked carbon nanomaterial films. | Patel SC, Lalwani G, Grover K, Qin YX, Sitharaman B | Scientific reports | 26018775 | Sci Rep | 2015 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/26018775 |
| Nanofilm generated non-pharmacological anabolic bone stimulus. | Talukdar Y, Rashkow JT, Patel S, Lalwani G, Bastidas J, Khan S, Sitharaman B | Journal of biomedical materials research. Part A | 31581364 | J Biomed Mater Res A | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31581364 |
| Enzymatic Degradation of Oxidized and Reduced Graphene Nanoribbons by Lignin Peroxidase. | Lalwani G, Xing W, Sitharaman B | Journal of materials chemistry. B | 25215188 | J Mater Chem B | 2014 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/25215188 |
| Structural disruption increases toxicity of graphene nanoribbons. | Mullick Chowdhury S, Dasgupta S, McElroy AE, Sitharaman B | Journal of applied toxicology : JAT | 25224919 | J Appl Toxicol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25224919 |
| Graphene nanoribbons as a drug delivery agent for lucanthone mediated therapy of glioblastoma multiforme. | Chowdhury SM, Surhland C, Sanchez Z, Chaudhary P, Suresh Kumar MA, Lee S, Peña LA, Waring M, Sitharaman B, Naidu M | Nanomedicine : nanotechnology, biology, and medicine | 25131339 | Nanomedicine | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25131339 |
| Graphene-based contrast agents for photoacoustic and thermoacoustic tomography. | Lalwani G, Cai X, Nie L, Wang LV, Sitharaman B | Photoacoustics | 24490141 | Photoacoustics | 2013 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/24490141 |
| Porous three-dimensional carbon nanotube scaffolds for tissue engineering. | Lalwani G, Gopalan A, D'Agati M, Sankaran JS, Judex S, Qin YX, Sitharaman B | Journal of biomedical materials research. Part A | 25788440 | J Biomed Mater Res A | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25788440 |
| Toxicology of graphene-based nanomaterials. | Lalwani G, D'Agati M, Khan AM, Sitharaman B | Advanced drug delivery reviews | 27154267 | Adv Drug Deliv Rev | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27154267 |
| Three-dimensional carbon nanotube scaffolds for long-term maintenance and expansion of human mesenchymal stem cells. | Lalwani G, D'agati M, Gopalan A, Patel SC, Talukdar Y, Sitharaman B | Journal of biomedical materials research. Part A | 28295953 | J Biomed Mater Res A | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28295953 |
| The magnetic, relaxometric, and optical properties of gadolinium-catalyzed single walled carbon nanotubes. | Sitharaman B, Jacobson BD, Wadghiri YZ, Bryant H, Frank J | Journal of applied physics | 23653487 | J Appl Phys | 2013 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/23653487 |
| Fabrication and Characterization of Three-Dimensional Macroscopic All-Carbon Scaffolds. | Lalwani G, Kwaczala AT, Kanakia S, Patel SC, Judex S, Sitharaman B | Carbon | 23436939 | Carbon N Y | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23436939 |
| Delivery of long chain C(16) and C(24) ceramide in HeLa cells using oxidized graphene nanoribbons. | Suhrland C, Truman JP, Obeid LM, Sitharaman B | Journal of biomedical materials research. Part B, Applied biomaterials | 31444959 | J Biomed Mater Res B Appl Biomater | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31444959 |
| Quantification of single-cell nanoparticle concentrations and the distribution of these concentrations in cell population. | Rashkow JT, Patel SC, Tappero R, Sitharaman B | Journal of the Royal Society, Interface | 24554576 | J R Soc Interface | 2014 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/24554576 |
| Two-dimensional nanostructure-reinforced biodegradable polymeric nanocomposites for bone tissue engineering. | Lalwani G, Henslee AM, Farshid B, Lin L, Kasper FK, Qin YX, Mikos AG, Sitharaman B | Biomacromolecules | 23405887 | Biomacromolecules | 2013 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/23405887 |
| Graphene-based platforms for cancer therapeutics. | Patel SC, Lee S, Lalwani G, Suhrland C, Chowdhury SM, Sitharaman B | Therapeutic delivery | 26769305 | Ther Deliv | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26769305 |
| Graphene nanoribbons elicit cell specific uptake and delivery via activation of epidermal growth factor receptor enhanced by human papillomavirus E5 protein. | Mullick Chowdhury S, Manepalli P, Sitharaman B | Acta biomaterialia | 24980059 | Acta Biomater | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24980059 |
| Synthesis, Characterization, In Vitro Phantom Imaging, and Cytotoxicity of A Novel Graphene-Based Multimodal Magnetic Resonance Imaging - X-Ray Computed Tomography Contrast Agent. | Lalwani G, Sundararaj JL, Schaefer K, Button T, Sitharaman B | Journal of materials chemistry. B | 24999431 | J Mater Chem B | 2014 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/24999431 |
| Cytotoxicity, cytocompatibility, cell-labeling efficiency, and in vitro cellular magnetic resonance imaging of gadolinium-catalyzed single-walled carbon nanotubes. | Avti PK, Caparelli ED, Sitharaman B | Journal of biomedical materials research. Part A | 23686792 | J Biomed Mater Res A | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23686792 |
| Interaction of graphene nanoribbons with components of the blood vascular system. | Chowdhury SM, Fang J, Sitharaman B | Future science OA | 26925250 | Future Sci OA | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26925250 |
| Interactions of 1D- and 2D-layered inorganic nanoparticles with fibroblasts and human mesenchymal stem cells. | Rashkow JT, Talukdar Y, Lalwani G, Sitharaman B | Nanomedicine (London, England) | 26080694 | Nanomedicine (Lond) | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26080694 |
| Boron nitride nanotubes and nanoplatelets as reinforcing agents of polymeric matrices for bone tissue engineering. | Farshid B, Lalwani G, Shir Mohammadi M, Simonsen J, Sitharaman B | Journal of biomedical materials research. Part B, Applied biomaterials | 26526153 | J Biomed Mater Res B Appl Biomater | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26526153 |
| In Vitro Bioactivity of One- and Two-Dimensional Nanoparticle-Incorporated Bone Tissue Engineering Scaffolds. | Rashkow JT, Lalwani G, Sitharaman B | Tissue engineering. Part A | 28762866 | Tissue Eng Part A | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28762866 |
| Multimodal ultrasound-photoacoustic imaging of tissue engineering scaffolds and blood oxygen saturation in and around the scaffolds. | Talukdar Y, Avti P, Sun J, Sitharaman B | Tissue engineering. Part C, Methods | 24107069 | Tissue Eng Part C Methods | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24107069 |
| Tungsten disulfide nanotubes reinforced biodegradable polymers for bone tissue engineering. | Lalwani G, Henslee AM, Farshid B, Parmar P, Lin L, Qin YX, Kasper FK, Mikos AG, Sitharaman B | Acta biomaterialia | 23727293 | Acta Biomater | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23727293 |
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| Real-time detection of lipid bilayer assembly and detergent-initiated solubilization using optical cavities. | Sun V, Armani AM | Applied physics letters | 25759510 | Appl Phys Lett | 2015 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/25759510 |
| Label free detection of 5'hydroxymethylcytosine within CpG islands using optical sensors. | Hawk RM, Armani AM | Biosensors & bioelectronics | 25461158 | Biosens Bioelectron | 2015 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/25461158 |
| Nanowatt threshold, alumina sensitized neodymium laser integrated on silicon. | Maker AJ, Armani AM | Optics express | 24216946 | Opt Express | 2013 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/24216946 |
| Attaching biological probes to silica optical biosensors using silane coupling agents. | Soteropulos CE, Hunt HK | Journal of visualized experiments : JoVE | 22588224 | J Vis Exp | 2012 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/22588224 |
| Determination of binding kinetics using whispering gallery mode microcavities. | Soteropulos CE, Hunt HK, Armani AM | Applied physics letters | 21990943 | Appl Phys Lett | 2011 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/21990943 |
| Selective patterning of Si-based biosensor surfaces using isotropic silicon etchants. | Biggs BW, Hunt HK, Armani AM | Journal of colloid and interface science | 22196345 | J Colloid Interface Sci | 2012 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/22196345 |
| Temperature sensor based on a hybrid ITO-silica resonant cavity. | Socorro AB, Soltani S, Del Villar I, Corres JM, Armani AM | Optics express | 25836065 | Opt Express | 2015 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/25836065 |
| A compressive sensing approach for glioma margin delineation using mass spectrometry. | Gholami B, Agar NY, Jolesz FA, Haddad WM, Tannenbaum AR | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255629 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255629 |
| First In Vivo Testing of Compounds Targeting Group 3 Medulloblastomas Using an Implantable Microdevice as a New Paradigm for Drug Development. | Jonas O, Calligaris D, Methuku KR, Poe MM, Francois JP, Tranghese F, Changelian A, Sieghart W, Ernst M, Krummel DA, Cook JM, Pomeroy SL, Cima M, Agar NY, Langer R, Sengupta S | Journal of biomedical nanotechnology | 27319222 | J Biomed Nanotechnol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27319222 |
| Mass spectrometry imaging as a tool for surgical decision-making. | Calligaris D, Norton I, Feldman DR, Ide JL, Dunn IF, Eberlin LS, Cooks RG, Jolesz FA, Golby AJ, Santagata S, Agar NY | Journal of mass spectrometry : JMS | 24259206 | J Mass Spectrom | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24259206 |
| Prostate cancer diagnosis and characterization with mass spectrometry imaging. | Kurreck A, Vandergrift LA, Fuss TL, Habbel P, Agar NYR, Cheng LL | Prostate cancer and prostatic diseases | 29209003 | Prostate Cancer Prostatic Dis | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29209003 |
| Application of desorption electrospray ionization mass spectrometry imaging in breast cancer margin analysis. | Calligaris D, Caragacianu D, Liu X, Norton I, Thompson CJ, Richardson AL, Golshan M, Easterling ML, Santagata S, Dillon DA, Jolesz FA, Agar NY | Proceedings of the National Academy of Sciences of the United States of America | 25246570 | Proc Natl Acad Sci U S A | 2014 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/25246570 |
| Intraoperative mass spectrometry mapping of an onco-metabolite to guide brain tumor surgery. | Santagata S, Eberlin LS, Norton I, Calligaris D, Feldman DR, Ide JL, Liu X, Wiley JS, Vestal ML, Ramkissoon SH, Orringer DA, Gill KK, Dunn IF, Dias-Santagata D, Ligon KL, Jolesz FA, Golby AJ, Cooks RG, Agar NY | Proceedings of the National Academy of Sciences of the United States of America | 24982150 | Proc Natl Acad Sci U S A | 2014 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/24982150 |
| Efficacy of PARP Inhibitor Rucaparib in Orthotopic Glioblastoma Xenografts Is Limited by Ineffective Drug Penetration into the Central Nervous System. | Parrish KE, Cen L, Murray J, Calligaris D, Kizilbash S, Mittapalli RK, Carlson BL, Schroeder MA, Sludden J, Boddy AV, Agar NY, Curtin NJ, Elmquist WF, Sarkaria JN | Molecular cancer therapeutics | 26438157 | Mol Cancer Ther | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26438157 |
| Classifying human brain tumors by lipid imaging with mass spectrometry. | Eberlin LS, Norton I, Dill AL, Golby AJ, Ligon KL, Santagata S, Cooks RG, Agar NY | Cancer research | 22139378 | Cancer Res | 2012 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/22139378 |
| Classification of astrocytomas and oligodendrogliomas from mass spectrometry data using sparse kernel machines. | Huang J, Gholami B, Agar NY, Norton I, Haddad WM, Tannenbaum AR | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22256188 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22256188 |
| Ambient mass spectrometry for the intraoperative molecular diagnosis of human brain tumors. | Eberlin LS, Norton I, Orringer D, Dunn IF, Liu X, Ide JL, Jarmusch AK, Ligon KL, Jolesz FA, Golby AJ, Santagata S, Agar NY, Cooks RG | Proceedings of the National Academy of Sciences of the United States of America | 23300285 | Proc Natl Acad Sci U S A | 2013 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/23300285 |
| Recursive feature elimination for brain tumor classification using desorption electrospray ionization mass spectrometry imaging. | Gholami B, Norton I, Tannenbaum AR, Agar NY | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23367115 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23367115 |
| Label-Free Neurosurgical Pathology with Stimulated Raman Imaging. | Lu FK, Calligaris D, Olubiyi OI, Norton I, Yang W, Santagata S, Xie XS, Golby AJ, Agar NY | Cancer research | 27197198 | Cancer Res | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27197198 |
| Profiling of adrenocorticotropic hormone and arginine vasopressin in human pituitary gland and tumor thin tissue sections using droplet-based liquid-microjunction surface-sampling-HPLC-ESI-MS-MS. | Kertesz V, Calligaris D, Feldman DR, Changelian A, Laws ER, Santagata S, Agar NY, Van Berkel GJ | Analytical and bioanalytical chemistry | 26084546 | Anal Bioanal Chem | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26084546 |
| The Efficacy of the Wee1 Inhibitor MK-1775 Combined with Temozolomide Is Limited by Heterogeneous Distribution across the Blood-Brain Barrier in Glioblastoma. | Pokorny JL, Calligaris D, Gupta SK, Iyekegbe DO Jr, Mueller D, Bakken KK, Carlson BL, Schroeder MA, Evans DL, Lou Z, Decker PA, Eckel-Passow JE, Pucci V, Ma B, Shumway SD, Elmquist WF, Agar NY, Sarkaria JN | Clinical cancer research : an official journal of the American Association for Cancer Research | 25609063 | Clin Cancer Res | 2015 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/25609063 |
| Molecular imaging of drug transit through the blood-brain barrier with MALDI mass spectrometry imaging. | Liu X, Ide JL, Norton I, Marchionni MA, Ebling MC, Wang LY, Davis E, Sauvageot CM, Kesari S, Kellersberger KA, Easterling ML, Santagata S, Stuart DD, Alberta J, Agar JN, Stiles CD, Agar NY | Scientific reports | 24091529 | Sci Rep | 2013 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/24091529 |
| Rapid, label-free detection of brain tumors with stimulated Raman scattering microscopy. | Ji M, Orringer DA, Freudiger CW, Ramkissoon S, Liu X, Lau D, Golby AJ, Norton I, Hayashi M, Agar NY, Young GS, Spino C, Santagata S, Camelo-Piragua S, Ligon KL, Sagher O, Xie XS | Science translational medicine | 24005159 | Sci Transl Med | 2013 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/24005159 |
| Reconstruction and Feature Selection for Desorption Electrospray Ionization Mass Spectroscopy Imagery. | Gao Y, Zhu L, Norton I, Agar NY, Tannenbaum A | Proceedings of SPIE--the International Society for Optical Engineering | 25302009 | Proc SPIE Int Soc Opt Eng | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/25302009 |
| A statistical modeling approach for tumor-type identification in surgical neuropathology using tissue mass spectrometry imaging. | Gholami B, Norton I, Eberlin LS, Agar NY | IEEE journal of biomedical and health informatics | 24592474 | IEEE J Biomed Health Inform | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/24592474 |
| Desorption electrospray ionization then MALDI mass spectrometry imaging of lipid and protein distributions in single tissue sections. | Eberlin LS, Liu X, Ferreira CR, Santagata S, Agar NY, Cooks RG | Analytical chemistry | 21975048 | Anal Chem | 2011 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/21975048 |
| Molecular typing of Meningiomas by Desorption Electrospray Ionization Mass Spectrometry Imaging for Surgical Decision-Making. | Calligaris D, Feldman DR, Norton I, Brastianos PK, Dunn IF, Santagata S, Agar NY | International journal of mass spectrometry | 25844057 | Int J Mass Spectrom | 2015 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/25844057 |
| MALDI mass spectrometry imaging analysis of pituitary adenomas for near-real-time tumor delineation. | Calligaris D, Feldman DR, Norton I, Olubiyi O, Changelian AN, Machaidze R, Vestal ML, Laws ER, Dunn IF, Santagata S, Agar NY | Proceedings of the National Academy of Sciences of the United States of America | 26216958 | Proc Natl Acad Sci U S A | 2015 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/26216958 |
| A review of bacteria-animal lateral gene transfer may inform our understanding of diseases like cancer. | Robinson KM, Sieber KB, Dunning Hotopp JC | PLoS genetics | 24146634 | PLoS Genet | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24146634 |
| Horizontal gene transfer between bacteria and animals. | Dunning Hotopp JC | Trends in genetics : TIG | 21334091 | Trends Genet | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21334091 |
| Targeted Enrichment and Sequencing of Recent Endosymbiont-Host Lateral Gene Transfers. | Dunning Hotopp JC, Slatko BE, Foster JM | Scientific reports | 28405008 | Sci Rep | 2017 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/28405008 |
| Lateral gene transfer between prokaryotes and eukaryotes. | Sieber KB, Bromley RE, Dunning Hotopp JC | Experimental cell research | 28189637 | Exp Cell Res | 2017 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28189637 |
| Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. | Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC | Microbiome | 28118849 | Microbiome | 2017 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/28118849 |
| Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. | Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC | BMC genomics | 25217238 | BMC Genomics | 2014 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/25217238 |
| Extensive duplication of the Wolbachia DNA in chromosome four of Drosophila ananassae. | Klasson L, Kumar N, Bromley R, Sieber K, Flowers M, Ott SH, Tallon LJ, Andersson SG, Dunning Hotopp JC | BMC genomics | 25496002 | BMC Genomics | 2014 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/25496002 |
| Genomics of Loa loa, a Wolbachia-free filarial parasite of humans. | Desjardins CA, Cerqueira GC, Goldberg JM, Dunning Hotopp JC, Haas BJ, Zucker J, Ribeiro JM, Saif S, Levin JZ, Fan L, Zeng Q, Russ C, Wortman JR, Fink DL, Birren BW, Nutman TB | Nature genetics | 23525074 | Nat Genet | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23525074 |
| Biology wars: the eukaryotes strike back. | Dunning Hotopp JC, Estes AM | Cell host & microbe | 25498339 | Cell Host Microbe | 2014 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/25498339 |
| Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples. | Kumar N, Lin M, Zhao X, Ott S, Santana-Cruz I, Daugherty S, Rikihisa Y, Sadzewicz L, Tallon LJ, Fraser CM, Dunning Hotopp JC | Scientific reports | 27713560 | Sci Rep | 2016 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/27713560 |
| The genome of Onchocerca volvulus, agent of river blindness. | Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S | Nature microbiology | 27869790 | Nat Microbiol | 2016 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/27869790 |
| Modeling the integration of bacterial rRNA fragments into the human cancer genome. | Sieber KB, Gajer P, Dunning Hotopp JC | BMC bioinformatics | 27001685 | BMC Bioinformatics | 2016 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/27001685 |
| Mobile elements and viral integrations prompt considerations for bacterial DNA integration as a novel carcinogen. | Robinson KM, Dunning Hotopp JC | Cancer letters | 24956175 | Cancer Lett | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/24956175 |
| Bacteria-human somatic cell lateral gene transfer is enriched in cancer samples. | Riley DR, Sieber KB, Robinson KM, White JR, Ganesan A, Nourbakhsh S, Dunning Hotopp JC | PLoS computational biology | 23840181 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23840181 |
| Extensively duplicated and transcriptionally active recent lateral gene transfer from a bacterial Wolbachia endosymbiont to its host filarial nematode Brugia malayi. | Ioannidis P, Johnston KL, Riley DR, Kumar N, White JR, Olarte KT, Ott S, Tallon LJ, Foster JM, Taylor MJ, Dunning Hotopp JC | BMC genomics | 24053607 | BMC Genomics | 2013 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/24053607 |
| MIWI2 and MILI Have Differential Effects on piRNA Biogenesis and DNA Methylation. | Manakov SA, Pezic D, Marinov GK, Pastor WA, Sachidanandam R, Aravin AA | Cell reports | 26279574 | Cell Rep | 2015 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/26279574 |
| Small but sturdy: small RNAs in cellular memory and epigenetics. | Stuwe E, Tóth KF, Aravin AA | Genes & development | 24589774 | Genes Dev | 2014 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24589774 |
| piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells. | Pezic D, Manakov SA, Sachidanandam R, Aravin AA | Genes & development | 24939875 | Genes Dev | 2014 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24939875 |
| MORC1 represses transposable elements in the mouse male germline. | Pastor WA, Stroud H, Nee K, Liu W, Pezic D, Manakov S, Lee SA, Moissiard G, Zamudio N, Bourc'his D, Aravin AA, Clark AT, Jacobsen SE | Nature communications | 25503965 | Nat Commun | 2014 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/25503965 |
| Cutoff Suppresses RNA Polymerase II Termination to Ensure Expression of piRNA Precursors. | Chen YA, Stuwe E, Luo Y, Ninova M, Le Thomas A, Rozhavskaya E, Li S, Vempati S, Laver JD, Patel DJ, Smibert CA, Lipshitz HD, Toth KF, Aravin AA | Molecular cell | 27292797 | Mol Cell | 2016 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/27292797 |
| Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. | Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ | Cell reports | 29996105 | Cell Rep | 2018 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/29996105 |
| A transgenerational process defines piRNA biogenesis in Drosophila virilis. | Le Thomas A, Marinov GK, Aravin AA | Cell reports | 25199836 | Cell Rep | 2014 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/25199836 |
| Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. | Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Tóth KF | Genes & development | 23392610 | Genes Dev | 2013 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/23392610 |
| Small RNA in the nucleus: the RNA-chromatin ping-pong. | Olovnikov I, Aravin AA, Fejes Toth K | Current opinion in genetics & development | 22349141 | Curr Opin Genet Dev | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22349141 |
| To be or not to be a piRNA: genomic origin and processing of piRNAs. | Le Thomas A, Tóth KF, Aravin AA | Genome biology | 24467990 | Genome Biol | 2014 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/24467990 |
| Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing. | Le Thomas A, Stuwe E, Li S, Du J, Marinov G, Rozhkov N, Chen YC, Luo Y, Sachidanandam R, Toth KF, Patel D, Aravin AA | Genes & development | 25085419 | Genes Dev | 2014 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/25085419 |
| A framework for piRNA cluster manipulation. | Olovnikov I, Le Thomas A, Aravin AA | Methods in molecular biology (Clifton, N.J.) | 24178556 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24178556 |
| Production of artificial piRNAs in flies and mice. | Muerdter F, Olovnikov I, Molaro A, Rozhkov NV, Czech B, Gordon A, Hannon GJ, Aravin AA | RNA (New York, N.Y.) | 22096018 | RNA | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22096018 |
| Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila. | Hur JK, Luo Y, Moon S, Ninova M, Marinov GK, Chung YD, Aravin AA | Genes & development | 27036967 | Genes Dev | 2016 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27036967 |
| Bacterial argonaute samples the transcriptome to identify foreign DNA. | Olovnikov I, Chan K, Sachidanandam R, Newman DK, Aravin AA | Molecular cell | 24034694 | Mol Cell | 2013 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/24034694 |
| Non-Coding RNAs in Transcriptional Regulation: The review for Current Molecular Biology Reports. | Chen YA, Aravin AA | Current molecular biology reports | 26120554 | Curr Mol Biol Rep | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26120554 |
| Prokaryotic Argonautes defend genomes against invasive DNA. | Hur JK, Olovnikov I, Aravin AA | Trends in biochemical sciences | 24836995 | Trends Biochem Sci | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24836995 |
| Aub and Ago3 Are Recruited to Nuage through Two Mechanisms to Form a Ping-Pong Complex Assembled by Krimper. | Webster A, Li S, Hur JK, Wachsmuth M, Bois JS, Perkins EM, Patel DJ, Aravin AA | Molecular cell | 26295961 | Mol Cell | 2015 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26295961 |
| Precision medicine for suicidality: from universality to subtypes and personalization. | Niculescu AB, Le-Niculescu H, Levey DF, Phalen PL, Dainton HL, Roseberry K, Niculescu EM, Niezer JO, Williams A, Graham DL, Jones TJ, Venugopal V, Ballew A, Yard M, Gelbart T, Kurian SM, Shekhar A, Schork NJ, Sandusky GE, Salomon DR | Molecular psychiatry | 28809398 | Mol Psychiatry | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28809398 |
| Convergent functional genomic studies of ω-3 fatty acids in stress reactivity, bipolar disorder and alcoholism. | Le-Niculescu H, Case NJ, Hulvershorn L, Patel SD, Bowker D, Gupta J, Bell R, Edenberg HJ, Tsuang MT, Kuczenski R, Geyer MA, Rodd ZA, Niculescu AB | Translational psychiatry | 22832392 | Transl Psychiatry | 2011 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/22832392 |
| Towards understanding and predicting suicidality in women: biomarkers and clinical risk assessment. | Levey DF, Niculescu EM, Le-Niculescu H, Dainton HL, Phalen PL, Ladd TB, Weber H, Belanger E, Graham DL, Khan FN, Vanipenta NP, Stage EC, Ballew A, Yard M, Gelbart T, Shekhar A, Schork NJ, Kurian SM, Sandusky GE, Salomon DR, Niculescu AB | Molecular psychiatry | 27046645 | Mol Psychiatry | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27046645 |
| Discovery and validation of blood biomarkers for suicidality. | Le-Niculescu H, Levey DF, Ayalew M, Palmer L, Gavrin LM, Jain N, Winiger E, Bhosrekar S, Shankar G, Radel M, Bellanger E, Duckworth H, Olesek K, Vergo J, Schweitzer R, Yard M, Ballew A, Shekhar A, Sandusky GE, Schork NJ, Kurian SM, Salomon DR, Niculescu AB 3rd | Molecular psychiatry | 23958961 | Mol Psychiatry | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23958961 |
| Convergent functional genomics of psychiatric disorders. | Niculescu AB | American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics | 23728881 | Am J Med Genet B Neuropsychiatr Genet | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23728881 |
| Psychiatric blood biomarkers: avoiding jumping to premature negative or positive conclusions. | Niculescu AB, Levey D, Le-Niculescu H, Niculescu E, Kurian SM, Salomon D | Molecular psychiatry | 25582618 | Mol Psychiatry | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25582618 |
| Precision medicine for mood disorders: objective assessment, risk prediction, pharmacogenomics, and repurposed drugs. | Le-Niculescu H, Roseberry K, Gill SS, Levey DF, Phalen PL, Mullen J, Williams A, Bhairo S, Voegtline T, Davis H, Shekhar A, Kurian SM, Niculescu AB | Molecular psychiatry | 33828235 | Mol Psychiatry | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33828235 |
| Towards precision medicine for stress disorders: diagnostic biomarkers and targeted drugs. | Le-Niculescu H, Roseberry K, Levey DF, Rogers J, Kosary K, Prabha S, Jones T, Judd S, McCormick MA, Wessel AR, Williams A, Phalen PL, Mamdani F, Sequeira A, Kurian SM, Niculescu AB | Molecular psychiatry | 30862937 | Mol Psychiatry | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/30862937 |
| Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction. | Ayalew M, Le-Niculescu H, Levey DF, Jain N, Changala B, Patel SD, Winiger E, Breier A, Shekhar A, Amdur R, Koller D, Nurnberger JI, Corvin A, Geyer M, Tsuang MT, Salomon D, Schork NJ, Fanous AH, O'Donovan MC, Niculescu AB | Molecular psychiatry | 22584867 | Mol Psychiatry | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22584867 |
| Understanding and predicting suicidality using a combined genomic and clinical risk assessment approach. | Niculescu AB, Levey DF, Phalen PL, Le-Niculescu H, Dainton HD, Jain N, Belanger E, James A, George S, Weber H, Graham DL, Schweitzer R, Ladd TB, Learman R, Niculescu EM, Vanipenta NP, Khan FN, Mullen J, Shankar G, Cook S, Humbert C, Ballew A, Yard M, Gelbart T, Shekhar A, Schork NJ, Kurian SM, Sandusky GE, Salomon DR | Molecular psychiatry | 26283638 | Mol Psychiatry | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26283638 |
| Dissecting Suicidality Using a Combined Genomic and Clinical Approach. | Niculescu AB, Le-Niculescu H | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 27909331 | Neuropsychopharmacology | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27909331 |
| A brief proposal for improving clinical trials. | Niculescu AB | Molecular psychiatry | 27021813 | Mol Psychiatry | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27021813 |
| Blood biomarkers for memory: toward early detection of risk for Alzheimer disease, pharmacogenomics, and repurposed drugs. | Niculescu AB, Le-Niculescu H, Roseberry K, Wang S, Hart J, Kaur A, Robertson H, Jones T, Strasburger A, Williams A, Kurian SM, Lamb B, Shekhar A, Lahiri DK, Saykin AJ | Molecular psychiatry | 31792364 | Mol Psychiatry | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31792364 |
| Genetic risk prediction and neurobiological understanding of alcoholism. | Levey DF, Le-Niculescu H, Frank J, Ayalew M, Jain N, Kirlin B, Learman R, Winiger E, Rodd Z, Shekhar A, Schork N, Kiefer F, Wodarz N, Müller-Myhsok B, Dahmen N, GESGA Consortium, Nöthen M, Sherva R, Farrer L, Smith AH, Kranzler HR, Rietschel M, Gelernter J, Niculescu AB | Translational psychiatry | 24844177 | Transl Psychiatry | 2014 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/24844177 |
| Convergent functional genomics of anxiety disorders: translational identification of genes, biomarkers, pathways and mechanisms. | Le-Niculescu H, Balaraman Y, Patel SD, Ayalew M, Gupta J, Kuczenski R, Shekhar A, Schork N, Geyer MA, Niculescu AB | Translational psychiatry | 22832404 | Transl Psychiatry | 2011 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/22832404 |
| Convergent functional genomics of stem cell-derived cells. | Niculescu AB | Translational psychiatry | 24022510 | Transl Psychiatry | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/24022510 |
| Towards precision medicine for pain: diagnostic biomarkers and repurposed drugs. | Niculescu AB, Le-Niculescu H, Levey DF, Roseberry K, Soe KC, Rogers J, Khan F, Jones T, Judd S, McCormick MA, Wessel AR, Williams A, Kurian SM, White FA | Molecular psychiatry | 30755720 | Mol Psychiatry | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30755720 |
| A hydrogel-endothelial cell implant mimics infantile hemangioma: modulation by survivin and the Hippo pathway. | Tsuneki M, Hardee S, Michaud M, Morotti R, Lavik E, Madri JA | Laboratory investigation; a journal of technical methods and pathology | 25961170 | Lab Invest | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25961170 |
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| Intravenously administered nanoparticles increase survival following blast trauma. | Lashof-Sullivan MM, Shoffstall E, Atkins KT, Keane N, Bir C, VandeVord P, Lavik EB | Proceedings of the National Academy of Sciences of the United States of America | 24982180 | Proc Natl Acad Sci U S A | 2014 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/24982180 |
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| Comparison of fMRI analysis methods for heterogeneous BOLD responses in block design studies. | Liu J, Duffy BA, Bernal-Casas D, Fang Z, Lee JH | NeuroImage | 27993672 | Neuroimage | 2017 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/27993672 |
| Activation of Direct and Indirect Pathway Medium Spiny Neurons Drives Distinct Brain-wide Responses. | Lee HJ, Weitz AJ, Bernal-Casas D, Duffy BA, Choy M, Kravitz AV, Kreitzer AC, Lee JH | Neuron | 27373834 | Neuron | 2016 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/27373834 |
| Tracing activity across the whole brain neural network with optogenetic functional magnetic resonance imaging. | Lee JH | Frontiers in neuroinformatics | 22046160 | Front Neuroinform | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22046160 |
| Informing brain connectivity with optogenetic functional magnetic resonance imaging. | Lee JH | NeuroImage | 22326987 | Neuroimage | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/22326987 |
| Studying Brain Circuit Function with Dynamic Causal Modeling for Optogenetic fMRI. | Bernal-Casas D, Lee HJ, Weitz AJ, Lee JH | Neuron | 28132829 | Neuron | 2017 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/28132829 |
| MRI compatible optrodes for simultaneous LFP and optogenetic fMRI investigation of seizure-like afterdischarges. | Duffy BA, Choy M, Chuapoco MR, Madsen M, Lee JH | NeuroImage | 26208873 | Neuroimage | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26208873 |
| Optogenetic fMRI reveals distinct, frequency-dependent networks recruited by dorsal and intermediate hippocampus stimulations. | Weitz AJ, Fang Z, Lee HJ, Fisher RS, Smith WC, Choy M, Liu J, Lin P, Rosenberg M, Lee JH | NeuroImage | 25462689 | Neuroimage | 2015 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/25462689 |
| Silicon coupled with plasmon nanocavity generates bright visible hot-luminescence. | Cho CH, Aspetti CO, Park J, Agarwal R | Nature photonics | 23710256 | Nat Photonics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23710256 |
| Enhanced second-harmonic generation from metal-integrated semiconductor nanowires via highly confined whispering gallery modes. | Ren ML, Liu W, Aspetti CO, Sun L, Agarwal R | Nature communications | 25388766 | Nat Commun | 2014 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/25388766 |
| Size-dependent chemical transformation, structural phase-change, and optical properties of nanowires. | Piccione B, Agarwal R, Jung Y, Agarwal R | Philosophical magazine (Abingdon, England) | 23997656 | Philos Mag (Abingdon) | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23997656 |
| Strain-induced large exciton energy shifts in buckled CdS nanowires. | Sun L, Kim DH, Oh KH, Agarwal R | Nano letters | 23899018 | Nano Lett | 2013 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/23899018 |
| Studies of hot photoluminescence in plasmonically coupled silicon via variable energy excitation and temperature-dependent spectroscopy. | Aspetti CO, Cho CH, Agarwal R, Agarwal R | Nano letters | 25120156 | Nano Lett | 2014 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/25120156 |
| Tailoring light-matter coupling in semiconductor and hybrid-plasmonic nanowires. | Piccione B, Aspetti CO, Cho CH, Agarwal R | Reports on progress in physics. Physical Society (Great Britain) | 25093385 | Rep Prog Phys | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25093385 |
| Ring-Opening Polymerization of γ-(4-Vinylbenzyl)-(L)-Glutamate N-Carboxyanhydride for the Synthesis of Functional Polypeptides. | Lu H, Bai Y, Wang J, Gabrielson NP, Wang F, Lin Y, Cheng J | Macromolecules | 22121300 | Macromolecules | 2011 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/22121300 |
| Water-Soluble Polypeptides with Elongated, Charged Side Chains Adopt Ultra-Stable Helical Conformations. | Zhang Y, Lu H, Lin Y, Cheng J | Macromolecules | 22049249 | Macromolecules | 2011 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/22049249 |
| Targeting tumor vasculature with aptamer-functionalized doxorubicin-polylactide nanoconjugates for enhanced cancer therapy. | Tang L, Tong R, Coyle VJ, Yin Q, Pondenis H, Borst LB, Cheng J, Fan TM | ACS nano | 25938427 | ACS Nano | 2015 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/25938427 |
| Dimeric drug polymeric nanoparticles with exceptionally high drug loading and quantitative loading efficiency. | Cai K, He X, Song Z, Yin Q, Zhang Y, Uckun FM, Jiang C, Cheng J | Journal of the American Chemical Society | 25741752 | J Am Chem Soc | 2015 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/25741752 |
| Nanoscale liposomal formulation of a SYK P-site inhibitor against B-precursor leukemia. | Uckun FM, Qazi S, Cely I, Sahin K, Shahidzadeh A, Ozercan I, Yin Q, Gaynon P, Termuhlen A, Cheng J, Yiv S | Blood | 23568490 | Blood | 2013 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/23568490 |
| Helical Poly(arginine) Mimics with Superior Cell-Penetrating and Molecular Transporting Properties. | Tang H, Yin L, Kim KH, Cheng J | Chemical science | 25400902 | Chem Sci | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25400902 |
| Cationic, helical polypeptide-based gene delivery for IMR-90 fibroblasts and human embryonic stem cells. | Yen J, Zhang Y, Gabrielson NP, Yin L, Guan L, Chaudhury I, Lu H, Wang F, Cheng J | Biomaterials science | 23997932 | Biomater Sci | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23997932 |
| Polypeptides with quaternary phosphonium side chains: synthesis, characterization, and cell-penetrating properties. | Song Z, Zheng N, Ba X, Yin L, Zhang R, Ma L, Cheng J | Biomacromolecules | 24635536 | Biomacromolecules | 2014 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/24635536 |
| In Vivo Targeting of Metabolically Labeled Cancers with Ultra-Small Silica Nanoconjugates. | Wang H, Tang L, Liu Y, Dobrucka IT, Dobrucki LW, Yin L, Cheng J | Theranostics | 27375793 | Theranostics | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27375793 |
| Pamidronate functionalized nanoconjugates for targeted therapy of focal skeletal malignant osteolysis. | Yin Q, Tang L, Cai K, Tong R, Sternberg R, Yang X, Dobrucki LW, Borst LB, Kamstock D, Song Z, Helferich WG, Cheng J, Fan TM | Proceedings of the National Academy of Sciences of the United States of America | 27457945 | Proc Natl Acad Sci U S A | 2016 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/27457945 |
| Dynamic urea bond for the design of reversible and self-healing polymers. | Ying H, Zhang Y, Cheng J | Nature communications | 24492620 | Nat Commun | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24492620 |
| Helical antimicrobial polypeptides with radial amphiphilicity. | Xiong M, Lee MW, Mansbach RA, Song Z, Bao Y, Peek RM Jr, Yao C, Chen LF, Ferguson AL, Wong GC, Cheng J | Proceedings of the National Academy of Sciences of the United States of America | 26460016 | Proc Natl Acad Sci U S A | 2015 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/26460016 |
| The effect of side-chain functionality and hydrophobicity on the gene delivery capabilities of cationic helical polypeptides. | Zhang R, Zheng N, Song Z, Yin L, Cheng J | Biomaterials | 24439403 | Biomaterials | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24439403 |
| Size-dependent tumor penetration and in vivo efficacy of monodisperse drug-silica nanoconjugates. | Tang L, Gabrielson NP, Uckun FM, Fan TM, Cheng J | Molecular pharmaceutics | 23301497 | Mol Pharm | 2013 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/23301497 |
| Synthesis of water-soluble poly(α-hydroxy acids) from living ring-opening polymerization of O-benzyl-L-serine carboxyanhydrides. | Lu Y, Yin L, Zhang Y, Zhonghai Z, Xu Y, Tong R, Cheng J | ACS macro letters | 23359651 | ACS Macro Lett | 2012 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/23359651 |
| Synthesis and biological response of size-specific, monodisperse drug-silica nanoconjugates. | Tang L, Fan TM, Borst LB, Cheng J | ACS nano | 22494403 | ACS Nano | 2012 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/22494403 |
| Water-soluble poly(L-serine)s with elongated and charged side-chains: synthesis, conformations, and cell-penetrating properties. | Tang H, Yin L, Lu H, Cheng J | Biomacromolecules | 22853191 | Biomacromolecules | 2012 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/22853191 |
| A cell-penetrating helical polymer for siRNA delivery to mammalian cells. | Gabrielson NP, Lu H, Yin L, Kim KH, Cheng J | Molecular therapy : the journal of the American Society of Gene Therapy | 22643866 | Mol Ther | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22643866 |
| Targeted Ultrasound-Assisted Cancer-Selective Chemical Labeling and Subsequent Cancer Imaging using Click Chemistry. | Wang H, Gauthier M, Kelly JR, Miller RJ, Xu M, O'Brien WD Jr, Cheng J | Angewandte Chemie (International ed. in English) | 27010510 | Angew Chem Int Ed Engl | 2016 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/27010510 |
| Anticancer Camptothecin-N-Poly(lactic acid) Nanoconjugates with Facile Hydrolysable Linker. | Yin Q, Tong R, Yin L, Fan TM, Cheng J | Polymer chemistry | 26005498 | Polym Chem | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/26005498 |
| Dual Stimuli-Responsive Poly(β-amino ester) Nanoparticles for On-Demand Burst Release. | Lee JS, Deng X, Han P, Cheng J | Macromolecular bioscience | 26036966 | Macromol Biosci | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26036966 |
| Non-invasive, real-time reporting drug release in vitro and in vivo. | Zhang Y, Yin Q, Yen J, Li J, Ying H, Wang H, Hua Y, Chaney EJ, Boppart SA, Cheng J | Chemical communications (Cambridge, England) | 25798457 | Chem Commun (Camb) | 2015 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/25798457 |
| Hydrolyzable polyureas bearing hindered urea bonds. | Ying H, Cheng J | Journal of the American Chemical Society | 25406025 | J Am Chem Soc | 2014 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/25406025 |
| CD22ΔE12 as a molecular target for RNAi therapy. | Uckun FM, Ma H, Cheng J, Myers DE, Qazi S | British journal of haematology | 25659406 | Br J Haematol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25659406 |
| Investigating the optimal size of anticancer nanomedicine. | Tang L, Yang X, Yin Q, Cai K, Wang H, Chaudhury I, Yao C, Zhou Q, Kwon M, Hartman JA, Dobrucki IT, Dobrucki LW, Borst LB, Lezmi S, Helferich WG, Ferguson AL, Fan TM, Cheng J | Proceedings of the National Academy of Sciences of the United States of America | 25316794 | Proc Natl Acad Sci U S A | 2014 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/25316794 |
| Reactive and bioactive cationic α-helical polypeptide template for nonviral gene delivery. | Gabrielson NP, Lu H, Yin L, Li D, Wang F, Cheng J | Angewandte Chemie (International ed. in English) | 22162307 | Angew Chem Int Ed Engl | 2012 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/22162307 |
| Synthesis of hybrid block copolymers via integrated ring-opening metathesis polymerization and polymerization of NCA. | Bai Y, Lu H, Ponnusamy E, Cheng J | Chemical communications (Cambridge, England) | 21869956 | Chem Commun (Camb) | 2011 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/21869956 |
| Trigger-responsive, fast-degradable poly(β-amino ester)s for enhanced DNA unpackaging and reduced toxicity. | Deng X, Zheng N, Song Z, Yin L, Cheng J | Biomaterials | 24674461 | Biomaterials | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24674461 |
| Redox-Responsive, Core Cross-Linked Polyester Micelles. | Zhang Z, Yin L, Tu C, Song Z, Zhang Y, Xu Y, Tong R, Zhou Q, Ren J, Cheng J | ACS macro letters | 23536920 | ACS Macro Lett | 2013 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/23536920 |
| In vivo cancer targeting via glycopolyester nanoparticle mediated metabolic cell labeling followed by click reaction. | Wang H, Bo Y, Liu Y, Xu M, Cai K, Wang R, Cheng J | Biomaterials | 31323538 | Biomaterials | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31323538 |
| Manipulating the membrane penetration mechanism of helical polypeptides via aromatic modification for efficient gene delivery. | Zheng N, Song Z, Yang J, Liu Y, Li F, Cheng J, Yin L | Acta biomaterialia | 28476586 | Acta Biomater | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28476586 |
| Ionic α-helical polypeptides toward nonviral gene delivery. | Zhang R, Song Z, Yin L, Zheng N, Tang H, Lu H, Gabrielson NP, Lin Y, Kim K, Cheng J | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 25377262 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2015 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/25377262 |
| Bioorthogonal Oxime Ligation Mediated In Vivo Cancer Targeting. | Tang L, Yin Q, Xu Y, Zhou Q, Cai K, Yen J, Dobrucki LW, Cheng J | Chemical science | 26146536 | Chem Sci | 2015 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/26146536 |
| Redox-Responsive Self-Assembled Chain-Shattering Polymeric Therapeutics. | Cai K, Yen J, Yin Q, Liu Y, Song Z, Lezmi S, Zhang Y, Yang X, Helferich WG, Cheng J | Biomaterials science | 26146551 | Biomater Sci | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26146551 |
| Enhanced Non-Viral Gene Delivery to Human Embryonic Stem Cells via Small Molecule-Mediated Transient Alteration of Cell Structure. | Yen J, Yin L, Cheng J | Journal of materials chemistry. B | 26005572 | J Mater Chem B | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/26005572 |
| Drug-initiated ring-opening polymerization of O-carboxyanhydrides for the preparation of anticancer drug-poly(O-carboxyanhydride) nanoconjugates. | Yin Q, Tong R, Xu Y, Baek K, Dobrucki LW, Fan TM, Cheng J | Biomacromolecules | 23445497 | Biomacromolecules | 2013 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/23445497 |
| Selective Delivery of an Anticancer Drug with Aptamer-Functionalized Liposomes to Breast Cancer Cells in Vitro and in Vivo. | Xing H, Tang L, Yang X, Hwang K, Wang W, Yin Q, Wong NY, Dobrucki LW, Yasui N, Katzenellenbogen JA, Helferich WG, Cheng J, Lu Y | Journal of materials chemistry. B | 24159374 | J Mater Chem B | 2013 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/24159374 |
| Poly(iohexol) nanoparticles as contrast agents for in vivo X-ray computed tomography imaging. | Yin Q, Yap FY, Yin L, Ma L, Zhou Q, Dobrucki LW, Fan TM, Gaba RC, Cheng J | Journal of the American Chemical Society | 23987119 | J Am Chem Soc | 2013 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/23987119 |
| Immunosuppressive Activity of Size-Controlled PEG-PLGA Nanoparticles Containing Encapsulated Cyclosporine A. | Tang L, Azzi J, Kwon M, Mounayar M, Tong R, Yin Q, Moore R, Skartsis N, Fan TM, Abdi R, Cheng J | Journal of transplantation | 22545201 | J Transplant | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22545201 |
| Selective in vivo metabolic cell-labeling-mediated cancer targeting. | Wang H, Wang R, Cai K, He H, Liu Y, Yen J, Wang Z, Xu M, Sun Y, Zhou X, Yin Q, Tang L, Dobrucki IT, Dobrucki LW, Chaney EJ, Boppart SA, Fan TM, Lezmi S, Chen X, Yin L, Cheng J | Nature chemical biology | 28192414 | Nat Chem Biol | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28192414 |
| Drug-Initiated, Controlled Ring-Opening Polymerization for the Synthesis of Polymer-Drug Conjugates. | Tong R, Cheng J | Macromolecules | 23357880 | Macromolecules | 2012 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/23357880 |
| Non-viral gene delivery via membrane-penetrating, mannose-targeting supramolecular self-assembled nanocomplexes. | Yin L, Song Z, Kim KH, Zheng N, Gabrielson NP, Cheng J | Advanced materials (Deerfield Beach, Fla.) | 23417835 | Adv Mater | 2013 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/23417835 |
| Facile functionalization of polyesters through thiol-yne chemistry for the design of degradable, cell-penetrating and gene delivery dual-functional agents. | Zhang Z, Yin L, Xu Y, Tong R, Lu Y, Ren J, Cheng J | Biomacromolecules | 23098261 | Biomacromolecules | 2012 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/23098261 |
| Chain-shattering polymeric therapeutics with on-demand drug-release capability. | Zhang Y, Yin Q, Yin L, Ma L, Tang L, Cheng J | Angewandte Chemie (International ed. in English) | 23650111 | Angew Chem Int Ed Engl | 2013 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/23650111 |
| Liposomal Nanoparticles of a Spleen Tyrosine Kinase P-Site Inhibitor Amplify the Potency of Low Dose Total Body Irradiation Against Aggressive B-Precursor Leukemia and Yield Superior Survival Outcomes in Mice. | Uckun FM, Myers DE, Cheng J, Qazi S | EBioMedicine | 26285772 | EBioMedicine | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26285772 |
| Reconfiguring the architectures of cationic helical polypeptides to control non-viral gene delivery. | Yin L, Song Z, Kim KH, Zheng N, Tang H, Lu H, Gabrielson N, Cheng J | Biomaterials | 23283350 | Biomaterials | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23283350 |
| Ionic polypeptides with unusual helical stability. | Lu H, Wang J, Bai Y, Lang JW, Liu S, Lin Y, Cheng J | Nature communications | 21343924 | Nat Commun | 2011 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/21343924 |
| Supramolecular self-assembled nanoparticles mediate oral delivery of therapeutic TNF-α siRNA against systemic inflammation. | Yin L, Song Z, Qu Q, Kim KH, Zheng N, Yao C, Chaudhury I, Tang H, Gabrielson NP, Uckun FM, Cheng J | Angewandte Chemie (International ed. in English) | 23610013 | Angew Chem Int Ed Engl | 2013 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/23610013 |
| Targeting Mantle Cell Lymphoma with Anti-SYK Nanoparticles. | Cely I, Yiv S, Yin Q, Shahidzadeh A, Tang L, Cheng J, Uckun FM | Journal of analytical oncology | 23730399 | J Anal Oncol | 2012 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/23730399 |
| Polymeric Nanomedicines Based on Poly(lactide) and Poly(lactide-co-glycolide). | Tong R, Gabrielson NP, Fan TM, Cheng J | Current opinion in solid state & materials science | 23914135 | Curr Opin Solid State Mater Sci | 2012 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/23914135 |
| Light-responsive helical polypeptides capable of reducing toxicity and unpacking DNA: toward nonviral gene delivery. | Yin L, Tang H, Kim KH, Zheng N, Song Z, Gabrielson NP, Lu H, Cheng J | Angewandte Chemie (International ed. in English) | 23832670 | Angew Chem Int Ed Engl | 2013 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/23832670 |
| Polyvalent mesoporous silica nanoparticle-aptamer bioconjugates target breast cancer cells. | Li LL, Yin Q, Cheng J, Lu Y | Advanced healthcare materials | 23184791 | Adv Healthc Mater | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23184791 |
| Maximizing gene delivery efficiencies of cationic helical polypeptides via balanced membrane penetration and cellular targeting. | Zheng N, Yin L, Song Z, Ma L, Tang H, Gabrielson NP, Lu H, Cheng J | Biomaterials | 24211080 | Biomaterials | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24211080 |
| Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant. | Feher VA, Schiffer JM, Mermelstein DJ, Mih N, Pierce LCT, McCammon JA, Amaro RE | Biophysical journal | 30606449 | Biophys J | 2019 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/30606449 |
| The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. | Bohl HO, Ieong P, Lee JK, Lee T, Kankanala J, Shi K, Demir Ö, Kurahashi K, Amaro RE, Wang Z, Aihara H | The Journal of biological chemistry | 29626094 | J Biol Chem | 2018 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/29626094 |
| Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A. | Schiffer JM, Feher VA, Malmstrom RD, Sida R, Amaro RE | Biophysical journal | 27760351 | Biophys J | 2016 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/27760351 |
| Progress towards automated Kepler scientific workflows for computer-aided drug discovery and molecular simulations. | Ieong PU, Sørensen J, Vemu PL, Wong CW, Demir Ö, Williams NP, Wang J, Crawl D, Swift RV, Malmstrom RD, Altintas I, Amaro RE | Procedia computer science | 29399238 | Procedia Comput Sci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/29399238 |
| Two Relations to Estimate Membrane Permeability Using Milestoning. | Votapka LW, Lee CT, Amaro RE | The journal of physical chemistry. B | 27154639 | J Phys Chem B | 2016 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/27154639 |
| Emerging Computational Methods for the Rational Discovery of Allosteric Drugs. | Wagner JR, Lee CT, Durrant JD, Malmstrom RD, Feher VA, Amaro RE | Chemical reviews | 27074285 | Chem Rev | 2016 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/27074285 |
| The Binding Interface between Human APOBEC3F and HIV-1 Vif Elucidated by Genetic and Computational Approaches. | Richards C, Albin JS, Demir Ö, Shaban NM, Luengas EM, Land AM, Anderson BD, Holten JR, Anderson JS, Harki DA, Amaro RE, Harris RS | Cell reports | 26628363 | Cell Rep | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26628363 |
| Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis. | Van Wart AT, Durrant J, Votapka L, Amaro RE | Journal of chemical theory and computation | 24803851 | J Chem Theory Comput | 2014 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/24803851 |
| Dynamics and Molecular Mechanisms of p53 Transcriptional Activation. | Offutt TL, Ieong PU, Demir Ö, Amaro RE | Biochemistry | 30388364 | Biochemistry | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30388364 |
| Determinants of Oligonucleotide Selectivity of APOBEC3B. | Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE | Journal of chemical information and modeling | 30130104 | J Chem Inf Model | 2019 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/30130104 |
| Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach. | Jagger BR, Lee CT, Amaro RE | The journal of physical chemistry letters | 30070844 | J Phys Chem Lett | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/30070844 |
| Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2. | Demir Ö, Amaro RE | Journal of chemical information and modeling | 22512810 | J Chem Inf Model | 2012 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/22512810 |
| Development of an AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases. | Prabhu L, Chen L, Wei H, Demir Ö, Safa A, Zeng L, Amaro RE, O'Neil BH, Zhang ZY, Lu T | Molecular bioSystems | 29099132 | Mol Biosyst | 2017 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/29099132 |
| Efficient Calculation of Accurate Reaction Energies-Assessment of Different Models in Electronic Structure Theory. | Friedrich J | Journal of chemical theory and computation | 26574443 | J Chem Theory Comput | 2015 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/26574443 |
| Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer. | Schiffer JM, Malmstrom RD, Parnell J, Ramirez-Sarmiento C, Reyes J, Amaro RE, Komives EA | Structure (London, England : 1993) | 27396830 | Structure | 2016 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/27396830 |
| WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. | Durrant JD, Amaro RE | BMC bioinformatics | 24886360 | BMC Bioinformatics | 2014 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/24886360 |
| Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme. | Swift RV, Ong CD, Amaro RE | Biochemistry | 23205906 | Biochemistry | 2012 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/23205906 |
| Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures. | Amaro RE, Mulholland AJ | Nature reviews. Chemistry | 30949587 | Nat Rev Chem | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30949587 |
| Designing novel inhibitors of Trypanosoma brucei. | Demir O, Amaro RE | Methods in molecular biology (Clifton, N.J.) | 23568474 | Methods Mol Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23568474 |
| Modeling the pharmacodynamics of passive membrane permeability. | Swift RV, Amaro RE | Journal of computer-aided molecular design | 22042376 | J Comput Aided Mol Des | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22042376 |
| Mechanism of 150-cavity formation in influenza neuraminidase. | Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM | Nature communications | 21750542 | Nat Commun | 2011 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/21750542 |
| Ensemble-based computational approach discriminates functional activity of p53 cancer and rescue mutants. | Demir Ö, Baronio R, Salehi F, Wassman CD, Hall L, Hatfield GW, Chamberlin R, Kaiser P, Lathrop RH, Amaro RE | PLoS computational biology | 22028641 | PLoS Comput Biol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22028641 |
| Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53. | Wassman CD, Baronio R, Demir Ö, Wallentine BD, Chen CK, Hall LV, Salehi F, Lin DW, Chung BP, Hatfield GW, Richard Chamberlin A, Luecke H, Lathrop RH, Kaiser P, Amaro RE | Nature communications | 23360998 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23360998 |
| Computational chemistry and drug discovery: a call to action. | Jansen JM, Amaro RE, Cornell W, Tseng YJ, Walters WP | Future medicinal chemistry | 23088271 | Future Med Chem | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23088271 |
| Exploring residue component contributions to dynamical network models of allostery. | Vanwart AT, Eargle J, Luthey-Schulten Z, Amaro RE | Journal of chemical theory and computation | 23139645 | J Chem Theory Comput | 2012 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/23139645 |
| Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. | Swift RV, Jusoh SA, Offutt TL, Li ES, Amaro RE | Journal of chemical information and modeling | 27097522 | J Chem Inf Model | 2016 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/27097522 |
| LipidWrapper: an algorithm for generating large-scale membrane models of arbitrary geometry. | Durrant JD, Amaro RE | PLoS computational biology | 25032790 | PLoS Comput Biol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25032790 |
| A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases. | Zimmermann S, Hall L, Riley S, Sørensen J, Amaro RE, Schnaufer A | Nucleic acids research | 26400159 | Nucleic Acids Res | 2016 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/26400159 |
| Computational approaches to mapping allosteric pathways. | Feher VA, Durrant JD, Van Wart AT, Amaro RE | Current opinion in structural biology | 24667124 | Curr Opin Struct Biol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24667124 |
| Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα. | P Barros E, Malmstrom RD, Nourbakhsh K, Del Rio JC, Kornev AP, Taylor SS, Amaro RE | Biochemistry | 28221775 | Biochemistry | 2017 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/28221775 |
| Conformational Switch Regulates the DNA Cytosine Deaminase Activity of Human APOBEC3B. | Shi K, Demir Ö, Carpenter MA, Wagner J, Kurahashi K, Harris RS, Amaro RE, Aihara H | Scientific reports | 29234087 | Sci Rep | 2017 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/29234087 |
| Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism. | Hirakis SP, Malmstrom RD, Amaro RE | Biochemistry | 28661131 | Biochemistry | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28661131 |
| Structural basis for ligand modulation of the CCR2 conformational landscape. | Taylor BC, Lee CT, Amaro RE | Proceedings of the National Academy of Sciences of the United States of America | 30975755 | Proc Natl Acad Sci U S A | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/30975755 |
| A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target. | Amaro RE, Ieong PU, Huber G, Dommer A, Steven AC, Bush RM, Durrant JD, Votapka LW | ACS central science | 30555910 | ACS Cent Sci | 2018 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/30555910 |
| Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. | Votapka LW, Amaro RE | PLoS computational biology | 26505480 | PLoS Comput Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26505480 |
| A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics. | Purawat S, Ieong PU, Malmstrom RD, Chan GJ, Yeung AK, Walker RC, Altintas I, Amaro RE | Biophysical journal | 28636905 | Biophys J | 2017 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/28636905 |
| Diversity of immunoglobulin lambda light chain gene usage over developmental stages in the horse. | Tallmadge RL, Tseng CT, Felippe MJ | Developmental and comparative immunology | 24726757 | Dev Comp Immunol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24726757 |
| Effects of autologous stromal cells and cytokines on differentiation of equine bone marrow-derived progenitor cells. | Schwab UE, Tallmadge RL, Matychak MB, Felippe MJB | American journal of veterinary research | 28945121 | Am J Vet Res | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28945121 |
| The Horse with Recurrent Fevers and Infections: Approach to Common Variable Immunodeficiency. | Mullen KR, Felippe MJB | The Veterinary clinics of North America. Equine practice | 38789347 | Vet Clin North Am Equine Pract | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38789347 |
| Developmental expression of B cell molecules in equine lymphoid tissues. | Prieto JMB, Tallmadge RL, Felippe MJB | Veterinary immunology and immunopathology | 28063478 | Vet Immunol Immunopathol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28063478 |
| Expression of essential B cell development genes in horses with common variable immunodeficiency. | Tallmadge RL, Such KA, Miller KC, Matychak MB, Felippe MJ | Molecular immunology | 22464097 | Mol Immunol | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22464097 |
| Developmental progression of equine immunoglobulin heavy chain variable region diversity. | Tallmadge RL, Tseng CT, King RA, Felippe MJ | Developmental and comparative immunology | 23567345 | Dev Comp Immunol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23567345 |
| Bone marrow transcriptome and epigenome profiles of equine common variable immunodeficiency patients unveil block of B lymphocyte differentiation. | Tallmadge RL, Shen L, Tseng CT, Miller SC, Barry J, Felippe MJ | Clinical immunology (Orlando, Fla.) | 25988861 | Clin Immunol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25988861 |
| Hematopoiesis in the equine fetal liver suggests immune preparedness. | Battista JM, Tallmadge RL, Stokol T, Felippe MJ | Immunogenetics | 25179685 | Immunogenetics | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25179685 |
| Equine common variable immunodeficiency: lessons from 100 clinical cases. | Julia M, Felippe B | Equine veterinary education | 39555145 | Equine Vet Educ | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39555145 |
| Microfluidic diagnostics for the developing world. | Mao X, Huang TJ | Lab on a chip | 22406768 | Lab Chip | 2012 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/22406768 |
| Surface acoustic wave microfluidics. | Ding X, Li P, Lin SC, Stratton ZS, Nama N, Guo F, Slotcavage D, Mao X, Shi J, Costanzo F, Huang TJ | Lab on a chip | 23900527 | Lab Chip | 2013 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/23900527 |
| Probing cell-cell communication with microfluidic devices. | Guo F, French JB, Li P, Zhao H, Chan CY, Fick JR, Benkovic SJ, Huang TJ | Lab on a chip | 23843092 | Lab Chip | 2013 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/23843092 |
| Multifunctional porous silicon nanopillar arrays: antireflection, superhydrophobicity, photoluminescence, and surface-enhanced Raman scattering. | Kiraly B, Yang S, Huang TJ | Nanotechnology | 23703091 | Nanotechnology | 2013 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/23703091 |
| Accelerating drug discovery via organs-on-chips. | Chan CY, Huang PH, Guo F, Ding X, Kapur V, Mai JD, Yuen PK, Huang TJ | Lab on a chip | 24193241 | Lab Chip | 2013 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/24193241 |
| A droplet-based, optofluidic device for high-throughput, quantitative bioanalysis. | Guo F, Lapsley MI, Nawaz AA, Zhao Y, Lin SC, Chen Y, Yang S, Zhao XZ, Huang TJ | Analytical chemistry | 23140515 | Anal Chem | 2012 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/23140515 |
| Microfluidic synthesis of multifunctional Janus particles for biomedical applications. | Yang S, Guo F, Kiraly B, Mao X, Lu M, Leong KW, Huang TJ | Lab on a chip | 22584998 | Lab Chip | 2012 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/22584998 |
| Three-dimensional hydrodynamic focusing method for polyplex synthesis. | Lu M, Ho YP, Grigsby CL, Nawaz AA, Leong KW, Huang TJ | ACS nano | 24341632 | ACS Nano | 2014 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/24341632 |
| Continuous enrichment of low-abundance cell samples using standing surface acoustic waves (SSAW). | Chen Y, Li S, Gu Y, Li P, Ding X, Wang L, McCoy JP, Levine SJ, Huang TJ | Lab on a chip | 24413889 | Lab Chip | 2014 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/24413889 |
| Shape-controlled synthesis of hybrid nanomaterials via three-dimensional hydrodynamic focusing. | Lu M, Yang S, Ho YP, Grigsby CL, Leong KW, Huang TJ | ACS nano | 25268035 | ACS Nano | 2014 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/25268035 |
| Standing surface acoustic wave based cell coculture. | Li S, Guo F, Chen Y, Ding X, Li P, Wang L, Cameron CE, Huang TJ | Analytical chemistry | 25232648 | Anal Chem | 2014 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/25232648 |
| Surface-Enhanced Raman Scattering Study on Graphene-Coated Metallic Nanostructure Substrates. | Hao Q, Wang B, Bossard JA, Kiraly B, Zeng Y, Chiang IK, Jensen L, Werner DH, Huang TJ | The journal of physical chemistry. C, Nanomaterials and interfaces | 24772200 | J Phys Chem C Nanomater Interfaces | 2012 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/24772200 |
| Label-free measurements of reaction kinetics using a droplet-based optofluidic device. | Mao Z, Guo F, Xie Y, Zhao Y, Lapsley MI, Wang L, Mai JD, Costanzo F, Huang TJ | Journal of laboratory automation | 25249275 | J Lab Autom | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25249275 |
| In situ fabrication of 3D Ag@ZnO nanostructures for microfluidic surface-enhanced Raman scattering systems. | Xie Y, Yang S, Mao Z, Li P, Zhao C, Cohick Z, Huang PH, Huang TJ | ACS nano | 25402207 | ACS Nano | 2014 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/25402207 |
| Acoustofluidic chemical waveform generator and switch. | Ahmed D, Muddana HS, Lu M, French JB, Ozcelik A, Fang Y, Butler PJ, Benkovic SJ, Manz A, Huang TJ | Analytical chemistry | 25405550 | Anal Chem | 2014 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/25405550 |
| FGF signaling regulates the number of posterior taste papillae by controlling progenitor field size. | Petersen CI, Jheon AH, Mostowfi P, Charles C, Ching S, Thirumangalathu S, Barlow LA, Klein OD | PLoS genetics | 21655085 | PLoS Genet | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21655085 |
| Spry1 and spry2 are essential for development of the temporomandibular joint. | Purcell P, Jheon A, Vivero MP, Rahimi H, Joo A, Klein OD | Journal of dental research | 22328578 | J Dent Res | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22328578 |
| On the cutting edge of organ renewal: Identification, regulation, and evolution of incisor stem cells. | Kuang-Hsien Hu J, Mushegyan V, Klein OD | Genesis (New York, N.Y. : 2000) | 24307456 | Genesis | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24307456 |
| Identification of novel Fgf enhancers and their role in dental evolution. | Tapaltsyan V, Charles C, Hu J, Mindell D, Ahituv N, Wilson GM, Black BL, Viriot L, Klein OD | Evolution & development | 26086993 | Evol Dev | 2016 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/26086993 |
| Spontaneous emergence of overgrown molar teeth in a colony of Prairie voles (Microtus ochrogaster). | Jheon AH, Prochazkova M, Sherman M, Manoli DS, Shah NM, Carbone L, Klein O | International journal of oral science | 25634121 | Int J Oral Sci | 2015 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/25634121 |
| Characterization of dental epithelial stem cells from the mouse incisor with two-dimensional and three-dimensional platforms. | Chavez MG, Yu W, Biehs B, Harada H, Snead ML, Lee JS, Desai TA, Klein OD | Tissue engineering. Part C, Methods | 22742471 | Tissue Eng Part C Methods | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22742471 |
| Stem cell and biomaterials research in dental tissue engineering and regeneration. | Horst OV, Chavez MG, Jheon AH, Desai T, Klein OD | Dental clinics of North America | 22835534 | Dent Clin North Am | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22835534 |
| Opposing activities of Notch and Wnt signaling regulate intestinal stem cells and gut homeostasis. | Tian H, Biehs B, Chiu C, Siebel CW, Wu Y, Costa M, de Sauvage FJ, Klein OD | Cell reports | 25818302 | Cell Rep | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25818302 |
| Sox2+ stem cells contribute to all epithelial lineages of the tooth via Sfrp5+ progenitors. | Juuri E, Saito K, Ahtiainen L, Seidel K, Tummers M, Hochedlinger K, Klein OD, Thesleff I, Michon F | Developmental cell | 22819339 | Dev Cell | 2012 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/22819339 |
| Regulation of tooth number by fine-tuning levels of receptor-tyrosine kinase signaling. | Charles C, Hovorakova M, Ahn Y, Lyons DB, Marangoni P, Churava S, Biehs B, Jheon A, Lesot H, Balooch G, Krumlauf R, Viriot L, Peterkova R, Klein OD | Development (Cambridge, England) | 21862563 | Development | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21862563 |
| A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable. | Tian H, Biehs B, Warming S, Leong KG, Rangell L, Klein OD, de Sauvage FJ | Nature | 21927002 | Nature | 2011 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/21927002 |
| Replaying evolutionary transitions from the dental fossil record. | Harjunmaa E, Seidel K, Häkkinen T, Renvoisé E, Corfe IJ, Kallonen A, Zhang ZQ, Evans AR, Mikkola ML, Salazar-Ciudad I, Klein OD, Jernvall J | Nature | 25079326 | Nature | 2014 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/25079326 |
| From molecules to mastication: the development and evolution of teeth. | Jheon AH, Seidel K, Biehs B, Klein OD | Wiley interdisciplinary reviews. Developmental biology | 24009032 | Wiley Interdiscip Rev Dev Biol | 2013 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/24009032 |
| Inhibition of Notch Signaling During Mouse Incisor Renewal Leads to Enamel Defects. | Jheon AH, Prochazkova M, Meng B, Wen T, Lim YJ, Naveau A, Espinoza R, Cox TC, Sone ED, Ganss B, Siebel CW, Klein OD | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 26179131 | J Bone Miner Res | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26179131 |
| Abnormal Ras signaling in Costello syndrome (CS) negatively regulates enamel formation. | Goodwin AF, Tidyman WE, Jheon AH, Sharir A, Zheng X, Charles C, Fagin JA, McMahon M, Diekwisch TG, Ganss B, Rauen KA, Klein OD | Human molecular genetics | 24057668 | Hum Mol Genet | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24057668 |
| Continuously growing rodent molars result from a predictable quantitative evolutionary change over 50 million years. | Tapaltsyan V, Eronen JT, Lawing AM, Sharir A, Janis C, Jernvall J, Klein OD | Cell reports | 25921530 | Cell Rep | 2015 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/25921530 |
| Developmental disorders of the dentition: an update. | Klein OD, Oberoi S, Huysseune A, Hovorakova M, Peterka M, Peterkova R | American journal of medical genetics. Part C, Seminars in medical genetics | 24124058 | Am J Med Genet C Semin Med Genet | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24124058 |
| Induction of ectopic taste buds by SHH reveals the competency and plasticity of adult lingual epithelium. | Castillo D, Seidel K, Salcedo E, Ahn C, de Sauvage FJ, Klein OD, Barlow LA | Development (Cambridge, England) | 24993944 | Development | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24993944 |
| Comprehensive mapping of the Escherichia coli flagellar regulatory network. | Fitzgerald DM, Bonocora RP, Wade JT | PLoS genetics | 25275371 | PLoS Genet | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25275371 |
| Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites. | Singh N, Wade JT | Methods in molecular biology (Clifton, N.J.) | 24318882 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24318882 |
| Widespread suppression of intragenic transcription initiation by H-NS. | Singh SS, Singh N, Bonocora RP, Fitzgerald DM, Wade JT, Grainger DC | Genes & development | 24449106 | Genes Dev | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24449106 |
| Coordinated regulation of acid resistance in Escherichia coli. | Aquino P, Honda B, Jaini S, Lyubetskaya A, Hosur K, Chiu JG, Ekladious I, Hu D, Jin L, Sayeg MK, Stettner AI, Wang J, Wong BG, Wong WS, Alexander SL, Ba C, Bensussen SI, Bernstein DB, Braff D, Cha S, Cheng DI, Cho JH, Chou K, Chuang J, Gastler DE, Grasso DJ, Greifenberger JS, Guo C, Hawes AK, Israni DV, Jain SR, Kim J, Lei J, Li H, Li D, Li Q, Mancuso CP, Mao N, Masud SF, Meisel CL, Mi J, Nykyforchyn CS, Park M, Peterson HM, Ramirez AK, Reynolds DS, Rim NG, Saffie JC, Su H, Su WR, Su Y, Sun M, Thommes MM, Tu T, Varongchayakul N, Wagner TE, Weinberg BH, Yang R, Yaroslavsky A, Yoon C, Zhao Y, Zollinger AJ, Stringer AM, Foster JW, Wade J, Raman S, Broude N, Wong WW, Galagan JE | BMC systems biology | 28061857 | BMC Syst Biol | 2017 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/28061857 |
| Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. | Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC | Nature microbiology | 28067866 | Nat Microbiol | 2017 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/28067866 |
| Determining the Specificity of Cascade Binding, Interference, and Primed Adaptation In Vivo in the Escherichia coli Type I-E CRISPR-Cas System. | Cooper LA, Stringer AM, Wade JT | mBio | 29666291 | mBio | 2018 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/29666291 |
| Genome-Wide Mapping of the Escherichia coli PhoB Regulon Reveals Many Transcriptionally Inert, Intragenic Binding Sites. | Fitzgerald DM, Stringer AM, Smith C, Lapierre P, Wade JT | mBio | 37067422 | mBio | 2023 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/37067422 |
| Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon. | Stringer AM, Currenti S, Bonocora RP, Baranowski C, Petrone BL, Palumbo MJ, Reilly AA, Zhang Z, Erill I, Wade JT | Journal of bacteriology | 24272778 | J Bacteriol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24272778 |
| FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica. | Stringer AM, Singh N, Yermakova A, Petrone BL, Amarasinghe JJ, Reyes-Diaz L, Mantis NJ, Wade JT | PloS one | 23028641 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23028641 |
| Identification of novel sRNAs in mycobacterial species. | Tsai CH, Baranowski C, Livny J, McDonough KA, Wade JT, Contreras LM | PloS one | 24244498 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24244498 |
| Non-canonical protein-DNA interactions identified by ChIP are not artifacts. | Bonocora RP, Fitzgerald DM, Stringer AM, Wade JT | BMC genomics | 23586855 | BMC Genomics | 2013 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/23586855 |
| Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding. | Bonocora RP, Smith C, Lapierre P, Wade JT | PLoS genetics | 26425847 | PLoS Genet | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26425847 |
| SuhB Associates with Nus Factors To Facilitate 30S Ribosome Biogenesis in Escherichia coli. | Singh N, Bubunenko M, Smith C, Abbott DM, Stringer AM, Shi R, Court DL, Wade JT | mBio | 26980831 | mBio | 2016 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/26980831 |
| Pervasive transcription: illuminating the dark matter of bacterial transcriptomes. | Wade JT, Grainger DC | Nature reviews. Microbiology | 25069631 | Nat Rev Microbiol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25069631 |
| MrpJ Directly Regulates Proteus mirabilis Virulence Factors, Including Fimbriae and Type VI Secretion, during Urinary Tract Infection. | Debnath I, Stringer AM, Smith SN, Bae E, Mobley HLT, Wade JT, Pearson MM | Infection and immunity | 30082479 | Infect Immun | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30082479 |
| Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping. | Adams PP, Baniulyte G, Esnault C, Chegireddy K, Singh N, Monge M, Dale RK, Storz G, Wade JT | eLife | 33460557 | Elife | 2021 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/33460557 |
| The BvgAS Regulon of Bordetella pertussis. | Moon K, Bonocora RP, Kim DD, Chen Q, Wade JT, Stibitz S, Hinton DM | mBio | 29018122 | mBio | 2017 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/29018122 |
| Maestro of regulation: Riboswitches orchestrate gene expression at the levels of translation, transcription and mRNA decay. | Bastet L, Turcotte P, Wade JT, Lafontaine DA | RNA biology | 29537923 | RNA Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29537923 |
| Chemical Inhibition of Kynureninase Reduces Pseudomonas aeruginosa Quorum Sensing and Virulence Factor Expression. | Kasper SH, Bonocora RP, Wade JT, Musah RA, Cady NC | ACS chemical biology | 26785289 | ACS Chem Biol | 2016 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/26785289 |
| ChIP-seq for genome-scale analysis of bacterial DNA-binding proteins. | Bonocora RP, Wade JT | Methods in molecular biology (Clifton, N.J.) | 25665574 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25665574 |
| Identification of regulatory targets for the bacterial Nus factor complex. | Baniulyte G, Singh N, Benoit C, Johnson R, Ferguson R, Paramo M, Stringer AM, Scott A, Lapierre P, Wade JT | Nature communications | 29229908 | Nat Commun | 2017 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/29229908 |
| Translational control and Rho-dependent transcription termination are intimately linked in riboswitch regulation. | Bastet L, Chauvier A, Singh N, Lussier A, Lamontagne AM, Prévost K, Massé E, Wade JT, Lafontaine DA | Nucleic acids research | 28520932 | Nucleic Acids Res | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28520932 |
| Identification of HilD-regulated genes in Salmonella enterica serovar Typhimurium. | Petrone BL, Stringer AM, Wade JT | Journal of bacteriology | 24375101 | J Bacteriol | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24375101 |
| Mapping the Regulatory Network for Salmonella enterica Serovar Typhimurium Invasion. | Smith C, Stringer AM, Mao C, Palumbo MJ, Wade JT | mBio | 27601571 | mBio | 2016 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/27601571 |
| A bacterial regulatory uORF senses multiple classes of ribosome-targeting antibiotics. | Baniulyte G, Wade JT | eLife | 40439554 | Elife | 2025 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/40439554 |
| Identification and characterization of small RNAs in Yersinia pestis. | Beauregard A, Smith EA, Petrone BL, Singh N, Karch C, McDonough KA, Wade JT | RNA biology | 23324607 | RNA Biol | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23324607 |
| Genome-Wide Transcriptional Response to Varying RpoS Levels in Escherichia coli K-12. | Wong GT, Bonocora RP, Schep AN, Beeler SM, Lee Fong AJ, Shull LM, Batachari LE, Dillon M, Evans C, Becker CJ, Bush EC, Hardin J, Wade JT, Stoebel DM | Journal of bacteriology | 28115545 | J Bacteriol | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28115545 |
| The evolutionary impact of intragenic FliA promoters in proteobacteria. | Fitzgerald DM, Smith C, Lapierre P, Wade JT | Molecular microbiology | 29476659 | Mol Microbiol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29476659 |
| Identification of bacterial sRNA regulatory targets using ribosome profiling. | Wang J, Rennie W, Liu C, Carmack CS, Prévost K, Caron MP, Massé E, Ding Y, Wade JT | Nucleic acids research | 26546513 | Nucleic Acids Res | 2015 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/26546513 |
| Genome-wide mapping of the Escherichia coli PhoB regulon reveals many transcriptionally inert, intragenic binding sites. | Fitzgerald D, Stringer A, Smith C, Lapierre P, Wade JT | bioRxiv : the preprint server for biology | 36798257 | bioRxiv | 2023 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/36798257 |
| Mapping the Escherichia coli DnaA-binding landscape reveals a preference for binding pairs of closely spaced DNA sites. | Stringer AM, Fitzgerald DM, Wade JT | Microbiology (Reading, England) | 39012340 | Microbiology (Reading) | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39012340 |
| Biosensor diagnosis of urinary tract infections: a path to better treatment? | Mach KE, Wong PK, Liao JC | Trends in pharmacological sciences | 21458868 | Trends Pharmacol Sci | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21458868 |
| Cellular self-organization by autocatalytic alignment feedback. | Junkin M, Leung SL, Whitman S, Gregorio CC, Wong PK | Journal of cell science | 22193956 | J Cell Sci | 2011 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/22193956 |
| Increased Cardiac Arrhythmogenesis Associated With Gap Junction Remodeling With Upregulation of RNA-Binding Protein FXR1. | Chu M, Novak SM, Cover C, Wang AA, Chinyere IR, Juneman EB, Zarnescu DC, Wong PK, Gregorio CC | Circulation | 29101288 | Circulation | 2018 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/29101288 |
| Notch1-Dll4 signalling and mechanical force regulate leader cell formation during collective cell migration. | Riahi R, Sun J, Wang S, Long M, Zhang DD, Wong PK | Nature communications | 25766473 | Nat Commun | 2015 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/25766473 |
| Electrokinetic focusing and separation of mammalian cells in conductive biological fluids. | Gao J, Riahi R, Sin ML, Zhang S, Wong PK | The Analyst | 22937529 | Analyst | 2012 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/22937529 |
| Advances in techniques for probing mechanoregulation of tissue morphogenesis. | Sun J, Xiao Y, Wang S, Slepian MJ, Wong PK | Journal of laboratory automation | 25331491 | J Lab Autom | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25331491 |
| Mapping photothermally induced gene expression in living cells and tissues by nanorod-locked nucleic acid complexes. | Riahi R, Wang S, Long M, Li N, Chiou PY, Zhang DD, Wong PK | ACS nano | 24645754 | ACS Nano | 2014 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/24645754 |
| A nanobiosensor for dynamic single cell analysis during microvascular self-organization. | Wang S, Sun J, Zhang DD, Wong PK | Nanoscale | 27547924 | Nanoscale | 2016 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/27547924 |
| Geometric control of capillary architecture via cell-matrix mechanical interactions. | Sun J, Jamilpour N, Wang FY, Wong PK | Biomaterials | 24439400 | Biomaterials | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24439400 |
| Single cell antimicrobial susceptibility testing by confined microchannels and electrokinetic loading. | Lu Y, Gao J, Zhang DD, Gau V, Liao JC, Wong PK | Analytical chemistry | 23445209 | Anal Chem | 2013 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/23445209 |
| A Microfiltration Device for Urogenital Schistosomiasis Diagnostics. | Xiao Y, Lu Y, Hsieh M, Liao J, Wong PK | PloS one | 27124499 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27124499 |
| Intercellular Tension Negatively Regulates Angiogenic Sprouting of Endothelial Tip Cells via Notch1-Dll4 Signaling. | Wang S, Sun J, Xiao Y, Lu Y, Zhang DD, Wong PK | Advanced biosystems | 30662935 | Adv Biosyst | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30662935 |
| Probing cell migration in confined environments by plasma lithography. | Junkin M, Wong PK | Biomaterials | 21134692 | Biomaterials | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21134692 |
| Electrokinetic stringency control in self-assembled monolayer-based biosensors for multiplex urinary tract infection diagnosis. | Liu T, Sin ML, Pyne JD, Gau V, Liao JC, Wong PK | Nanomedicine : nanotechnology, biology, and medicine | 23891989 | Nanomedicine | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23891989 |
| In situ electrokinetic enhancement for self-assembled-monolayer-based electrochemical biosensing. | Sin ML, Liu T, Pyne JD, Gau V, Liao JC, Wong PK | Analytical chemistry | 22397486 | Anal Chem | 2012 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/22397486 |
| Calcium wave propagation in networks of endothelial cells: model-based theoretical and experimental study. | Long J, Junkin M, Wong PK, Hoying J, Deymier P | PLoS computational biology | 23300426 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23300426 |
| A Universal Electrode Approach for Automated Electrochemical Molecular Analyses. | Sin ML, Gau V, Liao JC, Wong PK | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 24860248 | J Microelectromech Syst | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24860248 |
| Plasma lithography surface patterning for creation of cell networks. | Junkin M, Leung SL, Yang Y, Lu Y, Volmering J, Wong PK | Journal of visualized experiments : JoVE | 21694697 | J Vis Exp | 2011 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/21694697 |
| A microfluidic model for organ-specific extravasation of circulating tumor cells. | Riahi R, Yang YL, Kim H, Jiang L, Wong PK, Zohar Y | Biomicrofluidics | 24803959 | Biomicrofluidics | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24803959 |
| A gapmer aptamer nanobiosensor for real-time monitoring of transcription and translation in single cells. | Wang S, Xiao Y, Zhang DD, Wong PK | Biomaterials | 29190498 | Biomaterials | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29190498 |
| Collective Cell Migration in 3D Epithelial Wound Healing. | Xiao Y, Riahi R, Torab P, Zhang DD, Wong PK | ACS nano | 30758172 | ACS Nano | 2019 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/30758172 |
| Molecular detection of bacterial pathogens using microparticle enhanced double-stranded DNA probes. | Riahi R, Mach KE, Mohan R, Liao JC, Wong PK | Analytical chemistry | 21718053 | Anal Chem | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21718053 |
| Hybrid electrokinetic manipulation in high-conductivity media. | Gao J, Sin ML, Liu T, Gau V, Liao JC, Wong PK | Lab on a chip | 21487576 | Lab Chip | 2011 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/21487576 |
| Probing mechanoregulation of neuronal differentiation by plasma lithography patterned elastomeric substrates. | Nam KH, Jamilpour N, Mfoumou E, Wang FY, Zhang DD, Wong PK | Scientific reports | 25376886 | Sci Rep | 2014 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/25376886 |
| Spatiotemporal dynamics of microRNA during epithelial collective cell migration. | Dean ZS, Riahi R, Wong PK | Biomaterials | 25453946 | Biomaterials | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25453946 |
| Single cell nanobiosensors for dynamic gene expression profiling in native tissue microenvironments. | Wang S, Riahi R, Li N, Zhang DD, Wong PK | Advanced materials (Deerfield Beach, Fla.) | 26314800 | Adv Mater | 2015 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/26314800 |
| Long-range electrothermal fluid motion in microfluidic systems. | Lu Y, Ren Q, Liu T, Leung SL, Gau V, Liao JC, Chan CL, Wong PK | International journal of heat and mass transfer | 27127306 | Int J Heat Mass Transf | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27127306 |
| Cellular Architecture Regulates Collective Calcium Signaling and Cell Contractility. | Sun J, Hoying JB, Deymier PA, Zhang DD, Wong PK | PLoS computational biology | 27196735 | PLoS Comput Biol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27196735 |
| Single cell gene expression analysis in injury-induced collective cell migration. | Riahi R, Long M, Yang Y, Dean Z, Zhang DD, Slepian MJ, Wong PK | Integrative biology : quantitative biosciences from nano to macro | 24336811 | Integr Biol (Camb) | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24336811 |
| Intelligent Systems and Technology for Integrative and Predictive Medicine: An ACP Approach. | Wang FY, Wong PK | ACM transactions on intelligent systems and technology | 24883228 | ACM Trans Intell Syst Technol | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24883228 |
| Detection of mRNA in living cells by double-stranded locked nucleic acid probes. | Riahi R, Dean Z, Wu TH, Teitell MA, Chiou PY, Zhang DD, Wong PK | The Analyst | 23772441 | Analyst | 2013 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/23772441 |
| Knockout of Lmod2 results in shorter thin filaments followed by dilated cardiomyopathy and juvenile lethality. | Pappas CT, Mayfield RM, Henderson C, Jamilpour N, Cover C, Hernandez Z, Hutchinson KR, Chu M, Nam KH, Valdez JM, Wong PK, Granzier HL, Gregorio CC | Proceedings of the National Academy of Sciences of the United States of America | 26487682 | Proc Natl Acad Sci U S A | 2015 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/26487682 |
| An AC electrokinetics facilitated biosensor cassette for rapid pathogen identification. | Ouyang M, Mohan R, Lu Y, Liu T, Mach KE, Sin ML, McComb M, Joshi J, Gau V, Wong PK, Liao JC | The Analyst | 23626988 | Analyst | 2013 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/23626988 |
| Mechanically induced intercellular calcium communication in confined endothelial structures. | Junkin M, Lu Y, Long J, Deymier PA, Hoying JB, Wong PK | Biomaterials | 23267827 | Biomaterials | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23267827 |
| Advances in wound-healing assays for probing collective cell migration. | Riahi R, Yang Y, Zhang DD, Wong PK | Journal of laboratory automation | 22357609 | J Lab Autom | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22357609 |
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| A UAV-Mounted Whole Cell Biosensor System for Environmental Monitoring Applications. | Lu Y, Macias D, Dean ZS, Kreger NR, Wong PK | IEEE transactions on nanobioscience | 26584498 | IEEE Trans Nanobioscience | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26584498 |
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| Salmonella enterica Serovar Typhimurium Increases Functional PD-L1 Synergistically with Gamma Interferon in Intestinal Epithelial Cells via Salmonella Pathogenicity Island 2. | Sahler JM, Eade CR, Altier C, March JC | Infection and immunity | 29440366 | Infect Immun | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29440366 |
| Engineered commensal bacteria reprogram intestinal cells into glucose-responsive insulin-secreting cells for the treatment of diabetes. | Duan FF, Liu JH, March JC | Diabetes.. | 25626737 | Diabetes | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25626737 |
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| BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. | Orvis T, Hepperla A, Walter V, Song S, Simon J, Parker J, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman B | Cancer research | 25115300 | Cancer Res | 2014 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/25115300 |
| Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination. | Hast BE, Cloer EW, Goldfarb D, Li H, Siesser PF, Yan F, Walter V, Zheng N, Hayes DN, Major MB | Cancer research | 24322982 | Cancer Res | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24322982 |
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| SNF5/INI1 deficiency redefines chromatin remodeling complex composition during tumor development. | Wei D, Goldfarb D, Song S, Cannon C, Yan F, Sakellariou-Thompson D, Emanuele M, Major MB, Weissman BE, Kuwahara Y | Molecular cancer research : MCR | 25009291 | Mol Cancer Res | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25009291 |
| FOXP1 potentiates Wnt/β-catenin signaling in diffuse large B cell lymphoma. | Walker MP, Stopford CM, Cederlund M, Fang F, Jahn C, Rabinowitz AD, Goldfarb D, Graham DM, Yan F, Deal AM, Fedoriw Y, Richards KL, Davis IJ, Weidinger G, Damania B, Major MB | Science signaling | 25650440 | Sci Signal | 2015 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/25650440 |
| Modulation of Kaposi's sarcoma-associated herpesvirus interleukin-6 function by hypoxia-upregulated protein 1. | Giffin L, Yan F, Ben Major M, Damania B | Journal of virology | 24920810 | J Virol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24920810 |
| The mucolipidosis IV Ca2+ channel TRPML1 (MCOLN1) is regulated by the TOR kinase. | Onyenwoke RU, Sexton JZ, Yan F, Díaz MC, Forsberg LJ, Major MB, Brenman JE | The Biochemical journal | 26195823 | Biochem J | 2015 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/26195823 |
| Substrate trapping proteomics reveals targets of the βTrCP2/FBXW11 ubiquitin ligase. | Kim TY, Siesser PF, Rossman KL, Goldfarb D, Mackinnon K, Yan F, Yi X, MacCoss MJ, Moon RT, Der CJ, Major MB | Molecular and cellular biology | 25332235 | Mol Cell Biol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25332235 |
| Dynamics and evolution of β-catenin-dependent Wnt signaling revealed through massively parallel clonogenic screening. | Shah PK, Walker MP, Sims CE, Major MB, Allbritton NL | Integrative biology : quantitative biosciences from nano to macro | 24871928 | Integr Biol (Camb) | 2014 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/24871928 |
| USP6 oncogene promotes Wnt signaling by deubiquitylating Frizzleds. | Madan B, Walker MP, Young R, Quick L, Orgel KA, Ryan M, Gupta P, Henrich IC, Ferrer M, Marine S, Roberts BS, Arthur WT, Berndt JD, Oliveira AM, Moon RT, Virshup DM, Chou MM, Major MB | Proceedings of the National Academy of Sciences of the United States of America | 27162353 | Proc Natl Acad Sci U S A | 2016 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/27162353 |
| An integrated platform for genome engineering and gene expression perturbation in Plasmodium falciparum. | Nasamu AS, Falla A, Pasaje CFA, Wall BA, Wagner JC, Ganesan SM, Goldfless SJ, Niles JC | Scientific reports | 33431920 | Sci Rep | 2021 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33431920 |
| Quantification of labile heme in live malaria parasites using a genetically encoded biosensor. | Abshire JR, Rowlands CJ, Ganesan SM, So PT, Niles JC | Proceedings of the National Academy of Sciences of the United States of America | 28242687 | Proc Natl Acad Sci U S A | 2017 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/28242687 |
| An integrated strategy for efficient vector construction and multi-gene expression in Plasmodium falciparum. | Wagner JC, Goldfless SJ, Ganesan SM, Lee MC, Fidock DA, Niles JC | Malaria journal | 24160265 | Malar J | 2013 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/24160265 |
| Synthetic RNA-protein modules integrated with native translation mechanisms to control gene expression in malaria parasites. | Ganesan SM, Falla A, Goldfless SJ, Nasamu AS, Niles JC | Nature communications | 26925876 | Nat Commun | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26925876 |
| Ancient human sialic acid variant restricts an emerging zoonotic malaria parasite. | Dankwa S, Lim C, Bei AK, Jiang RH, Abshire JR, Patel SD, Goldberg JM, Moreno Y, Kono M, Niles JC, Duraisingh MT | Nature communications | 27041489 | Nat Commun | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27041489 |
| Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum. | Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC | Nature methods | 25108687 | Nat Methods | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25108687 |
| Plasmodium Niemann-Pick type C1-related protein is a druggable target required for parasite membrane homeostasis. | Istvan ES, Das S, Bhatnagar S, Beck JR, Owen E, Llinas M, Ganesan SM, Niles JC, Winzeler E, Vaidya AB, Goldberg DE | eLife | 30888318 | Elife | 2019 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/30888318 |
| Small molecule inhibition of apicomplexan FtsH1 disrupts plastid biogenesis in human pathogens. | Amberg-Johnson K, Hari SB, Ganesan SM, Lorenzi HA, Sauer RT, Niles JC, Yeh E | eLife | 28826494 | Elife | 2017 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/28826494 |
| Identification of malaria parasite-infected red blood cell surface aptamers by inertial microfluidic SELEX (I-SELEX). | Birch CM, Hou HW, Han J, Niles JC | Scientific reports | 26126714 | Sci Rep | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/26126714 |
| Direct and specific chemical control of eukaryotic translation with a synthetic RNA-protein interaction. | Goldfless SJ, Belmont BJ, de Paz AM, Liu JF, Niles JC | Nucleic acids research | 22275521 | Nucleic Acids Res | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22275521 |
| A Genome-wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes. | Sidik SM, Huet D, Ganesan SM, Huynh MH, Wang T, Nasamu AS, Thiru P, Saeij JPJ, Carruthers VB, Niles JC, Lourido S | Cell | 27594426 | Cell | 2016 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/27594426 |
| Inducible control of subcellular RNA localization using a synthetic protein-RNA aptamer interaction. | Belmont BJ, Niles JC | PloS one | 23056498 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23056498 |
| ATG8 Is Essential Specifically for an Autophagy-Independent Function in Apicoplast Biogenesis in Blood-Stage Malaria Parasites. | Walczak M, Ganesan SM, Niles JC, Yeh E | mBio | 29295911 | mBio | 2018 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/29295911 |
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| The epithelial cell-derived atopic dermatitis cytokine TSLP activates neurons to induce itch. | Wilson SR, Thé L, Batia LM, Beattie K, Katibah GE, McClain SP, Pellegrino M, Estandian DM, Bautista DM | Cell | 24094650 | Cell | 2013 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/24094650 |
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| The star-nosed mole reveals clues to the molecular basis of mammalian touch. | Gerhold KA, Pellegrino M, Tsunozaki M, Morita T, Leitch DB, Tsuruda PR, Brem RB, Catania KC, Bautista DM | PloS one | 23383028 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23383028 |
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| Detection and avoidance of a carnivore odor by prey. | Ferrero DM, Lemon JK, Fluegge D, Pashkovski SL, Korzan WJ, Datta SR, Spehr M, Fendt M, Liberles SD | Proceedings of the National Academy of Sciences of the United States of America | 21690383 | Proc Natl Acad Sci U S A | 2011 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/21690383 |
| Distinct representations of olfactory information in different cortical centres. | Sosulski DL, Bloom ML, Cutforth T, Axel R, Datta SR | Nature | 21451525 | Nature | 2011 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/21451525 |
| Shh-proteoglycan interactions regulate maturation of olfactory glomerular circuitry. | Persson L, Witt RM, Galligan M, Greer PL, Eisner A, Pazyra-Murphy MF, Datta SR, Segal RA | Developmental neurobiology | 24913191 | Dev Neurobiol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24913191 |
| Olfactory maps, circuits and computations. | Giessel AJ, Datta SR | Current opinion in neurobiology | 24492088 | Curr Opin Neurobiol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24492088 |
| Click-assembled, oxygen-sensing nanoconjugates for depth-resolved, near-infrared imaging in a 3D cancer model. | Nichols AJ, Roussakis E, Klein OJ, Evans CL | Angewandte Chemie (International ed. in English) | 24590700 | Angew Chem Int Ed Engl | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24590700 |
| An Integrin-Targeted, Highly Diffusive Construct for Photodynamic Therapy. | Klein OJ, Yuan H, Nowell NH, Kaittanis C, Josephson L, Evans CL | Scientific reports | 29042620 | Sci Rep | 2017 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/29042620 |
| Bright, "Clickable" Porphyrins for the Visualization of Oxygenation under Ambient Light. | Roussakis E, Li Z, Nowell NH, Nichols AJ, Evans CL | Angewandte Chemie (International ed. in English) | 26510549 | Angew Chem Int Ed Engl | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26510549 |
| Promotion of Proapoptotic Signals by Lysosomal Photodamage: Mechanistic Aspects and Influence of Autophagy. | Kessel D, Evans CL | Photochemistry and photobiology | 27096545 | Photochem Photobiol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27096545 |
| Longitudinal, quantitative monitoring of therapeutic response in 3D in vitro tumor models with OCT for high-content therapeutic screening. | Klein OJ, Jung YK, Evans CL | Methods (San Diego, Calif.) | 24013042 | Methods | 2014 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/24013042 |
| In vitro optimization of EtNBS-PDT against hypoxic tumor environments with a tiered, high-content, 3D model optical screening platform. | Klein OJ, Bhayana B, Park YJ, Evans CL | Molecular pharmaceutics | 22946843 | Mol Pharm | 2012 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/22946843 |
| Longitudinal, label-free, quantitative tracking of cell death and viability in a 3D tumor model with OCT. | Jung Y, Klein OJ, Wang H, Evans CL | Scientific reports | 27248849 | Sci Rep | 2016 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/27248849 |
| Non-invasive transdermal two-dimensional mapping of cutaneous oxygenation with a rapid-drying liquid bandage. | Li Z, Roussakis E, Koolen PG, Ibrahim AM, Kim K, Rose LF, Wu J, Nichols AJ, Baek Y, Birngruber R, Apiou-Sbirlea G, Matyal R, Huang T, Chan R, Lin SJ, Evans CL | Biomedical optics express | 25426308 | Biomed Opt Express | 2014 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/25426308 |
| Killing hypoxic cell populations in a 3D tumor model with EtNBS-PDT. | Evans CL, Abu-Yousif AO, Park YJ, Klein OJ, Celli JP, Rizvi I, Zheng X, Hasan T | PloS one | 21876751 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21876751 |
| Longitudinal, 3D in vivo imaging of sebaceous glands by coherent anti-stokes Raman scattering microscopy: normal function and response to cryotherapy. | Jung Y, Tam J, Ray Jalian H, Rox Anderson R, Evans CL | The Journal of investigative dermatology | 25026458 | J Invest Dermatol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25026458 |
| Structure-function relationships of Nile blue (EtNBS) derivatives as antimicrobial photosensitizers. | Vecchio D, Bhayana B, Huang L, Carrasco E, Evans CL, Hamblin MR | European journal of medicinal chemistry | 24561676 | Eur J Med Chem | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/24561676 |
| Video-rate scanning confocal microscopy and microendoscopy. | Nichols AJ, Evans CL | Journal of visualized experiments : JoVE | 22042305 | J Vis Exp | 2011 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/22042305 |
| Label-Free, Longitudinal Visualization of PDT Response In Vitro with Optical Coherence Tomography. | Jung Y, Nichols AJ, Klein OJ, Roussakis E, Evans CL | Israel journal of chemistry | 23316088 | Isr J Chem | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23316088 |
| PLGA nanoparticle encapsulation reduces toxicity while retaining the therapeutic efficacy of EtNBS-PDT in vitro. | Hung HI, Klein OJ, Peterson SW, Rokosh SR, Osseiran S, Nowell NH, Evans CL | Scientific reports | 27686626 | Sci Rep | 2016 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/27686626 |
| Comprehensive evaluation of peripheral nerve regeneration in the acute healing phase using tissue clearing and optical microscopy in a rodent model. | Jung Y, Ng JH, Keating CP, Senthil-Kumar P, Zhao J, Randolph MA, Winograd JM, Evans CL | PloS one | 24714405 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24714405 |
| 3D-resolved targeting of photodynamic therapy using temporal focusing. | Rowlands CJ, Wu J, Uzel SG, Klein O, Evans CL, So PT | Laser physics letters | 25620902 | Laser Phys Lett | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25620902 |
| Strain tunes proteolytic degradation and diffusive transport in fibrin networks. | Adhikari AS, Mekhdjian AH, Dunn AR | Biomacromolecules | 22185486 | Biomacromolecules | 2012 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/22185486 |
| Spatial distribution of cell-cell and cell-ECM adhesions regulates force balance while main-taining E-cadherin molecular tension in cell pairs. | Sim JY, Moeller J, Hart KC, Ramallo D, Vogel V, Dunn AR, Nelson WJ, Pruitt BL | Molecular biology of the cell | 25971797 | Mol Biol Cell | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/25971797 |
| The CDC42-interacting protein 4 controls epithelial cell cohesion and tumor dissemination. | Rolland Y, Marighetti P, Malinverno C, Confalonieri S, Luise C, Ducano N, Palamidessi A, Bisi S, Kajiho H, Troglio F, Shcherbakova OG, Dunn AR, Oldani A, Lanzetti L, Di Fiore PP, Disanza A, Scita G | Developmental cell | 25203208 | Dev Cell | 2014 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/25203208 |
| Quantification of nanowire penetration into living cells. | Xu AM, Aalipour A, Leal-Ortiz S, Mekhdjian AH, Xie X, Dunn AR, Garner CC, Melosh NA | Nature communications | 24710350 | Nat Commun | 2014 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/24710350 |
| A force balance can explain local and global cell movements during early zebrafish development. | Chai J, Hamilton AL, Krieg M, Buckley CD, Riedel-Kruse IH, Dunn AR | Biophysical journal | 26200877 | Biophys J | 2015 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/26200877 |
| E-cadherin is under constitutive actomyosin-generated tension that is increased at cell-cell contacts upon externally applied stretch. | Borghi N, Sorokina M, Shcherbakova OG, Weis WI, Pruitt BL, Nelson WJ, Dunn AR | Proceedings of the National Academy of Sciences of the United States of America | 22802638 | Proc Natl Acad Sci U S A | 2012 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/22802638 |
| Molecular tension sensors report forces generated by single integrin molecules in living cells. | Morimatsu M, Mekhdjian AH, Adhikari AS, Dunn AR | Nano letters | 23859772 | Nano Lett | 2013 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/23859772 |
| Mechanical systems biology of C. elegans touch sensation. | Krieg M, Dunn AR, Goodman MB | BioEssays : news and reviews in molecular, cellular and developmental biology | 25597279 | Bioessays | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25597279 |
| Mechanical load induces a 100-fold increase in the rate of collagen proteolysis by MMP-1. | Adhikari AS, Chai J, Dunn AR | Journal of the American Chemical Society | 21247159 | J Am Chem Soc | 2011 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/21247159 |
| Single Molecule Force Measurements in Living Cells Reveal a Minimally Tensioned Integrin State. | Chang AC, Mekhdjian AH, Morimatsu M, Denisin AK, Pruitt BL, Dunn AR | ACS nano | 27779848 | ACS Nano | 2016 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/27779848 |
| Sphingosine 1-phosphate receptor 1 regulates the directional migration of lymphatic endothelial cells in response to fluid shear stress. | Surya VN, Michalaki E, Huang EY, Fuller GG, Dunn AR | Journal of the Royal Society, Interface | 27974574 | J R Soc Interface | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27974574 |
| How Hydra Eats. | Dunn AR | Biophysical journal | 27074672 | Biophys J | 2016 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/27074672 |
| Visualizing the interior architecture of focal adhesions with high-resolution traction maps. | Morimatsu M, Mekhdjian AH, Chang AC, Tan SJ, Dunn AR | Nano letters | 25730141 | Nano Lett | 2015 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/25730141 |
| Multiplexed Fluid Flow Device to Study Cellular Response to Tunable Shear Stress Gradients. | Ostrowski MA, Huang EY, Surya VN, Poplawski C, Barakat JM, Lin GL, Fuller GG, Dunn AR | Annals of biomedical engineering | 26589597 | Ann Biomed Eng | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26589597 |
| Conformational dynamics accompanying the proteolytic degradation of trimeric collagen I by collagenases. | Adhikari AS, Glassey E, Dunn AR | Journal of the American Chemical Society | 22720833 | J Am Chem Soc | 2012 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/22720833 |
| Multiplexed single-molecule force proteolysis measurements using magnetic tweezers. | Adhikari AS, Chai J, Dunn AR | Journal of visualized experiments : JoVE | 22871786 | J Vis Exp | 2012 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/22871786 |
| Cell adhesion. The minimal cadherin-catenin complex binds to actin filaments under force. | Buckley CD, Tan J, Anderson KL, Hanein D, Volkmann N, Weis WI, Nelson WJ, Dunn AR | Science (New York, N.Y.) | 25359979 | Science | 2014 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/25359979 |
| Mechanical control of the sense of touch by β-spectrin. | Krieg M, Dunn AR, Goodman MB | Nature cell biology | 24561618 | Nat Cell Biol | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24561618 |
| Microvascular endothelial cells migrate upstream and align against the shear stress field created by impinging flow. | Ostrowski MA, Huang NF, Walker TW, Verwijlen T, Poplawski C, Khoo AS, Cooke JP, Fuller GG, Dunn AR | Biophysical journal | 24461011 | Biophys J | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24461011 |
| HSF1 physically neutralizes amyloid oligomers to empower overgrowth and bestow neuroprotection. | Tang Z, Su KH, Xu M, Dai C | Science advances | 33177089 | Sci Adv | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33177089 |
| Suppression of the HSF1-mediated proteotoxic stress response by the metabolic stress sensor AMPK. | Dai S, Tang Z, Cao J, Zhou W, Li H, Sampson S, Dai C | The EMBO journal | 25425574 | EMBO J | 2015 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/25425574 |
| HSF1: Guardian of Proteostasis in Cancer. | Dai C, Sampson SB | Trends in cell biology | 26597576 | Trends Cell Biol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26597576 |
| Iron addiction: a novel therapeutic target in ovarian cancer. | Basuli D, Tesfay L, Deng Z, Paul B, Yamamoto Y, Ning G, Xian W, McKeon F, Lynch M, Crum CP, Hegde P, Brewer M, Wang X, Miller LD, Dyment N, Torti FM, Torti SV | Oncogene | 28319068 | Oncogene | 2017 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/28319068 |
| Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response. | Xu M, Lin L, Ram BM, Shriwas O, Chuang KH, Dai S, Su KH, Tang Z, Dai C | Cell reports | 37224019 | Cell Rep | 2023 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/37224019 |
| Metabolic control of the proteotoxic stress response: implications in diabetes mellitus and neurodegenerative disorders. | Su KH, Dai C | Cellular and molecular life sciences : CMLS | 27289378 | Cell Mol Life Sci | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27289378 |
| Visualization of RAS/MAPK Signaling In Situ by the Proximity Ligation Assay (PLA). | Tang Z, Dai C | Methods in molecular biology (Clifton, N.J.) | 27924568 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/27924568 |
| MEK guards proteome stability and inhibits tumor-suppressive amyloidogenesis via HSF1. | Tang Z, Dai S, He Y, Doty RA, Shultz LD, Sampson SB, Dai C | Cell | 25679764 | Cell | 2015 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/25679764 |
| Loss of tumor suppressor NF1 activates HSF1 to promote carcinogenesis. | Dai C, Santagata S, Tang Z, Shi J, Cao J, Kwon H, Bronson RT, Whitesell L, Lindquist S | The Journal of clinical investigation | 22945628 | J Clin Invest | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22945628 |
| HSF1 critically attunes proteotoxic stress sensing by mTORC1 to combat stress and promote growth. | Su KH, Cao J, Tang Z, Dai S, He Y, Sampson SB, Benjamin IJ, Dai C | Nature cell biology | 27043084 | Nat Cell Biol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27043084 |
| Metabolic stressors disrupt proteome homeostasis to suppress malignancy. | Dai C | Molecular & cellular oncology | 26973866 | Mol Cell Oncol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26973866 |
| Proteotoxic stress of cancer: implication of the heat-shock response in oncogenesis. | Dai C, Dai S, Cao J | Journal of cellular physiology | 22105155 | J Cell Physiol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22105155 |
| Calcium ion gradients modulate the zinc affinity and antibacterial activity of human calprotectin. | Brophy MB, Hayden JA, Nolan EM | Journal of the American Chemical Society | 23082970 | J Am Chem Soc | 2012 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/23082970 |
| Molecular basis for self-assembly of a human host-defense peptide that entraps bacterial pathogens. | Chairatana P, Nolan EM | Journal of the American Chemical Society | 25158166 | J Am Chem Soc | 2014 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/25158166 |
| Disulfide cross-linking influences symbiotic activities of nodule peptide NCR247. | Shabab M, Arnold MF, Penterman J, Wommack AJ, Bocker HT, Price PA, Griffitts JS, Nolan EM, Walker GC | Proceedings of the National Academy of Sciences of the United States of America | 27551097 | Proc Natl Acad Sci U S A | 2016 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/27551097 |
| Defensins, lectins, mucins, and secretory immunoglobulin A: microbe-binding biomolecules that contribute to mucosal immunity in the human gut. | Chairatana P, Nolan EM | Critical reviews in biochemistry and molecular biology | 27841019 | Crit Rev Biochem Mol Biol | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27841019 |
| Manganese binding properties of human calprotectin under conditions of high and low calcium: X-ray crystallographic and advanced electron paramagnetic resonance spectroscopic analysis. | Gagnon DM, Brophy MB, Bowman SE, Stich TA, Drennan CL, Britt RD, Nolan EM | Journal of the American Chemical Society | 25597447 | J Am Chem Soc | 2015 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/25597447 |
| Visualizing attack of Escherichia coli by the antimicrobial peptide human defensin 5. | Chileveru HR, Lim SA, Chairatana P, Wommack AJ, Chiang IL, Nolan EM | Biochemistry | 25664683 | Biochemistry | 2015 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/25664683 |
| Human defensin 5 disulfide array mutants: disulfide bond deletion attenuates antibacterial activity against Staphylococcus aureus. | Wanniarachchi YA, Kaczmarek P, Wan A, Nolan EM | Biochemistry | 21861459 | Biochemistry | 2011 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/21861459 |
| Proteolysis Triggers Self-Assembly and Unmasks Innate Immune Function of a Human α-Defensin Peptide. | Chairatana P, Chu H, Castillo PA, Shen B, Bevins CL, Nolan EM | Chemical science | 27076903 | Chem Sci | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/27076903 |
| Human α-Defensin 6: A Small Peptide That Self-Assembles and Protects the Host by Entangling Microbes. | Chairatana P, Nolan EM | Accounts of chemical research | 28296382 | Acc Chem Res | 2017 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/28296382 |
| Discovery and characterization of a disulfide-locked C(2)-symmetric defensin peptide. | Wommack AJ, Ziarek JJ, Tomaras J, Chileveru HR, Zhang Y, Wagner G, Nolan EM | Journal of the American Chemical Society | 25181039 | J Am Chem Soc | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/25181039 |
| A bacterial mutant library as a tool to study the attack of a defensin peptide. | Moser S, Chileveru HR, Tomaras J, Nolan EM | Chembiochem : a European journal of chemical biology | 25430675 | Chembiochem | 2014 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/25430675 |
| Reduction of human defensin 5 affords a high-affinity zinc-chelating peptide. | Zhang Y, Cougnon FB, Wanniarachchi YA, Hayden JA, Nolan EM | ACS chemical biology | 23841778 | ACS Chem Biol | 2013 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/23841778 |
| Human calprotectin is an iron-sequestering host-defense protein. | Nakashige TG, Zhang B, Krebs C, Nolan EM | Nature chemical biology | 26302479 | Nat Chem Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26302479 |
| Calcium Ions Tune the Zinc-Sequestering Properties and Antimicrobial Activity of Human S100A12. | Cunden LS, Gaillard A, Nolan EM | Chemical science | 26913170 | Chem Sci | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26913170 |
| The Hexahistidine Motif of Host-Defense Protein Human Calprotectin Contributes to Zinc Withholding and Its Functional Versatility. | Nakashige TG, Stephan JR, Cunden LS, Brophy MB, Wommack AJ, Keegan BC, Shearer JM, Nolan EM | Journal of the American Chemical Society | 27541598 | J Am Chem Soc | 2016 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/27541598 |
| NMR solution structure and condition-dependent oligomerization of the antimicrobial peptide human defensin 5. | Wommack AJ, Robson SA, Wanniarachchi YA, Wan A, Turner CJ, Wagner G, Nolan EM | Biochemistry | 23163963 | Biochemistry | 2012 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/23163963 |
| Calcium-induced Tetramerization and Zinc Chelation Shield Human Calprotectin from Degradation by Host and Bacterial Extracellular Proteases. | Stephan JR, Nolan EM | Chemical science | 26925211 | Chem Sci | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26925211 |
| Manganese and microbial pathogenesis: sequestration by the Mammalian immune system and utilization by microorganisms. | Brophy MB, Nolan EM | ACS chemical biology | 25594606 | ACS Chem Biol | 2015 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/25594606 |
| Modeling lung deformation: a combined deformable image registration method with spatially varying Young's modulus estimates. | Li M, Castillo E, Zheng XL, Luo HY, Castillo R, Wu Y, Guerrero T | Medical physics | 23927316 | Med Phys | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23927316 |
| Morphometry-based measurements of the structural response to whole-brain radiation. | Fuentes D, Contreras J, Yu J, He R, Castillo E, Castillo R, Guerrero T | International journal of computer assisted radiology and surgery | 25408306 | Int J Comput Assist Radiol Surg | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25408306 |
| Deformable image registration for temporal subtraction of chest radiographs. | Li M, Castillo E, Luo HY, Zheng XL, Castillo R, Meshkov D, Guerrero T | International journal of computer assisted radiology and surgery | 24078349 | Int J Comput Assist Radiol Surg | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24078349 |
| Pre-radiotherapy FDG PET predicts radiation pneumonitis in lung cancer. | Castillo R, Pham N, Ansari S, Meshkov D, Castillo S, Li M, Olanrewaju A, Hobbs B, Castillo E, Guerrero T | Radiation oncology (London, England) | 24625207 | Radiat Oncol | 2014 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24625207 |
| A reference dataset for deformable image registration spatial accuracy evaluation using the COPDgene study archive. | Castillo R, Castillo E, Fuentes D, Ahmad M, Wood AM, Ludwig MS, Guerrero T | Physics in medicine and biology | 23571679 | Phys Med Biol | 2013 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/23571679 |
| Computing global minimizers to a constrained B-spline image registration problem from optimal l1 perturbations to block match data. | Castillo E, Castillo R, Fuentes D, Guerrero T | Medical physics | 24694135 | Med Phys | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24694135 |
| Evaluation of image registration spatial accuracy using a Bayesian hierarchical model. | Liu S, Yuan Y, Castillo R, Guerrero T, Johnson VE | Biometrics | 24575781 | Biometrics | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24575781 |
| Results of a Multi-Institutional Phase 2 Clinical Trial for 4DCT-Ventilation Functional Avoidance Thoracic Radiation Therapy. | Vinogradskiy Y, Castillo R, Castillo E, Schubert L, Jones BL, Faught A, Gaspar LE, Kwak J, Bowles DW, Waxweiler T, Dougherty JM, Gao D, Stevens C, Miften M, Kavanagh B, Grills I, Rusthoven CG, Guerrero T | International journal of radiation oncology, biology, physics | 34767934 | Int J Radiat Oncol Biol Phys | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/34767934 |
| Quality assurance assessment of diagnostic and radiation therapy-simulation CT image registration for head and neck radiation therapy: anatomic region of interest-based comparison of rigid and deformable algorithms. | Mohamed AS, Ruangskul MN, Awan MJ, Baron CA, Kalpathy-Cramer J, Castillo R, Castillo E, Guerrero TM, Kocak-Uzel E, Yang J, Court LE, Kantor ME, Gunn GB, Colen RR, Frank SJ, Garden AS, Rosenthal DI, Fuller CD | Radiology | 25380454 | Radiology | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25380454 |
| Pre-Radiation Therapy Fluorine 18 Fluorodeoxyglucose PET Helps Identify Patients with Esophageal Cancer at High Risk for Radiation Pneumonitis. | Castillo R, Pham N, Castillo E, Aso-Gonzalez S, Ansari S, Hobbs B, Palacio D, Skinner H, Guerrero TM | Radiology | 25584706 | Radiology | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25584706 |
| Least median of squares filtering of locally optimal point matches for compressible flow image registration. | Castillo E, Castillo R, White B, Rojo J, Guerrero T | Physics in medicine and biology | 22797602 | Phys Med Biol | 2012 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/22797602 |
| Clinical validation of 4-dimensional computed tomography ventilation with pulmonary function test data. | Brennan D, Schubert L, Diot Q, Castillo R, Castillo E, Guerrero T, Martel MK, Linderman D, Gaspar LE, Miften M, Kavanagh BD, Vinogradskiy Y | International journal of radiation oncology, biology, physics | 25817531 | Int J Radiat Oncol Biol Phys | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/25817531 |
| Assessment of a quantitative metric for 4D CT artifact evaluation by observer consensus. | Castillo SJ, Castillo R, Balter P, Pan T, Ibbott G, Hobbs B, Yuan Y, Guerrero T | Journal of applied clinical medical physics | 24892346 | J Appl Clin Med Phys | 2014 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/24892346 |
| Use of 4-dimensional computed tomography-based ventilation imaging to correlate lung dose and function with clinical outcomes. | Vinogradskiy Y, Castillo R, Castillo E, Tucker SL, Liao Z, Guerrero T, Martel MK | International journal of radiation oncology, biology, physics | 23474113 | Int J Radiat Oncol Biol Phys | 2013 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/23474113 |
| Spatial correspondence of 4D CT ventilation and SPECT pulmonary perfusion defects in patients with malignant airway stenosis. | Castillo R, Castillo E, McCurdy M, Gomez DR, Block AM, Bergsma D, Joy S, Guerrero T | Physics in medicine and biology | 22411124 | Phys Med Biol | 2012 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/22411124 |
| Proton therapy radiation pneumonitis local dose-response in esophagus cancer patients. | Echeverria AE, McCurdy M, Castillo R, Bernard V, Ramos NV, Buckley W, Castillo E, Liu P, Martinez J, Guerrero T | Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology | 23127772 | Radiother Oncol | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23127772 |
| Evaluation of 4D CT acquisition methods designed to reduce artifacts. | Castillo SJ, Castillo R, Castillo E, Pan T, Ibbott G, Balter P, Hobbs B, Guerrero T | Journal of applied clinical medical physics | 26103169 | J Appl Clin Med Phys | 2015 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/26103169 |
| Comparison of 4-dimensional computed tomography ventilation with nuclear medicine ventilation-perfusion imaging: a clinical validation study. | Vinogradskiy Y, Koo PJ, Castillo R, Castillo E, Guerrero T, Gaspar LE, Miften M, Kavanagh BD | International journal of radiation oncology, biology, physics | 24725702 | Int J Radiat Oncol Biol Phys | 2014 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24725702 |
| Factors accounting for a missed diagnosis of cystic fibrosis after newborn screening. | Rock MJ, Levy H, Zaleski C, Farrell PM | Pediatric pulmonology | 22081556 | Pediatr Pulmonol | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22081556 |
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| Gut-tropic T cells that express integrin α4β7 and CCR9 are required for induction of oral immune tolerance in mice. | Cassani B, Villablanca EJ, Quintana FJ, Love PE, Lacy-Hulbert A, Blaner WS, Sparwasser T, Snapper SB, Weiner HL, Mora JR | Gastroenterology | 21925467 | Gastroenterology | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21925467 |
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| Cardiac structural and sarcomere genes associated with cardiomyopathy exhibit marked intolerance of genetic variation. | Pan S, Caleshu CA, Dunn KE, Foti MJ, Moran MK, Soyinka O, Ashley EA | Circulation. Cardiovascular genetics | 23074333 | Circ Cardiovasc Genet | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23074333 |
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| Molecular diagnosis of long QT syndrome at 10 days of life by rapid whole genome sequencing. | Priest JR, Ceresnak SR, Dewey FE, Malloy-Walton LE, Dunn K, Grove ME, Perez MV, Maeda K, Dubin AM, Ashley EA | Heart rhythm | 24973560 | Heart Rhythm | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24973560 |
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| Correlation of outer nuclear layer thickness with cone density values in patients with retinitis pigmentosa and healthy subjects. | Menghini M, Lujan BJ, Zayit-Soudry S, Syed R, Porco TC, Bayabo K, Carroll J, Roorda A, Duncan JL | Investigative ophthalmology & visual science | 25515570 | Invest Ophthalmol Vis Sci | 2014 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/25515570 |
| Neuronal pentraxins mediate silent synapse conversion in the developing visual system. | Koch SM, Ullian EM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 20392962 | J Neurosci | 2010 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/20392962 |
| Astrocyte-encoded positional cues maintain sensorimotor circuit integrity. | Molofsky AV, Kelley KW, Tsai HH, Redmond SA, Chang SM, Madireddy L, Chan JR, Baranzini SE, Ullian EM, Rowitch DH | Nature | 24776795 | Nature | 2014 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/24776795 |
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| PKLR promotes colorectal cancer liver colonization through induction of glutathione synthesis. | Nguyen A, Loo JM, Mital R, Weinberg EM, Man FY, Zeng Z, Paty PB, Saltz L, Janjigian YY, de Stanchina E, Tavazoie SF | The Journal of clinical investigation | 26784545 | J Clin Invest | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26784545 |
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| An old drug for new ideas: metformin promotes adult neurogenesis and spatial memory formation. | Potts MB, Lim DA | Cell stem cell | 22770236 | Cell Stem Cell | 2012 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/22770236 |
| Chromatin-based epigenetics of adult subventricular zone neural stem cells. | Gonzales-Roybal G, Lim DA | Frontiers in genetics | 24115953 | Front Genet | 2013 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/24115953 |
| Analysis of Mll1 deficiency identifies neurogenic transcriptional modules and Brn4 as a factor for direct astrocyte-to-neuron reprogramming. | Potts MB, Siu JJ, Price JD, Salinas RD, Cho MJ, Ramos AD, Hahn J, Margeta M, Oldham MC, Lim DA | Neurosurgery | 24887289 | Neurosurgery | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24887289 |
| Interventional magnetic resonance imaging-guided cell transplantation into the brain with radially branched deployment. | Silvestrini MT, Yin D, Martin AJ, Coppes VG, Mann P, Larson PS, Starr PA, Zeng X, Gupta N, Panter SS, Desai TA, Lim DA | Molecular therapy : the journal of the American Society of Gene Therapy | 25138755 | Mol Ther | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25138755 |
| Adult neural stem cells stake their ground. | Lim DA, Alvarez-Buylla A | Trends in neurosciences | 25223700 | Trends Neurosci | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25223700 |
| Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo. | Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, Gonzales-Roybal G, Oldham MC, Song JS, Lim DA | Cell stem cell | 23583100 | Cell Stem Cell | 2013 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/23583100 |
| Normalization, bias correction, and peak calling for ChIP-seq. | Diaz A, Park K, Lim DA, Song JS | Statistical applications in genetics and molecular biology | 22499706 | Stat Appl Genet Mol Biol | 2012 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/22499706 |
| Distinct and separable roles for EZH2 in neurogenic astroglia. | Hwang WW, Salinas RD, Siu JJ, Kelley KW, Delgado RN, Paredes MF, Alvarez-Buylla A, Oldham MC, Lim DA | eLife | 24867641 | Elife | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24867641 |
| The Ink4a/Arf locus is a barrier to direct neuronal transdifferentiation. | Price JD, Park KY, Chen J, Salinas RD, Cho MJ, Kriegstein AR, Lim DA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 25209293 | J Neurosci | 2014 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/25209293 |
| Radially branched deployment for more efficient cell transplantation at the scale of the human brain. | Silvestrini MT, Yin D, Coppes VG, Mann P, Martin AJ, Larson PS, Starr PA, Gupta N, Panter SS, Desai TA, Lim DA | Stereotactic and functional neurosurgery | 23343609 | Stereotact Funct Neurosurg | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23343609 |
| Activation of neuronal gene expression by the JMJD3 demethylase is required for postnatal and adult brain neurogenesis. | Park DH, Hong SJ, Salinas RD, Liu SJ, Sun SW, Sgualdino J, Testa G, Matzuk MM, Iwamori N, Lim DA | Cell reports | 25176653 | Cell Rep | 2014 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/25176653 |
| Embryonic Nkx2.1-expressing neural precursor cells contribute to the regional heterogeneity of adult V-SVZ neural stem cells. | Delgado RN, Lim DA | Developmental biology | 26387477 | Dev Biol | 2015 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/26387477 |
| The long noncoding RNA Pnky regulates neuronal differentiation of embryonic and postnatal neural stem cells. | Ramos AD, Andersen RE, Liu SJ, Nowakowski TJ, Hong SJ, Gertz C, Salinas RD, Zarabi H, Kriegstein AR, Lim DA | Cell stem cell | 25800779 | Cell Stem Cell | 2015 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/25800779 |
| Maintenance of neural stem cell positional identity by mixed-lineage leukemia 1. | Delgado RN, Mansky B, Ahanger SH, Lu C, Andersen RE, Dou Y, Alvarez-Buylla A, Lim DA | Science (New York, N.Y.) | 32241942 | Science | 2020 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/32241942 |
| Early impact of social isolation and breast tumor progression in mice. | Madden KS, Szpunar MJ, Brown EB | Brain, behavior, and immunity | 22610067 | Brain Behav Immun | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22610067 |
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| Second harmonic generation microscopy reveals altered collagen microstructure in usual interstitial pneumonia versus healthy lung. | Kottmann RM, Sharp J, Owens K, Salzman P, Xiao GQ, Phipps RP, Sime PJ, Brown EB, Perry SW | Respiratory research | 26013144 | Respir Res | 2015 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/26013144 |
| Mitochondrial membrane potential probes and the proton gradient: a practical usage guide. | Perry SW, Norman JP, Barbieri J, Brown EB, Gelbard HA | BioTechniques | 21486251 | Biotechniques | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21486251 |
| Measurement of the ratio of forward-propagating to back-propagating second harmonic signal using a single objective. | Han X, Brown E | Optics express | 20588906 | Opt Express | 2010 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/20588906 |
| Second harmonic generation reveals matrix alterations during breast tumor progression. | Burke K, Tang P, Brown E | Journal of biomedical optics | 23172133 | J Biomed Opt | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23172133 |
| Tumor-associated macrophages and stromal TNF-α regulate collagen structure in a breast tumor model as visualized by second harmonic generation. | Burke RM, Madden KS, Perry SW, Zettel ML, Brown EB 3rd | Journal of biomedical optics | 23912760 | J Biomed Opt | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23912760 |
| Fluoxetine modulates breast cancer metastasis to the brain in a murine model. | Shapovalov Y, Zettel M, Spielman SC, Amico-Ruvio SA, Kelly EA, Sipe GO, Dickerson IM, Majewska AK, Brown EB | BMC cancer | 25129445 | BMC Cancer | 2014 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/25129445 |
| Chronic Stress Exposure Suppresses Mammary Tumor Growth and Reduces Circulating Exosome TGF-β Content via β-Adrenergic Receptor Signaling in MMTV-PyMT Mice. | Dawes RP, Burke KA, Byun DK, Xu Z, Stastka P, Chan L, Brown EB, Madden KS | Breast cancer : basic and clinical research | 32595275 | Breast Cancer (Auckl) | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32595275 |
| Engineering superficial zone features in tissue engineered cartilage. | Chen T, Hilton MJ, Brown EB, Zuscik MJ, Awad HA | Biotechnology and bioengineering | 23239161 | Biotechnol Bioeng | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23239161 |
| β-Adrenergic receptors (β-AR) regulate VEGF and IL-6 production by divergent pathways in high β-AR-expressing breast cancer cell lines. | Madden KS, Szpunar MJ, Brown EB | Breast cancer research and treatment | 21234673 | Breast Cancer Res Treat | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21234673 |
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| The role of the lymphatic system in inflammatory-erosive arthritis. | Bouta EM, Li J, Ju Y, Brown EB, Ritchlin CT, Xing L, Schwarz EM | Seminars in cell & developmental biology | 25598390 | Semin Cell Dev Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25598390 |
| Measuring intranodal pressure and lymph viscosity to elucidate mechanisms of arthritic flare and therapeutic outcomes. | Bouta EM, Wood RW, Perry SW, Brown EB, Ritchlin CT, Xing L, Schwarz EM | Annals of the New York Academy of Sciences | 22172039 | Ann N Y Acad Sci | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22172039 |
| Two-photon and second harmonic microscopy in clinical and translational cancer research. | Perry SW, Burke RM, Brown EB | Annals of biomedical engineering | 22258888 | Ann Biomed Eng | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22258888 |
| In vivo quantification of lymph viscosity and pressure in lymphatic vessels and draining lymph nodes of arthritic joints in mice. | Bouta EM, Wood RW, Brown EB, Rahimi H, Ritchlin CT, Schwarz EM | The Journal of physiology | 24421350 | J Physiol | 2014 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/24421350 |
| Spatiotemporal Analyses of Osteogenesis and Angiogenesis via Intravital Imaging in Cranial Bone Defect Repair. | Huang C, Ness VP, Yang X, Chen H, Luo J, Brown EB, Zhang X | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 25640220 | J Bone Miner Res | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25640220 |
| Using second harmonic generation to predict patient outcome in solid tumors. | Burke K, Smid M, Dawes RP, Timmermans MA, Salzman P, van Deurzen CH, Beer DG, Foekens JA, Brown E | BMC cancer | 26603532 | BMC Cancer | 2015 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/26603532 |
| Stromal matrix metalloprotease-13 knockout alters Collagen I structure at the tumor-host interface and increases lung metastasis of C57BL/6 syngeneic E0771 mammary tumor cells. | Perry SW, Schueckler JM, Burke K, Arcuri GL, Brown EB | BMC cancer | 24010522 | BMC Cancer | 2013 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/24010522 |
| Power Doppler ultrasound phenotyping of expanding versus collapsed popliteal lymph nodes in murine inflammatory arthritis. | Bouta EM, Ju Y, Rahimi H, de Mesy-Bentley KL, Wood RW, Xing L, Schwarz EM | PloS one | 24040061 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24040061 |
| The antidepressant desipramine and α2-adrenergic receptor activation promote breast tumor progression in association with altered collagen structure. | Szpunar MJ, Burke KA, Dawes RP, Brown EB, Madden KS | Cancer prevention research (Philadelphia, Pa.) | 24309563 | Cancer Prev Res (Phila) | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24309563 |
| Second-harmonic generation scattering directionality predicts tumor cell motility in collagen gels. | Burke KA, Dawes RP, Cheema MK, Van Hove A, Benoit DS, Perry SW, Brown E | Journal of biomedical optics | 25625899 | J Biomed Opt | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25625899 |
| Physical and chemical strategies for therapeutic delivery by using polymeric nanoparticles. | Morachis JM, Mahmoud EA, Almutairi A | Pharmacological reviews | 22544864 | Pharmacol Rev | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22544864 |
| Low power upconverted near-IR light for efficient polymeric nanoparticle degradation and cargo release. | Viger ML, Grossman M, Fomina N, Almutairi A | Advanced materials (Deerfield Beach, Fla.) | 23722298 | Adv Mater | 2013 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/23722298 |
| In vivo time-gated fluorescence imaging with biodegradable luminescent porous silicon nanoparticles. | Gu L, Hall DJ, Qin Z, Anglin E, Joo J, Mooney DJ, Howell SB, Sailor MJ | Nature communications | 23933660 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23933660 |
| A Single UV or Near IR Triggering Event Leads to Polymer Degradation into Small Molecules. | de Gracia Lux C, McFearin CL, Joshi-Barr S, Sankaranarayanan J, Fomina N, Almutairi A | ACS macro letters | 23066523 | ACS Macro Lett | 2012 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/23066523 |
| Biocompatible polymeric nanoparticles degrade and release cargo in response to biologically relevant levels of hydrogen peroxide. | de Gracia Lux C, Joshi-Barr S, Nguyen T, Mahmoud E, Schopf E, Fomina N, Almutairi A | Journal of the American Chemical Society | 22946840 | J Am Chem Soc | 2012 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/22946840 |
| UV and near-IR triggered release from polymeric nanoparticles. | Fomina N, McFearin C, Sermsakdi M, Edigin O, Almutairi A | Journal of the American Chemical Society | 20568765 | J Am Chem Soc | 2010 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/20568765 |
| Inflammation responsive logic gate nanoparticles for the delivery of proteins. | Mahmoud EA, Sankaranarayanan J, Morachis JM, Kim G, Almutairi A | Bioconjugate chemistry | 21688843 | Bioconjug Chem | 2011 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/21688843 |
| A model for neural development and treatment of Rett syndrome using human induced pluripotent stem cells. | Marchetto MC, Carromeu C, Acab A, Yu D, Yeo GW, Mu Y, Chen G, Gage FH, Muotri AR | Cell | 21074045 | Cell | 2010 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/21074045 |
| Modeling of TREX1-Dependent Autoimmune Disease using Human Stem Cells Highlights L1 Accumulation as a Source of Neuroinflammation. | Thomas CA, Tejwani L, Trujillo CA, Negraes PD, Herai RH, Mesci P, Macia A, Crow YJ, Muotri AR | Cell stem cell | 28803918 | Cell Stem Cell | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28803918 |
| Modeling anorexia nervosa: transcriptional insights from human iPSC-derived neurons. | Negraes PD, Cugola FR, Herai RH, Trujillo CA, Cristino AS, Chailangkarn T, Muotri AR, Duvvuri V | Translational psychiatry | 28291261 | Transl Psychiatry | 2017 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/28291261 |
| Evolution, development, and plasticity of the human brain: from molecules to bones. | Hrvoj-Mihic B, Bienvenu T, Stefanacci L, Muotri AR, Semendeferi K | Frontiers in human neuroscience | 24194709 | Front Hum Neurosci | 2013 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/24194709 |
| Species-specific maturation profiles of human, chimpanzee and bonobo neural cells. | Marchetto MC, Hrvoj-Mihic B, Kerman BE, Yu DX, Vadodaria KC, Linker SB, Narvaiza I, Santos R, Denli AM, Mendes AP, Oefner R, Cook J, McHenry L, Grasmick JM, Heard K, Fredlender C, Randolph-Moore L, Kshirsagar R, Xenitopoulos R, Chou G, Hah N, Muotri AR, Padmanabhan K, Semendeferi K, Gage FH | eLife | 30730291 | Elife | 2019 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/30730291 |
| The Human Model: Changing Focus on Autism Research. | Muotri AR | Biological psychiatry | 25861701 | Biol Psychiatry | 2016 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/25861701 |
| Exercise induces age-dependent changes on epigenetic parameters in rat hippocampus: a preliminary study. | Elsner VR, Lovatel GA, Moysés F, Bertoldi K, Spindler C, Cechinel LR, Muotri AR, Siqueira IR | Experimental gerontology | 23201423 | Exp Gerontol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23201423 |
| Stem cells and modeling of autism spectrum disorders. | Freitas BC, Trujillo CA, Carromeu C, Yusupova M, Herai RH, Muotri AR | Experimental neurology | 23036599 | Exp Neurol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23036599 |
| Treadmill exercise induces age-related changes in aversive memory, neuroinflammatory and epigenetic processes in the rat hippocampus. | Lovatel GA, Elsner VR, Bertoldi K, Vanzella C, Moysés Fdos S, Vizuete A, Spindler C, Cechinel LR, Netto CA, Muotri AR, Siqueira IR | Neurobiology of learning and memory | 23357282 | Neurobiol Learn Mem | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23357282 |
| Kinin-B2 receptor activity determines the differentiation fate of neural stem cells. | Trujillo CA, Negraes PD, Schwindt TT, Lameu C, Carromeu C, Muotri AR, Pesquero JB, Cerqueira DM, Pillat MM, de Souza HD, Turaça LT, Abreu JG, Ulrich H | The Journal of biological chemistry | 23132855 | J Biol Chem | 2012 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/23132855 |
| Modeling autism spectrum disorders with human neurons. | Beltrão-Braga PC, Muotri AR | Brain research | 26854137 | Brain Res | 2017 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26854137 |
| The Use of Induced Pluripotent Stem Cell Technology to Advance Autism Research and Treatment. | Acab A, Muotri AR | Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics | 25851569 | Neurotherapeutics | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25851569 |
| Systematic optimization of human pluripotent stem cells media using Design of Experiments. | Marinho PA, Chailangkarn T, Muotri AR | Scientific reports | 25940691 | Sci Rep | 2015 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/25940691 |
| Brains, genes, and primates. | Izpisua Belmonte JC, Callaway EM, Caddick SJ, Churchland P, Feng G, Homanics GE, Lee KF, Leopold DA, Miller CT, Mitchell JF, Mitalipov S, Moutri AR, Movshon JA, Okano H, Reynolds JH, Ringach D, Sejnowski TJ, Silva AC, Strick PL, Wu J, Zhang F | Neuron | 25950631 | Neuron | 2015 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/25950631 |
| LINE-1: creators of neuronal diversity. | Thomas CA, Muotri AR | Frontiers in bioscience (Elite edition) | 22201983 | Front Biosci (Elite Ed) | 2012 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/22201983 |
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| Loss of MXD3 induces apoptosis of Reh human precursor B acute lymphoblastic leukemia cells. | Barisone GA, Satake N, Lewis C, Duong C, Chen C, Lam KS, Nolta J, Dίaz E | Blood cells, molecules & diseases | 25554682 | Blood Cells Mol Dis | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25554682 |
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| Designing artificial enzymes by intuition and computation. | Nanda V, Koder RL | Nature chemistry | 21124375 | Nat Chem | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21124375 |
| Parallels between DNA and collagen - comparing elastic models of the double and triple helix. | Xu F, Zheng H, Clauvelin N, Lu XJ, Olson WK, Nanda V | Scientific reports | 29038480 | Sci Rep | 2017 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/29038480 |
| Structural principles for computational and de novo design of 4Fe-4S metalloproteins. | Nanda V, Senn S, Pike DH, Rodriguez-Granillo A, Hansen WA, Khare SD, Noy D | Biochimica et biophysica acta | 26449207 | Biochim Biophys Acta | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26449207 |
| Methacrylation induces rapid, temperature-dependent, reversible self-assembly of type-I collagen. | Drzewiecki KE, Parmar AS, Gaudet ID, Branch JR, Pike DH, Nanda V, Shreiber DI | Langmuir : the ACS journal of surfaces and colloids | 25208340 | Langmuir | 2014 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/25208340 |
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| Self-assembly of left- and right-handed molecular screws. | Xu F, Khan IJ, McGuinness K, Parmar AS, Silva T, Murthy NS, Nanda V | Journal of the American Chemical Society | 24283407 | J Am Chem Soc | 2013 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/24283407 |
| Dissecting Electrostatic Contributions to Folding and Self-Assembly Using Designed Multicomponent Peptide Systems. | Parmar AS, James JK, Grisham DR, Pike DH, Nanda V | Journal of the American Chemical Society | 26966815 | J Am Chem Soc | 2016 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/26966815 |
| Metal Stabilization of Collagen and de Novo Designed Mimetic Peptides. | Parmar AS, Xu F, Pike DH, Belure SV, Hasan NF, Drzewiecki KE, Shreiber DI, Nanda V | Biochemistry | 26225466 | Biochemistry | 2015 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/26225466 |
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| Hydrodynamic radius coincides with the slip plane position in the electrokinetic behavior of lysozyme. | Grisham DR, Nanda V | Proteins | 29383755 | Proteins | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29383755 |
| Collagen mimetic peptide discs promote assembly of a broad range of natural protein fibers through hydrophobic interactions. | McGuinness K, Nanda V | Organic & biomolecular chemistry | 28678287 | Org Biomol Chem | 2017 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/28678287 |
| Compositional control of higher order assembly using synthetic collagen peptides. | Xu F, Li J, Jain V, Tu RS, Huang Q, Nanda V | Journal of the American Chemical Society | 22171825 | J Am Chem Soc | 2012 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/22171825 |
| Circular permutation directs orthogonal assembly in complex collagen peptide mixtures. | Xu F, Silva T, Joshi M, Zahid S, Nanda V | The Journal of biological chemistry | 24043622 | J Biol Chem | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24043622 |
| Zeta Potential Prediction from Protein Structure in General Aqueous Electrolyte Solutions. | Grisham DR, Nanda V | Langmuir : the ACS journal of surfaces and colloids | 33186035 | Langmuir | 2020 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/33186035 |
| Design of net-charged abc-type collagen heterotrimers. | Parmar AS, Zahid S, Belure SV, Young R, Hasan N, Nanda V | Journal of structural biology | 23603270 | J Struct Biol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23603270 |
| Sequence recombination improves target specificity in a redesigned collagen peptide abc-type heterotrimer. | Giddu S, Xu F, Nanda V | Proteins | 23042255 | Proteins | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23042255 |
| Control of Collagen Stability and Heterotrimer Specificity through Repulsive Electrostatic Interactions. | Parmar AS, Joshi M, Nosker PL, Hasan NF, Nanda V | Biomolecules | 24970200 | Biomolecules | 2013 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/24970200 |
| Circular Dichroism Spectroscopy of Collagen Fibrillogenesis: A New Use for an Old Technique. | Drzewiecki KE, Grisham DR, Parmar AS, Nanda V, Shreiber DI | Biophysical journal | 27926839 | Biophys J | 2016 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/27926839 |
| Marginal protein stability drives subcellular proteome isoelectric point. | Loell K, Nanda V | Proceedings of the National Academy of Sciences of the United States of America | 30385634 | Proc Natl Acad Sci U S A | 2018 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/30385634 |
| Morphological diversity and polymorphism of self-assembling collagen peptides controlled by length of hydrophobic domains. | McGuinness K, Khan IJ, Nanda V | ACS nano | 25390880 | ACS Nano | 2014 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/25390880 |
| Microfluidic analysis of extracellular matrix-bFGF crosstalk on primary human myoblast chemoproliferation, chemokinesis, and chemotaxis. | Ferreira MM, Dewi RE, Heilshorn SC | Integrative biology : quantitative biosciences from nano to macro | 25909157 | Integr Biol (Camb) | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25909157 |
| Complex chemoattractive and chemorepellent Kit signals revealed by direct imaging of murine mast cells in microfluidic gradient chambers. | Shamloo A, Manchandia M, Ferreira M, Mani M, Nguyen C, Jahn T, Weinberg K, Heilshorn S | Integrative biology : quantitative biosciences from nano to macro | 23835699 | Integr Biol (Camb) | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23835699 |
| Photoreactive elastin-like proteins for use as versatile bioactive materials and surface coatings. | Raphel J, Parisi-Amon A, Heilshorn S | Journal of materials chemistry | 23015764 | J Mater Chem | 2012 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/23015764 |
| Design of three-dimensional engineered protein hydrogels for tailored control of neurite growth. | Lampe KJ, Antaris AL, Heilshorn SC | Acta biomaterialia | 23128159 | Acta Biomater | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23128159 |
| Microfluidic investigation of BDNF-enhanced neural stem cell chemotaxis in CXCL12 gradients. | Xu H, Heilshorn SC | Small (Weinheim an der Bergstrasse, Germany) | 23109183 | Small | 2013 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/23109183 |
| Matrix RGD ligand density and L1CAM-mediated Schwann cell interactions synergistically enhance neurite outgrowth. | Romano NH, Madl CM, Heilshorn SC | Acta biomaterialia | 25308870 | Acta Biomater | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25308870 |
| Hybrid elastin-like polypeptide-polyethylene glycol (ELP-PEG) hydrogels with improved transparency and independent control of matrix mechanics and cell ligand density. | Wang H, Cai L, Paul A, Enejder A, Heilshorn SC | Biomacromolecules | 25111283 | Biomacromolecules | 2014 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/25111283 |
| Protein-engineered hydrogel encapsulation for 3-D culture of murine cochlea. | Chang DT, Chai R, DiMarco R, Heilshorn SC, Cheng AG | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | 25111520 | Otol Neurotol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25111520 |
| One-pot Synthesis of Elastin-like Polypeptide Hydrogels with Grafted VEGF-Mimetic Peptides. | Cai L, Dinh CB, Heilshorn SC | Biomaterials science | 24729868 | Biomater Sci | 2014 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24729868 |
| Small-molecule axon-polarization studies enabled by a shear-free microfluidic gradient generator. | Xu H, Ferreira MM, Heilshorn SC | Lab on a chip | 24781157 | Lab Chip | 2014 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/24781157 |
| Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids. | DiMarco RL, Su J, Yan KS, Dewi R, Kuo CJ, Heilshorn SC | Integrative biology : quantitative biosciences from nano to macro | 24343706 | Integr Biol (Camb) | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24343706 |
| Avidity-controlled delivery of angiogenic peptides from injectable molecular-recognition hydrogels. | Mulyasasmita W, Cai L, Hori Y, Heilshorn SC | Tissue engineering. Part A | 24490588 | Tissue Eng Part A | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24490588 |
| Multifunctional materials through modular protein engineering. | DiMarco RL, Heilshorn SC | Advanced materials (Deerfield Beach, Fla.) | 22730248 | Adv Mater | 2012 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/22730248 |
| Sequence-specific crosslinking of electrospun, elastin-like protein preserves bioactivity and native-like mechanics. | Benitez PL, Sweet JA, Fink H, Chennazhi KP, Nair SV, Enejder A, Heilshorn SC | Advanced healthcare materials | 23184558 | Adv Healthc Mater | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23184558 |
| Tetrakis(hydroxymethyl) phosphonium chloride as a covalent cross-linking agent for cell encapsulation within protein-based hydrogels. | Chung C, Lampe KJ, Heilshorn SC | Biomacromolecules | 23151175 | Biomacromolecules | 2012 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/23151175 |
| Building stem cell niches from the molecule up through engineered peptide materials. | Lampe KJ, Heilshorn SC | Neuroscience letters | 22322073 | Neurosci Lett | 2012 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/22322073 |
| Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids. | DiMarco RL, Dewi RE, Bernal G, Kuo C, Heilshorn SC | Biomaterials science | 26371971 | Biomater Sci | 2015 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/26371971 |
| Matrix interactions modulate neurotrophin-mediated neurite outgrowth and pathfinding. | Madl CM, Heilshorn SC | Neural regeneration research | 26170800 | Neural Regen Res | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26170800 |
| Improving viability of stem cells during syringe needle flow through the design of hydrogel cell carriers. | Aguado BA, Mulyasasmita W, Su J, Lampe KJ, Heilshorn SC | Tissue engineering. Part A | 22011213 | Tissue Eng Part A | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22011213 |
| Protein-engineered biomaterials: nanoscale mimics of the extracellular matrix. | Romano NH, Sengupta D, Chung C, Heilshorn SC | Biochimica et biophysica acta | 20647034 | Biochim Biophys Acta | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20647034 |
| Matrix density mediates polarization and lumen formation of endothelial sprouts in VEGF gradients. | Shamloo A, Heilshorn SC | Lab on a chip | 20820484 | Lab Chip | 2010 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/20820484 |
| Essential regulation of CNS angiogenesis by the orphan G protein-coupled receptor GPR124. | Kuhnert F, Mancuso MR, Shamloo A, Wang HT, Choksi V, Florek M, Su H, Fruttiger M, Young WL, Heilshorn SC, Kuo CJ | Science (New York, N.Y.) | 21071672 | Science | 2010 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/21071672 |
| Mechanisms of vascular endothelial growth factor-induced pathfinding by endothelial sprouts in biomaterials. | Shamloo A, Xu H, Heilshorn S | Tissue engineering. Part A | 21888475 | Tissue Eng Part A | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21888475 |
| Microfluidic gradients reveal enhanced neurite outgrowth but impaired guidance within 3D matrices with high integrin ligand densities. | Romano NH, Lampe KJ, Xu H, Ferreira MM, Heilshorn SC | Small (Weinheim an der Bergstrasse, Germany) | 25315156 | Small | 2015 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/25315156 |
| Adaptable hydrogel networks with reversible linkages for tissue engineering. | Wang H, Heilshorn SC | Advanced materials (Deerfield Beach, Fla.) | 25989348 | Adv Mater | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/25989348 |
| Avidity-controlled hydrogels for injectable co-delivery of induced pluripotent stem cell-derived endothelial cells and growth factors. | Mulyasasmita W, Cai L, Dewi RE, Jha A, Ullmann SD, Luong RH, Huang NF, Heilshorn SC | Journal of controlled release : official journal of the Controlled Release Society | 24848744 | J Control Release | 2014 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/24848744 |
| Molecular-level engineering of protein physical hydrogels for predictive sol-gel phase behavior. | Mulyasasmita W, Lee JS, Heilshorn SC | Biomacromolecules | 21861461 | Biomacromolecules | 2011 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/21861461 |
| Protein-engineered biomaterials to generate human skeletal muscle mimics. | Sengupta D, Gilbert PM, Johnson KJ, Blau HM, Heilshorn SC | Advanced healthcare materials | 23184832 | Adv Healthc Mater | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23184832 |
| Protein-engineered injectable hydrogel to improve retention of transplanted adipose-derived stem cells. | Parisi-Amon A, Mulyasasmita W, Chung C, Heilshorn SC | Advanced healthcare materials | 23184882 | Adv Healthc Mater | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23184882 |
| Hydrogel crosslinking density regulates temporal contractility of human embryonic stem cell-derived cardiomyocytes in 3D cultures. | Chung C, Anderson E, Pera RR, Pruitt BL, Heilshorn SC | Soft matter | 23226161 | Soft Matter | 2012 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/23226161 |
| Designing ECM-mimetic materials using protein engineering. | Cai L, Heilshorn SC | Acta biomaterialia | 24365704 | Acta Biomater | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24365704 |
| A microfluidic-based genetic screen to identify microbial virulence factors that inhibit dendritic cell migration. | McLaughlin LM, Xu H, Carden SE, Fisher S, Reyes M, Heilshorn SC, Monack DM | Integrative biology : quantitative biosciences from nano to macro | 24599496 | Integr Biol (Camb) | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24599496 |
| Injectable Hydrogels with In Situ Double Network Formation Enhance Retention of Transplanted Stem Cells. | Cai L, Dewi RE, Heilshorn SC | Advanced functional materials | 26273242 | Adv Funct Mater | 2015 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/26273242 |
| Spontaneous cardiomyocyte differentiation of mouse embryoid bodies regulated by hydrogel crosslink density. | Chung C, Pruitt BL, Heilshorn SC | Biomaterials science | 24748962 | Biomater Sci | 2013 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/24748962 |
| Chemotaxis of human induced pluripotent stem cell-derived endothelial cells. | Huang NF, Dewi RE, Okogbaa J, Lee JC, Jalilrufaihah A, Heilshorn SC, Cooke JP | American journal of translational research | 23977410 | Am J Transl Res | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23977410 |
| Cutting edge: identification of autoreactive CD4+ and CD8+ T cell subsets resistant to PD-1 pathway blockade. | Pauken KE, Nelson CE, Martinov T, Spanier JA, Heffernan JR, Sahli NL, Quarnstrom CF, Osum KC, Schenkel JM, Jenkins MK, Blazar BR, Vezys V, Fife BT | Journal of immunology (Baltimore, Md. : 1950) | 25769925 | J Immunol | 2015 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/25769925 |
| Shortened Intervals during Heterologous Boosting Preserve Memory CD8 T Cell Function but Compromise Longevity. | Thompson EA, Beura LK, Nelson CE, Anderson KG, Vezys V | Journal of immunology (Baltimore, Md. : 1950) | 26903479 | J Immunol | 2016 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/26903479 |
| Cutting edge: generation of effector cells that localize to mucosal tissues and form resident memory CD8 T cells is controlled by mTOR. | Sowell RT, Rogozinska M, Nelson CE, Vezys V, Marzo AL | Journal of immunology (Baltimore, Md. : 1950) | 25070853 | J Immunol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25070853 |
| Robust Iterative Stimulation with Self-Antigens Overcomes CD8(+) T Cell Tolerance to Self- and Tumor Antigens. | Nelson CE, Thompson EA, Quarnstrom CF, Fraser KA, Seelig DM, Bhela S, Burbach BJ, Masopust D, Vezys V | Cell reports | 31533033 | Cell Rep | 2019 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/31533033 |
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| Imaging lysosomal enzyme activity in live cells using self-quenched substrates. | Humphries WH 4th, Payne CK | Analytical biochemistry | 22387398 | Anal Biochem | 2012 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/22387398 |
| Nanoparticles act as protein carriers during cellular internalization. | Doorley GW, Payne CK | Chemical communications (Cambridge, England) | 22328990 | Chem Commun (Camb) | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22328990 |
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| Impact of Serum Proteins on MRI Contrast Agents: Cellular Binding and T(2) relaxation. | Hill A, Payne CK | RSC advances | 25485101 | RSC Adv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25485101 |
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| Cellular binding of nanoparticles in the presence of serum proteins. | Doorley GW, Payne CK | Chemical communications (Cambridge, England) | 20886139 | Chem Commun (Camb) | 2011 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/20886139 |
| Cellular binding of nanoparticles disrupts the membrane potential. | Warren EA, Payne CK | RSC advances | 25685328 | RSC Adv | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25685328 |
| Lysosome transport as a function of lysosome diameter. | Bandyopadhyay D, Cyphersmith A, Zapata JA, Kim YJ, Payne CK | PloS one | 24497985 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24497985 |
| Endo-lysosomal vesicles positive for Rab7 and LAMP1 are terminal vesicles for the transport of dextran. | Humphries WH 4th, Szymanski CJ, Payne CK | PloS one | 22039519 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22039519 |
| Differential cathepsin responses to inhibitor-induced feedback: E-64 and cystatin C elevate active cathepsin S and suppress active cathepsin L in breast cancer cells. | Wilder CL, Walton C, Watson V, Stewart FAA, Johnson J, Peyton SR, Payne CK, Odero-Marah V, Platt MO | The international journal of biochemistry & cell biology | 27592448 | Int J Biochem Cell Biol | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27592448 |
| Membrane potential mediates the cellular binding of nanoparticles. | Shin EH, Li Y, Kumar U, Sureka HV, Zhang X, Payne CK | Nanoscale | 23698734 | Nanoscale | 2013 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/23698734 |
| Cellular Binding of Anionic Nanoparticles is Inhibited by Serum Proteins Independent of Nanoparticle Composition. | Fleischer CC, Kumar U, Payne CK | Biomaterials science | 23956836 | Biomater Sci | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23956836 |
| Secondary structure of corona proteins determines the cell surface receptors used by nanoparticles. | Fleischer CC, Payne CK | The journal of physical chemistry. B | 24779411 | J Phys Chem B | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/24779411 |
| Different cortical involvement pattern of generalized and localized spasms: a magnetoencephalography study. | Kakisaka Y, Gupta A, Wang ZI, Dubarry AS, Alexopoulos AV, Mosher JC, Burgess RC | Epilepsy & behavior : E&B | 21944062 | Epilepsy Behav | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21944062 |
| Functional Magnetic Resonance Imaging Correlates of Ventral Striatal Deep Brain Stimulation for Poststroke Pain. | Jones SE, Lempka SF, Gopalakrishnan R, Baker KB, Beall EB, Bhattacharyya P, Huang X, Lin J, Chen J, Lowe MJ, Malone DA, Machado AG | Neuromodulation : journal of the International Neuromodulation Society | 32744789 | Neuromodulation | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32744789 |
| The use of contact heat evoked potential stimulator (CHEPS) in magnetoencephalography for pain research. | Gopalakrishnan R, Machado AG, Burgess RC, Mosher JC | Journal of neuroscience methods | 23994044 | J Neurosci Methods | 2013 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/23994044 |
| Effectiveness and neural mechanisms associated with tDCS delivered to premotor cortex in stroke rehabilitation: study protocol for a randomized controlled trial. | Plow EB, Cunningham DA, Beall E, Jones S, Wyant A, Bonnett C, Yue GH, Lowe M, Wang XF, Sakaie K, Machado A | Trials | 24119615 | Trials | 2013 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/24119615 |
| Deep brain stimulation of the ventral striatum/anterior limb of the internal capsule in thalamic pain syndrome: study protocol for a pilot randomized controlled trial. | Plow EB, Malone DA Jr, Machado A | Trials | 23902631 | Trials | 2013 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/23902631 |
| Brain stimulation in the treatment of chronic neuropathic and non-cancerous pain. | Plow EB, Pascual-Leone A, Machado A | The journal of pain | 22484179 | J Pain | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22484179 |
| A magnetoencephalography study of multi-modal processing of pain anticipation in primary sensory cortices. | Gopalakrishnan R, Burgess RC, Plow EB, Floden DP, Machado AG | Neuroscience | 26210576 | Neuroscience | 2015 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/26210576 |
| Challenges in Recruitment for the Study of Noninvasive Brain Stimulation in Stroke: Lessons from Deep Brain Stimulation. | Potter-Baker KA, Bonnett CE, Chabra P, Roelle S, Varnerin N, Cunningham DA, Sankarasubramanian V, Pundik S, Conforto AB, Machado AG, Plow EB | Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association | 26851211 | J Stroke Cerebrovasc Dis | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26851211 |
| Central neuromodulation for refractory pain. | Moore NZ, Lempka SF, Machado A | Neurosurgery clinics of North America | 24262901 | Neurosurg Clin N Am | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24262901 |
| Voxel-based morphometric MRI post-processing in MRI-negative focal cortical dysplasia followed by simultaneously recorded MEG and stereo-EEG. | Wang ZI, Jones SE, Ristic AJ, Wong C, Kakisaka Y, Jin K, Schneider F, Gonzalez-Martinez JA, Mosher JC, Nair D, Burgess RC, Najm IM, Alexopoulos AV | Epilepsy research | 22391138 | Epilepsy Res | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22391138 |
| Clinical evidence for the utility of movement compensation algorithm in magnetoencephalography: successful localization during focal seizure. | Kakisaka Y, Wang ZI, Mosher JC, Dubarry AS, Alexopoulos AV, Enatsu R, Kotagal P, Burgess RC | Epilepsy research | 22503605 | Epilepsy Res | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22503605 |
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| Magnetoencephalography's higher sensitivity to epileptic spikes may elucidate the profile of electroencephalographically negative epileptic seizures. | Kakisaka Y, Wang ZI, Mosher JC, Nair DR, Alexopoulos AV, Burgess RC | Epilepsy & behavior : E&B | 22227034 | Epilepsy Behav | 2012 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22227034 |
| Cerebral stimulation for the affective component of neuropathic pain. | Machado AG, Baker KB, Plow E, Malone DA | Neuromodulation : journal of the International Neuromodulation Society | 23094938 | Neuromodulation | 2013 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/23094938 |
| Deep brain stimulation of the ventral striatal area for poststroke pain syndrome: a magnetoencephalography study. | Gopalakrishnan R, Burgess RC, Malone DA, Lempka SF, Gale JT, Floden DP, Baker KB, Machado AG | Journal of neurophysiology | 29384450 | J Neurophysiol | 2018 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/29384450 |
| Early event related fields during visually evoked pain anticipation. | Gopalakrishnan R, Burgess RC, Plow EB, Floden DP, Machado AG | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 26733321 | Clin Neurophysiol | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26733321 |
| Randomized clinical trial of deep brain stimulation for poststroke pain. | Lempka SF, Malone DA Jr, Hu B, Baker KB, Wyant A, Ozinga JG 4th, Plow EB, Pandya M, Kubu CS, Ford PJ, Machado AG | Annals of neurology | 28380672 | Ann Neurol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28380672 |
| Preexisting high frequencies of memory CD8+ T cells favor rapid memory differentiation and preservation of proliferative potential upon boosting. | Fraser KA, Schenkel JM, Jameson SC, Vezys V, Masopust D | Immunity | 23890070 | Immunity | 2013 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/23890070 |
| Intravascular staining for discrimination of vascular and tissue leukocytes. | Anderson KG, Mayer-Barber K, Sung H, Beura L, James BR, Taylor JJ, Qunaj L, Griffith TS, Vezys V, Barber DL, Masopust D | Nature protocols | 24385150 | Nat Protoc | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24385150 |
| The integration of T cell migration, differentiation and function. | Masopust D, Schenkel JM | Nature reviews. Immunology | 23598650 | Nat Rev Immunol | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23598650 |
| T cell memory. Resident memory CD8 T cells trigger protective innate and adaptive immune responses. | Schenkel JM, Fraser KA, Beura LK, Pauken KE, Vezys V, Masopust D | Science (New York, N.Y.) | 25170049 | Science | 2014 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/25170049 |
| Sensing and alarm function of resident memory CD8⁺ T cells. | Schenkel JM, Fraser KA, Vezys V, Masopust D | Nature immunology | 23542740 | Nat Immunol | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23542740 |
| Cutting edge: resident memory CD8 T cells occupy frontline niches in secondary lymphoid organs. | Schenkel JM, Fraser KA, Masopust D | Journal of immunology (Baltimore, Md. : 1950) | 24600038 | J Immunol | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24600038 |
| Does the potential for chaos constrain the embryonic cell-cycle oscillator? | McIsaac RS, Huang KC, Sengupta A, Wingreen NS | PLoS computational biology | 21779158 | PLoS Comput Biol | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21779158 |
| How Does the Xenopus laevis Embryonic Cell Cycle Avoid Spatial Chaos? | Gelens L, Huang KC, Ferrell JE Jr | Cell reports | 26212326 | Cell Rep | 2015 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/26212326 |
| Interplay between the localization and kinetics of phosphorylation in flagellar pole development of the bacterium Caulobacter crescentus. | Tropini C, Huang KC | PLoS computational biology | 22876167 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22876167 |
| Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations. | Hsin J, Gopinathan A, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 22647609 | Proc Natl Acad Sci U S A | 2012 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/22647609 |
| De novo morphogenesis in L-forms via geometric control of cell growth. | Billings G, Ouzounov N, Ursell T, Desmarais SM, Shaevitz J, Gitai Z, Huang KC | Molecular microbiology | 24995493 | Mol Microbiol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24995493 |
| Motility enhancement through surface modification is sufficient for cyanobacterial community organization during phototaxis. | Ursell T, Chau RM, Wisen S, Bhaya D, Huang KC | PLoS computational biology | 24039562 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24039562 |
| Chiral twisting in a bacterial cytoskeletal polymer affects filament size and orientation. | Shi H, Quint DA, Grason GM, Gopinathan A, Huang KC | Nature communications | 32179732 | Nat Commun | 2020 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/32179732 |
| Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance. | Aranda-Díaz A, Obadia B, Dodge R, Thomsen T, Hallberg ZF, Güvener ZT, Ludington WB, Huang KC | eLife | 31995029 | Elife | 2020 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/31995029 |
| The molecular origins of chiral growth in walled cells. | Huang KC, Ehrhardt DW, Shaevitz JW | Current opinion in microbiology | 23194654 | Curr Opin Microbiol | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23194654 |
| Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs. | Ng KM, Aranda-Díaz A, Tropini C, Frankel MR, Van Treuren W, O'Loughlin CT, Merrill BD, Yu FB, Pruss KM, Oliveira RA, Higginbottom SK, Neff NF, Fischbach MA, Xavier KB, Sonnenburg JL, Huang KC | Cell host & microbe | 31726029 | Cell Host Microbe | 2019 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/31726029 |
| Mechanical consequences of cell-wall turnover in the elongation of a Gram-positive bacterium. | Misra G, Rojas ER, Gopinathan A, Huang KC | Biophysical journal | 23746506 | Biophys J | 2013 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/23746506 |
| Dimer dynamics and filament organization of the bacterial cell division protein FtsA. | Hsin J, Fu R, Huang KC | Journal of molecular biology | 23871894 | J Mol Biol | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23871894 |
| The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction. | Sundararajan K, Miguel A, Desmarais SM, Meier EL, Casey Huang K, Goley ED | Nature communications | 26099469 | Nat Commun | 2015 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/26099469 |
| How and why cells grow as rods. | Chang F, Huang KC | BMC biology | 25185019 | BMC Biol | 2014 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/25185019 |
| The bacterial actin MreB rotates, and rotation depends on cell-wall assembly. | van Teeffelen S, Wang S, Furchtgott L, Huang KC, Wingreen NS, Shaevitz JW, Gitai Z | Proceedings of the National Academy of Sciences of the United States of America | 21903929 | Proc Natl Acad Sci U S A | 2011 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/21903929 |
| Response of Escherichia coli growth rate to osmotic shock. | Rojas E, Theriot JA, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24821776 | Proc Natl Acad Sci U S A | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24821776 |
| Mechanisms for maintaining cell shape in rod-shaped Gram-negative bacteria. | Furchtgott L, Wingreen NS, Huang KC | Molecular microbiology | 21501250 | Mol Microbiol | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21501250 |
| GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell wall synthesis. | Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao J | Science (New York, N.Y.) | 28209899 | Science | 2017 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/28209899 |
| FtsZ-Dependent Elongation of a Coccoid Bacterium. | Pereira AR, Hsin J, Król E, Tavares AC, Flores P, Hoiczyk E, Ng N, Dajkovic A, Brun YV, VanNieuwenhze MS, Roemer T, Carballido-Lopez R, Scheffers DJ, Huang KC, Pinho MG | mBio | 27601570 | mBio | 2016 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/27601570 |
| How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction. | Shi H, Bratton BP, Gitai Z, Huang KC | Cell | 29522748 | Cell | 2018 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/29522748 |
| Spatial gradient of protein phosphorylation underlies replicative asymmetry in a bacterium. | Chen YE, Tropini C, Jonas K, Tsokos CG, Huang KC, Laub MT | Proceedings of the National Academy of Sciences of the United States of America | 21191097 | Proc Natl Acad Sci U S A | 2011 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/21191097 |
| Dynamic SpoIIIE assembly mediates septal membrane fission during Bacillus subtilis sporulation. | Fleming TC, Shin JY, Lee SH, Becker E, Huang KC, Bustamante C, Pogliano K | Genes & development | 20516200 | Genes Dev | 2010 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/20516200 |
| Principles of bacterial cell-size determination revealed by cell-wall synthesis perturbations. | Tropini C, Lee TK, Hsin J, Desmarais SM, Ursell T, Monds RD, Huang KC | Cell reports | 25456140 | Cell Rep | 2014 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/25456140 |
| Systematic perturbation of cytoskeletal function reveals a linear scaling relationship between cell geometry and fitness. | Monds RD, Lee TK, Colavin A, Ursell T, Quan S, Cooper TF, Huang KC | Cell reports | 25456141 | Cell Rep | 2014 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/25456141 |
| Bacterial division. Mechanical crack propagation drives millisecond daughter cell separation in Staphylococcus aureus. | Zhou X, Halladin DK, Rojas ER, Koslover EF, Lee TK, Huang KC, Theriot JA | Science (New York, N.Y.) | 25931560 | Science | 2015 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/25931560 |
| Effects of polymerization and nucleotide identity on the conformational dynamics of the bacterial actin homolog MreB. | Colavin A, Hsin J, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24550504 | Proc Natl Acad Sci U S A | 2014 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/24550504 |
| Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization. | Ursell TS, Nguyen J, Monds RD, Colavin A, Billings G, Ouzounov N, Gitai Z, Shaevitz JW, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24550515 | Proc Natl Acad Sci U S A | 2014 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/24550515 |
| The role of hydrolases in bacterial cell-wall growth. | Lee TK, Huang KC | Current opinion in microbiology | 24035761 | Curr Opin Microbiol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24035761 |
| Optimal dynamics for quality control in spatially distributed mitochondrial networks. | Patel PK, Shirihai O, Huang KC | PLoS computational biology | 23874166 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23874166 |
| FtsZ protofilaments use a hinge-opening mechanism for constrictive force generation. | Li Y, Hsin J, Zhao L, Cheng Y, Shang W, Huang KC, Wang HW, Ye S | Science (New York, N.Y.) | 23888039 | Science | 2013 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/23888039 |
| Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates. | Shi H, Colavin A, Lee TK, Huang KC | Nature protocols | 28125106 | Nat Protoc | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28125106 |
| A Comprehensive, CRISPR-based Functional Analysis of Essential Genes in Bacteria. | Peters JM, Colavin A, Shi H, Czarny TL, Larson MH, Wong S, Hawkins JS, Lu CHS, Koo BM, Marta E, Shiver AL, Whitehead EH, Weissman JS, Brown ED, Qi LS, Huang KC, Gross CA | Cell | 27238023 | Cell | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27238023 |
| Physical constraints on the establishment of intracellular spatial gradients in bacteria. | Tropini C, Rabbani N, Huang KC | BMC biophysics | 22931750 | BMC Biophys | 2012 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/22931750 |
| RodZ modulates geometric localization of the bacterial actin MreB to regulate cell shape. | Colavin A, Shi H, Huang KC | Nature communications | 29599448 | Nat Commun | 2018 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/29599448 |
| Isolation and preparation of bacterial cell walls for compositional analysis by ultra performance liquid chromatography. | Desmarais SM, Cava F, de Pedro MA, Huang KC | Journal of visualized experiments : JoVE | 24457605 | J Vis Exp | 2014 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/24457605 |
| Single-molecule imaging reveals modulation of cell wall synthesis dynamics in live bacterial cells. | Lee TK, Meng K, Shi H, Huang KC | Nature communications | 27774981 | Nat Commun | 2016 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/27774981 |
| Posttranslational acetylation of α-tubulin constrains protofilament number in native microtubules. | Cueva JG, Hsin J, Huang KC, Goodman MB | Current biology : CB | 22658592 | Curr Biol | 2012 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/22658592 |
| Peptidoglycan at its peaks: how chromatographic analyses can reveal bacterial cell wall structure and assembly. | Desmarais SM, De Pedro MA, Cava F, Huang KC | Molecular microbiology | 23679048 | Mol Microbiol | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23679048 |
| Macromolecules that prefer their membranes curvy. | Huang KC, Ramamurthi KS | Molecular microbiology | 20444099 | Mol Microbiol | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20444099 |
| Helical insertion of peptidoglycan produces chiral ordering of the bacterial cell wall. | Wang S, Furchtgott L, Huang KC, Shaevitz JW | Proceedings of the National Academy of Sciences of the United States of America | 22343529 | Proc Natl Acad Sci U S A | 2012 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/22343529 |
| Analysis of surface protein expression reveals the growth pattern of the gram-negative outer membrane. | Ursell TS, Trepagnier EH, Huang KC, Theriot JA | PLoS computational biology | 23028278 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23028278 |
| Mechanics of membrane bulging during cell-wall disruption in gram-negative bacteria. | Daly KE, Huang KC, Wingreen NS, Mukhopadhyay R | Physical review. E, Statistical, nonlinear, and soft matter physics | 21599215 | Phys Rev E Stat Nonlin Soft Matter Phys | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21599215 |
| The contractile ring coordinates curvature-dependent septum assembly during fission yeast cytokinesis. | Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F | Molecular biology of the cell | 25355954 | Mol Biol Cell | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25355954 |
| High-throughput, Highly Sensitive Analyses of Bacterial Morphogenesis Using Ultra Performance Liquid Chromatography. | Desmarais SM, Tropini C, Miguel A, Cava F, Monds RD, de Pedro MA, Huang KC | The Journal of biological chemistry | 26468288 | J Biol Chem | 2015 Dec 25 | https://www.ncbi.nlm.nih.gov/pubmed/26468288 |
| Disruption of lipid homeostasis in the Gram-negative cell envelope activates a novel cell death pathway. | Sutterlin HA, Shi H, May KL, Miguel A, Khare S, Huang KC, Silhavy TJ | Proceedings of the National Academy of Sciences of the United States of America | 26929379 | Proc Natl Acad Sci U S A | 2016 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/26929379 |
| A Periplasmic Polymer Curves Vibrio cholerae and Promotes Pathogenesis. | Bartlett TM, Bratton BP, Duvshani A, Miguel A, Sheng Y, Martin NR, Nguyen JP, Persat A, Desmarais SM, VanNieuwenhze MS, Huang KC, Zhu J, Shaevitz JW, Gitai Z | Cell | 28086090 | Cell | 2017 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/28086090 |
| Rapid, precise quantification of bacterial cellular dimensions across a genomic-scale knockout library. | Ursell T, Lee TK, Shiomi D, Shi H, Tropini C, Monds RD, Colavin A, Billings G, Bhaya-Grossman I, Broxton M, Huang BE, Niki H, Huang KC | BMC biology | 28222723 | BMC Biol | 2017 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/28222723 |
| Homeostatic Cell Growth Is Accomplished Mechanically through Membrane Tension Inhibition of Cell-Wall Synthesis. | Rojas ER, Huang KC, Theriot JA | Cell systems | 29203279 | Cell Syst | 2017 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/29203279 |
| Precise regulation of the relative rates of surface area and volume synthesis in bacterial cells growing in dynamic environments. | Shi H, Hu Y, Odermatt PD, Gonzalez CG, Zhang L, Elias JE, Chang F, Huang KC | Nature communications | 33785742 | Nat Commun | 2021 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/33785742 |
| Variations in the binding pocket of an inhibitor of the bacterial division protein FtsZ across genotypes and species. | Miguel A, Hsin J, Liu T, Tang G, Altman RB, Huang KC | PLoS computational biology | 25811761 | PLoS Comput Biol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25811761 |
| Physics of Intracellular Organization in Bacteria. | Wingreen NS, Huang KC | Annual review of microbiology | 26488278 | Annu Rev Microbiol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26488278 |
| Cutting the Gordian Knot of the Microbiota. | Vasquez KS, Shiver AL, Huang KC | Molecular cell | 29883604 | Mol Cell | 2018 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/29883604 |
| A dynamically assembled cell wall synthesis machinery buffers cell growth. | Lee TK, Tropini C, Hsin J, Desmarais SM, Ursell TS, Gong E, Gitai Z, Monds RD, Huang KC | Proceedings of the National Academy of Sciences of the United States of America | 24550500 | Proc Natl Acad Sci U S A | 2014 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/24550500 |
| Normal morphogenesis of epithelial tissues and progression of epithelial tumors. | Wang CC, Jamal L, Janes KA | Wiley interdisciplinary reviews. Systems biology and medicine | 21898857 | Wiley Interdiscip Rev Syst Biol Med | 2012 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/21898857 |
| An ERK-p38 subnetwork coordinates host cell apoptosis and necrosis during coxsackievirus B3 infection. | Jensen KJ, Garmaroudi FS, Zhang J, Lin J, Boroomand S, Zhang M, Luo Z, Yang D, Luo H, McManus BM, Janes KA | Cell host & microbe | 23332156 | Cell Host Microbe | 2013 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/23332156 |
| Parameterizing cell-to-cell regulatory heterogeneities via stochastic transcriptional profiles. | Bajikar SS, Fuchs C, Roller A, Theis FJ, Janes KA | Proceedings of the National Academy of Sciences of the United States of America | 24449900 | Proc Natl Acad Sci U S A | 2014 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/24449900 |
| Nucleocytoplasmic transport of active HER2 causes fractional escape from the DCIS-like state. | Wang L, Paudel BB, McKnight RA, Janes KA | Nature communications | 37055441 | Nat Commun | 2023 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/37055441 |
| Identifying single-cell molecular programs by stochastic profiling. | Janes KA, Wang CC, Holmberg KJ, Cabral K, Brugge JS | Nature methods | 20228812 | Nat Methods | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20228812 |
| Multiscale models of cell signaling. | Bajikar SS, Janes KA | Annals of biomedical engineering | 22476894 | Ann Biomed Eng | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22476894 |
| TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors. | Chitforoushzadeh Z, Ye Z, Sheng Z, LaRue S, Fry RC, Lauffenburger DA, Janes KA | Science signaling | 27273097 | Sci Signal | 2016 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/27273097 |
| RUNX1 and its understudied role in breast cancer. | Janes KA | Cell cycle (Georgetown, Tex.) | 22024923 | Cell Cycle | 2011 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/22024923 |
| Paring down signaling complexity. | Janes KA | Nature biotechnology | 20622836 | Nat Biotechnol | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20622836 |
| Tumor-Suppressor Inactivation of GDF11 Occurs by Precursor Sequestration in Triple-Negative Breast Cancer. | Bajikar SS, Wang CC, Borten MA, Pereira EJ, Atkins KA, Janes KA | Developmental cell | 29161592 | Dev Cell | 2017 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/29161592 |
| Simultaneous profiling of 194 distinct receptor transcripts in human cells. | Kang BH, Jensen KJ, Hatch JA, Janes KA | Science signaling | 23921087 | Sci Signal | 2013 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/23921087 |
| Models of signalling networks - what cell biologists can gain from them and give to them. | Janes KA, Lauffenburger DA | Journal of cell science | 23720376 | J Cell Sci | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23720376 |
| Stochastic profiling of transcriptional regulatory heterogeneities in tissues, tumors and cultured cells. | Wang L, Janes KA | Nature protocols | 23306461 | Nat Protoc | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23306461 |
| A time- and matrix-dependent TGFBR3-JUND-KRT5 regulatory circuit in single breast epithelial cells and basal-like premalignancies. | Wang CC, Bajikar SS, Jamal L, Atkins KA, Janes KA | Nature cell biology | 24658685 | Nat Cell Biol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24658685 |
| Pairwise network mechanisms in the host signaling response to coxsackievirus B3 infection. | Garmaroudi FS, Marchant D, Si X, Khalili A, Bashashati A, Wong BW, Tabet A, Ng RT, Murphy K, Luo H, Janes KA, McManus BM | Proceedings of the National Academy of Sciences of the United States of America | 20833815 | Proc Natl Acad Sci U S A | 2010 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/20833815 |
| Intersection of FOXO- and RUNX1-mediated gene expression programs in single breast epithelial cells during morphogenesis and tumor progression. | Wang L, Brugge JS, Janes KA | Proceedings of the National Academy of Sciences of the United States of America | 21873240 | Proc Natl Acad Sci U S A | 2011 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/21873240 |
| Modeling the latent dimensions of multivariate signaling datasets. | Jensen KJ, Janes KA | Physical biology | 22871687 | Phys Biol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22871687 |
| A high-throughput assay for phosphoprotein-specific phosphatase activity in cellular extracts. | Bose AK, Janes KA | Molecular & cellular proteomics : MCP | 23233447 | Mol Cell Proteomics | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23233447 |
| Network Architecture Predisposes an Enzyme to Either Pharmacologic or Genetic Targeting. | Jensen KJ, Moyer CB, Janes KA | Cell systems | 26942229 | Cell Syst | 2016 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/26942229 |
| A microfluidic platform for systems pathology: multiparameter single-cell signaling measurements of clinical brain tumor specimens. | Sun J, Masterman-Smith MD, Graham NA, Jiao J, Mottahedeh J, Laks DR, Ohashi M, DeJesus J, Kamei K, Lee KB, Wang H, Yu ZT, Lu YT, Hou S, Li K, Liu M, Zhang N, Wang S, Angenieux B, Panosyan E, Samuels ER, Park J, Williams D, Konkankit V, Nathanson D, van Dam RM, Phelps ME, Wu H, Liau LM, Mischel PS, Lazareff JA, Kornblum HI, Yong WH, Graeber TG, Tseng HR | Cancer research | 20631065 | Cancer Res | 2010 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/20631065 |
| Stem cell-based gene therapy activated using magnetic hyperthermia to enhance the treatment of cancer. | Yin PT, Shah S, Pasquale NJ, Garbuzenko OB, Minko T, Lee KB | Biomaterials | 26720500 | Biomaterials | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26720500 |
| Controlling differentiation of adipose-derived stem cells using combinatorial graphene hybrid-pattern arrays. | Kim TH, Shah S, Yang L, Yin PT, Hossain MK, Conley B, Choi JW, Lee KB | ACS nano | 25840606 | ACS Nano | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25840606 |
| Engineering Stem Cells for Biomedical Applications. | Yin PT, Han E, Lee KB | Advanced healthcare materials | 25772134 | Adv Healthc Mater | 2016 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/25772134 |
| An upconversion nanoparticle with orthogonal emissions using dual NIR excitations for controlled two-way photoswitching. | Lai J, Zhang Y, Pasquale N, Lee KB | Angewandte Chemie (International ed. in English) | 25349100 | Angew Chem Int Ed Engl | 2014 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/25349100 |
| A step closer to complete chemical reprogramming for generating iPS cells. | Solanki A, Lee KB | Chembiochem : a European journal of chemical biology | 20183843 | Chembiochem | 2010 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/20183843 |
| Multimodal magnetic core-shell nanoparticles for effective stem-cell differentiation and imaging. | Shah B, Yin PT, Ghoshal S, Lee KB | Angewandte Chemie (International ed. in English) | 23650180 | Angew Chem Int Ed Engl | 2013 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/23650180 |
| Versatile fluorescence resonance energy transfer-based mesoporous silica nanoparticles for real-time monitoring of drug release. | Lai J, Shah BP, Garfunkel E, Lee KB | ACS nano | 23445171 | ACS Nano | 2013 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/23445171 |
| Hybrid upconversion nanomaterials for optogenetic neuronal control. | Shah S, Liu JJ, Pasquale N, Lai J, McGowan H, Pang ZP, Lee KB | Nanoscale | 26415758 | Nanoscale | 2015 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/26415758 |
| Large-Scale Nanoelectrode Arrays to Monitor the Dopaminergic Differentiation of Human Neural Stem Cells. | Kim TH, Yea CH, Chueng ST, Yin PT, Conley B, Dardir K, Pak Y, Jung GY, Choi JW, Lee KB | Advanced materials (Deerfield Beach, Fla.) | 26390254 | Adv Mater | 2015 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/26390254 |
| Incorporation of functionalized gold nanoparticles into nanofibers for enhanced attachment and differentiation of mammalian cells. | Jung D, Minami I, Patel S, Lee J, Jiang B, Yuan Q, Li L, Kobayashi S, Chen Y, Lee KB, Nakatsuji N | Journal of nanobiotechnology | 22686683 | J Nanobiotechnology | 2012 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/22686683 |
| Generation of a library of non-toxic quantum dots for cellular imaging and siRNA delivery. | Subramaniam P, Lee SJ, Shah S, Patel S, Starovoytov V, Lee KB | Advanced materials (Deerfield Beach, Fla.) | 22744954 | Adv Mater | 2012 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/22744954 |
| Combined magnetic nanoparticle-based microRNA and hyperthermia therapy to enhance apoptosis in brain cancer cells. | Yin PT, Shah BP, Lee KB | Small (Weinheim an der Bergstrasse, Germany) | 24947843 | Small | 2014 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/24947843 |
| Core-shell nanoparticle-based peptide therapeutics and combined hyperthermia for enhanced cancer cell apoptosis. | Shah BP, Pasquale N, De G, Tan T, Ma J, Lee KB | ACS nano | 25133971 | ACS Nano | 2014 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/25133971 |
| Graphene-encapsulated nanoparticle-based biosensor for the selective detection of cancer biomarkers. | Myung S, Solanki A, Kim C, Park J, Kim KS, Lee KB | Advanced materials (Deerfield Beach, Fla.) | 21469221 | Adv Mater | 2011 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/21469221 |
| Synergistic induction of apoptosis in brain cancer cells by targeted codelivery of siRNA and anticancer drugs. | Kim C, Shah BP, Subramaniam P, Lee KB | Molecular pharmaceutics | 21793576 | Mol Pharm | 2011 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/21793576 |
| Guiding stem cell differentiation into oligodendrocytes using graphene-nanofiber hybrid scaffolds. | Shah S, Yin PT, Uehara TM, Chueng ST, Yang L, Lee KB | Advanced materials (Deerfield Beach, Fla.) | 24668911 | Adv Mater | 2014 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/24668911 |
| Label-free polypeptide-based enzyme detection using a graphene-nanoparticle hybrid sensor. | Myung S, Yin PT, Kim C, Park J, Solanki A, Reyes PI, Lu Y, Kim KS, Lee KB | Advanced materials (Deerfield Beach, Fla.) | 22961629 | Adv Mater | 2012 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/22961629 |
| Polarization-controlled differentiation of human neural stem cells using synergistic cues from the patterns of carbon nanotube monolayer coating. | Park SY, Choi DS, Jin HJ, Park J, Byun KE, Lee KB, Hong S | ACS nano | 21568294 | ACS Nano | 2011 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/21568294 |
| Carbon nanotube monolayer cues for osteogenesis of mesenchymal stem cells. | Baik KY, Park SY, Heo K, Lee KB, Hong S | Small (Weinheim an der Bergstrasse, Germany) | 21425459 | Small | 2011 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/21425459 |
| Microfluidic image cytometry for quantitative single-cell profiling of human pluripotent stem cells in chemically defined conditions. | Kamei K, Ohashi M, Gschweng E, Ho Q, Suh J, Tang J, For Yu ZT, Clark AT, Pyle AD, Teitell MA, Lee KB, Witte ON, Tseng HR | Lab on a chip | 20390128 | Lab Chip | 2010 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/20390128 |
| Design, synthesis, and characterization of graphene-nanoparticle hybrid materials for bioapplications. | Yin PT, Shah S, Chhowalla M, Lee KB | Chemical reviews | 25692385 | Chem Rev | 2015 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/25692385 |
| Nanotechnology-Based Approaches for Guiding Neural Regeneration. | Shah S, Solanki A, Lee KB | Accounts of chemical research | 26653885 | Acc Chem Res | 2016 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/26653885 |
| 3D graphene oxide-encapsulated gold nanoparticles to detect neural stem cell differentiation. | Kim TH, Lee KB, Choi JW | Biomaterials | 23937915 | Biomaterials | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23937915 |
| Multidimensional nanomaterials for the control of stem cell fate. | Chueng SD, Yang L, Zhang Y, Lee KB | Nano convergence | 28191433 | Nano Converg | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28191433 |
| Advanced Gene Manipulation Methods for Stem Cell Theranostics. | Rathnam C, Chueng SD, Yang L, Lee KB | Theranostics | 28824715 | Theranostics | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28824715 |
| Development of Photoactivated Fluorescent N-Hydroxyoxindoles and Their Application for Cell-Selective Imaging. | Lai J, Yu A, Yang L, Zhang Y, Shah BP, Lee KB | Chemistry (Weinheim an der Bergstrasse, Germany) | 27004772 | Chemistry | 2016 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/27004772 |
| NanoScript: a nanoparticle-based artificial transcription factor for effective gene regulation. | Patel S, Jung D, Yin PT, Carlton P, Yamamoto M, Bando T, Sugiyama H, Lee KB | ACS nano | 25133310 | ACS Nano | 2014 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/25133310 |
| Selective inhibition of human brain tumor cells through multifunctional quantum-dot-based siRNA delivery. | Jung J, Solanki A, Memoli KA, Kamei K, Kim H, Drahl MA, Williams LJ, Tseng HR, Lee K | Angewandte Chemie (International ed. in English) | 19950159 | Angew Chem Int Ed Engl | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/19950159 |
| Thickness dependence of the MoO(3) blocking layers on ZnO nanorod-inverted organic photovoltaic devices. | Wang M, Li Y, Huang H, Peterson ED, Nie W, Zhou W, Zeng W, Huang W, Fang G, Sun N, Zhao X, Carroll DL | Applied physics letters | 21464889 | Appl Phys Lett | 2011 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/21464889 |
| Controlling differentiation of neural stem cells using extracellular matrix protein patterns. | Solanki A, Shah S, Memoli KA, Park SY, Hong S, Lee KB | Small (Weinheim an der Bergstrasse, Germany) | 20859950 | Small | 2010 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/20859950 |
| Graphite-coated magnetic nanoparticles as multimodal imaging probes and cooperative therapeutic agents for tumor cells. | Park JK, Jung J, Subramaniam P, Shah BP, Kim C, Lee JK, Cho JH, Lee C, Lee KB | Small (Weinheim an der Bergstrasse, Germany) | 21560243 | Small | 2011 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/21560243 |
| Single vehicular delivery of siRNA and small molecules to control stem cell differentiation. | Shah S, Solanki A, Sasmal PK, Lee KB | Journal of the American Chemical Society | 24106916 | J Am Chem Soc | 2013 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/24106916 |
| Real-Time Monitoring of ATP-Responsive Drug Release Using Mesoporous-Silica-Coated Multicolor Upconversion Nanoparticles. | Lai J, Shah BP, Zhang Y, Yang L, Lee KB | ACS nano | 25859611 | ACS Nano | 2015 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/25859611 |
| Probing stem cell behavior using nanoparticle-based approaches. | Patel S, Lee KB | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 25903468 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2015 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/25903468 |
| Integrating epigenetic modulators into NanoScript for enhanced chondrogenesis of stem cells. | Patel S, Pongkulapa T, Yin PT, Pandian GN, Rathnam C, Bando T, Vaijayanthi T, Sugiyama H, Lee KB | Journal of the American Chemical Society | 25789886 | J Am Chem Soc | 2015 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/25789886 |
| Inducing Stem Cell Myogenesis Using NanoScript. | Patel S, Yin PT, Sugiyama H, Lee KB | ACS nano | 26108385 | ACS Nano | 2015 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/26108385 |
| Photo-triggerable Hydrogel-Nanoparticle Hybrid Scaffolds for Remotely Controlled Drug Delivery. | Shah S, Sasmal PK, Lee KB | Journal of materials chemistry. B | 25580246 | J Mater Chem B | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25580246 |
| Toward unmasking the dynamics of visual perception. | Singer J, Kreiman G | Neuron | 19945387 | Neuron | 2009 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/19945387 |
| Widespread transcription at neuronal activity-regulated enhancers. | Kim TK, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S, Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME | Nature | 20393465 | Nature | 2010 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/20393465 |
| Can Deep Learning Recognize Subtle Human Activities? | Jacquot V, Ying Z, Kreiman G | Conference on Computer Vision and Pattern Recognition Workshops. IEEE Computer Society Conference on Computer Vision and Pattern Recognition. Workshops | 34290902 | Conf Comput Vis Pattern Recognit Workshops | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34290902 |
| Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites. | Hemberg M, Gray JM, Cloonan N, Kuersten S, Grimmond S, Greenberg ME, Kreiman G | Nucleic acids research | 22684627 | Nucleic Acids Res | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22684627 |
| Robust selectivity to two-object images in human visual cortex. | Agam Y, Liu H, Papanastassiou A, Buia C, Golby AJ, Madsen JR, Kreiman G | Current biology : CB | 20417105 | Curr Biol | 2010 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/20417105 |
| Timing, timing, timing: fast decoding of object information from intracranial field potentials in human visual cortex. | Liu H, Agam Y, Madsen JR, Kreiman G | Neuron | 19409272 | Neuron | 2009 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/19409272 |
| Spatiotemporal dynamics underlying object completion in human ventral visual cortex. | Tang H, Buia C, Madhavan R, Crone NE, Madsen JR, Anderson WS, Kreiman G | Neuron | 25043420 | Neuron | 2014 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/25043420 |
| Neuroscience: what we cannot model, we do not understand. | Anderson WS, Kreiman G | Current biology : CB | 21300278 | Curr Biol | 2011 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/21300278 |
| Internally generated preactivation of single neurons in human medial frontal cortex predicts volition. | Fried I, Mukamel R, Kreiman G | Neuron | 21315264 | Neuron | 2011 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/21315264 |
| Measuring sparseness in the brain: comment on Bowers (2009). | Quian Quiroga R, Kreiman G | Psychological review | 20063978 | Psychol Rev | 2010 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20063978 |
| From neurons to circuits: linear estimation of local field potentials. | Rasch M, Logothetis NK, Kreiman G | The Journal of neuroscience : the official journal of the Society for Neuroscience | 19889990 | J Neurosci | 2009 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/19889990 |
| Cascade of neural processing orchestrates cognitive control in human frontal cortex. | Tang H, Yu HY, Chou CC, Crone NE, Madsen JR, Anderson WS, Kreiman G | eLife | 26888070 | Elife | 2016 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/26888070 |
| Face recognition: vision and emotions beyond the bubble. | Tang H, Kreiman G | Current biology : CB | 22075428 | Curr Biol | 2011 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/22075428 |
| Theory on the coupled stochastic dynamics of transcription and splice-site recognition. | Murugan R, Kreiman G | PLoS computational biology | 23133354 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23133354 |
| Short temporal asynchrony disrupts visual object recognition. | Singer JM, Kreiman G | Journal of vision | 24819738 | J Vis | 2014 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/24819738 |
| How cortical neurons help us see: visual recognition in the human brain. | Blumberg J, Kreiman G | The Journal of clinical investigation | 20811161 | J Clin Invest | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20811161 |
| Genome-wide activity-dependent MeCP2 phosphorylation regulates nervous system development and function. | Cohen S, Gabel HW, Hemberg M, Hutchinson AN, Sadacca LA, Ebert DH, Harmin DA, Greenberg RS, Verdine VK, Zhou Z, Wetsel WC, West AE, Greenberg ME | Neuron | 21982370 | Neuron | 2011 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/21982370 |
| Mesoscopic physiological interactions in the human brain reveal small-world properties. | Wang J, Tao A, Anderson WS, Madsen JR, Kreiman G | Cell reports | 34433053 | Cell Rep | 2021 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/34433053 |
| Mechanical derivation of functional myotubes from adipose-derived stem cells. | Choi YS, Vincent LG, Lee AR, Dobke MK, Engler AJ | Biomaterials | 22197570 | Biomaterials | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22197570 |
| In situ mechanical analysis of myofibrillar perturbation and aging on soft, bilayered Drosophila myocardium. | Kaushik G, Fuhrmann A, Cammarato A, Engler AJ | Biophysical journal | 22261050 | Biophys J | 2011 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/22261050 |
| Nanoscopic mechanical anisotropy in hydrogel surfaces. | Flores-Merino MV, Chirasatitsin S, Lopresti C, Reilly GC, Battaglia G, Engler AJ | Soft matter | 20953281 | Soft Matter | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/20953281 |
| Stimulation of adipogenesis of adult adipose-derived stem cells using substrates that mimic the stiffness of adipose tissue. | Young DA, Choi YS, Engler AJ, Christman KL | Biomaterials | 23953825 | Biomaterials | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23953825 |
| Cation type specific cell remodeling regulates attachment strength. | Fuhrmann A, Li J, Chien S, Engler AJ | PloS one | 25014042 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25014042 |
| Digital Plasmonic Patterning for Localized Tuning of Hydrogel Stiffness. | Hribar KC, Choi YS, Ondeck M, Engler AJ, Chen S | Advanced functional materials | 26120293 | Adv Funct Mater | 2014 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26120293 |
| Rotator cuff tear state modulates self-renewal and differentiation capacity of human skeletal muscle progenitor cells. | Thomas KA, Gibbons MC, Lane JG, Singh A, Ward SR, Engler AJ | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 27699827 | J Orthop Res | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27699827 |
| High content image analysis of focal adhesion-dependent mechanosensitive stem cell differentiation. | Holle AW, McIntyre AJ, Kehe J, Wijesekara P, Young JL, Vincent LG, Engler AJ | Integrative biology : quantitative biosciences from nano to macro | 27723854 | Integr Biol (Camb) | 2016 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/27723854 |
| Mesenchymal stem cell durotaxis depends on substrate stiffness gradient strength. | Vincent LG, Choi YS, Alonso-Latorre B, del Álamo JC, Engler AJ | Biotechnology journal | 23390141 | Biotechnol J | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23390141 |
| Traction forces mediated by integrin signaling are necessary for definitive endoderm specification. | Taylor-Weiner H, Ravi N, Engler AJ | Journal of cell science | 25908864 | J Cell Sci | 2015 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/25908864 |
| 3D surface topology guides stem cell adhesion and differentiation. | Viswanathan P, Ondeck MG, Chirasatitsin S, Ngamkham K, Reilly GC, Engler AJ, Battaglia G | Biomaterials | 25818420 | Biomaterials | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25818420 |
| Haptotaxis is cell type specific and limited by substrate adhesiveness. | Wen JH, Choi O, Taylor-Weiner H, Fuhrmann A, Karpiak JV, Almutairi A, Engler AJ | Cellular and molecular bioengineering | 26640598 | Cell Mol Bioeng | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26640598 |
| Extracellular matrix regulation in the muscle satellite cell niche. | Thomas K, Engler AJ, Meyer GA | Connective tissue research | 25047058 | Connect Tissue Res | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25047058 |
| Wet nanoscale imaging and testing of polymersomes. | Battaglia G, LoPresti C, Massignani M, Warren NJ, Madsen J, Forster S, Vasilev C, Hobbs JK, Armes SP, Chirasatitsin S, Engler AJ | Small (Weinheim an der Bergstrasse, Germany) | 21695783 | Small | 2011 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/21695783 |
| Extracellular matrix downregulation in the Drosophila heart preserves contractile function and improves lifespan. | Sessions AO, Kaushik G, Parker S, Raedschelders K, Bodmer R, Van Eyk JE, Engler AJ | Matrix biology : journal of the International Society for Matrix Biology | 27793636 | Matrix Biol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27793636 |
| Mechanically patterned neuromuscular junctions-in-a-dish have improved functional maturation. | Happe CL, Tenerelli KP, Gromova AK, Kolb F, Engler AJ | Molecular biology of the cell | 28495800 | Mol Biol Cell | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28495800 |
| Stiffness gradients mimicking in vivo tissue variation regulate mesenchymal stem cell fate. | Tse JR, Engler AJ | PloS one | 21246050 | PLoS One | 2011 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/21246050 |
| Acute shear stress direction dictates adherent cell remodeling and verifies shear profile of spinning disk assays. | Fuhrmann A, Engler AJ | Physical biology | 25619322 | Phys Biol | 2015 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/25619322 |
| Vinculin network-mediated cytoskeletal remodeling regulates contractile function in the aging heart. | Kaushik G, Spenlehauer A, Sessions AO, Trujillo AS, Fuhrmann A, Fu Z, Venkatraman V, Pohl D, Tuler J, Wang M, Lakatta EG, Ocorr K, Bodmer R, Bernstein SI, Van Eyk JE, Cammarato A, Engler AJ | Science translational medicine | 26084806 | Sci Transl Med | 2015 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/26084806 |
| A Drosophila melanogaster model of diastolic dysfunction and cardiomyopathy based on impaired troponin-T function. | Viswanathan MC, Kaushik G, Engler AJ, Lehman W, Cammarato A | Circulation research | 24221941 | Circ Res | 2014 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/24221941 |
| In situ mechanotransduction via vinculin regulates stem cell differentiation. | Holle AW, Tang X, Vijayraghavan D, Vincent LG, Fuhrmann A, Choi YS, del Álamo JC, Engler AJ | Stem cells (Dayton, Ohio) | 23897765 | Stem Cells | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23897765 |
| A co-culture device with a tunable stiffness to understand combinatorial cell-cell and cell-matrix interactions. | Rao N, Grover GN, Vincent LG, Evans SC, Choi YS, Spencer KH, Hui EE, Engler AJ, Christman KL | Integrative biology : quantitative biosciences from nano to macro | 24061208 | Integr Biol (Camb) | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24061208 |
| The alignment and fusion assembly of adipose-derived stem cells on mechanically patterned matrices. | Choi YS, Vincent LG, Lee AR, Kretchmer KC, Chirasatitsin S, Dobke MK, Engler AJ | Biomaterials | 22800539 | Biomaterials | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22800539 |
| Cell instructive microporous scaffolds through interface engineering. | Viswanathan P, Chirasatitsin S, Ngamkham K, Engler AJ, Battaglia G | Journal of the American Chemical Society | 23163574 | J Am Chem Soc | 2012 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/23163574 |
| Dynamic and reversible surface topography influences cell morphology. | Kiang JD, Wen JH, del Álamo JC, Engler AJ | Journal of biomedical materials research. Part A | 23355509 | J Biomed Mater Res A | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23355509 |
| The cytoskeleton regulates cell attachment strength. | Fuhrmann A, Engler AJ | Biophysical journal | 26153702 | Biophys J | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26153702 |
| Materials as stem cell regulators. | Murphy WL, McDevitt TC, Engler AJ | Nature materials | 24845994 | Nat Mater | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24845994 |
| Hydrogels with time-dependent material properties enhance cardiomyocyte differentiation in vitro. | Young JL, Engler AJ | Biomaterials | 21071078 | Biomaterials | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21071078 |
| Detecting cell-adhesive sites in extracellular matrix using force spectroscopy mapping. | Chirasatitsin S, Engler AJ | Journal of physics. Condensed matter : an Institute of Physics journal | 21152375 | J Phys Condens Matter | 2010 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/21152375 |
| More than a feeling: discovering, understanding, and influencing mechanosensing pathways. | Holle AW, Engler AJ | Current opinion in biotechnology | 21536426 | Curr Opin Biotechnol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21536426 |
| Effect of platelet-rich plasma on degeneration change of rotator cuff muscles: In vitro and in vivo evaluations. | Takase F, Inui A, Mifune Y, Sakata R, Muto T, Harada Y, Ueda Y, Kokubu T, Kurosaka M | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 27684960 | J Orthop Res | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27684960 |
| Metastatic State of Cancer Cells May Be Indicated by Adhesion Strength. | Fuhrmann A, Banisadr A, Beri P, Tlsty TD, Engler AJ | Biophysical journal | 28256233 | Biophys J | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28256233 |
| Stem cell migration and mechanotransduction on linear stiffness gradient hydrogels. | Hadden WJ, Young JL, Holle AW, McFetridge ML, Kim DY, Wijesinghe P, Taylor-Weiner H, Wen JH, Lee AR, Bieback K, Vo BN, Sampson DD, Kennedy BF, Spatz JP, Engler AJ, Choi YS | Proceedings of the National Academy of Sciences of the United States of America | 28507138 | Proc Natl Acad Sci U S A | 2017 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/28507138 |
| Epimuscular Fat in the Human Rotator Cuff Is a Novel Beige Depot. | Meyer GA, Gibbons MC, Sato E, Lane JG, Ward SR, Engler AJ | Stem cells translational medicine | 25999520 | Stem Cells Transl Med | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25999520 |
| Mechanical Characterization of a Dynamic and Tunable Methacrylated Hyaluronic Acid Hydrogel. | Ondeck MG, Engler AJ | Journal of biomechanical engineering | 26746491 | J Biomech Eng | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26746491 |
| RAP2 mediates mechanoresponses of the Hippo pathway. | Meng Z, Qiu Y, Lin KC, Kumar A, Placone JK, Fang C, Wang KC, Lu S, Pan M, Hong AW, Moroishi T, Luo M, Plouffe SW, Diao Y, Ye Z, Park HW, Wang X, Yu FX, Chien S, Wang CY, Ren B, Engler AJ, Guan KL | Nature | 30135582 | Nature | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30135582 |
| Muscle progenitor cell regenerative capacity in the torn rotator cuff. | Meyer GA, Farris AL, Sato E, Gibbons M, Lane JG, Ward SR, Engler AJ | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 25410765 | J Orthop Res | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25410765 |
| Interplay of matrix stiffness and protein tethering in stem cell differentiation. | Wen JH, Vincent LG, Fuhrmann A, Choi YS, Hribar KC, Taylor-Weiner H, Chen S, Engler AJ | Nature materials | 25108614 | Nat Mater | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25108614 |
| Mechanical regulation of cardiac fibroblast profibrotic phenotypes. | Herum KM, Choppe J, Kumar A, Engler AJ, McCulloch AD | Molecular biology of the cell | 28468977 | Mol Biol Cell | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28468977 |
| An automated compound screening for anti-aging effects on the function of C. elegans sensory neurons. | Bazopoulou D, Chaudhury AR, Pantazis A, Chronis N | Scientific reports | 28839194 | Sci Rep | 2017 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/28839194 |
| A Biochip with a 3D microfluidic architecture for trapping white blood cells. | Tripathi A, Riddell J 4th, Chronis N | Sensors and actuators. B, Chemical | 23935241 | Sens Actuators B Chem | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/23935241 |
| A doublet microlens array for imaging micron-sized objects. | Tripathi A, Chronis N | Journal of micromechanics and microengineering : structures, devices, and systems | 22003271 | J Micromech Microeng | 2011 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22003271 |
| Chemically induced oxidative stress affects ASH neuronal function and behavior in C. elegans. | Gourgou E, Chronis N | Scientific reports | 27922032 | Sci Rep | 2016 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/27922032 |
| Global hormone profiling of murine placenta reveals Secretin expression. | Knox K, Leuenberger D, Penn AA, Baker JC | Placenta | 21944867 | Placenta | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21944867 |
| Sex differences in a hypoxia model of preterm brain damage. | Mayoral SR, Omar G, Penn AA | Pediatric research | 19542909 | Pediatr Res | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19542909 |
| Correlation of preterm infant illness severity with placental histology. | Chisholm KM, Heerema-McKenney A, Tian L, Rajani AK, Saria S, Koller D, Penn AA | Placenta | 26992676 | Placenta | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26992676 |
| Plasma vasopressin concentrations positively predict cerebrospinal fluid vasopressin concentrations in human neonates. | Carson DS, Howerton CL, Garner JP, Hyde SA, Clark CL, Hardan AY, Penn AA, Parker KJ | Peptides | 25148831 | Peptides | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25148831 |
| Integration of early physiological responses predicts later illness severity in preterm infants. | Saria S, Rajani AK, Gould J, Koller D, Penn AA | Science translational medicine | 20826840 | Sci Transl Med | 2010 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/20826840 |
| Controversies in preterm brain injury. | Penn AA, Gressens P, Fleiss B, Back SA, Gallo V | Neurobiology of disease | 26477300 | Neurobiol Dis | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26477300 |
| Neonatal CSF oxytocin levels are associated with parent report of infant soothability and sociability. | Clark CL, St John N, Pasca AM, Hyde SA, Hornbeak K, Abramova M, Feldman H, Parker KJ, Penn AA | Psychoneuroendocrinology | 23507187 | Psychoneuroendocrinology | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23507187 |
| Placental function assessed visually using half-Fourier acquisition single-shot turbo spin-echo (HASTE) magnetic resonance imaging. | Himoto Y, Kido A, Mogami H, Moribata Y, Minamiguchi S, Shitano F, Kiguchi K, Kurata Y, Konishi I, Togashi K | Placenta | 26992675 | Placenta | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26992675 |
| Sex-specific cognitive deficits and regional brain volume loss in mice exposed to chronic, sublethal hypoxia. | Lan WC, Priestley M, Mayoral SR, Tian L, Shamloo M, Penn AA | Pediatric research | 21436761 | Pediatr Res | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21436761 |
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| Drug treatment combined with BCG vaccination reduces disease reactivation in guinea pigs infected with Mycobacterium tuberculosis. | Shang S, Shanley CA, Caraway ML, Orme EA, Henao-Tamayo M, Hascall-Dove L, Ackart D, Orme IM, Ordway DJ, Basaraba RJ | Vaccine | 22244979 | Vaccine | 2012 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/22244979 |
| Differential Mycobacterium bovis BCG vaccine-derived efficacy in C3Heb/FeJ and C3H/HeOuJ mice exposed to a clinical strain of Mycobacterium tuberculosis. | Henao-Tamayo M, Obregón-Henao A, Creissen E, Shanley C, Orme I, Ordway DJ | Clinical and vaccine immunology : CVI | 25392011 | Clin Vaccine Immunol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25392011 |
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| Mycobacterium bovis BCG-mediated protection against W-Beijing strains of Mycobacterium tuberculosis is diminished concomitant with the emergence of regulatory T cells. | Ordway DJ, Shang S, Henao-Tamayo M, Obregon-Henao A, Nold L, Caraway M, Shanley CA, Basaraba RJ, Duncan CG, Orme IM | Clinical and vaccine immunology : CVI | 21795460 | Clin Vaccine Immunol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21795460 |
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| Beijing sublineages of Mycobacterium tuberculosis differ in pathogenicity in the guinea pig. | Kato-Maeda M, Shanley CA, Ackart D, Jarlsberg LG, Shang S, Obregon-Henao A, Harton M, Basaraba RJ, Henao-Tamayo M, Barrozo JC, Rose J, Kawamura LM, Coscolla M, Fofanov VY, Koshinsky H, Gagneux S, Hopewell PC, Ordway DJ, Orme IM | Clinical and vaccine immunology : CVI | 22718126 | Clin Vaccine Immunol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22718126 |
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| Effect of bacillus Calmette-Guérin vaccination on CD4+Foxp3+ T cells during acquired immune response to Mycobacterium tuberculosis infection. | Henao-Tamayo MI, Obregón-Henao A, Arnett K, Shanley CA, Podell B, Orme IM, Ordway DJ | Journal of leukocyte biology | 26590147 | J Leukoc Biol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26590147 |
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| Monitoring cotranslational protein folding in mammalian cells at codon resolution. | Han Y, David A, Liu B, Magadán JG, Bennink JR, Yewdell JW, Qian SB | Proceedings of the National Academy of Sciences of the United States of America | 22802618 | Proc Natl Acad Sci U S A | 2012 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/22802618 |
| Viewing folding of nascent polypeptide chains from ribosomes. | Liu B, Conn CS, Qian SB | Expert review of proteomics | 23256666 | Expert Rev Proteomics | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23256666 |
| Genome-Wide Profiling of Alternative Translation Initiation Sites. | Gao X, Wan J, Qian SB | Methods in molecular biology (Clifton, N.J.) | 26463392 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26463392 |
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| Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. | Lee S, Liu B, Lee S, Huang SX, Shen B, Qian SB | Proceedings of the National Academy of Sciences of the United States of America | 22927429 | Proc Natl Acad Sci U S A | 2012 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/22927429 |
| TISdb: a database for alternative translation initiation in mammalian cells. | Wan J, Qian SB | Nucleic acids research | 24203712 | Nucleic Acids Res | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24203712 |
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| Nutrient signaling in protein homeostasis: an increase in quantity at the expense of quality. | Conn CS, Qian SB | Science signaling | 23592839 | Sci Signal | 2013 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/23592839 |
| Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation. | Han Y, Gao X, Liu B, Wan J, Zhang X, Qian SB | Cell research | 24903108 | Cell Res | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24903108 |
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| Structure and Dimerization of IreB, a Negative Regulator of Cephalosporin Resistance in Enterococcus faecalis. | Hall CL, Lytle BL, Jensen D, Hoff JS, Peterson FC, Volkman BF, Kristich CJ | Journal of molecular biology | 28551334 | J Mol Biol | 2017 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/28551334 |
| Modulators of Enterococcus faecalis Cell Envelope Integrity and Antimicrobial Resistance Influence Stable Colonization of the Mammalian Gastrointestinal Tract. | Banla IL, Kommineni S, Hayward M, Rodrigues M, Palmer KL, Salzman NH, Kristich CJ | Infection and immunity | 29038125 | Infect Immun | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29038125 |
| Ceftriaxone Administration Disrupts Intestinal Homeostasis, Mediating Noninflammatory Proliferation and Dissemination of Commensal Enterococci. | Chakraborty R, Lam V, Kommineni S, Stromich J, Hayward M, Kristich CJ, Salzman NH | Infection and immunity | 30224553 | Infect Immun | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30224553 |
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| Convergence of PASTA Kinase and Two-Component Signaling in Response to Cell Wall Stress in Enterococcus faecalis. | Kellogg SL, Kristich CJ | Journal of bacteriology | 29632091 | J Bacteriol | 2018 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/29632091 |
| Growth- and Stress-Induced PASTA Kinase Phosphorylation in Enterococcus faecalis. | Labbe BD, Kristich CJ | Journal of bacteriology | 28808126 | J Bacteriol | 2017 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/28808126 |
| Functional Dissection of the CroRS Two-Component System Required for Resistance to Cell Wall Stressors in Enterococcus faecalis. | Kellogg SL, Kristich CJ | Journal of bacteriology | 26883822 | J Bacteriol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26883822 |
| Nutritional control of antibiotic resistance via an interface between the phosphotransferase system and a two-component signaling system. | Snyder H, Kellogg SL, Skarda LM, Little JL, Kristich CJ | Antimicrobial agents and chemotherapy | 24277024 | Antimicrob Agents Chemother | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24277024 |
| Genetic basis for vancomycin-enhanced cephalosporin susceptibility in vancomycin-resistant enterococci revealed using counterselection with dominant-negative thymidylate synthase. | Kristich CJ, Djorić D, Little JL | Antimicrobial agents and chemotherapy | 24366749 | Antimicrob Agents Chemother | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24366749 |
| Bacteriocin production augments niche competition by enterococci in the mammalian gastrointestinal tract. | Kommineni S, Bretl DJ, Lam V, Chakraborty R, Hayward M, Simpson P, Cao Y, Bousounis P, Kristich CJ, Salzman NH | Nature | 26479034 | Nature | 2015 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/26479034 |
| Requirement of the CroRS Two-Component System for Resistance to Cell Wall-Targeting Antimicrobials in Enterococcus faecium. | Kellogg SL, Little JL, Hoff JS, Kristich CJ | Antimicrobial agents and chemotherapy | 28223383 | Antimicrob Agents Chemother | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28223383 |
| Functional Characterization of the Basal Amygdala-Dorsal BNST Pathway during Contextual Fear Conditioning. | Sasaki Russell J, Trouche S, Reijmers LG | eNeuro | 32601096 | eNeuro | 2020 Jul/Aug | https://www.ncbi.nlm.nih.gov/pubmed/32601096 |
| A transgenic mouse line for collecting ribosome-bound mRNA using the tetracycline transactivator system. | Drane L, Ainsley JA, Mayford MR, Reijmers LG | Frontiers in molecular neuroscience | 25400545 | Front Mol Neurosci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25400545 |
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| Translational profiling of clock cells reveals circadianly synchronized protein synthesis. | Huang Y, Ainsley JA, Reijmers LG, Jackson FR | PLoS biology | 24348200 | PLoS Biol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24348200 |
| A retrograde adeno-associated virus for collecting ribosome-bound mRNA from anatomically defined projection neurons. | Cook-Snyder DR, Jones A, Reijmers LG | Frontiers in molecular neuroscience | 26557053 | Front Mol Neurosci | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26557053 |
| Natural amyloid-β oligomers acutely impair the formation of a contextual fear memory in mice. | Kittelberger KA, Piazza F, Tesco G, Reijmers LG | PloS one | 22238679 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22238679 |
| Fear extinction causes target-specific remodeling of perisomatic inhibitory synapses. | Trouche S, Sasaki JM, Tu T, Reijmers LG | Neuron | 24183705 | Neuron | 2013 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/24183705 |
| Essential gene pathways for glioblastoma stem cells: clinical implications for prevention of tumor recurrence. | Yamada K, Tso J, Ye F, Choe J, Liu Y, Liau LM, Tso CL | Cancers | 24212792 | Cancers (Basel) | 2011 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/24212792 |
| Protective properties of radio-chemoresistant glioblastoma stem cell clones are associated with metabolic adaptation to reduced glucose dependence. | Ye F, Zhang Y, Liu Y, Yamada K, Tso JL, Menjivar JC, Tian JY, Yong WH, Schaue D, Mischel PS, Cloughesy TF, Nelson SF, Liau LM, McBride W, Tso CL | PloS one | 24260384 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24260384 |
| Autocrine endothelin-3/endothelin receptor B signaling maintains cellular and molecular properties of glioblastoma stem cells. | Liu Y, Ye F, Yamada K, Tso JL, Zhang Y, Nguyen DH, Dong Q, Soto H, Choe J, Dembo A, Wheeler H, Eskin A, Schmid I, Yong WH, Mischel PS, Cloughesy TF, Kornblum HI, Nelson SF, Liau LM, Tso CL | Molecular cancer research : MCR | 22013079 | Mol Cancer Res | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22013079 |
| Bone morphogenetic protein 7 sensitizes O6-methylguanine methyltransferase expressing-glioblastoma stem cells to clinically relevant dose of temozolomide. | Tso JL, Yang S, Menjivar JC, Yamada K, Zhang Y, Hong I, Bui Y, Stream A, McBride WH, Liau LM, Nelson SF, Cloughesy TF, Yong WH, Lai A, Tso CL | Molecular cancer | 26546412 | Mol Cancer | 2015 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/26546412 |
| Ribosomal Proteins RPS11 and RPS20, Two Stress-Response Markers of Glioblastoma Stem Cells, Are Novel Predictors of Poor Prognosis in Glioblastoma Patients. | Yong WH, Shabihkhani M, Telesca D, Yang S, Tso JL, Menjivar JC, Wei B, Lucey GM, Mareninov S, Chen Z, Liau LM, Lai A, Nelson SF, Cloughesy TF, Tso CL | PloS one | 26506620 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26506620 |
| Compact, light-weight and cost-effective microscope based on lensless incoherent holography for telemedicine applications. | Mudanyali O, Tseng D, Oh C, Isikman SO, Sencan I, Bishara W, Oztoprak C, Seo S, Khademhosseini B, Ozcan A | Lab on a chip | 20401422 | Lab Chip | 2010 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/20401422 |
| Lensfree microscopy on a cellphone. | Tseng D, Mudanyali O, Oztoprak C, Isikman SO, Sencan I, Yaglidere O, Ozcan A | Lab on a chip | 20445943 | Lab Chip | 2010 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/20445943 |
| High-throughput lens-free blood analysis on a chip. | Seo S, Isikman SO, Sencan I, Mudanyali O, Su TW, Bishara W, Erlinger A, Ozcan A | Analytical chemistry | 20450181 | Anal Chem | 2010 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/20450181 |
| On-chip differential interference contrast microscopy using lensless digital holography. | Oh C, Isikman SO, Khademhosseinieh B, Ozcan A | Optics express | 20389485 | Opt Express | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/20389485 |
| Lens-free optical tomographic microscope with a large imaging volume on a chip. | Isikman SO, Bishara W, Mavandadi S, Yu FW, Feng S, Lau R, Ozcan A | Proceedings of the National Academy of Sciences of the United States of America | 21504943 | Proc Natl Acad Sci U S A | 2011 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/21504943 |
| Combined reflection and transmission microscope for telemedicine applications in field settings. | Biener G, Greenbaum A, Isikman SO, Lee K, Tseng D, Ozcan A | Lab on a chip | 21709875 | Lab Chip | 2011 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/21709875 |
| Lensless fluorescent microscopy on a chip. | Coskun AF, Su TW, Sencan I, Ozcan A | Journal of visualized experiments : JoVE | 21876522 | J Vis Exp | 2011 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/21876522 |
| Partially coherent lensfree tomographic microscopy [Invited]. | Isikman SO, Bishara W, Ozcan A | Applied optics | 22193016 | Appl Opt | 2011 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/22193016 |
| Optofluidic Tomography on a Chip. | Isikman SO, Bishara W, Zhu H, Ozcan A | Applied physics letters | 21580801 | Appl Phys Lett | 2011 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/21580801 |
| Portable and cost-effective pixel super-resolution on-chip microscope for telemedicine applications. | Bishara W, Sikora U, Mudanyali O, Su TW, Yaglidere O, Luckhart S, Ozcan A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22256247 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22256247 |
| Holographic opto-fluidic microscopy. | Bishara W, Zhu H, Ozcan A | Optics express | 21197025 | Opt Express | 2010 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/21197025 |
| Lensfree fluorescent on-chip imaging of transgenic Caenorhabditis elegans over an ultra-wide field-of-view. | Coskun AF, Sencan I, Su TW, Ozcan A | PloS one | 21253611 | PLoS One | 2011 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/21253611 |
| Quantification of plant chlorophyll content using Google Glass. | Cortazar B, Koydemir HC, Tseng D, Feng S, Ozcan A | Lab on a chip | 25669673 | Lab Chip | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25669673 |
| High-throughput and label-free single nanoparticle sizing based on time-resolved on-chip microscopy. | McLeod E, Dincer TU, Veli M, Ertas YN, Nguyen C, Luo W, Greenbaum A, Feizi A, Ozcan A | ACS nano | 25688665 | ACS Nano | 2015 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/25688665 |
| Wide-field computational color imaging using pixel super-resolved on-chip microscopy. | Greenbaum A, Feizi A, Akbari N, Ozcan A | Optics express | 23736466 | Opt Express | 2013 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/23736466 |
| Smart-phone based computational microscopy using multi-frame contact imaging on a fiber-optic array. | Navruz I, Coskun AF, Wong J, Mohammad S, Tseng D, Nagi R, Phillips S, Ozcan A | Lab on a chip | 23939637 | Lab Chip | 2013 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/23939637 |
| High-throughput lensfree 3D tracking of human sperms reveals rare statistics of helical trajectories. | Su TW, Xue L, Ozcan A | Proceedings of the National Academy of Sciences of the United States of America | 22988076 | Proc Natl Acad Sci U S A | 2012 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/22988076 |
| Imaging without lenses: achievements and remaining challenges of wide-field on-chip microscopy. | Greenbaum A, Luo W, Su TW, Göröcs Z, Xue L, Isikman SO, Coskun AF, Mudanyali O, Ozcan A | Nature methods | 22936170 | Nat Methods | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22936170 |
| Giga-pixel lensfree holographic microscopy and tomography using color image sensors. | Isikman SO, Greenbaum A, Luo W, Coskun AF, Ozcan A | PloS one | 22984606 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22984606 |
| Lensfree optofluidic plasmonic sensor for real-time and label-free monitoring of molecular binding events over a wide field-of-view. | Coskun AF, Cetin AE, Galarreta BC, Alvarez DA, Altug H, Ozcan A | Scientific reports | 25346102 | Sci Rep | 2014 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/25346102 |
| Biomedical imaging and sensing using flatbed scanners. | Göröcs Z, Ozcan A | Lab on a chip | 24965011 | Lab Chip | 2014 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/24965011 |
| Lensfree On-Chip Microscopy and Tomography for Bio-Medical Applications. | Isikman SO, Bishara W, Mudanyali O, Sencan I, Su TW, Tseng D, Yaglidere O, Sikora U, Ozcan A | IEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society | 24478572 | IEEE J Sel Top Quantum Electron | 2011 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/24478572 |
| Analysis of Diffractive Optical Neural Networks and Their Integration with Electronic Neural Networks. | Mengu D, Luo Y, Rivenson Y, Ozcan A | IEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society | 33223801 | IEEE J Sel Top Quantum Electron | 2020 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/33223801 |
| Nanofabrication using near-field optical probes. | McLeod E, Ozcan A | Journal of laboratory automation | 22713756 | J Lab Autom | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22713756 |
| Lensfree holographic imaging of antibody microarrays for high-throughput detection of leukocyte numbers and function. | Stybayeva G, Mudanyali O, Seo S, Silangcruz J, Macal M, Ramanculov E, Dandekar S, Erlinger A, Ozcan A, Revzin A | Analytical chemistry | 20359168 | Anal Chem | 2010 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/20359168 |
| Giga-pixel fluorescent imaging over an ultra-large field-of-view using a flatbed scanner. | Göröcs Z, Ling Y, Yu MD, Karahalios D, Mogharabi K, Lu K, Wei Q, Ozcan A | Lab on a chip | 24080766 | Lab Chip | 2013 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/24080766 |
| Field-portable pixel super-resolution colour microscope. | Greenbaum A, Akbari N, Feizi A, Luo W, Ozcan A | PloS one | 24086742 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24086742 |
| On-chip cytometry using plasmonic nanoparticle enhanced lensfree holography. | Wei Q, McLeod E, Qi H, Wan Z, Sun R, Ozcan A | Scientific reports | 23608952 | Sci Rep | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23608952 |
| Wide-field optical detection of nanoparticles using on-chip microscopy and self-assembled nanolenses. | Mudanyali O, McLeod E, Luo W, Greenbaum A, Coskun AF, Hennequin Y, Allier CP, Ozcan A | Nature photonics | 24358054 | Nat Photonics | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24358054 |
| Computational imaging, sensing and diagnostics for global health applications. | Coskun AF, Ozcan A | Current opinion in biotechnology | 24484875 | Curr Opin Biotechnol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24484875 |
| Albumin testing in urine using a smart-phone. | Coskun AF, Nagi R, Sadeghi K, Phillips S, Ozcan A | Lab on a chip | 23995895 | Lab Chip | 2013 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/23995895 |
| Lensfree computational microscopy tools for cell and tissue imaging at the point-of-care and in low-resource settings. | Isikman SO, Greenbaum A, Lee M, Bishara W, Mudanyali O, Su TW, Ozcan A | Analytical cellular pathology (Amsterdam) | 22433451 | Anal Cell Pathol (Amst) | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22433451 |
| Maskless imaging of dense samples using pixel super-resolution based multi-height lensfree on-chip microscopy. | Greenbaum A, Ozcan A | Optics express | 22330550 | Opt Express | 2012 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/22330550 |
| Sperm trajectories form chiral ribbons. | Su TW, Choi I, Feng J, Huang K, McLeod E, Ozcan A | Scientific reports | 23588811 | Sci Rep | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23588811 |
| Cost-effective and rapid blood analysis on a cell-phone. | Zhu H, Sencan I, Wong J, Dimitrov S, Tseng D, Nagashima K, Ozcan A | Lab on a chip | 23392286 | Lab Chip | 2013 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/23392286 |
| Flexible Plasmonic Sensors. | Shir D, Ballard ZS, Ozcan A | IEEE journal of selected topics in quantum electronics : a publication of the IEEE Lasers and Electro-optics Society | 27547023 | IEEE J Sel Top Quantum Electron | 2016 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/27547023 |
| Democratization of Nanoscale Imaging and Sensing Tools Using Photonics. | McLeod E, Wei Q, Ozcan A | Analytical chemistry | 26068279 | Anal Chem | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26068279 |
| Tunable vapor-condensed nanolenses. | McLeod E, Nguyen C, Huang P, Luo W, Veli M, Ozcan A | ACS nano | 24979060 | ACS Nano | 2014 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/24979060 |
| Automated single-cell motility analysis on a chip using lensfree microscopy. | Pushkarsky I, Liu Y, Weaver W, Su TW, Mudanyali O, Ozcan A, Di Carlo D | Scientific reports | 24739819 | Sci Rep | 2014 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/24739819 |
| Crowd-sourced BioGames: managing the big data problem for next-generation lab-on-a-chip platforms. | Mavandadi S, Dimitrov S, Feng S, Yu F, Yu R, Sikora U, Ozcan A | Lab on a chip | 22918378 | Lab Chip | 2012 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/22918378 |
| On-chip biomedical imaging. | Göröcs Z, Ozcan A | IEEE reviews in biomedical engineering | 23558399 | IEEE Rev Biomed Eng | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23558399 |
| Wide field-of-view lens-free fluorescent imaging on a chip. | Coskun AF, Su TW, Ozcan A | Lab on a chip | 20379564 | Lab Chip | 2010 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/20379564 |
| Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy. | Su TW, Erlinger A, Tseng D, Ozcan A | Analytical chemistry | 20836503 | Anal Chem | 2010 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/20836503 |
| Smart technology for global access to healthcare. | Ozcan A | SPIE newsroom | 20582244 | SPIE Newsroom | 2010 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/20582244 |
| Multi-angle lensless digital holography for depth resolved imaging on a chip. | Su TW, Isikman SO, Bishara W, Tseng D, Erlinger A, Ozcan A | Optics express | 20588819 | Opt Express | 2010 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/20588819 |
| Lensless wide-field fluorescent imaging on a chip using compressive decoding of sparse objects. | Coskun AF, Sencan I, Su TW, Ozcan A | Optics express | 20588904 | Opt Express | 2010 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/20588904 |
| Lensfree on-chip microscopy over a wide field-of-view using pixel super-resolution. | Bishara W, Su TW, Coskun AF, Ozcan A | Optics express | 20588977 | Opt Express | 2010 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/20588977 |
| Optofluidic on-chip tomography. | Isikman SO, Bishara W, Zhu H, Ozcan A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22256312 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22256312 |
| Toward giga-pixel nanoscopy on a chip: a computational wide-field look at the nano-scale without the use of lenses. | McLeod E, Luo W, Mudanyali O, Greenbaum A, Ozcan A | Lab on a chip | 23592185 | Lab Chip | 2013 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/23592185 |
| Wide-field fluorescent microscopy on a cell-phone. | Zhu H, Yaglidere O, Su TW, Tseng D, Ozcan A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255900 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255900 |
| Optical detection and sizing of single nanoparticles using continuous wetting films. | Hennequin Y, Allier CP, McLeod E, Mudanyali O, Migliozzi D, Ozcan A, Dinten JM | ACS nano | 23889001 | ACS Nano | 2013 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/23889001 |
| Integrated rapid-diagnostic-test reader platform on a cellphone. | Mudanyali O, Dimitrov S, Sikora U, Padmanabhan S, Navruz I, Ozcan A | Lab on a chip | 22596243 | Lab Chip | 2012 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/22596243 |
| A personalized food allergen testing platform on a cellphone. | Coskun AF, Wong J, Khodadadi D, Nagi R, Tey A, Ozcan A | Lab on a chip | 23254910 | Lab Chip | 2013 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/23254910 |
| High-throughput screening of large volumes of whole blood using structured illumination and fluorescent on-chip imaging. | Arpali SA, Arpali C, Coskun AF, Chiang HH, Ozcan A | Lab on a chip | 23047492 | Lab Chip | 2012 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/23047492 |
| Spectral demultiplexing in holographic and fluorescent on-chip microscopy. | Sencan I, Coskun AF, Sikora U, Ozcan A | Scientific reports | 24441627 | Sci Rep | 2014 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/24441627 |
| Optoelectronic tweezers integrated with lensfree holographic microscopy for wide-field interactive cell and particle manipulation on a chip. | Huang KW, Su TW, Ozcan A, Chiou PY | Lab on a chip | 23661233 | Lab Chip | 2013 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/23661233 |
| Cellphone-based detection platform for rbST biomarker analysis in milk extracts using a microsphere fluorescence immunoassay. | Ludwig SK, Zhu H, Phillips S, Shiledar A, Feng S, Tseng D, van Ginkel LA, Nielen MW, Ozcan A | Analytical and bioanalytical chemistry | 24972876 | Anal Bioanal Chem | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24972876 |
| Lens-free computational imaging of capillary morphogenesis within three-dimensional substrates. | Weidling J, Isikman SO, Greenbaum A, Ozcan A, Botvinick E | Journal of biomedical optics | 23235893 | J Biomed Opt | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23235893 |
| Killing of targets by CD8 T cells in the mouse spleen follows the law of mass action. | Ganusov VV, Barber DL, De Boer RJ | PloS one | 21283669 | PLoS One | 2011 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/21283669 |
| Wide-field lensless fluorescent microscopy using a tapered fiber-optic faceplate on a chip. | Coskun AF, Sencan I, Su TW, Ozcan A | The Analyst | 21283900 | Analyst | 2011 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/21283900 |
| Holographic pixel super-resolution in portable lensless on-chip microscopy using a fiber-optic array. | Bishara W, Sikora U, Mudanyali O, Su TW, Yaglidere O, Luckhart S, Ozcan A | Lab on a chip | 21365087 | Lab Chip | 2011 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/21365087 |
| Quantum dot enabled detection of Escherichia coli using a cell-phone. | Zhu H, Sikora U, Ozcan A | The Analyst | 22396952 | Analyst | 2012 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/22396952 |
| Wide-field fluorescent microscopy and fluorescent imaging flow cytometry on a cell-phone. | Zhu H, Ozcan A | Journal of visualized experiments : JoVE | 23603893 | J Vis Exp | 2013 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/23603893 |
| BioGames: A Platform for Crowd-Sourced Biomedical Image Analysis and Telediagnosis. | Mavandadi S, Feng S, Yu F, Dimitrov S, Yu R, Ozcan A | Games for health journal | 23724363 | Games Health J | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/23724363 |
| Detection of waterborne parasites using field-portable and cost-effective lensfree microscopy. | Mudanyali O, Oztoprak C, Tseng D, Erlinger A, Ozcan A | Lab on a chip | 20694255 | Lab Chip | 2010 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/20694255 |
| Color and monochrome lensless on-chip imaging of Caenorhabditis elegans over a wide field-of-view. | Isikman SO, Sencan I, Mudanyali O, Bishara W, Oztoprak C, Ozcan A | Lab on a chip | 20390127 | Lab Chip | 2010 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/20390127 |
| Lensless fluorescent on-chip microscopy using a fiber-optic taper. | Coskun AF, Sencan I, Su TW, Ozcan A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255702 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22255702 |
| Lensfree on-chip holography facilitates novel microscopy applications. | Ozcan A, Isikman S, Mudanyali O, Tseng D, Sencan I | SPIE newsroom | 21643449 | SPIE Newsroom | 2010 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/21643449 |
| Lensfree Fluorescent On-Chip Imaging using Compressive Sampling. | Coskun AF, Su TW, Sencan I, Ozcan A | Optics and photonics news | 21546979 | Opt Photonics News | 2010 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/21546979 |
| Field-portable lensfree tomographic microscope. | Isikman SO, Bishara W, Sikora U, Yaglidere O, Yeah J, Ozcan A | Lab on a chip | 21573311 | Lab Chip | 2011 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/21573311 |
| Optofluidic fluorescent imaging cytometry on a cell phone. | Zhu H, Mavandadi S, Coskun AF, Yaglidere O, Ozcan A | Analytical chemistry | 21774454 | Anal Chem | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21774454 |
| Lensfree super-resolution holographic microscopy using wetting films on a chip. | Mudanyali O, Bishara W, Ozcan A | Optics express | 21935102 | Opt Express | 2011 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/21935102 |
| Field-portable reflection and transmission microscopy based on lensless holography. | Lee M, Yaglidere O, Ozcan A | Biomedical optics express | 21991559 | Biomed Opt Express | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21991559 |
| Optical imaging techniques for point-of-care diagnostics. | Zhu H, Isikman SO, Mudanyali O, Greenbaum A, Ozcan A | Lab on a chip | 23044793 | Lab Chip | 2013 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/23044793 |
| A mathematical framework for combining decisions of multiple experts toward accurate and remote diagnosis of malaria using tele-microscopy. | Mavandadi S, Feng S, Yu F, Dimitrov S, Nielsen-Saines K, Prescott WR, Ozcan A | PloS one | 23071544 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23071544 |
| Cellphone-based devices for bioanalytical sciences. | Vashist SK, Mudanyali O, Schneider EM, Zengerle R, Ozcan A | Analytical and bioanalytical chemistry | 24287630 | Anal Bioanal Chem | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24287630 |
| Detection and spatial mapping of mercury contamination in water samples using a smart-phone. | Wei Q, Nagi R, Sadeghi K, Feng S, Yan E, Ki SJ, Caire R, Tseng D, Ozcan A | ACS nano | 24437470 | ACS Nano | 2014 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/24437470 |
| Fluorescent imaging of single nanoparticles and viruses on a smart phone. | Wei Q, Qi H, Luo W, Tseng D, Ki SJ, Wan Z, Göröcs Z, Bentolila LA, Wu TT, Sun R, Ozcan A | ACS nano | 24016065 | ACS Nano | 2013 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/24016065 |
| Cost-effective and compact wide-field fluorescent imaging on a cell-phone. | Zhu H, Yaglidere O, Su TW, Tseng D, Ozcan A | Lab on a chip | 21063582 | Lab Chip | 2011 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/21063582 |
| Immunochromatographic diagnostic test analysis using Google Glass. | Feng S, Caire R, Cortazar B, Turan M, Wong A, Ozcan A | ACS nano | 24571349 | ACS Nano | 2014 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/24571349 |
| Mobile phones democratize and cultivate next-generation imaging, diagnostics and measurement tools. | Ozcan A | Lab on a chip | 24647550 | Lab Chip | 2014 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/24647550 |
| Nano-imaging enabled via self-assembly. | McLeod E, Ozcan A | Nano today | 25506387 | Nano Today | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/25506387 |
| Organohalogen and organophosphorous pesticide method for ginseng root--a comparison of gas chromatography-single quadrupole mass spectrometry with high resolution time-of-flight mass spectrometry. | Hayward DG, Wong JW | Analytical chemistry | 19548696 | Anal Chem | 2009 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/19548696 |
| Multiresidue pesticide analysis in ginseng and spinach by nontargeted and targeted screening procedures. | Hayward DG, Wong JW, Zhang K, Chang J, Shi F, Banerjee K, Yang P | Journal of AOAC International | 22320080 | J AOAC Int | 2011 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/22320080 |
| RNA Chromatin Immunoprecipitation (RNA-ChIP) in Caenorhabditis elegans. | Cecere G, Grishok A | Bio-protocol | 29170745 | Bio Protoc | 2014 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/29170745 |
| The ZFP-1(AF10)/DOT-1 complex opposes H2B ubiquitination to reduce Pol II transcription. | Cecere G, Hoersch S, Jensen MB, Dixit S, Grishok A | Molecular cell | 23806335 | Mol Cell | 2013 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/23806335 |
| CSR-1 RNAi pathway positively regulates histone expression in C. elegans. | Avgousti DC, Palani S, Sherman Y, Grishok A | The EMBO journal | 22863779 | EMBO J | 2012 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/22863779 |
| Promoters recognized by forkhead proteins exist for individual 21U-RNAs. | Cecere G, Zheng GX, Mansisidor AR, Klymko KE, Grishok A | Molecular cell | 22819322 | Mol Cell | 2012 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/22819322 |
| A conserved PHD finger protein and endogenous RNAi modulate insulin signaling in Caenorhabditis elegans. | Mansisidor AR, Cecere G, Hoersch S, Jensen MB, Kawli T, Kennedy LM, Chavez V, Tan MW, Lieb JD, Grishok A | PLoS genetics | 21980302 | PLoS Genet | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21980302 |
| Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape. | Cecere G, Hoersch S, O'Keeffe S, Sachidanandam R, Grishok A | Nature structural & molecular biology | 24681887 | Nat Struct Mol Biol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24681887 |
| Development and interlaboratory validation of a QuEChERS-based liquid chromatography-tandem mass spectrometry method for multiresidue pesticide analysis. | Wong J, Hao C, Zhang K, Yang P, Banerjee K, Hayward D, Iftakhar I, Schreiber A, Tech K, Sack C, Smoker M, Chen X, Utture SC, Oulkar DP | Journal of agricultural and food chemistry | 20196606 | J Agric Food Chem | 2010 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/20196606 |
| Neuronal migration is regulated by endogenous RNAi and chromatin-binding factor ZFP-1/AF10 in Caenorhabditis elegans. | Kennedy LM, Grishok A | Genetics | 24558261 | Genetics | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24558261 |
| Biology and Mechanisms of Short RNAs in Caenorhabditis elegans. | Grishok A | Advances in genetics | 23890211 | Adv Genet | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23890211 |
| Analysis of organophosphorus pesticides in dried ground ginseng root by capillary gas chromatography-mass spectrometry and -flame photometric detection. | Wong JW, Hennessy MK, Hayward DG, Krynitsky AJ, Cassias I, Schenck FJ | Journal of agricultural and food chemistry | 17249685 | J Agric Food Chem | 2007 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/17249685 |
| The conserved PHD1-PHD2 domain of ZFP-1/AF10 is a discrete functional module essential for viability in Caenorhabditis elegans. | Avgousti DC, Cecere G, Grishok A | Molecular and cellular biology | 23263989 | Mol Cell Biol | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23263989 |
| Endogenous RNAi and adaptation to environment in C. elegans. | Grishok A | Worm | 24058837 | Worm | 2012 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24058837 |
| A nuclear perspective on RNAi pathways in metazoans. | Cecere G, Grishok A | Biochimica et biophysica acta | 24361586 | Biochim Biophys Acta | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24361586 |
| Enantiospecific synthesis of genetically encodable fluorescent unnatural amino acid L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid. | Xiang Z, Wang L | The Journal of organic chemistry | 21732687 | J Org Chem | 2011 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/21732687 |
| RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. | Johnson DB, Xu J, Shen Z, Takimoto JK, Schultz MD, Schmitz RJ, Xiang Z, Ecker JR, Briggs SP, Wang L | Nature chemical biology | 21926996 | Nat Chem Biol | 2011 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/21926996 |
| Genetically encoding an electrophilic amino acid for protein stapling and covalent binding to native receptors. | Chen XH, Xiang Z, Hu YS, Lacey VK, Cang H, Wang L | ACS chemical biology | 25010185 | ACS Chem Biol | 2014 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/25010185 |
| Proximity-enabled protein crosslinking through genetically encoding haloalkane unnatural amino acids. | Xiang Z, Lacey VK, Ren H, Xu J, Burban DJ, Jennings PA, Wang L | Angewandte Chemie (International ed. in English) | 24449339 | Angew Chem Int Ed Engl | 2014 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/24449339 |
| Optical Control of a Neuronal Protein Using a Genetically Encoded Unnatural Amino Acid in Neurons. | Kang JY, Kawaguchi D, Wang L | Journal of visualized experiments : JoVE | 27078635 | J Vis Exp | 2016 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/27078635 |
| In Situ Formation of an Azo Bridge on Proteins Controllable by Visible Light. | Hoppmann C, Maslennikov I, Choe S, Wang L | Journal of the American Chemical Society | 26301538 | J Am Chem Soc | 2015 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/26301538 |
| Expanding the genetic code for biological studies. | Wang Q, Parrish AR, Wang L | Chemistry & biology | 19318213 | Chem Biol | 2009 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/19318213 |
| In vivo expression of a light-activatable potassium channel using unnatural amino acids. | Kang JY, Kawaguchi D, Coin I, Xiang Z, O'Leary DD, Slesinger PA, Wang L | Neuron | 24139041 | Neuron | 2013 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/24139041 |
| Release factor one is nonessential in Escherichia coli. | Johnson DB, Wang C, Xu J, Schultz MD, Schmitz RJ, Ecker JR, Wang L | ACS chemical biology | 22662873 | ACS Chem Biol | 2012 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/22662873 |
| Response and adaptation of Escherichia coli to suppression of the amber stop codon. | Wang Q, Sun T, Xu J, Shen Z, Briggs SP, Zhou D, Wang L | Chembiochem : a European journal of chemical biology | 25044429 | Chembiochem | 2014 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/25044429 |
| A fluorescent reporter of the phosphorylation status of the substrate protein STAT3. | Lacey VK, Parrish AR, Han S, Shen Z, Briggs SP, Ma Y, Wang L | Angewandte Chemie (International ed. in English) | 21805546 | Angew Chem Int Ed Engl | 2011 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/21805546 |
| Genetic incorporation of unnatural amino acids into proteins in yeast. | Wang Q, Wang L | Methods in molecular biology (Clifton, N.J.) | 21956564 | Methods Mol Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/21956564 |
| Esterification of an unnatural amino acid structurally deviating from canonical amino acids promotes its uptake and incorporation into proteins in mammalian cells. | Takimoto JK, Xiang Z, Kang JY, Wang L | Chembiochem : a European journal of chemical biology | 20872394 | Chembiochem | 2010 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20872394 |
| Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. | Xiang Z, Ren H, Hu YS, Coin I, Wei J, Cang H, Wang L | Nature methods | 23913257 | Nat Methods | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23913257 |
| Expression of fluorescent cyclotides using protein trans-splicing for easy monitoring of cyclotide-protein interactions. | Jagadish K, Borra R, Lacey V, Majumder S, Shekhtman A, Wang L, Camarero JA | Angewandte Chemie (International ed. in English) | 23322720 | Angew Chem Int Ed Engl | 2013 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/23322720 |
| Photo-cross-linkers incorporated into G-protein-coupled receptors in mammalian cells: a ligand comparison. | Coin I, Perrin MH, Vale WW, Wang L | Angewandte Chemie (International ed. in English) | 21751313 | Angew Chem Int Ed Engl | 2011 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/21751313 |
| Engineering the Genetic Code in Cells and Animals: Biological Considerations and Impacts. | Wang L | Accounts of chemical research | 28984438 | Acc Chem Res | 2017 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/28984438 |
| Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. | Parrish AR, She X, Xiang Z, Coin I, Shen Z, Briggs SP, Dillin A, Wang L | ACS chemical biology | 22554080 | ACS Chem Biol | 2012 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/22554080 |
| Imprints of the genetic code in the ribosome. | Johnson DB, Wang L | Proceedings of the National Academy of Sciences of the United States of America | 20385807 | Proc Natl Acad Sci U S A | 2010 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/20385807 |
| Stereochemical basis for engineered pyrrolysyl-tRNA synthetase and the efficient in vivo incorporation of structurally divergent non-native amino acids. | Takimoto JK, Dellas N, Noel JP, Wang L | ACS chemical biology | 21545173 | ACS Chem Biol | 2011 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/21545173 |
| Genetically encoding unnatural amino acids in neural stem cells and optically reporting voltage-sensitive domain changes in differentiated neurons. | Shen B, Xiang Z, Miller B, Louie G, Wang W, Noel JP, Gage FH, Wang L | Stem cells (Dayton, Ohio) | 21681861 | Stem Cells | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21681861 |
| Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. | Coin I, Katritch V, Sun T, Xiang Z, Siu FY, Beyermann M, Stevens RC, Wang L | Cell | 24290358 | Cell | 2013 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/24290358 |
| Expanding the library and substrate diversity of the pyrrolysyl-tRNA synthetase to incorporate unnatural amino acids containing conjugated rings. | Lacey VK, Louie GV, Noel JP, Wang L | Chembiochem : a European journal of chemical biology | 24019075 | Chembiochem | 2013 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/24019075 |
| Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells. | Hoppmann C, Lacey VK, Louie GV, Wei J, Noel JP, Wang L | Angewandte Chemie (International ed. in English) | 24615769 | Angew Chem Int Ed Engl | 2014 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/24615769 |
| miR-30b/30d regulation of GalNAc transferases enhances invasion and immunosuppression during metastasis. | Gaziel-Sovran A, Segura MF, Di Micco R, Collins MK, Hanniford D, Vega-Saenz de Miera E, Rakus JF, Dankert JF, Shang S, Kerbel RS, Bhardwaj N, Shao Y, Darvishian F, Zavadil J, Erlebacher A, Mahal LK, Osman I, Hernando E | Cancer cell | 21741600 | Cancer Cell | 2011 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/21741600 |
| Identification of a conserved glycan signature for microvesicles. | Batista BS, Eng WS, Pilobello KT, Hendricks-Muñoz KD, Mahal LK | Journal of proteome research | 21859146 | J Proteome Res | 2011 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/21859146 |
| Complex N-linked glycans serve as a determinant for exosome/microvesicle cargo recruitment. | Liang Y, Eng WS, Colquhoun DR, Dinglasan RR, Graham DR, Mahal LK | The Journal of biological chemistry | 25261472 | J Biol Chem | 2014 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/25261472 |
| Glycomic analysis: an array of technologies. | Krishnamoorthy L, Mahal LK | ACS chemical biology | 19728746 | ACS Chem Biol | 2009 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/19728746 |
| Insights into miRNA regulation of the human glycome. | Kasper BT, Koppolu S, Mahal LK | Biochemical and biophysical research communications | 24463102 | Biochem Biophys Res Commun | 2014 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/24463102 |
| Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. | Sun N, Yazawa M, Liu J, Han L, Sanchez-Freire V, Abilez OJ, Navarrete EG, Hu S, Wang L, Lee A, Pavlovic A, Lin S, Chen R, Hajjar RJ, Snyder MP, Dolmetsch RE, Butte MJ, Ashley EA, Longaker MT, Robbins RC, Wu JC | Science translational medicine | 22517884 | Sci Transl Med | 2012 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/22517884 |
| Dynamic microRNA expression programs during cardiac differentiation of human embryonic stem cells: role for miR-499. | Wilson KD, Hu S, Venkatasubrahmanyam S, Fu JD, Sun N, Abilez OJ, Baugh JJ, Jia F, Ghosh Z, Li RA, Butte AJ, Wu JC | Circulation. Cardiovascular genetics | 20733065 | Circ Cardiovasc Genet | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20733065 |
| Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. | Churko JM, Mantalas GL, Snyder MP, Wu JC | Circulation research | 23743227 | Circ Res | 2013 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/23743227 |
| Sacrificial layer technique for axial force post assay of immature cardiomyocytes. | Taylor RE, Kim K, Sun N, Park SJ, Sim JY, Fajardo G, Bernstein D, Wu JC, Pruitt BL | Biomedical microdevices | 23007494 | Biomed Microdevices | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23007494 |
| Atomic force mechanobiology of pluripotent stem cell-derived cardiomyocytes. | Liu J, Sun N, Bruce MA, Wu JC, Butte MJ | PloS one | 22624048 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22624048 |
| Drug screening using a library of human induced pluripotent stem cell-derived cardiomyocytes reveals disease-specific patterns of cardiotoxicity. | Liang P, Lan F, Lee AS, Gong T, Sanchez-Freire V, Wang Y, Diecke S, Sallam K, Knowles JW, Wang PJ, Nguyen PK, Bers DM, Robbins RC, Wu JC | Circulation | 23519760 | Circulation | 2013 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/23519760 |
| Epigenetic Modulations of Induced Pluripotent Stem Cells: Novel Therapies and Disease Models. | Huang C, Wu JC | Drug discovery today. Disease models | 23646061 | Drug Discov Today Dis Models | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23646061 |
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| Model organisms reveal insight into human neurodegenerative disease: ataxin-2 intermediate-length polyglutamine expansions are a risk factor for ALS. | Bonini NM, Gitler AD | Journal of molecular neuroscience : MN | 21660502 | J Mol Neurosci | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21660502 |
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| Molecular determinants and genetic modifiers of aggregation and toxicity for the ALS disease protein FUS/TLS. | Sun Z, Diaz Z, Fang X, Hart MP, Chesi A, Shorter J, Gitler AD | PLoS biology | 21541367 | PLoS Biol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21541367 |
| The modulation of Amyotrophic Lateral Sclerosis risk by ataxin-2 intermediate polyglutamine expansions is a specific effect. | Gispert S, Kurz A, Waibel S, Bauer P, Liepelt I, Geisen C, Gitler AD, Becker T, Weber M, Berg D, Andersen PM, Krüger R, Riess O, Ludolph AC, Auburger G | Neurobiology of disease | 21889984 | Neurobiol Dis | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21889984 |
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| The role of the Parkinson's disease gene PARK9 in essential cellular pathways and the manganese homeostasis network in yeast. | Chesi A, Kilaru A, Fang X, Cooper AA, Gitler AD | PloS one | 22457822 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22457822 |
| High-throughput yeast plasmid overexpression screen. | Fleming MS, Gitler AD | Journal of visualized experiments : JoVE | 21841759 | J Vis Exp | 2011 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/21841759 |
| Profilin 1 associates with stress granules and ALS-linked mutations alter stress granule dynamics. | Figley MD, Bieri G, Kolaitis RM, Taylor JP, Gitler AD | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24920614 | J Neurosci | 2014 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/24920614 |
| Alpha-synuclein is part of a diverse and highly conserved interaction network that includes PARK9 and manganese toxicity. | Gitler AD, Chesi A, Geddie ML, Strathearn KE, Hamamichi S, Hill KJ, Caldwell KA, Caldwell GA, Cooper AA, Rochet JC, Lindquist S | Nature genetics | 19182805 | Nat Genet | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19182805 |
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| TDP-43 is intrinsically aggregation-prone, and amyotrophic lateral sclerosis-linked mutations accelerate aggregation and increase toxicity. | Johnson BS, Snead D, Lee JJ, McCaffery JM, Shorter J, Gitler AD | The Journal of biological chemistry | 19465477 | J Biol Chem | 2009 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/19465477 |
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| Therapeutic modulation of eIF2α phosphorylation rescues TDP-43 toxicity in amyotrophic lateral sclerosis disease models. | Kim HJ, Raphael AR, LaDow ES, McGurk L, Weber RA, Trojanowski JQ, Lee VM, Finkbeiner S, Gitler AD, Bonini NM | Nature genetics | 24336168 | Nat Genet | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24336168 |
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| Graphene-Dielectric Integration for Graphene Transistors. | Liao L, Duan X | Materials science & engineering. R, Reports : a review journal | 21278913 | Mater Sci Eng R Rep | 2010 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/21278913 |
| Unveiling the formation pathway of single crystalline porous silicon nanowires. | Zhong X, Qu Y, Lin YC, Liao L, Duan X | ACS applied materials & interfaces | 21244020 | ACS Appl Mater Interfaces | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/21244020 |
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| Nanoscale morphology, dimensional control, and electrical properties of oligoanilines. | Wang Y, Tran HD, Liao L, Duan X, Kaner RB | Journal of the American Chemical Society | 20662516 | J Am Chem Soc | 2010 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/20662516 |
| pH-Operated mechanized porous silicon nanoparticles. | Xue M, Zhong X, Shaposhnik Z, Qu Y, Tamanoi F, Duan X, Zink JI | Journal of the American Chemical Society | 21595466 | J Am Chem Soc | 2011 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/21595466 |
| Rational design and synthesis of freestanding photoelectric nanodevices as highly efficient photocatalysts. | Qu Y, Liao L, Cheng R, Wang Y, Lin YC, Huang Y, Duan X | Nano letters | 20373781 | Nano Lett | 2010 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/20373781 |
| Top-gated graphene nanoribbon transistors with ultrathin high-k dielectrics. | Liao L, Bai J, Cheng R, Lin YC, Jiang S, Huang Y, Duan X | Nano letters | 20380441 | Nano Lett | 2010 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/20380441 |
| Plasmonic modulation of the upconversion fluorescence in NaYF4 :Yb/Tm hexaplate nanocrystals using gold nanoparticles or nanoshells. | Zhang H, Li Y, Ivanov IA, Qu Y, Huang Y, Duan X | Angewandte Chemie (International ed. in English) | 20235253 | Angew Chem Int Ed Engl | 2010 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/20235253 |
| Single-layer graphene on Al2O3/Si substrate: better contrast and higher performance of graphene transistors. | Liao L, Bai J, Qu Y, Huang Y, Duan X | Nanotechnology | 19946170 | Nanotechnology | 2010 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/19946170 |
| Rational fabrication of graphene nanoribbons using a nanowire etch mask. | Bai J, Duan X, Huang Y | Nano letters | 19344151 | Nano Lett | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19344151 |
| Electrically conductive and optically active porous silicon nanowires. | Qu Y, Liao L, Li Y, Zhang H, Huang Y, Duan X | Nano letters | 19807130 | Nano Lett | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19807130 |
| Porous silicon nanowires. | Qu Y, Zhou H, Duan X | Nanoscale | 21869999 | Nanoscale | 2011 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/21869999 |
| Very large magnetoresistance in graphene nanoribbons. | Bai J, Cheng R, Xiu F, Liao L, Wang M, Shailos A, Wang KL, Huang Y, Duan X | Nature nanotechnology | 20693988 | Nat Nanotechnol | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20693988 |
| Domain wall motion in synthetic Co2Si nanowires. | Liu G, Lin YC, Liao L, Liu L, Chen Y, Liu Y, Weiss NO, Zhou H, Huang Y, Duan X | Nano letters | 22469009 | Nano Lett | 2012 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/22469009 |
| Highly spectral dependent enhancement of upconversion emission with sputtered gold island films. | Zhang H, Xu D, Huang Y, Duan X | Chemical communications (Cambridge, England) | 21079884 | Chem Commun (Camb) | 2011 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/21079884 |
| High-speed graphene transistors with a self-aligned nanowire gate. | Liao L, Lin YC, Bao M, Cheng R, Bai J, Liu Y, Qu Y, Wang KL, Huang Y, Duan X | Nature | 20811365 | Nature | 2010 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/20811365 |
| Sub-100 nm channel length graphene transistors. | Liao L, Bai J, Cheng R, Lin YC, Jiang S, Qu Y, Huang Y, Duan X | Nano letters | 20815334 | Nano Lett | 2010 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/20815334 |
| Photocatalytic Properties of Porous Silicon Nanowires. | Qu Y, Zhong X, Li Y, Liao L, Huang Y, Duan X | Journal of materials chemistry | 22190767 | J Mater Chem | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/22190767 |
| Heterointegration of Pt/Si/Ag Nanowire Photodiodes and Their Photocatalytic Properties. | Qu Y, Xue T, Zhong X, Lin YC, Liao L, Choi J, Duan X | Advanced functional materials | 21629399 | Adv Funct Mater | 2010 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/21629399 |
| Toward tunable band gap and tunable dirac point in bilayer graphene with molecular doping. | Yu WJ, Liao L, Chae SH, Lee YH, Duan X | Nano letters | 21985035 | Nano Lett | 2011 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/21985035 |
| Plasmonic enhancements of photocatalytic activity of Pt/n-Si/Ag photodiodes using Au/Ag core/shell nanorods. | Qu Y, Cheng R, Su Q, Duan X | Journal of the American Chemical Society | 21961900 | J Am Chem Soc | 2011 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/21961900 |
| Graphene nanomesh. | Bai J, Zhong X, Jiang S, Huang Y, Duan X | Nature nanotechnology | 20154685 | Nat Nanotechnol | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20154685 |
| High-performance top-gated graphene-nanoribbon transistors using zirconium oxide nanowires as high-dielectric-constant gate dielectrics. | Liao L, Bai J, Lin YC, Qu Y, Huang Y, Duan X | Advanced materials (Deerfield Beach, Fla.) | 20526997 | Adv Mater | 2010 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/20526997 |
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| High-kappa oxide nanoribbons as gate dielectrics for high mobility top-gated graphene transistors. | Liao L, Bai J, Qu Y, Lin YC, Li Y, Huang Y, Duan X | Proceedings of the National Academy of Sciences of the United States of America | 20308584 | Proc Natl Acad Sci U S A | 2010 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/20308584 |
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| Antibacterial and cell-adhesive polypeptide and poly(ethylene glycol) hydrogel as a potential scaffold for wound healing. | Song A, Rane AA, Christman KL | Acta biomaterialia | 22023748 | Acta Biomater | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22023748 |
| Human cardiomyogenesis and the need for systems biology analysis. | Young DA, DeQuach JA, Christman KL | Wiley interdisciplinary reviews. Systems biology and medicine | 21197666 | Wiley Interdiscip Rev Syst Biol Med | 2011 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/21197666 |
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| Decellularized porcine brain matrix for cell culture and tissue engineering scaffolds. | DeQuach JA, Yuan SH, Goldstein LS, Christman KL | Tissue engineering. Part A | 21883047 | Tissue Eng Part A | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21883047 |
| Injectable materials for the treatment of myocardial infarction and heart failure: the promise of decellularized matrices. | Singelyn JM, Christman KL | Journal of cardiovascular translational research | 20632221 | J Cardiovasc Transl Res | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20632221 |
| Increased infarct wall thickness by a bio-inert material is insufficient to prevent negative left ventricular remodeling after myocardial infarction. | Rane AA, Chuang JS, Shah A, Hu DP, Dalton ND, Gu Y, Peterson KL, Omens JH, Christman KL | PloS one | 21731777 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/21731777 |
| Injectable extracellular matrix derived hydrogel provides a platform for enhanced retention and delivery of a heparin-binding growth factor. | Seif-Naraghi SB, Horn D, Schup-Magoffin PJ, Christman KL | Acta biomaterialia | 22750737 | Acta Biomater | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22750737 |
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| Injectable skeletal muscle matrix hydrogel promotes neovascularization and muscle cell infiltration in a hindlimb ischemia model. | DeQuach JA, Lin JE, Cam C, Hu D, Salvatore MA, Sheikh F, Christman KL | European cells & materials | 22665162 | Eur Cell Mater | 2012 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/22665162 |
| Award winner for outstanding research in the PhD category, 2014 Society for Biomaterials annual meeting and exposition, Denver, Colorado, April 16-19, 2014: Decellularized adipose matrix hydrogels stimulate in vivo neovascularization and adipose formation. | Adam Young D, Bajaj V, Christman KL | Journal of biomedical materials research. Part A | 24510423 | J Biomed Mater Res A | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24510423 |
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| Catheter-deliverable hydrogel derived from decellularized ventricular extracellular matrix increases endogenous cardiomyocytes and preserves cardiac function post-myocardial infarction. | Singelyn JM, Sundaramurthy P, Johnson TD, Schup-Magoffin PJ, Hu DP, Faulk DM, Wang J, Mayle KM, Bartels K, Salvatore M, Kinsey AM, Demaria AN, Dib N, Christman KL | Journal of the American College of Cardiology | 22340268 | J Am Coll Cardiol | 2012 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/22340268 |
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| Patient-to-patient variability in autologous pericardial matrix scaffolds for cardiac repair. | Seif-Naraghi SB, Horn D, Schup-Magoffin PA, Madani MM, Christman KL | Journal of cardiovascular translational research | 21695575 | J Cardiovasc Transl Res | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21695575 |
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| Characterization of the mutagenic spectrum of 4-nitroquinoline 1-oxide (4-NQO) in Aspergillus nidulans by whole genome sequencing. | Downes DJ, Chonofsky M, Tan K, Pfannenstiel BT, Reck-Peterson SL, Todd RB | G3 (Bethesda, Md.) | 25352541 | G3 (Bethesda) | 2014 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/25352541 |
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| Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies. | Bielas SL, Silhavy JL, Brancati F, Kisseleva MV, Al-Gazali L, Sztriha L, Bayoumi RA, Zaki MS, Abdel-Aleem A, Rosti RO, Kayserili H, Swistun D, Scott LC, Bertini E, Boltshauser E, Fazzi E, Travaglini L, Field SJ, Gayral S, Jacoby M, Schurmans S, Dallapiccola B, Majerus PW, Valente EM, Gleeson JG | Nature genetics | 19668216 | Nat Genet | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19668216 |
| Receptor tyrosine kinases and TLR/IL1Rs unexpectedly activate myeloid cell PI3kγ, a single convergent point promoting tumor inflammation and progression. | Schmid MC, Avraamides CJ, Dippold HC, Franco I, Foubert P, Ellies LG, Acevedo LM, Manglicmot JR, Song X, Wrasidlo W, Blair SL, Ginsberg MH, Cheresh DA, Hirsch E, Field SJ, Varner JA | Cancer cell | 21665146 | Cancer Cell | 2011 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/21665146 |
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| Role of phosphatidylinositol 4-phosphate (PI4P) and its binding protein GOLPH3 in hepatitis C virus secretion. | Bishé B, Syed GH, Field SJ, Siddiqui A | The Journal of biological chemistry | 22745132 | J Biol Chem | 2012 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/22745132 |
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| GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch and shape the Golgi to promote budding. | Dippold HC, Ng MM, Farber-Katz SE, Lee SK, Kerr ML, Peterman MC, Sim R, Wiharto PA, Galbraith KA, Madhavarapu S, Fuchs GJ, Meerloo T, Farquhar MG, Zhou H, Field SJ | Cell | 19837035 | Cell | 2009 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/19837035 |
| Regulation of Drosophila mesoderm migration by phosphoinositides and the PH domain of the Rho GTP exchange factor Pebble. | Murray MJ, Ng MM, Fraval H, Tan J, Liu W, Smallhorn M, Brill JA, Field SJ, Saint R | Developmental biology | 23000359 | Dev Biol | 2012 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/23000359 |
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| Carbon-fiber microelectrode amperometry reveals sickle-cell-induced inflammation and chronic morphine effects on single mast cells. | Manning BM, Hebbel RP, Gupta K, Haynes CL | ACS chemical biology | 22217155 | ACS Chem Biol | 2012 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/22217155 |
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| Analytical characterization of the role of phospholipids in platelet adhesion and secretion. | Koseoglu S, Meyer AF, Kim D, Meyer BM, Wang Y, Dalluge JJ, Haynes CL | Analytical chemistry | 25439269 | Anal Chem | 2015 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/25439269 |
| Checkpoints for Preliminary Identification of Small Molecules found Enriched in Autophagosomes and Activated Mast Cell Secretions Analyzed by Comparative UPLC/MS(e). | Satori CP, Ramezani M, Koopmeiners JS, Meyer AF, Rodriguez-Navarro JA, Kuhns MM, Taylor TH, Haynes CL, Dalluge JJ, Arriaga EA | Analytical methods : advancing methods and applications | 28194233 | Anal Methods | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28194233 |
| Cytoskeletal F-actin, not the circumferential coil of microtubules, regulates platelet dense-body granule secretion. | Ge S, White JG, Haynes CL | Platelets | 21988315 | Platelets | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/21988315 |
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| Neuropeptide-Induced Mast Cell Degranulation and Characterization of Signaling Modulation in Response to IgE Conditioning. | Manning BM, Gruba SM, Meyer AF, Haynes CL | ACS chemical biology | 27580075 | ACS Chem Biol | 2016 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/27580075 |
| Platelet membrane variations and their effects on δ-granule secretion kinetics and aggregation spreading among different species. | Gruba SM, Koseoglu S, Meyer AF, Meyer BM, Maurer-Jones MA, Haynes CL | Biochimica et biophysica acta | 25906946 | Biochim Biophys Acta | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25906946 |
| Microfluidics-based in vivo mimetic systems for the study of cellular biology. | Kim D, Wu X, Young AT, Haynes CL | Accounts of chemical research | 24555566 | Acc Chem Res | 2014 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/24555566 |
| On-chip evaluation of platelet adhesion and aggregation upon exposure to mesoporous silica nanoparticles. | Kim D, Finkenstaedt-Quinn S, Hurley KR, Buchman JT, Haynes CL | The Analyst | 24300894 | Analyst | 2014 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/24300894 |
| Critical role of membrane cholesterol in exocytosis revealed by single platelet study. | Ge S, White JG, Haynes CL | ACS chemical biology | 20590163 | ACS Chem Biol | 2010 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/20590163 |
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| Exploring inflammatory disease drug effects on neutrophil function. | Wu X, Kim D, Young AT, Haynes CL | The Analyst | 24946254 | Analyst | 2014 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/24946254 |
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| Neutrophil chemotaxis within a competing gradient of chemoattractants. | Kim D, Haynes CL | Analytical chemistry | 22816782 | Anal Chem | 2012 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/22816782 |
| On-chip evaluation of neutrophil activation and neutrophil-endothelial cell interaction during neutrophil chemotaxis. | Kim D, Haynes CL | Analytical chemistry | 24127752 | Anal Chem | 2013 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/24127752 |
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| Neutrophils confer T cell resistance to myeloid-derived suppressor cell-mediated suppression to promote chronic inflammation. | Ryan SO, Johnson JL, Cobb BA | Journal of immunology (Baltimore, Md. : 1950) | 23576679 | J Immunol | 2013 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/23576679 |
| Carbohydrate oxidation acidifies endosomes, regulating antigen processing and TLR9 signaling. | Lewis CJ, Cobb BA | Journal of immunology (Baltimore, Md. : 1950) | 20200279 | J Immunol | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20200279 |
| Glycobiology of immune responses. | Rabinovich GA, van Kooyk Y, Cobb BA | Annals of the New York Academy of Sciences | 22524422 | Ann N Y Acad Sci | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22524422 |
| Myeloid glycosylation defects lead to a spontaneous common variable immunodeficiency-like condition with associated hemolytic anemia and antilymphocyte autoimmunity. | Ryan SO, Abbott DW, Cobb BA | Journal of immunology (Baltimore, Md. : 1950) | 24795453 | J Immunol | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24795453 |
| Host glycans and antigen presentation. | Ryan SO, Cobb BA | Microbes and infection | 22580092 | Microbes Infect | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22580092 |
| Glycoantigens induce human peripheral Tr1 cell differentiation with gut-homing specialization. | Kreisman LS, Cobb BA | The Journal of biological chemistry | 21228275 | J Biol Chem | 2011 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/21228275 |
| Structural characterization and MHCII-dependent immunological properties of the zwitterionic O-chain antigen of Morganella morganii. | Young NM, Kreisman LS, Stupak J, MacLean LL, Cobb BA, Richards JC | Glycobiology | 21321054 | Glycobiology | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21321054 |
| Mycobacterium tuberculosis synergizes with ATP to induce release of microvesicles and exosomes containing major histocompatibility complex class II molecules capable of antigen presentation. | Ramachandra L, Qu Y, Wang Y, Lewis CJ, Cobb BA, Takatsu K, Boom WH, Dubyak GR, Harding CV | Infection and immunity | 20837713 | Infect Immun | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20837713 |
| B-cell-independent sialylation of IgG. | Jones MB, Oswald DM, Joshi S, Whiteheart SW, Orlando R, Cobb BA | Proceedings of the National Academy of Sciences of the United States of America | 27303031 | Proc Natl Acad Sci U S A | 2016 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/27303031 |
| Roles for major histocompatibility complex glycosylation in immune function. | Ryan SO, Cobb BA | Seminars in immunopathology | 22461020 | Semin Immunopathol | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22461020 |
| The regulatory power of glycans and their binding partners in immunity. | Johnson JL, Jones MB, Ryan SO, Cobb BA | Trends in immunology | 23485517 | Trends Immunol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23485517 |
| Interaction of the Capsular Polysaccharide A from Bacteroides fragilis with DC-SIGN on Human Dendritic Cells is Necessary for Its Processing and Presentation to T Cells. | Bloem K, García-Vallejo JJ, Vuist IM, Cobb BA, van Vliet SJ, van Kooyk Y | Frontiers in immunology | 23653626 | Front Immunol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23653626 |
| Polysaccharide A from the capsule of Bacteroides fragilis induces clonal CD4+ T cell expansion. | Johnson JL, Jones MB, Cobb BA | The Journal of biological chemistry | 25540199 | J Biol Chem | 2015 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/25540199 |
| Infection, inflammation and host carbohydrates: a Glyco-Evasion Hypothesis. | Kreisman LS, Cobb BA | Glycobiology | 22492234 | Glycobiology | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22492234 |
| Bacterial capsular polysaccharide prevents the onset of asthma through T-cell activation. | Johnson JL, Jones MB, Cobb BA | Glycobiology | 25347992 | Glycobiology | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25347992 |
| Type I Streptococcus pneumoniae carbohydrate utilizes a nitric oxide and MHC II-dependent pathway for antigen presentation. | Velez CD, Lewis CJ, Kasper DL, Cobb BA | Immunology | 18778282 | Immunology | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/18778282 |
| Mgat2 ablation in the myeloid lineage leads to defective glycoantigen T cell responses. | Ryan SO, Leal SM Jr, Abbott DW, Pearlman E, Cobb BA | Glycobiology | 24310166 | Glycobiology | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24310166 |
| Adaptive immune defects against glycoantigens in chronic granulomatous disease via dysregulated nitric oxide production. | Lewis CJ, Cobb BA | European journal of immunology | 21630251 | Eur J Immunol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21630251 |
| MHCII glycosylation modulates Bacteroides fragilis carbohydrate antigen presentation. | Ryan SO, Bonomo JA, Zhao F, Cobb BA | The Journal of experimental medicine | 21502329 | J Exp Med | 2011 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/21502329 |
| Pan-neuronal maturation but not neuronal subtype differentiation of adult neural stem cells is mechanosensitive. | Keung AJ, Dong M, Schaffer DV, Kumar S | Scientific reports | 23660869 | Sci Rep | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23660869 |
| Vinculin tension distributions of individual stress fibers within cell-matrix adhesions. | Chang CW, Kumar S | Journal of cell science | 23687380 | J Cell Sci | 2013 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/23687380 |
| Combining mechanical and optical approaches to dissect cellular mechanobiology. | Sen S, Kumar S | Journal of biomechanics | 19819457 | J Biomech | 2010 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/19819457 |
| Independent regulation of tumor cell migration by matrix stiffness and confinement. | Pathak A, Kumar S | Proceedings of the National Academy of Sciences of the United States of America | 22689955 | Proc Natl Acad Sci U S A | 2012 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/22689955 |
| Cell-matrix mechanobiology: applications to brain tumors and design of tissue engineering scaffolds. | Kumar S | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 19964076 | Annu Int Conf IEEE Eng Med Biol Soc | 2009 | https://www.ncbi.nlm.nih.gov/pubmed/19964076 |
| Presentation counts: microenvironmental regulation of stem cells by biophysical and material cues. | Keung AJ, Kumar S, Schaffer DV | Annual review of cell and developmental biology | 20590452 | Annu Rev Cell Dev Biol | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20590452 |
| Soft microenvironments promote the early neurogenic differentiation but not self-renewal of human pluripotent stem cells. | Keung AJ, Asuri P, Kumar S, Schaffer DV | Integrative biology : quantitative biosciences from nano to macro | 22854634 | Integr Biol (Camb) | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22854634 |
| Biophysical regulation of tumor cell invasion: moving beyond matrix stiffness. | Pathak A, Kumar S | Integrative biology : quantitative biosciences from nano to macro | 21210057 | Integr Biol (Camb) | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21210057 |
| Dissecting regional variations in stress fiber mechanics in living cells with laser nanosurgery. | Tanner K, Boudreau A, Bissell MJ, Kumar S | Biophysical journal | 21044574 | Biophys J | 2010 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/21044574 |
| Microtopographical assembly of cardiomyocytes. | Patel AA, Desai TA, Kumar S | Integrative biology : quantitative biosciences from nano to macro | 21863181 | Integr Biol (Camb) | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21863181 |
| Rho GTPases mediate the mechanosensitive lineage commitment of neural stem cells. | Keung AJ, de Juan-Pardo EM, Schaffer DV, Kumar S | Stem cells (Dayton, Ohio) | 21956892 | Stem Cells | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21956892 |
| A genetic strategy for the dynamic and graded control of cell mechanics, motility, and matrix remodeling. | MacKay JL, Keung AJ, Kumar S | Biophysical journal | 22325265 | Biophys J | 2012 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/22325265 |
| A fluorescent peroxidase probe increases the sensitivity of commercial ELISAs by two orders of magnitude. | Acharya AP, Nafisi PM, Gardner A, Mackay JL, Kundu K, Kumar S, Murthy N | Chemical communications (Cambridge, England) | 24071916 | Chem Commun (Camb) | 2013 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/24071916 |
| Microenvironmental stiffness enhances glioma cell proliferation by stimulating epidermal growth factor receptor signaling. | Umesh V, Rape AD, Ulrich TA, Kumar S | PloS one | 25000176 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25000176 |
| Constitutive activation of myosin-dependent contractility sensitizes glioma tumor-initiating cells to mechanical inputs and reduces tissue invasion. | Wong SY, Ulrich TA, Deleyrolle LP, MacKay JL, Lin JM, Martuscello RT, Jundi MA, Reynolds BA, Kumar S | Cancer research | 25634210 | Cancer Res | 2015 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/25634210 |
| Cell-Matrix De-Adhesion Dynamics Reflect Contractile Mechanics. | Sen S, Kumar S | Cellular and molecular bioengineering | 21297858 | Cell Mol Bioeng | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21297858 |
| Measuring the elastic properties of living cells with atomic force microscopy indentation. | Mackay JL, Kumar S | Methods in molecular biology (Clifton, N.J.) | 23027009 | Methods Mol Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23027009 |
| Mechanics, malignancy, and metastasis: the force journey of a tumor cell. | Kumar S, Weaver VM | Cancer metastasis reviews | 19153673 | Cancer Metastasis Rev | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19153673 |
| Differential Contributions of Nonmuscle Myosin II Isoforms and Functional Domains to Stress Fiber Mechanics. | Chang CW, Kumar S | Scientific reports | 26336830 | Sci Rep | 2015 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/26336830 |
| CD44-mediated adhesion to hyaluronic acid contributes to mechanosensing and invasive motility. | Kim Y, Kumar S | Molecular cancer research : MCR | 24962319 | Mol Cancer Res | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24962319 |
| The mechanical rigidity of the extracellular matrix regulates the structure, motility, and proliferation of glioma cells. | Ulrich TA, de Juan Pardo EM, Kumar S | Cancer research | 19435897 | Cancer Res | 2009 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/19435897 |
| Elucidating the mechanobiology of malignant brain tumors using a brain matrix-mimetic hyaluronic acid hydrogel platform. | Ananthanarayanan B, Kim Y, Kumar S | Biomaterials | 21820737 | Biomaterials | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/21820737 |
| From molecular signal activation to locomotion: an integrated, multiscale analysis of cell motility on defined matrices. | Pathak A, Kumar S | PloS one | 21483802 | PLoS One | 2011 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/21483802 |
| Microscale mechanisms of agarose-induced disruption of collagen remodeling. | Ulrich TA, Lee TG, Shon HK, Moon DW, Kumar S | Biomaterials | 21575987 | Biomaterials | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21575987 |
| Simultaneous and independent tuning of RhoA and Rac1 activity with orthogonally inducible promoters. | MacKay JL, Kumar S | Integrative biology : quantitative biosciences from nano to macro | 25044255 | Integr Biol (Camb) | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25044255 |
| A composite hydrogel platform for the dissection of tumor cell migration at tissue interfaces. | Rape AD, Kumar S | Biomaterials | 25047626 | Biomaterials | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25047626 |
| Probing cellular mechanobiology in three-dimensional culture with collagen-agarose matrices. | Ulrich TA, Jain A, Tanner K, MacKay JL, Kumar S | Biomaterials | 19926126 | Biomaterials | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19926126 |
| Cyclic Mechanical Loading Is Essential for Rac1-Mediated Elongation and Remodeling of the Embryonic Mitral Valve. | Gould RA, Yalcin HC, MacKay JL, Sauls K, Norris R, Kumar S, Butcher JT | Current biology : CB | 26725196 | Curr Biol | 2016 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/26725196 |
| Transforming potential and matrix stiffness co-regulate confinement sensitivity of tumor cell migration. | Pathak A, Kumar S | Integrative biology : quantitative biosciences from nano to macro | 23832051 | Integr Biol (Camb) | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23832051 |
| Contractility dominates adhesive ligand density in regulating cellular de-adhesion and retraction kinetics. | Sen S, Ng WP, Kumar S | Annals of biomedical engineering | 21046466 | Ann Biomed Eng | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21046466 |
| Extracellular matrix rigidity modulates neuroblastoma cell differentiation and N-myc expression. | Lam WA, Cao L, Umesh V, Keung AJ, Sen S, Kumar S | Molecular cancer | 20144241 | Mol Cancer | 2010 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/20144241 |
| Contributions of talin-1 to glioma cell-matrix tensional homeostasis. | Sen S, Ng WP, Kumar S | Journal of the Royal Society, Interface | 22158841 | J R Soc Interface | 2012 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/22158841 |
| Three-dimensional patterning of multiple cell populations through orthogonal genetic control of cell motility. | MacKay JL, Sood A, Kumar S | Soft matter | 24622945 | Soft Matter | 2014 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/24622945 |
| Modulating malignant epithelial tumor cell adhesion, migration and mechanics with nanorod surfaces. | Lee J, Chu BH, Sen S, Gupte A, Chancellor TJ, Chang CY, Ren F, Kumar S, Lele TP | Biomedical microdevices | 20830527 | Biomed Microdevices | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20830527 |
| Biophysics and dynamics of natural and engineered stem cell microenvironments. | Keung AJ, Healy KE, Kumar S, Schaffer DV | Wiley interdisciplinary reviews. Systems biology and medicine | 20836010 | Wiley Interdiscip Rev Syst Biol Med | 2010 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/20836010 |
| Isoform-specific contributions of alpha-actinin to glioma cell mechanobiology. | Sen S, Dong M, Kumar S | PloS one | 20037648 | PLoS One | 2009 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/20037648 |
| Aldehyde dehydrogenase in combination with CD133 defines angiogenic ovarian cancer stem cells that portend poor patient survival. | Silva IA, Bai S, McLean K, Yang K, Griffith K, Thomas D, Ginestier C, Johnston C, Kueck A, Reynolds RK, Wicha MS, Buckanovich RJ | Cancer research | 21498635 | Cancer Res | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21498635 |
| EGFL6 Regulates the Asymmetric Division, Maintenance, and Metastasis of ALDH+ Ovarian Cancer Cells. | Bai S, Ingram P, Chen YC, Deng N, Pearson A, Niknafs YS, O'Hayer P, Wang Y, Zhang ZY, Boscolo E, Bischoff J, Yoon E, Buckanovich RJ | Cancer research | 27803106 | Cancer Res | 2016 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/27803106 |
| Metformin targets ovarian cancer stem cells in vitro and in vivo. | Shank JJ, Yang K, Ghannam J, Cabrera L, Johnston CJ, Reynolds RK, Buckanovich RJ | Gynecologic oncology | 22864111 | Gynecol Oncol | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22864111 |
| A novel model for evaluating therapies targeting human tumor vasculature and human cancer stem-like cells. | Burgos-Ojeda D, McLean K, Bai S, Pulaski H, Gong Y, Silva I, Skorecki K, Tzukerman M, Buckanovich RJ | Cancer research | 23576551 | Cancer Res | 2013 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23576551 |
| Ovarian cancer stem cell markers: prognostic and therapeutic implications. | Burgos-Ojeda D, Rueda BR, Buckanovich RJ | Cancer letters | 22334034 | Cancer Lett | 2012 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/22334034 |
| F3-targeted cisplatin-hydrogel nanoparticles as an effective therapeutic that targets both murine and human ovarian tumor endothelial cells in vivo. | Winer I, Wang S, Lee YE, Fan W, Gong Y, Burgos-Ojeda D, Spahlinger G, Kopelman R, Buckanovich RJ | Cancer research | 20959470 | Cancer Res | 2010 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/20959470 |
| Genome-wide chromatin interactions of the Nanog locus in pluripotency, differentiation, and reprogramming. | Apostolou E, Ferrari F, Walsh RM, Bar-Nur O, Stadtfeld M, Cheloufi S, Stuart HT, Polo JM, Ohsumi TK, Borowsky ML, Kharchenko PV, Park PJ, Hochedlinger K | Cell stem cell | 23665121 | Cell Stem Cell | 2013 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/23665121 |
| A high-efficiency system for the generation and study of human induced pluripotent stem cells. | Maherali N, Ahfeldt T, Rigamonti A, Utikal J, Cowan C, Hochedlinger K | Cell stem cell | 18786420 | Cell Stem Cell | 2008 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/18786420 |
| Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. | Maherali N, Sridharan R, Xie W, Utikal J, Eminli S, Arnold K, Stadtfeld M, Yachechko R, Tchieu J, Jaenisch R, Plath K, Hochedlinger K | Cell stem cell | 18371336 | Cell Stem Cell | 2007 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/18371336 |
| Immortalization eliminates a roadblock during cellular reprogramming into iPS cells. | Utikal J, Polo JM, Stadtfeld M, Maherali N, Kulalert W, Walsh RM, Khalil A, Rheinwald JG, Hochedlinger K | Nature | 19668190 | Nature | 2009 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/19668190 |
| Dose-dependent roles for canonical Wnt signalling in de novo crypt formation and cell cycle properties of the colonic epithelium. | Hirata A, Utikal J, Yamashita S, Aoki H, Watanabe A, Yamamoto T, Okano H, Bardeesy N, Kunisada T, Ushijima T, Hara A, Jaenisch R, Hochedlinger K, Yamada Y | Development (Cambridge, England) | 23222438 | Development | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23222438 |
| Reprogramming of pancreatic beta cells into induced pluripotent stem cells. | Stadtfeld M, Brennand K, Hochedlinger K | Current biology : CB | 18501604 | Curr Biol | 2008 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/18501604 |
| Induced pluripotent stem cell generation using a single lentiviral stem cell cassette. | Sommer CA, Stadtfeld M, Murphy GJ, Hochedlinger K, Kotton DN, Mostoslavsky G | Stem cells (Dayton, Ohio) | 19096035 | Stem Cells | 2009 Mar | https://www.ncbi.nlm.nih.gov/pubmed/19096035 |
| Sox2(+) adult stem and progenitor cells are important for tissue regeneration and survival of mice. | Arnold K, Sarkar A, Yram MA, Polo JM, Bronson R, Sengupta S, Seandel M, Geijsen N, Hochedlinger K | Cell stem cell | 21982232 | Cell Stem Cell | 2011 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/21982232 |
| Tgfbeta signal inhibition cooperates in the induction of iPSCs and replaces Sox2 and cMyc. | Maherali N, Hochedlinger K | Current biology : CB | 19765992 | Curr Biol | 2009 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/19765992 |
| Differentiation stage determines potential of hematopoietic cells for reprogramming into induced pluripotent stem cells. | Eminli S, Foudi A, Stadtfeld M, Maherali N, Ahfeldt T, Mostoslavsky G, Hock H, Hochedlinger K | Nature genetics | 19668214 | Nat Genet | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/19668214 |
| Anti-DNA:RNA antibodies and silicon photonic microring resonators: increased sensitivity for multiplexed microRNA detection. | Qavi AJ, Kindt JT, Gleeson MA, Bailey RC | Analytical chemistry | 21711056 | Anal Chem | 2011 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/21711056 |
| Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology. | Bailey RC | Bioanalysis | 21083072 | Bioanalysis | 2009 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21083072 |
| Multiplexed evaluation of capture agent binding kinetics using arrays of silicon photonic microring resonators. | Byeon JY, Bailey RC | The Analyst | 21085731 | Analyst | 2011 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/21085731 |
| Magnetically-actuated, bead-enhanced silicon photonic immunosensor. | Valera E, McClellan MS, Bailey RC | Analytical methods : advancing methods and applications | 26528374 | Anal Methods | 2015 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/26528374 |
| Subpicogram per milliliter detection of interleukins using silicon photonic microring resonators and an enzymatic signal enhancement strategy. | Kindt JT, Luchansky MS, Qavi AJ, Lee SH, Bailey RC | Analytical chemistry | 24171505 | Anal Chem | 2013 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/24171505 |
| Label-free virus detection using silicon photonic microring resonators. | McClellan MS, Domier LL, Bailey RC | Biosensors & bioelectronics | 22138465 | Biosens Bioelectron | 2012 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/22138465 |
| Label-free technologies for quantitative multiparameter biological analysis. | Qavi AJ, Washburn AL, Byeon JY, Bailey RC | Analytical and bioanalytical chemistry | 19221722 | Anal Bioanal Chem | 2009 May | https://www.ncbi.nlm.nih.gov/pubmed/19221722 |
| Label-free quantitation of a cancer biomarker in complex media using silicon photonic microring resonators. | Washburn AL, Gunn LC, Bailey RC | Analytical chemistry | 19848413 | Anal Chem | 2009 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/19848413 |
| Efficient bioconjugation of protein capture agents to biosensor surfaces using aniline-catalyzed hydrazone ligation. | Byeon JY, Limpoco FT, Bailey RC | Langmuir : the ACS journal of surfaces and colloids | 20809595 | Langmuir | 2010 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/20809595 |
| Characterization of the evanescent field profile and bound mass sensitivity of a label-free silicon photonic microring resonator biosensing platform. | Luchansky MS, Washburn AL, Martin TA, Iqbal M, Gunn LC, Bailey RC | Biosensors & bioelectronics | 20708399 | Biosens Bioelectron | 2010 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/20708399 |
| Isothermal discrimination of single-nucleotide polymorphisms via real-time kinetic desorption and label-free detection of DNA using silicon photonic microring resonator arrays. | Qavi AJ, Mysz TM, Bailey RC | Analytical chemistry | 21834517 | Anal Chem | 2011 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/21834517 |
| Grand challenge commentary: Informative diagnostics for personalized medicine. | Bailey RC | Nature chemical biology | 21079587 | Nat Chem Biol | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21079587 |
| Photonics-on-a-chip: recent advances in integrated waveguides as enabling detection elements for real-world, lab-on-a-chip biosensing applications. | Washburn AL, Bailey RC | The Analyst | 20957245 | Analyst | 2011 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/20957245 |
| Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators. | Marty MT, Sloan CD, Bailey RC, Sligar SG | Analytical chemistry | 22686186 | Anal Chem | 2012 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/22686186 |
| Multiplexed detection and label-free quantitation of microRNAs using arrays of silicon photonic microring resonators. | Qavi AJ, Bailey RC | Angewandte Chemie (International ed. in English) | 20491114 | Angew Chem Int Ed Engl | 2010 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/20491114 |
| Silicon photonic microring resonators for quantitative cytokine detection and T-cell secretion analysis. | Luchansky MS, Bailey RC | Analytical chemistry | 20143780 | Anal Chem | 2010 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/20143780 |
| Quantitative, label-free detection of five protein biomarkers using multiplexed arrays of silicon photonic microring resonators. | Washburn AL, Luchansky MS, Bowman AL, Bailey RC | Analytical chemistry | 20000326 | Anal Chem | 2010 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/20000326 |
| Multiplexed cancer biomarker detection using chip-integrated silicon photonic sensor arrays. | Washburn AL, Shia WW, Lenkeit KA, Lee SH, Bailey RC | The Analyst | 27400767 | Analyst | 2016 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/27400767 |
| Single domain antibodies for the detection of ricin using silicon photonic microring resonator arrays. | Shia WW, Bailey RC | Analytical chemistry | 23268548 | Anal Chem | 2013 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/23268548 |
| High-Q optical sensors for chemical and biological analysis. | Luchansky MS, Bailey RC | Analytical chemistry | 22111937 | Anal Chem | 2012 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/22111937 |
| Real-time monitoring of surface-initiated atom transfer radical polymerization using silicon photonic microring resonators: implications for combinatorial screening of polymer brush growth conditions. | Limpoco FT, Bailey RC | Journal of the American Chemical Society | 21899288 | J Am Chem Soc | 2011 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/21899288 |
| Biomolecular analysis with microring resonators: applications in multiplexed diagnostics and interaction screening. | Kindt JT, Bailey RC | Current opinion in chemical biology | 23871688 | Curr Opin Chem Biol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23871688 |
| Label-free, multiplexed detection of bacterial tmRNA using silicon photonic microring resonators. | Scheler O, Kindt JT, Qavi AJ, Kaplinski L, Glynn B, Barry T, Kurg A, Bailey RC | Biosensors & bioelectronics | 22541813 | Biosens Bioelectron | 2012 Jun-Jul | https://www.ncbi.nlm.nih.gov/pubmed/22541813 |
| Chaperone probes and bead-based enhancement to improve the direct detection of mRNA using silicon photonic sensor arrays. | Kindt JT, Bailey RC | Analytical chemistry | 22913333 | Anal Chem | 2012 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/22913333 |
| Interfacing lipid bilayer nanodiscs and silicon photonic sensor arrays for multiplexed protein-lipid and protein-membrane protein interaction screening. | Sloan CD, Marty MT, Sligar SG, Bailey RC | Analytical chemistry | 23425255 | Anal Chem | 2013 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/23425255 |
| Sizing up the future of microRNA analysis. | Qavi AJ, Kindt JT, Bailey RC | Analytical and bioanalytical chemistry | 20680616 | Anal Bioanal Chem | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20680616 |
| DNA-encoding to improve performance and allow parallel evaluation of the binding characteristics of multiple antibodies in a surface-bound immunoassay format. | Washburn AL, Gomez J, Bailey RC | Analytical chemistry | 21438633 | Anal Chem | 2011 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/21438633 |
| Sensitive on-chip detection of a protein biomarker in human serum and plasma over an extended dynamic range using silicon photonic microring resonators and sub-micron beads. | Luchansky MS, Washburn AL, McClellan MS, Bailey RC | Lab on a chip | 21541438 | Lab Chip | 2011 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/21541438 |
| The mammalian disaggregase machinery: Hsp110 synergizes with Hsp70 and Hsp40 to catalyze protein disaggregation and reactivation in a cell-free system. | Shorter J | PloS one | 22022600 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22022600 |
| RNA-Binding Proteins in Amyotrophic Lateral Sclerosis and Neurodegeneration. | Ugras SE, Shorter J | Neurology research international | 22919483 | Neurol Res Int | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22919483 |
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| Independent optical excitation of distinct neural populations. | Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Boyden ES | Nature methods | 24509633 | Nat Methods | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24509633 |
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| Face-selective electrostatic control of hydrothermal zinc oxide nanowire synthesis. | Joo J, Chow BY, Prakash M, Boyden ES, Jacobson JM | Nature materials | 21743451 | Nat Mater | 2011 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/21743451 |
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| Prosthetic systems for therapeutic optical activation and silencing of genetically-targeted neurons. | Bernstein JG, Han X, Henninger MA, Ko EY, Qian X, Franzesi GT, McConnell JP, Stern P, Desimone R, Boyden ES | Proceedings of SPIE--the International Society for Optical Engineering | 18458792 | Proc SPIE Int Soc Opt Eng | 2008 | https://www.ncbi.nlm.nih.gov/pubmed/18458792 |
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| Multidimensional screening yields channelrhodopsin variants having improved photocurrent and order-of-magnitude reductions in calcium and proton currents. | Cho YK, Park D, Yang A, Chen F, Chuong AS, Klapoetke NC, Boyden ES | The Journal of biological chemistry | 30610117 | J Biol Chem | 2019 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/30610117 |
| Tradition and reinvention: the making and unmaking of herbal medicines in the UK. | Urquiza-Haas N, Cloatre E | Journal of law and society | 35915840 | J Law Soc | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35915840 |
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| Crystal structure of the conserved herpesvirus fusion regulator complex gH-gL. | Chowdary TK, Cairns TM, Atanasiu D, Cohen GH, Eisenberg RJ, Heldwein EE | Nature structural & molecular biology | 20601960 | Nat Struct Mol Biol | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20601960 |
| Data publication with the structural biology data grid supports live analysis. | Meyer PA, Socias S, Key J, Ransey E, Tjon EC, Buschiazzo A, Lei M, Botka C, Withrow J, Neau D, Rajashankar K, Anderson KS, Baxter RH, Blacklow SC, Boggon TJ, Bonvin AM, Borek D, Brett TJ, Caflisch A, Chang CI, Chazin WJ, Corbett KD, Cosgrove MS, Crosson S, Dhe-Paganon S, Di Cera E, Drennan CL, Eck MJ, Eichman BF, Fan QR, Ferré-D'Amaré AR, Fromme JC, Garcia KC, Gaudet R, Gong P, Harrison SC, Heldwein EE, Jia Z, Keenan RJ, Kruse AC, Kvansakul M, McLellan JS, Modis Y, Nam Y, Otwinowski Z, Pai EF, Pereira PJ, Petosa C, Raman CS, Rapoport TA, Roll-Mecak A, Rosen MK, Rudenko G, Schlessinger J, Schwartz TU, Shamoo Y, Sondermann H, Tao YJ, Tolia NH, Tsodikov OV, Westover KD, Wu H, Foster I, Fraser JS, Maia FR, Gonen T, Kirchhausen T, Diederichs K, Crosas M, Sliz P | Nature communications | 26947396 | Nat Commun | 2016 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/26947396 |
| Crystal structure of the herpesvirus inner tegument protein UL37 supports its essential role in control of viral trafficking. | Pitts JD, Klabis J, Richards AL, Smith GA, Heldwein EE | Journal of virology | 24599989 | J Virol | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24599989 |
| Extensive mutagenesis of the HSV-1 gB ectodomain reveals remarkable stability of its postfusion form. | Vitu E, Sharma S, Stampfer SD, Heldwein EE | Journal of molecular biology | 23500487 | J Mol Biol | 2013 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/23500487 |
| Membrane requirement for folding of the herpes simplex virus 1 gB cytodomain suggests a unique mechanism of fusion regulation. | Silverman JL, Greene NG, King DS, Heldwein EE | Journal of virology | 22623783 | J Virol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22623783 |
| Capturing the herpes simplex virus core fusion complex (gB-gH/gL) in an acidic environment. | Cairns TM, Whitbeck JC, Lou H, Heldwein EE, Chowdary TK, Eisenberg RJ, Cohen GH | Journal of virology | 21507973 | J Virol | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21507973 |
| Entry of herpesviruses into cells: more than one way to pull the trigger. | Heldwein EE | Structure (London, England : 1993) | 19217384 | Structure | 2009 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/19217384 |
| Fusion-deficient insertion mutants of herpes simplex virus type 1 glycoprotein B adopt the trimeric postfusion conformation. | Silverman JL, Sharma S, Cairns TM, Heldwein EE | Journal of virology | 19939928 | J Virol | 2010 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19939928 |
| Syncytial phenotype of C-terminally truncated herpes simplex virus type 1 gB is associated with diminished membrane interactions. | Chowdary TK, Heldwein EE | Journal of virology | 20200237 | J Virol | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20200237 |
| Characterization of Vesicular Stomatitis Virus Pseudotypes Bearing Essential Entry Glycoproteins gB, gD, gH, and gL of Herpes Simplex Virus 1. | Rogalin HB, Heldwein EE | Journal of virology | 27605677 | J Virol | 2016 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/27605677 |
| Structural basis of local, pH-dependent conformational changes in glycoprotein B from herpes simplex virus type 1. | Stampfer SD, Lou H, Cohen GH, Eisenberg RJ, Heldwein EE | Journal of virology | 20943984 | J Virol | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20943984 |
| Expression, purification, and crystallization of HSV-1 glycoproteins for structure determination. | Stampfer SD, Heldwein EE | Methods in molecular biology (Clifton, N.J.) | 24671689 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24671689 |
| Expression, Purification, and Crystallization of HSV-1 Glycoproteins for Structure Determination. | White EM, Stampfer SD, Heldwein EE | Methods in molecular biology (Clifton, N.J.) | 31617192 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/31617192 |
| HCMV gB shares structural and functional properties with gB proteins from other herpesviruses. | Sharma S, Wisner TW, Johnson DC, Heldwein EE | Virology | 23089254 | Virology | 2013 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/23089254 |
| Mutations in the cytoplasmic tail of herpes simplex virus 1 gH reduce the fusogenicity of gB in transfected cells. | Silverman JL, Heldwein EE | Journal of virology | 23843635 | J Virol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23843635 |
| Stuck in the middle: structural insights into the role of the gH/gL heterodimer in herpesvirus entry. | Stampfer SD, Heldwein EE | Current opinion in virology | 23107819 | Curr Opin Virol | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23107819 |
| Expression, Purification, and Crystallization of Full-Length HSV-1 gB for Structure Determination. | Cooper RS, Heldwein EE | Methods in molecular biology (Clifton, N.J.) | 31617193 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/31617193 |
| A metastasis biomarker (MetaSite Breast™ Score) is associated with distant recurrence in hormone receptor-positive, HER2-negative early-stage breast cancer. | Sparano JA, Gray R, Oktay MH, Entenberg D, Rohan T, Xue X, Donovan M, Peterson M, Shuber A, Hamilton DA, D'Alfonso T, Goldstein LJ, Gertler F, Davidson NE, Condeelis J, Jones J | NPJ breast cancer | 29138761 | NPJ Breast Cancer | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29138761 |
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| Divergent allosteric control of the IRE1α endoribonuclease using kinase inhibitors. | Wang L, Perera BG, Hari SB, Bhhatarai B, Backes BJ, Seeliger MA, Schürer SC, Oakes SA, Papa FR, Maly DJ | Nature chemical biology | 23086298 | Nat Chem Biol | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23086298 |
| The UPR and cell fate at a glance. | Merksamer PI, Papa FR | Journal of cell science | 20332117 | J Cell Sci | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20332117 |
| Caspase-2 cleavage of BID is a critical apoptotic signal downstream of endoplasmic reticulum stress. | Upton JP, Austgen K, Nishino M, Coakley KM, Hagen A, Han D, Papa FR, Oakes SA | Molecular and cellular biology | 18426910 | Mol Cell Biol | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18426910 |
| IRE1α cleaves select microRNAs during ER stress to derepress translation of proapoptotic Caspase-2. | Upton JP, Wang L, Han D, Wang ES, Huskey NE, Lim L, Truitt M, McManus MT, Ruggero D, Goga A, Papa FR, Oakes SA | Science (New York, N.Y.) | 23042294 | Science | 2012 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/23042294 |
| Signaling cell death from the endoplasmic reticulum stress response. | Shore GC, Papa FR, Oakes SA | Current opinion in cell biology | 21146390 | Curr Opin Cell Biol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21146390 |
| Real-time redox measurements during endoplasmic reticulum stress reveal interlinked protein folding functions. | Merksamer PI, Trusina A, Papa FR | Cell | 19026441 | Cell | 2008 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/19026441 |
| Allosteric inhibition of the IRE1α RNase preserves cell viability and function during endoplasmic reticulum stress. | Ghosh R, Wang L, Wang ES, Perera BG, Igbaria A, Morita S, Prado K, Thamsen M, Caswell D, Macias H, Weiberth KF, Gliedt MJ, Alavi MV, Hari SB, Mitra AK, Bhhatarai B, Schürer SC, Snapp EL, Gould DB, German MS, Backes BJ, Maly DJ, Oakes SA, Papa FR | Cell | 25018104 | Cell | 2014 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/25018104 |
| Druggable sensors of the unfolded protein response. | Maly DJ, Papa FR | Nature chemical biology | 25325700 | Nat Chem Biol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25325700 |
| Chaperone-mediated reflux of secretory proteins to the cytosol during endoplasmic reticulum stress. | Igbaria A, Merksamer PI, Trusina A, Tilahun F, Johnson JR, Brandman O, Krogan NJ, Weissman JS, Papa FR | Proceedings of the National Academy of Sciences of the United States of America | 31101715 | Proc Natl Acad Sci U S A | 2019 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/31101715 |
| IRE1α induces thioredoxin-interacting protein to activate the NLRP3 inflammasome and promote programmed cell death under irremediable ER stress. | Lerner AG, Upton JP, Praveen PV, Ghosh R, Nakagawa Y, Igbaria A, Shen S, Nguyen V, Backes BJ, Heiman M, Heintz N, Greengard P, Hui S, Tang Q, Trusina A, Oakes SA, Papa FR | Cell metabolism | 22883233 | Cell Metab | 2012 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/22883233 |
| Mycobacterial shuttle vectors designed for high-level protein expression in infected macrophages. | Eitson JL, Medeiros JJ, Hoover AR, Srivastava S, Roybal KT, Aínsa JA, Hansen EJ, Gumbo T, van Oers NS | Applied and environmental microbiology | 22820329 | Appl Environ Microbiol | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22820329 |
| Efflux-pump-derived multiple drug resistance to ethambutol monotherapy in Mycobacterium tuberculosis and the pharmacokinetics and pharmacodynamics of ethambutol. | Srivastava S, Musuka S, Sherman C, Meek C, Leff R, Gumbo T | The Journal of infectious diseases | 20210628 | J Infect Dis | 2010 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/20210628 |
| Sterilizing Effect of Ertapenem-Clavulanate in a Hollow-Fiber Model of Tuberculosis and Implications on Clinical Dosing. | van Rijn SP, Srivastava S, Wessels MA, van Soolingen D, Alffenaar JC, Gumbo T | Antimicrobial agents and chemotherapy | 28696238 | Antimicrob Agents Chemother | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28696238 |
| Therapy duration and long-term outcomes in extra-pulmonary tuberculosis. | Pusch T, Pasipanodya JG, Hall RG 2nd, Gumbo T | BMC infectious diseases | 24580808 | BMC Infect Dis | 2014 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/24580808 |
| Redefining multidrug-resistant tuberculosis based on clinical response to combination therapy. | Gumbo T, Pasipanodya JG, Wash P, Burger A, McIlleron H | Antimicrobial agents and chemotherapy | 25092691 | Antimicrob Agents Chemother | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25092691 |
| Clinical and toxicodynamic evidence that high-dose pyrazinamide is not more hepatotoxic than the low doses currently used. | Pasipanodya JG, Gumbo T | Antimicrobial agents and chemotherapy | 20439617 | Antimicrob Agents Chemother | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20439617 |
| Pharmacokinetics-pharmacodynamics of pyrazinamide in a novel in vitro model of tuberculosis for sterilizing effect: a paradigm for faster assessment of new antituberculosis drugs. | Gumbo T, Dona CS, Meek C, Leff R | Antimicrobial agents and chemotherapy | 19451303 | Antimicrob Agents Chemother | 2009 Aug | https://www.ncbi.nlm.nih.gov/pubmed/19451303 |
| Transformation Morphisms and Time-to-Extinction Analysis That Map Therapy Duration From Preclinical Models to Patients With Tuberculosis: Translating From Apples to Oranges. | Magombedze G, Pasipanodya JG, Srivastava S, Deshpande D, Visser ME, Chigutsa E, McIlleron H, Gumbo T | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 30496464 | Clin Infect Dis | 2018 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/30496464 |
| Efficacy Versus Hepatotoxicity of High-dose Rifampin, Pyrazinamide, and Moxifloxacin to Shorten Tuberculosis Therapy Duration: There Is Still Fight in the Old Warriors Yet! | Srivastava S, Deshpande D, Magombedze G, Gumbo T | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 30496465 | Clin Infect Dis | 2018 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/30496465 |
| Susceptibility Testing of Antibiotics That Degrade Faster than the Doubling Time of Slow-Growing Mycobacteria: Ertapenem Sterilizing Effect versus Mycobacterium tuberculosis. | Srivastava S, van Rijn SP, Wessels AM, Alffenaar JW, Gumbo T | Antimicrobial agents and chemotherapy | 26926650 | Antimicrob Agents Chemother | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26926650 |
| Pegylated interferon fractal pharmacokinetics: individualized dosing for hepatitis C virus infection. | Jain MK, Pasipanodya JG, Alder L, Lee WM, Gumbo T | Antimicrobial agents and chemotherapy | 23183434 | Antimicrob Agents Chemother | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23183434 |
| Thioridazine as Chemotherapy for Mycobacterium avium Complex Diseases. | Deshpande D, Srivastava S, Musuka S, Gumbo T | Antimicrobial agents and chemotherapy | 27216055 | Antimicrob Agents Chemother | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27216055 |
| Thioridazine pharmacokinetic-pharmacodynamic parameters "Wobble" during treatment of tuberculosis: a theoretical basis for shorter-duration curative monotherapy with congeners. | Musuka S, Srivastava S, Siyambalapitiyage Dona CW, Meek C, Leff R, Pasipanodya J, Gumbo T | Antimicrobial agents and chemotherapy | 24041886 | Antimicrob Agents Chemother | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24041886 |
| Clofazimine for the Treatment of Mycobacterium kansasii. | Srivastava S, Gumbo T | Antimicrobial agents and chemotherapy | 29844047 | Antimicrob Agents Chemother | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29844047 |
| Serum drug concentrations predictive of pulmonary tuberculosis outcomes. | Pasipanodya JG, McIlleron H, Burger A, Wash PA, Smith P, Gumbo T | The Journal of infectious diseases | 23901086 | J Infect Dis | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/23901086 |
| A Long-term Co-perfused Disseminated Tuberculosis-3D Liver Hollow Fiber Model for Both Drug Efficacy and Hepatotoxicity in Babies. | Srivastava S, Pasipanodya JG, Ramachandran G, Deshpande D, Shuford S, Crosswell HE, Cirrincione KN, Sherman CM, Swaminathan S, Gumbo T | EBioMedicine | 27211555 | EBioMedicine | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27211555 |
| Failure of the azithromycin and ethambutol combination regimen in the hollow-fibre system model of pulmonary Mycobacterium avium infection is due to acquired resistance. | Srivastava S, Deshpande D, Gumbo T | The Journal of antimicrobial chemotherapy | 28922805 | J Antimicrob Chemother | 2017 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/28922805 |
| A new evolutionary and pharmacokinetic-pharmacodynamic scenario for rapid emergence of resistance to single and multiple anti-tuberculosis drugs. | Pasipanodya JG, Gumbo T | Current opinion in pharmacology | 21807559 | Curr Opin Pharmacol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21807559 |
| Rapid drug tolerance and dramatic sterilizing effect of moxifloxacin monotherapy in a novel hollow-fiber model of intracellular Mycobacterium kansasii disease. | Srivastava S, Pasipanodya J, Sherman CM, Meek C, Leff R, Gumbo T | Antimicrobial agents and chemotherapy | 25645830 | Antimicrob Agents Chemother | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25645830 |
| In vitro activity of RX-P873 against Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. | Flamm RK, Rhomberg PR, Jones RN, Farrell DJ | Antimicrobial agents and chemotherapy | 25645834 | Antimicrob Agents Chemother | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25645834 |
| The antibiotic resistance arrow of time: efflux pump induction is a general first step in the evolution of mycobacterial drug resistance. | Schmalstieg AM, Srivastava S, Belkaya S, Deshpande D, Meek C, Leff R, van Oers NS, Gumbo T | Antimicrobial agents and chemotherapy | 22751536 | Antimicrob Agents Chemother | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22751536 |
| An oracle: antituberculosis pharmacokinetics-pharmacodynamics, clinical correlation, and clinical trial simulations to predict the future. | Pasipanodya J, Gumbo T | Antimicrobial agents and chemotherapy | 20937778 | Antimicrob Agents Chemother | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/20937778 |
| New susceptibility breakpoints for first-line antituberculosis drugs based on antimicrobial pharmacokinetic/pharmacodynamic science and population pharmacokinetic variability. | Gumbo T | Antimicrobial agents and chemotherapy | 20086150 | Antimicrob Agents Chemother | 2010 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20086150 |
| Spatial Network Mapping of Pulmonary Multidrug-Resistant Tuberculosis Cavities Using RNA Sequencing. | Dheda K, Lenders L, Srivastava S, Magombedze G, Wainwright H, Raj P, Bush SJ, Pollara G, Steyn R, Davids M, Pooran A, Pennel T, Linegar A, McNerney R, Moodley L, Pasipanodya JG, Turner CT, Noursadeghi M, Warren RM, Wakeland E, Gumbo T | American journal of respiratory and critical care medicine | 30694692 | Am J Respir Crit Care Med | 2019 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/30694692 |
| Viral transduction of the neonatal brain delivers controllable genetic mosaicism for visualising and manipulating neuronal circuits in vivo. | Kim JY, Ash RT, Ceballos-Diaz C, Levites Y, Golde TE, Smirnakis SM, Jankowsky JL | The European journal of neuroscience | 23347239 | Eur J Neurosci | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23347239 |
| Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease. | Badea A, Johnson GA, Jankowsky JL | NeuroImage | 20035883 | Neuroimage | 2010 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/20035883 |
| Genetic suppression of transgenic APP rescues Hypersynchronous network activity in a mouse model of Alzeimer's disease. | Born HA, Kim JY, Savjani RR, Das P, Dabaghian YA, Guo Q, Yoo JW, Schuler DR, Cirrito JR, Zheng H, Golde TE, Noebels JL, Jankowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24623762 | J Neurosci | 2014 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/24623762 |
| Specificity and efficiency of reporter expression in adult neural progenitors vary substantially among nestin-CreER(T2) lines. | Sun MY, Yetman MJ, Lee TC, Chen Y, Jankowsky JL | The Journal of comparative neurology | 24519019 | J Comp Neurol | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24519019 |
| Transgene expression in the Nop-tTA driver line is not inherently restricted to the entorhinal cortex. | Yetman MJ, Lillehaug S, Bjaalie JG, Leergaard TB, Jankowsky JL | Brain structure & function | 25869275 | Brain Struct Funct | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/25869275 |
| Wild-type neural progenitors divide and differentiate normally in an amyloid-rich environment. | Yetman MJ, Jankowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24174666 | J Neurosci | 2013 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/24174666 |
| Impairments in experience-dependent scaling and stability of hippocampal place fields limit spatial learning in a mouse model of Alzheimer's disease. | Zhao R, Fowler SW, Chiang AC, Ji D, Jankowsky JL | Hippocampus | 24752989 | Hippocampus | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24752989 |
| Neuronal aggregates are associated with phenotypic onset in the R6/2 Huntington's disease transgenic mouse. | Cowin RM, Roscic A, Bui N, Graham D, Paganetti P, Jankowsky JL, Weiss A, Paylor R | Behavioural brain research | 22306231 | Behav Brain Res | 2012 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/22306231 |
| Strain background influences neurotoxicity and behavioral abnormalities in mice expressing the tetracycline transactivator. | Han HJ, Allen CC, Buchovecky CM, Yetman MJ, Born HA, Marin MA, Rodgers SP, Song BJ, Lu HC, Justice MJ, Probst FJ, Jankowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22855807 | J Neurosci | 2012 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/22855807 |
| Amyloid-β plaques disrupt axon initial segments. | Marin MA, Ziburkus J, Jankowsky J, Rasband MN | Experimental neurology | 27109181 | Exp Neurol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27109181 |
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| Crystal structure of arginase from Plasmodium falciparum and implications for L-arginine depletion in malarial infection . | Dowling DP, Ilies M, Olszewski KL, Portugal S, Mota MM, Llinás M, Christianson DW | Biochemistry | 20527960 | Biochemistry | 2010 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/20527960 |
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| Central carbon metabolism of Plasmodium parasites. | Olszewski KL, Llinás M | Molecular and biochemical parasitology | 20849882 | Mol Biochem Parasitol | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20849882 |
| Targeting NAD+ metabolism in the human malaria parasite Plasmodium falciparum. | O'Hara JK, Kerwin LJ, Cobbold SA, Tai J, Bedell TA, Reider PJ, Llinás M | PloS one | 24747974 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24747974 |
| Evolution of Fitness Cost-Neutral Mutant PfCRT Conferring P. falciparum 4-Aminoquinoline Drug Resistance Is Accompanied by Altered Parasite Metabolism and Digestive Vacuole Physiology. | Gabryszewski SJ, Dhingra SK, Combrinck JM, Lewis IA, Callaghan PS, Hassett MR, Siriwardana A, Henrich PP, Lee AH, Gnädig NF, Musset L, Llinás M, Egan TJ, Roepe PD, Fidock DA | PLoS pathogens | 27832198 | PLoS Pathog | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27832198 |
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| Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions. | Beck A, Gabler-Pamer L, Alencastro Veiga Cruzeiro G, Lambo S, Englinger B, Shaw ML, Hack OA, Liu I, Haase RD, de Biagi CAO Jr, Baumgartner A, Nascimento Silva AD, Klenner M, Freidel PS, Herms J, von Baumgarten L, Tonn JC, Thon N, Bruckner K, Madlener S, Mayr L, Senfter D, Peyrl A, Slavc I, Lötsch D, Dorfer C, Geyregger R, Amberg N, Haberler C, Mack N, Schwalm B, Pfister SM, Korshunov A, Baird LC, Yang E, Chi SN, Alexandrescu S, Gojo J, Kool M, Hovestadt V, Filbin MG | Nature cancer | 40419763 | Nat Cancer | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40419763 |
| Associations Between Brain Metabolites Measured With MR Spectroscopy and Head Impacts in High School American Football Athletes. | Liu Z, Dudley JA, Diekfuss JA, Ahmed N, Edmondson AD, Cecil KM, Yuan W, Zuleger TM, Slutsky-Ganesh AB, Barber Foss KD, Myer GD, Fleischer CC | Journal of magnetic resonance imaging : JMRI | 39177233 | J Magn Reson Imaging | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39177233 |
| Reply to "Letter to the Editor - Critical Omissions Compromise Internal Validity in Jugular Vein Compression Collar Studies". | Fleischer CC, authors of the original manuscript | Journal of magnetic resonance imaging : JMRI | 39506603 | J Magn Reson Imaging | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39506603 |
| Climate change and neurological diseases: report from the Hot Brain 2: Climate Change and Brain Health meeting, 2024. | Mills JD, Gulcebi MI, Allatt J, Amos A, Atkinson J, Berwick J, Clayton S, Dijk DJ, Doell KC, Ebi K, Fleischer CC, Hajat S, Howarth C, Jones O, Maslin M, Page L, Romanello M, Vanhala L, Sisodiya SM | BMJ neurology open | 39737344 | BMJ Neurol Open | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39737344 |
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| An Update on MR Spectroscopy in Cancer Management: Advances in Instrumentation, Acquisition, and Analysis. | Martinez Luque E, Liu Z, Sung D, Goldberg RM, Agarwal R, Bhattacharya A, Ahmed NS, Allen JW, Fleischer CC | Radiology. Imaging cancer | 38578207 | Radiol Imaging Cancer | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38578207 |
| Estimating muscle activation from EMG using deep learning-based dynamical systems models. | Wimalasena LN, Braun JF, Keshtkaran MR, Hofmann D, Gallego JÁ, Alessandro C, Tresch MC, Miller LE, Pandarinath C | Journal of neural engineering | 35366649 | J Neural Eng | 2022 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/35366649 |
| Reducing power requirements for high-accuracy decoding in iBCIs. | Karpowicz BM, Bhaduri B, Nason-Tomaszewski SR, Jacques BG, Ali YH, Flint RD, Bechefsky PH, Hochberg LR, AuYong N, Slutzky MW, Pandarinath C | Journal of neural engineering | 39423832 | J Neural Eng | 2024 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/39423832 |
| Pseudo-linear summation explains neural geometry of multi-finger movements in human premotor cortex. | Shah NP, Avansino D, Kamdar F, Nicolas C, Kapitonava A, Vargas-Irwin C, Hochberg LR, Pandarinath C, Shenoy KV, Willett FR, Henderson JM | Nature communications | 40442062 | Nat Commun | 2025 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/40442062 |
| A deep learning framework for inference of single-trial neural population dynamics from calcium imaging with subframe temporal resolution. | Zhu F, Grier HA, Tandon R, Cai C, Agarwal A, Giovannucci A, Kaufman MT, Pandarinath C | Nature neuroscience | 36424431 | Nat Neurosci | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36424431 |
| Expressive dynamics models with nonlinear injective readouts enable reliable recovery of latent features from neural activity. | Versteeg C, Sedler AR, McCart JD, Pandarinath C | ArXiv | 37744459 | ArXiv | 2023 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/37744459 |
| Computation-through-Dynamics Benchmark: Simulated datasets and quality metrics for dynamical models of neural activity. | Versteeg C, McCart JD, Ostrow M, Zoltowski DM, Washington CB, Driscoll L, Codol O, Michaels JA, Linderman SW, Sussillo D, Pandarinath C | bioRxiv : the preprint server for biology | 39975240 | bioRxiv | 2025 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/39975240 |
| Expressive architectures enhance interpretability of dynamics-based neural population models. | Sedler AR, Versteeg C, Pandarinath C | Neurons, behavior, data analysis, and theory | 38699512 | Neuron Behav Data Anal Theory | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38699512 |
| Identifying Distinct Neural Features between the Initial and Corrective Phases of Precise Reaching Using AutoLFADS. | Lee WH, Karpowicz BM, Pandarinath C, Rouse AG | The Journal of neuroscience : the official journal of the Society for Neuroscience | 38538142 | J Neurosci | 2024 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/38538142 |
| Spinal interneuron population dynamics underlying flexible pattern generation. | Wimalasena LN, Pandarinath C, Yong NA | bioRxiv : the preprint server for biology | 38948833 | bioRxiv | 2024 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/38948833 |
| Myomatrix arrays for high-definition muscle recording. | Chung B, Zia M, Thomas KA, Michaels JA, Jacob A, Pack A, Williams MJ, Nagapudi K, Teng LH, Arrambide E, Ouellette L, Oey N, Gibbs R, Anschutz P, Lu J, Wu Y, Kashefi M, Oya T, Kersten R, Mosberger AC, O'Connell S, Wang R, Marques H, Mendes AR, Lenschow C, Kondakath G, Kim JJ, Olson W, Quinn KN, Perkins P, Gatto G, Thanawalla A, Coltman S, Kim T, Smith T, Binder-Markey B, Zaback M, Thompson CK, Giszter S, Person A, Goulding M, Azim E, Thakor N, O'Connor D, Trimmer B, Lima SQ, Carey MR, Pandarinath C, Costa RM, Pruszynski JA, Bakir M, Sober SJ | eLife | 38113081 | Elife | 2023 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/38113081 |
| BRAND: a platform for closed-loop experiments with deep network models. | Ali YH, Bodkin K, Rigotti-Thompson M, Patel K, Card NS, Bhaduri B, Nason-Tomaszewski SR, Mifsud DM, Hou X, Nicolas C, Allcroft S, Hochberg LR, Au Yong N, Stavisky SD, Miller LE, Brandman DM, Pandarinath C | Journal of neural engineering | 38579696 | J Neural Eng | 2024 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/38579696 |
| Myomatrix arrays for high-definition muscle recording. | Chung B, Zia M, Thomas KA, Michaels JA, Jacob A, Pack A, Williams MJ, Nagapudi K, Teng LH, Arrambide E, Ouellette L, Oey N, Gibbs R, Anschutz P, Lu J, Wu Y, Kashefi M, Oya T, Kersten R, Mosberger AC, O'Connell S, Wang R, Marques H, Mendes AR, Lenschow C, Kondakath G, Kim JJ, Olson W, Quinn KN, Perkins P, Gatto G, Thanawalla A, Coltman S, Kim T, Smith T, Binder-Markey B, Zaback M, Thompson CK, Giszter S, Person A, Goulding M, Azim E, Thakor N, O'Connor D, Trimmer B, Lima SQ, Carey MR, Pandarinath C, Costa RM, Pruszynski JA, Bakir M, Sober SJ | bioRxiv : the preprint server for biology | 36865176 | bioRxiv | 2023 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/36865176 |
| Stabilizing brain-computer interfaces through alignment of latent dynamics. | Karpowicz BM, Ali YH, Wimalasena LN, Sedler AR, Keshtkaran MR, Bodkin K, Ma X, Rubin DB, Williams ZM, Cash SS, Hochberg LR, Miller LE, Pandarinath C | Nature communications | 40389429 | Nat Commun | 2025 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/40389429 |
| Diffusion-Based Generation of Neural Activity from Disentangled Latent Codes. | McCart JD, Sedler AR, Versteeg C, Mifsud D, Rigotti-Thompson M, Pandarinath C | ArXiv | 39130199 | ArXiv | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39130199 |
| A large-scale neural network training framework for generalized estimation of single-trial population dynamics. | Keshtkaran MR, Sedler AR, Chowdhury RH, Tandon R, Basrai D, Nguyen SL, Sohn H, Jazayeri M, Miller LE, Pandarinath C | Nature methods | 36443486 | Nat Methods | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36443486 |
| High-performance neural population dynamics modeling enabled by scalable computational infrastructure. | Patel AN, Sedler AR, Huang J, Pandarinath C, Gilja V | Journal of open source software | 37520691 | J Open Source Softw | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37520691 |
| A DRG genetic toolkit reveals molecular, morphological, and functional diversity of somatosensory neuron subtypes. | Qi L, Iskols M, Shi D, Reddy P, Walker C, Lezgiyeva K, Voisin T, Pawlak M, Kuchroo VK, Chiu I, Ginty DD, Sharma N | bioRxiv : the preprint server for biology | 37131664 | bioRxiv | 2023 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/37131664 |
| Activity-dependent development of the body's touch receptors. | Santiago C, Siegrist J, Africawala N, Handler A, Tasnim A, Anjum R, Turecek J, Lehnert BP, Renauld S, Choi J, Nolan-Tamariz M, Iskols M, Magee AR, Paradis S, Sharma N, Ginty DD | Neuron | 40381613 | Neuron | 2025 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/40381613 |
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| DRG afferents that mediate physiologic and pathologic mechanosensation from the distal colon. | Wolfson RL, Abdelaziz A, Rankin G, Kushner S, Qi L, Mazor O, Choi S, Sharma N, Ginty DD | Cell | 37541195 | Cell | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37541195 |
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| Self-Aligned Multilayered Nitrogen Vacancy Diamond Nanoparticles for High Spatial Resolution Magnetometry of Microelectronic Currents. | Gokhale Y, Coventry BS, Rogers T, Lines M, Vena A, Phillips J, Zhu T, Bok I, Troche D, Glodowski M, Vareberg A, Bhatt S, Ashtiani AO, Eliceiri KW, Hai A | Nano letters | 40387807 | Nano Lett | 2025 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/40387807 |
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| Positive Controls in Adults and Children Support That Very Few, If Any, New Neurons Are Born in the Adult Human Hippocampus. | Sorrells SF, Paredes MF, Zhang Z, Kang G, Pastor-Alonso O, Biagiotti S, Page CE, Sandoval K, Knox A, Connolly A, Huang EJ, Garcia-Verdugo JM, Oldham MC, Yang Z, Alvarez-Buylla A | The Journal of neuroscience : the official journal of the Society for Neuroscience | 33762407 | J Neurosci | 2021 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/33762407 |
| Cell-Type Specificity of Mosaic Chromosome 1q Gain Resolved by snRNA-seq in a Case of Epilepsy With Hyaline Protoplasmic Astrocytopathy. | Leng K, Cadwell CR, Devine WP, Tihan T, Qi Z, Singhal NS, Glenn OA, Kamiya S, Wiita AP, Berger AC, Shieh JT, Titus EW, Paredes MF, Upadhyay V | Neurology. Genetics | 38586598 | Neurol Genet | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38586598 |
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| β-Adrenergic Signaling Promotes Morphological Maturation of Astrocytes in Female Mice. | Rosenberg MF, Godoy MI, Wade SD, Paredes MF, Zhang Y, Molofsky AV | The Journal of neuroscience : the official journal of the Society for Neuroscience | 37845031 | J Neurosci | 2023 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/37845031 |
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| K(ATP) channel-dependent electrical signaling links capillary pericytes to arterioles during neurovascular coupling. | Isaacs D, Xiang L, Hariharan A, Longden TA | Proceedings of the National Academy of Sciences of the United States of America | 39630860 | Proc Natl Acad Sci U S A | 2024 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/39630860 |
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| Pathologically Entangled: Brain Trauma-Evoked ROS Imbalance Disrupts Kir Channel Function in Distant Peripheral Vessels. | Weir N, Longden TA | Function (Oxford, England) | 35330675 | Function (Oxf) | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35330675 |
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| Tetris in the Nervous System: What Principles of Neuronal Tiling Can Tell Us About How Glia Play the Game. | DeSantis DF, Smith CJ | Frontiers in cellular neuroscience | 34512272 | Front Cell Neurosci | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34512272 |
| A Subset of Oligodendrocyte Lineage Cells Interact With the Developing Dorsal Root Entry Zone During Its Genesis. | Green LA, Gallant RM, Brandt JP, Nichols EL, Smith CJ | Frontiers in cellular neuroscience | 35734217 | Front Cell Neurosci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35734217 |
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| Defining the molecular identity and morphology of glia limitans superficialis astrocytes in vertebrates. | Hasel P, Cooper ML, Marchildon AE, Rufen-Blanchette U, Kim RD, Ma TC, Groh AMR, Hill EJ, Lewis EM, Januszewski M, Light SEW, Smith CJ, Stratton JA, Sloan SA, Kang UJ, Chao MV, Liddelow SA | Cell reports | 39982817 | Cell Rep | 2025 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/39982817 |
| Pioneer Axons Utilize a Dcc Signaling-Mediated Invasion Brake to Precisely Complete Their Pathfinding Odyssey. | Kikel-Coury NL, Green LA, Nichols EL, Zellmer AM, Pai S, Hedlund SA, Marsden KC, Smith CJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34131031 | J Neurosci | 2021 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/34131031 |
| An ultrastructural map of a spinal sensorimotor circuit reveals the potential of astroglial modulation. | Koh ZM, Arceo RA, Hammer J, Chau K, Light SEW, Dolojan A, Januszewski M, Svara F, Smith CJ | bioRxiv : the preprint server for biology | 40093104 | bioRxiv | 2025 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/40093104 |
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| Identification of astroglia-like cardiac nexus glia that are critical regulators of cardiac development and function. | Kikel-Coury NL, Brandt JP, Correia IA, O'Dea MR, DeSantis DF, Sterling F, Vaughan K, Ozcebe G, Zorlutuna P, Smith CJ | PLoS biology | 34793438 | PLoS Biol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34793438 |
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| A call for a unified and multimodal definition of cellular identity in the enteric nervous system. | Majd H, Cesiulis A, Samuel RM, Richter MN, Elder N, Guyer RA, Hao MM, Stamp LA, Goldstein AM, Fattahi F | bioRxiv : the preprint server for biology | 38293133 | bioRxiv | 2024 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/38293133 |
| Generation of Schwann cell derived melanocytes from hPSCs identifies pro-metastatic factors in melanoma. | Samuel RM, Navickas A, Maynard A, Gaylord EA, Garcia K, Bhat S, Majd H, Richter MN, Elder N, Le D, Nguyen P, Shibata B, Llabata ML, Selleri L, Laird DJ, Darmanis S, Goodarzi H, Fattahi F | bioRxiv : the preprint server for biology | 36945537 | bioRxiv | 2023 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/36945537 |
| Combined GWAS and single cell transcriptomics uncover the underlying genes and cell types in disorders of gut-brain interaction. | Majd A, Richter MN, Samuel RM, Cesiulis A, Ghazizadeh Z, Wang J, Fattahi F | medRxiv : the preprint server for health sciences | 37333423 | medRxiv | 2023 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/37333423 |
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| High-Throughput Screening on Primary Tumor-Associated Microglia and Macrophages Identifies HDAC Inhibitors as Enhancers of Phagocytosis and Potent Partners for Immunotherapy in Glioblastoma. | Khalaj M, Gutierrez ML, Nejad P, Raveh T, Fattahi F, Weissman IL | bioRxiv : the preprint server for biology | 40196519 | bioRxiv | 2025 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/40196519 |
| Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. | Ghazizadeh Z, Majd H, Richter M, Samuel R, Zekavat SM, Asgharian H, Farahvashi S, Kalantari A, Ramirez J, Zhao H, Natarajan P, Goodarzi H, Fattahi F | bioRxiv : the preprint server for biology | 32511360 | bioRxiv | 2020 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/32511360 |
| Distinct differentiation trajectories leave lasting impacts on gene regulation and function of V2a interneurons. | Elder NH, Majd A, Bulger EA, Samuel RM, Zholudeva LV, McDevitt TC, Fattahi F | bioRxiv : the preprint server for biology | 39677634 | bioRxiv | 2024 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/39677634 |
| Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. | Samuel RM, Majd H, Richter MN, Ghazizadeh Z, Zekavat SM, Navickas A, Ramirez JT, Asgharian H, Simoneau CR, Bonser LR, Koh KD, Garcia-Knight M, Tassetto M, Sunshine S, Farahvashi S, Kalantari A, Liu W, Andino R, Zhao H, Natarajan P, Erle DJ, Ott M, Goodarzi H, Fattahi F | Cell stem cell | 33232663 | Cell Stem Cell | 2020 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/33232663 |
| Stem Cell-Based Models for Studying the Effects of Cancer and Cancer Therapies on the Peripheral Nervous System. | Richter MN, Fattahi F | Advanced biology | 35666079 | Adv Biol (Weinh) | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35666079 |
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| TWISP: A Transgenic Worm for Interrogating Signal Propagation in C. elegans. | Sharma AK, Randi F, Kumar S, Dvali S, Leifer AM | bioRxiv : the preprint server for biology | 37577580 | bioRxiv | 2023 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/37577580 |
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| A high-throughput method to deliver targeted optogenetic stimulation to moving C. elegans populations. | Liu M, Kumar S, Sharma AK, Leifer AM | PLoS biology | 35089912 | PLoS Biol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35089912 |
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| A Novel Single Vector Intersectional AAV Strategy for Interrogating Cellular Diversity and Brain Function. | Hughes AC, Pollard BG, Xu B, Gammons JW, Chapman P, Bikoff JB, Schwarz LA | bioRxiv : the preprint server for biology | 36798174 | bioRxiv | 2023 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/36798174 |
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| Vimentin Coordinates Protein Turnover at the Aggresome during Neural Stem Cell Quiescence Exit. | Morrow CS, Porter TJ, Xu N, Arndt ZP, Ako-Asare K, Heo HJ, Thompson EAN, Moore DL | Cell stem cell | 32109376 | Cell Stem Cell | 2020 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/32109376 |
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| Autofluorescence is a biomarker of neural stem cell activation state. | Morrow CS, Tweed K, Farhadova S, Walsh AJ, Lear BP, Roopra A, Risgaard RD, Klosa PC, Arndt ZP, Peterson ER, Chi MM, Harris AG, Skala MC, Moore DL | Cell stem cell | 38521057 | Cell Stem Cell | 2024 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/38521057 |
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| Auditory cues reveal intended movement information in middle frontal gyrus neuronal ensemble activity of a person with tetraplegia. | Hosman T, Hynes JB, Saab J, Wilcoxen KG, Buchbinder BR, Schmansky N, Cash SS, Eskandar EN, Simeral JD, Franco B, Kelemen J, Vargas-Irwin CE, Hochberg LR | Scientific reports | 33431994 | Sci Rep | 2021 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33431994 |
| Reward expectation extinction restructures and degrades CA1 spatial maps through loss of a dopaminergic reward proximity signal. | Krishnan S, Heer C, Cherian C, Sheffield MEJ | Nature communications | 36333323 | Nat Commun | 2022 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/36333323 |
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| The Precision of Place Fields Governs Their Fate across Epochs of Experience. | Chiu Y, Dong C, Krishnan S, Sheffield MEJ | eNeuro | 37973379 | eNeuro | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37973379 |
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| Analysis of PEG-lipid anchor length on lipid nanoparticle pharmacokinetics and activity in a mouse model of traumatic brain injury. | Waggoner LE, Miyasaki KF, Kwon EJ | Biomaterials science | 36987922 | Biomater Sci | 2023 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/36987922 |
| Infusible Extracellular Matrix Biomaterial Promotes Vascular Integrity and Modulates the Inflammatory Response in Acute Traumatic Brain Injury. | Diaz MD, Kandell RM, Wu JR, Chen A, Christman KL, Kwon EJ | Advanced healthcare materials | 37390094 | Adv Healthc Mater | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37390094 |
| Targeting the Extracellular Matrix in Traumatic Brain Injury Increases Signal Generation from an Activity-Based Nanosensor. | Kandell RM, Kudryashev JA, Kwon EJ | ACS nano | 34870408 | ACS Nano | 2021 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/34870408 |
| Spatial Measurement and Inhibition of Calpain Activity in Traumatic Brain Injury with an Activity-Based Nanotheranostic Platform. | Madias MI, Stessman LN, Warlof SJ, Kudryashev JA, Kwon EJ | ACS nano | 39236689 | ACS Nano | 2024 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/39236689 |
| PEGylated Multimeric RNA Nanoparticles for siRNA Delivery in Traumatic Brain Injury. | Han S, Yoo W, Carton O, Joo J, Kwon EJ | Small (Weinheim an der Bergstrasse, Germany) | 39498752 | Small | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39498752 |
| Pharmacokinetic Analysis of Peptide-Modified Nanoparticles with Engineered Physicochemical Properties in a Mouse Model of Traumatic Brain Injury. | Waggoner LE, Madias MI, Hurtado AA, Kwon EJ | The AAPS journal.. | 34401968 | AAPS J | 2021 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/34401968 |
| An Activity-Based Nanosensor for Traumatic Brain Injury. | Kudryashev JA, Waggoner LE, Leng HT, Mininni NH, Kwon EJ | ACS sensors | 32100994 | ACS Sens | 2020 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/32100994 |
| Reprograming Clots for In Vivo Chemical Targeting in Traumatic Brain Injury. | Kandell RM, Wu JR, Kwon EJ | Advanced materials (Deerfield Beach, Fla.) | 38780012 | Adv Mater | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38780012 |
| Engineered nanomaterials that exploit blood-brain barrier dysfunction for delivery to the brain. | Wu JR, Hernandez Y, Miyasaki KF, Kwon EJ | Advanced drug delivery reviews | 37054953 | Adv Drug Deliv Rev | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37054953 |
| Porous Silicon Nanoparticles Targeted to the Extracellular Matrix for Therapeutic Protein Delivery in Traumatic Brain Injury. | Waggoner LE, Kang J, Zuidema JM, Vijayakumar S, Hurtado AA, Sailor MJ, Kwon EJ | Bioconjugate chemistry | 36017941 | Bioconjug Chem | 2022 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/36017941 |
| Nanomedicine for Acute Brain Injuries: Insight from Decades of Cancer Nanomedicine. | Kandell RM, Waggoner LE, Kwon EJ | Molecular pharmaceutics | 32584042 | Mol Pharm | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/32584042 |
| An Activity-Based Nanosensor for Minimally-Invasive Measurement of Protease Activity in Traumatic Brain Injury. | Kudryashev JA, Madias MI, Kandell RM, Lin QX, Kwon EJ | Advanced functional materials | 37873031 | Adv Funct Mater | 2023 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/37873031 |
| Mechanobiological Modulation of In Vitro Astrocyte Reactivity Using Variable Gel Stiffness. | C Benincasa J, Madias MI, Kandell RM, Delgado-Garcia LM, Engler AJ, Kwon EJ, Porcionatto MA | ACS biomaterials science & engineering | 38870483 | ACS Biomater Sci Eng | 2024 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/38870483 |
| Robust genome and cell engineering via in vitro and in situ circularized RNAs. | Tong M, Palmer N, Dailamy A, Kumar A, Khaliq H, Han S, Finburgh E, Wing M, Hong C, Xiang Y, Miyasaki K, Portell A, Rainaldi J, Suhardjo A, Nourreddine S, Chew WL, Kwon EJ, Mali P | Nature biomedical engineering | 39187662 | Nat Biomed Eng | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39187662 |
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| Accurate neuron segmentation method for one-photon calcium imaging videos combining convolutional neural networks and clustering. | Bao Y, Gong Y | Communications biology | 39122882 | Commun Biol | 2024 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/39122882 |
| Genetically Encoded Fluorescent Indicators for Imaging Brain Chemistry. | Bi X, Beck C, Gong Y | Biosensors | 33920418 | Biosensors (Basel) | 2021 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/33920418 |
| Rational engineering of ratiometric calcium sensors with bright green and red fluorescent proteins. | Zhang D, Redington E, Gong Y | Communications biology | 34326458 | Commun Biol | 2021 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/34326458 |
| Identifying properties of pattern completion neurons in a computational model of the visual cortex. | Baker CM, Gong Y | PLoS computational biology | 37279242 | PLoS Comput Biol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37279242 |
| A high-speed, bright, red fluorescent voltage sensor to detect neural activity. | Beck C, Gong Y | Scientific reports | 31685893 | Sci Rep | 2019 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/31685893 |
| A Semi-supervised Pipeline for Accurate Neuron Segmentation with Fewer Ground Truth Labels. | Baker CM, Gong Y | eNeuro | 38242690 | eNeuro | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38242690 |
| Segmentation of Neurons from Fluorescence Calcium Recordings Beyond Real-time. | Bao Y, Soltanian-Zadeh S, Farsiu S, Gong Y | Nature machine intelligence | 34485824 | Nat Mach Intell | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34485824 |
| Enhanced genetically encoded voltage indicators advance their applications in neuroscience. | Beck C, Zhang D, Gong Y | Current opinion in biomedical engineering | 32864526 | Curr Opin Biomed Eng | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32864526 |
| Decontaminate Traces From Fluorescence Calcium Imaging Videos Using Targeted Non-negative Matrix Factorization. | Bao Y, Redington E, Agarwal A, Gong Y | Frontiers in neuroscience | 35126042 | Front Neurosci | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35126042 |
| A kinetic-optimized CoChR variant with enhanced high-frequency spiking fidelity. | Bi X, Beck C, Gong Y | Biophysical journal | 36151721 | Biophys J | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36151721 |
| DNP-Assisted NMR Investigation of Proteins at Endogenous Levels in Cellular Milieu. | Costello WN, Xiao Y, Frederick KK | Methods in enzymology | 30638534 | Methods Enzymol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30638534 |
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| Stability of the nitroxide biradical AMUPol in intact and lysed mammalian cells. | Ghosh R, Dumarieh R, Xiao Y, Frederick KK | Journal of magnetic resonance (San Diego, Calif. : 1997) | 35151975 | J Magn Reson | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35151975 |
| Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells. | Lagasca D, Ghosh R, Xiao Y, Frederick KK | bioRxiv : the preprint server for biology | 39605460 | bioRxiv | 2024 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/39605460 |
| In cell NMR reveals cells selectively amplify and structurally remodel amyloid fibrils. | Ansari S, Lagasca D, Dumarieh R, Xiao Y, Krishna S, Li Y, Frederick KK | bioRxiv : the preprint server for biology | 39314304 | bioRxiv | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/39314304 |
| Cryogenic Sample Loading into a Magic Angle Spinning Nuclear Magnetic Resonance Spectrometer that Preserves Cellular Viability. | Ghosh R, Kragelj J, Xiao Y, Frederick KK | Journal of visualized experiments : JoVE | 32955491 | J Vis Exp | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32955491 |
| Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells. | Kragelj J, Ghosh R, Xiao Y, Dumarieh R, Lagasca D, Krishna S, Frederick KK | bioRxiv : the preprint server for biology | 37961511 | bioRxiv | 2025 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/37961511 |
| Michler's hydrol blue elucidates structural differences in prion strains. | Xiao Y, Rocha S, Kitts CC, Reymer A, Beke-Somfai T, Frederick KK, Nordén B | Proceedings of the National Academy of Sciences of the United States of America | 33168711 | Proc Natl Acad Sci U S A | 2020 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/33168711 |
| In-Cell NMR of Intact Mammalian Cells Preserved with the Cryoprotectants DMSO and Glycerol Have Similar DNP Performance. | Xiao Y, Ghosh R, Frederick KK | Frontiers in molecular biosciences | 35145995 | Front Mol Biosci | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35145995 |
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| Structural context modulates the conformational ensemble of the intrinsically disordered amino terminus of α-synuclein. | Dumarieh R, Lagasca D, Krishna S, Kragelj J, Xiao Y, Frederick KK | bioRxiv : the preprint server for biology | 39553926 | bioRxiv | 2024 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/39553926 |
| Structural Context Modulates the Conformational Ensemble of the Intrinsically Disordered Amino Terminus of α-Synuclein. | Dumarieh R, Lagasca D, Krishna S, Kragelj J, Xiao Y, Ansari S, Frederick KK | Journal of the American Chemical Society | 40147456 | J Am Chem Soc | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/40147456 |
| Spatially resolved DNP-assisted NMR illuminates the conformational ensemble of α-synuclein in intact viable cells. | Kragelj J, Ghosh R, Xiao Y, Dumarieh R, Lagasca D, Krishna S, Frederick KK | Proceedings of the National Academy of Sciences of the United States of America | 40465629 | Proc Natl Acad Sci U S A | 2025 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/40465629 |
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| Transcriptional determinants of goal-directed learning and representational drift in the parahippocampal cortex. | McLachlan CA, Lee DG, Kwon O, Delgado KM, Manjrekar N, Yao Z, Zeng H, Tasic B, Chen JL | Cell reports | 39792551 | Cell Rep | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39792551 |
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| PERIRHINAL CORTEX LEARNS A PREDICTIVE MAP (INTERNAL MODEL) OF THE TASK ENVIRONMENT. | Lee DG, McLachlan CA, Nogueira R, Kwon O, Carey AE, House G, Lagani GD, LaMay D, Fusi S, Chen JL | bioRxiv : the preprint server for biology | 36993645 | bioRxiv | 2023 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/36993645 |
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| ActuAtor, a Listeria-inspired molecular tool for physical manipulation of intracellular organizations through de novo actin polymerization. | Nakamura H, Rho E, Lee CT, Itoh K, Deng D, Watanabe S, Razavi S, Matsubayashi HT, Zhu C, Jung E, Rangamani P, Watanabe S, Inoue T | Cell reports | 37734382 | Cell Rep | 2023 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/37734382 |
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| Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. | Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Ogunmowo TH, Ho A, Mackay JP, Ha T, Watanabe S, Robinson PJ | The EMBO journal | 38907032 | EMBO J | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38907032 |
| Ultrastructural membrane dynamics of mouse and human cortical synapses. | Eddings CR, Fan M, Imoto Y, Itoh K, McDonald X, Eilers J, Anderson WS, Worley PF, Lippmann K, Nauen DW, Watanabe S | bioRxiv : the preprint server for biology | 39763840 | bioRxiv | 2024 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/39763840 |
| Asynchronous release sites align with NMDA receptors in mouse hippocampal synapses. | Li S, Raychaudhuri S, Lee SA, Brockmann MM, Wang J, Kusick G, Prater C, Syed S, Falahati H, Ramos R, Bartol TM, Hosy E, Watanabe S | Nature communications | 33514725 | Nat Commun | 2021 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/33514725 |
| Rapid and reversible optogenetic silencing of synaptic transmission by clustering of synaptic vesicles. | Vettkötter D, Schneider M, Goulden BD, Dill H, Liewald J, Zeiler S, Guldan J, Ateş YA, Watanabe S, Gottschalk A | Nature communications | 36535932 | Nat Commun | 2022 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/36535932 |
| Synaptic Vesicle Endocytosis in Different Model Systems. | Gan Q, Watanabe S | Frontiers in cellular neuroscience | 30002619 | Front Cell Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30002619 |
| The Synaptic Vesicle Cycle Revisited: New Insights into the Modes and Mechanisms. | Chanaday NL, Cousin MA, Milosevic I, Watanabe S, Morgan JR | The Journal of neuroscience : the official journal of the Society for Neuroscience | 31619489 | J Neurosci | 2019 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/31619489 |
| Transient docking of synaptic vesicles: Implications and mechanisms. | Kusick GF, Ogunmowo TH, Watanabe S | Current opinion in neurobiology | 35398664 | Curr Opin Neurobiol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35398664 |
| Dynamin 1xA interacts with Endophilin A1 via its spliced long C-terminus for ultrafast endocytosis. | Imoto Y, Xue J, Luo L, Raychaudhuri S, Itoh K, Ma Y, Craft GE, Kwan AH, Mackay JP, Ha T, Watanabe S, Robinson PJ | bioRxiv : the preprint server for biology | 37790502 | bioRxiv | 2023 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/37790502 |
| Membrane mechanics dictate axonal morphology and function. | Griswold JM, Bonilla-Quintana M, Pepper R, Lee CT, Raychaudhuri S, Ma S, Gan Q, Syed S, Zhu C, Bell M, Suga M, Yamaguchi Y, Chéreau R, Nägerl UV, Knott G, Rangamani P, Watanabe S | bioRxiv : the preprint server for biology | 37503105 | bioRxiv | 2023 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/37503105 |
| Dynamin is primed at endocytic sites for ultrafast endocytosis. | Imoto Y, Raychaudhuri S, Ma Y, Fenske P, Sandoval E, Itoh K, Blumrich EM, Matsubayashi HT, Mamer L, Zarebidaki F, Söhl-Kielczynski B, Trimbuch T, Nayak S, Iwasa JH, Liu J, Wu B, Ha T, Inoue T, Jorgensen EM, Cousin MA, Rosenmund C, Watanabe S | Neuron | 35809574 | Neuron | 2022 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/35809574 |
| Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis. | Ogunmowo TH, Jing H, Raychaudhuri S, Kusick GF, Imoto Y, Li S, Itoh K, Ma Y, Jafri H, Dalva MB, Chapman ER, Ha T, Watanabe S, Liu J | Nature communications | 37210439 | Nat Commun | 2023 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/37210439 |
| Membrane mechanics dictate axonal pearls-on-a-string morphology and function. | Griswold JM, Bonilla-Quintana M, Pepper R, Lee CT, Raychaudhuri S, Ma S, Gan Q, Syed S, Zhu C, Bell M, Suga M, Yamaguchi Y, Chéreau R, Nägerl UV, Knott G, Rangamani P, Watanabe S | Nature neuroscience | 39623218 | Nat Neurosci | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39623218 |
| Effects of mexiletine on hyperexcitability in sporadic amyotrophic lateral sclerosis: Preliminary findings from a small phase II randomized controlled trial. | Weiss MD, Macklin EA, McIlduff CE, Vucic S, Wainger BJ, Kiernan MC, Goutman SA, Goyal NA, Rutkove SB, Ladha SS, Chen IA, Harms MB, Brannagan TH, Lacomis D, Zivkovic S, Ma M, Wang LH, Simmons Z, Rivner MH, Shefner JM, Cudkowicz ME, Atassi N, Mexiletine-2 ALS Study Group | Muscle & nerve | 33340120 | Muscle Nerve | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33340120 |
| iPSC motor neurons, but not other derived cell types, capture gene expression changes in postmortem sporadic ALS motor neurons. | Held A, Adler M, Marques C, Reyes CJ, Kavuturu AS, Quadros ARAA, Ndayambaje IS, Lara E, Ward M, Lagier-Tourenne C, Wainger BJ | Cell reports | 37651231 | Cell Rep | 2023 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/37651231 |
| Phenotypic screen identifies the natural product silymarin as a novel anti-inflammatory analgesic. | DuBreuil DM, Lai X, Zhu K, Chahyadinata G, Perner C, Chiang BM, Battenberg A, Sokol CL, Wainger BJ | Molecular pain | 36526437 | Mol Pain | 2023 Jan-Dec | https://www.ncbi.nlm.nih.gov/pubmed/36526437 |
| Heat But Not Mechanical Hypersensitivity Depends on Voltage-Gated Ca(V)2.2 Calcium Channel Activity in Peripheral Axon Terminals Innervating Skin. | DuBreuil DM, Lopez Soto EJ, Daste S, Meir R, Li D, Wainger B, Fleischmann A, Lipscombe D | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34353899 | J Neurosci | 2021 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/34353899 |
| Pharmacological Profiling of Purified Human Stem Cell-Derived and Primary Mouse Motor Neurons. | Moakley D, Koh J, Pereira JD, DuBreuil DM, Devlin AC, Berezovski E, Zhu K, Wainger BJ | Scientific reports | 31346219 | Sci Rep | 2019 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/31346219 |
| Modeling cell-autonomous motor neuron phenotypes in ALS using iPSCs. | Hawrot J, Imhof S, Wainger BJ | Neurobiology of disease | 31759135 | Neurobiol Dis | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31759135 |
| Neuronal STING activation in amyotrophic lateral sclerosis and frontotemporal dementia. | Marques C, Held A, Dorfman K, Sung J, Song C, Kavuturu AS, Aguilar C, Russo T, Oakley DH, Albers MW, Hyman BT, Petrucelli L, Lagier-Tourenne C, Wainger BJ | Acta neuropathologica | 38478117 | Acta Neuropathol | 2024 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/38478117 |
| Effect of Ezogabine on Cortical and Spinal Motor Neuron Excitability in Amyotrophic Lateral Sclerosis: A Randomized Clinical Trial. | Wainger BJ, Macklin EA, Vucic S, McIlduff CE, Paganoni S, Maragakis NJ, Bedlack R, Goyal NA, Rutkove SB, Lange DJ, Rivner MH, Goutman SA, Ladha SS, Mauricio EA, Baloh RH, Simmons Z, Pothier L, Kassis SB, La T, Hall M, Evora A, Klements D, Hurtado A, Pereira JD, Koh J, Celnik PA, Chaudhry V, Gable K, Juel VC, Phielipp N, Marei A, Rosenquist P, Meehan S, Oskarsson B, Lewis RA, Kaur D, Kiskinis E, Woolf CJ, Eggan K, Weiss MD, Berry JD, David WS, Davila-Perez P, Camprodon JA, Pascual-Leone A, Kiernan MC, Shefner JM, Atassi N, Cudkowicz ME | JAMA neurology | 33226425 | JAMA Neurol | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33226425 |
| A high-content platform for physiological profiling and unbiased classification of individual neurons. | DuBreuil DM, Chiang BM, Zhu K, Lai X, Flynn P, Sapir Y, Wainger BJ | Cell reports methods | 34318289 | Cell Rep Methods | 2021 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/34318289 |
| Human sensorimotor organoids derived from healthy and amyotrophic lateral sclerosis stem cells form neuromuscular junctions. | Pereira JD, DuBreuil DM, Devlin AC, Held A, Sapir Y, Berezovski E, Hawrot J, Dorfman K, Chander V, Wainger BJ | Nature communications | 34362895 | Nat Commun | 2021 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/34362895 |
| Functional Electrical Stimulation and the Modulation of the Axon Regeneration Program. | Jara JS, Agger S, Hollis ER 2nd | Frontiers in cell and developmental biology | 33015031 | Front Cell Dev Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33015031 |
| Cortical Reorganization of Sensorimotor Systems and the Role of Intracortical Circuits After Spinal Cord Injury. | Mohammed H, Hollis ER 2nd | Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics | 29882081 | Neurotherapeutics | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29882081 |
| Task-specific modulation of corticospinal neuron activity during motor learning in mice. | Serradj N, Marino F, Moreno-López Y, Bernstein A, Agger S, Soliman M, Sloan A, Hollis E | Nature communications | 37169765 | Nat Commun | 2023 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/37169765 |
| Corticospinal Modulation of Precision Movements. | Marino F, Moreno-López Y, Hollis E | Neuroscience insights | 38680210 | Neurosci Insights | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38680210 |
| A Kinematic Deviation Index (KDI) for Evaluation of Forelimb Function in Rodents. | Torres-Espin A, Bernstein A, Soliman M, Jara JS, Moreno-López Y, Hollis E | bioRxiv : the preprint server for biology | 39386493 | bioRxiv | 2024 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/39386493 |
| Basal Forebrain Cholinergic Neurons Selectively Drive Coordinated Motor Learning in Mice. | Li Y, Hollis E | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34750228 | J Neurosci | 2021 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/34750228 |
| Nicotinic acetylcholine signaling is required for motor learning but not for rehabilitation from spinal cord injury. | Li Y, Hollis Ii ER | Neural regeneration research | 35900431 | Neural Regen Res | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35900431 |
| Acute Extrinsic Activation of the RANKL Pathway Decreases Wound Healing and Functional Recovery After Spinal Cord Injury in Mice. | Vivinetto AL, Bernstein A, Soliman M, Cave JW, Hollis E | Glia | 39828951 | Glia | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39828951 |
| Disruption of ATRX-RNA interactions uncovers roles in ATRX localization and PRC2 function. | Ren W, Medeiros N, Warneford-Thomson R, Wulfridge P, Yan Q, Bian J, Sidoli S, Garcia BA, Skordalakes E, Joyce E, Bonasio R, Sarma K | Nature communications | 32376827 | Nat Commun | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/32376827 |
| Targeted Nuclease Approaches for Mapping Native R-Loops. | Wulfridge P, Yan Q, Sarma K | Methods in molecular biology (Clifton, N.J.) | 35704205 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35704205 |
| Targeting the IRE1α/XBP1s pathway suppresses CARM1-expressing ovarian cancer. | Lin J, Liu H, Fukumoto T, Zundell J, Yan Q, Tang CA, Wu S, Zhou W, Guo D, Karakashev S, Hu CA, Sarma K, Kossenkov AV, Zhang R | Nature communications | 34493732 | Nat Commun | 2021 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/34493732 |
| Targeted Enhancer Activation by a Subunit of the Integrator Complex. | Barbieri E, Trizzino M, Welsh SA, Owens TA, Calabretta B, Carroll M, Sarma K, Gardini A | Molecular cell | 30008316 | Mol Cell | 2018 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/30008316 |
| Proximity labeling identifies a repertoire of site-specific R-loop modulators. | Yan Q, Wulfridge P, Doherty J, Fernandez-Luna JL, Real PJ, Tang HY, Sarma K | Nature communications | 35013239 | Nat Commun | 2022 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/35013239 |
| SF3B1 homeostasis is critical for survival and therapeutic response in T cell leukemia. | Han C, Khodadadi-Jamayran A, Lorch AH, Jin Q, Serafin V, Zhu P, Politanska Y, Sun L, Gutierrez-Diaz BT, Pryzhkova MV, Abdala-Valencia H, Bartom ET, Buldini B, Basso G, Velu SE, Sarma K, Mattamana BB, Cho BK, Obeng RC, Goo YA, Jordan PW, Tsirigos A, Zhou Y, Ntziachristos P | Science advances | 35061527 | Sci Adv | 2022 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/35061527 |
| ATRX histone binding and helicase activities have distinct roles in neuronal differentiation. | Bieluszewska A, Wulfridge P, Doherty J, Ren W, Sarma K | Nucleic acids research | 35998910 | Nucleic Acids Res | 2022 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/35998910 |
| TET deficiency perturbs mature B cell homeostasis and promotes oncogenesis associated with accumulation of G-quadruplex and R-loop structures. | Shukla V, Samaniego-Castruita D, Dong Z, González-Avalos E, Yan Q, Sarma K, Rao A | Nature immunology | 34937926 | Nat Immunol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34937926 |
| A nuclease- and bisulfite-based strategy captures strand-specific R-loops genome-wide. | Wulfridge P, Sarma K | eLife | 33620319 | Elife | 2021 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/33620319 |
| MapR: A Method for Identifying Native R-Loops Genome Wide. | Yan Q, Sarma K | Current protocols in molecular biology | 31943854 | Curr Protoc Mol Biol | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31943854 |
| Mapping Native R-Loops Genome-wide Using a Targeted Nuclease Approach. | Yan Q, Shields EJ, Bonasio R, Sarma K | Cell reports | 31665646 | Cell Rep | 2019 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/31665646 |
| G-quadruplexes associated with R-loops promote CTCF binding. | Wulfridge P, Yan Q, Rell N, Doherty J, Jacobson S, Offley S, Deliard S, Feng K, Phillips-Cremins JE, Gardini A, Sarma K | Molecular cell | 37552993 | Mol Cell | 2023 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/37552993 |
| Modulation of tactile feedback for the execution of dexterous movement. | Conner JM, Bohannon A, Igarashi M, Taniguchi J, Baltar N, Azim E | Science (New York, N.Y.) | 34648327 | Science | 2021 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/34648327 |
| Selective Targeting of a Defined Subpopulation of Corticospinal Neurons using a Novel Klhl14-Cre Mouse Line Enables Molecular and Anatomical Investigations through Development into Maturity. | Lustig J, Lammers A, Kaiser J, Patel P, Raghu A, Conner JM, Nguyen P, Azim E, Sahni V | bioRxiv : the preprint server for biology | 39713479 | bioRxiv | 2024 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/39713479 |
| Gain control in the sensorimotor system. | Azim E, Seki K | Current opinion in physiology | 31403088 | Curr Opin Physiol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31403088 |
| Anipose: A toolkit for robust markerless 3D pose estimation. | Karashchuk P, Rupp KL, Dickinson ES, Walling-Bell S, Sanders E, Azim E, Brunton BW, Tuthill JC | Cell reports | 34592148 | Cell Rep | 2021 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/34592148 |
| Reverse-translational identification of a cerebellar satiation network. | Low AYT, Goldstein N, Gaunt JR, Huang KP, Zainolabidin N, Yip AKK, Carty JRE, Choi JY, Miller AM, Ho HST, Lenherr C, Baltar N, Azim E, Sessions OM, Ch'ng TH, Bruce AS, Martin LE, Halko MA, Brady RO Jr, Holsen LM, Alhadeff AL, Chen AI, Betley JN | Nature | 34789878 | Nature | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34789878 |
| The Cerebellar Nuclei and Dexterous Limb Movements. | Thanawalla AR, Chen AI, Azim E | Neuroscience | 32652173 | Neuroscience | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/32652173 |
| Proprioception. | Tuthill JC, Azim E | Current biology : CB | 29510103 | Curr Biol | 2018 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/29510103 |
| Large-scale capture of hidden fluorescent labels for training generalizable markerless motion capture models. | Butler DJ, Keim AP, Ray S, Azim E | Nature communications | 37752123 | Nat Commun | 2023 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/37752123 |
| The dorsal column nuclei scale mechanical sensitivity in naive and neuropathic pain states. | Upadhyay A, Gradwell MA, Vajtay TJ, Conner J, Sanyal AA, Azadegan C, Patel KR, Thackray JK, Bohic M, Imai F, Ogundare SO, Yoshida Y, Abdus-Saboor I, Azim E, Abraira VE | Cell reports | 40202848 | Cell Rep | 2025 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/40202848 |
| Behavioral and Neural Bases of Tactile Shape Discrimination Learning in Head-Fixed Mice. | Kim J, Erskine A, Cheung JA, Hires SA | Neuron | 33002411 | Neuron | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33002411 |
| Dynamic cues for whisker-based object localization: An analytical solution to vibration during active whisker touch. | Vaxenburg R, Wyche I, Svoboda K, Efros AL, Hires SA | PLoS computational biology | 29584719 | PLoS Comput Biol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29584719 |
| The Sensorimotor Basis of Whisker-Guided Anteroposterior Object Localization in Head-Fixed Mice. | Cheung J, Maire P, Kim J, Sy J, Hires SA | Current biology : CB | 31474537 | Curr Biol | 2019 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/31474537 |
| Posterior amygdala regulates sexual and aggressive behaviors in male mice. | Yamaguchi T, Wei D, Song SC, Lim B, Tritsch NX, Lin D | Nature neuroscience | 32719562 | Nat Neurosci | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32719562 |
| Inhibitory co-transmission from midbrain dopamine neurons relies on presynaptic GABA uptake. | Melani R, Tritsch NX | Cell reports | 35443174 | Cell Rep | 2022 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/35443174 |
| Unraveling the dynamics of dopamine release and its actions on target cells. | Sippy T, Tritsch NX | Trends in neurosciences | 36635111 | Trends Neurosci | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36635111 |
| GABA co-released from striatal dopamine axons dampens phasic dopamine release through autoregulatory GABA(A) receptors. | Patel JC, Sherpa AD, Melani R, Witkovsky P, Wiseman MR, O'Neill B, Aoki C, Tritsch NX, Rice ME | Cell reports | 38431842 | Cell Rep | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38431842 |
| A Hypothalamic Midbrain Pathway Essential for Driving Maternal Behaviors. | Fang YY, Yamaguchi T, Song SC, Tritsch NX, Lin D | Neuron | 29621487 | Neuron | 2018 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/29621487 |
| Cell-type-specific disruption of cortico-striatal circuitry drives repetitive patterns of behavior in fragile X syndrome model mice. | Longo F, Aryal S, Anastasiades PG, Maltese M, Baimel C, Albanese F, Tabor J, Zhu JD, Oliveira MM, Gastaldo D, Bagni C, Santini E, Tritsch NX, Carter AG, Klann E | Cell reports | 37505982 | Cell Rep | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37505982 |
| Dopamine differentially modulates the size of projection neuron ensembles in the intact and dopamine-depleted striatum. | Maltese M, March JR, Bashaw AG, Tritsch NX | eLife | 33983121 | Elife | 2021 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/33983121 |
| Intrinsic dopamine and acetylcholine dynamics in the striatum of mice. | Krok AC, Maltese M, Mistry P, Miao X, Li Y, Tritsch NX | Nature | 37558873 | Nature | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37558873 |
| Acetylcholine waves and dopamine release in the striatum. | Matityahu L, Gilin N, Sarpong GA, Atamna Y, Tiroshi L, Tritsch NX, Wickens JR, Goldberg JA | Nature communications | 37891198 | Nat Commun | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37891198 |
| G protein-coupled receptors cooperate to silence dopamine neurons. | Liu H, Tritsch NX | The Journal of physiology | 36214545 | J Physiol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36214545 |
| Nongenetic Optical Methods for Measuring and Modulating Neuronal Response. | Zimmerman JF, Tian B | ACS nano | 29727159 | ACS Nano | 2018 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/29727159 |
| Texturing Silicon Nanowires for Highly Localized Optical Modulation of Cellular Dynamics. | Fang Y, Jiang Y, Acaron Ledesma H, Yi J, Gao X, Weiss DE, Shi F, Tian B | Nano letters | 29894630 | Nano Lett | 2018 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/29894630 |
| Photoelectrochemical modulation of neuronal activity with free-standing coaxial silicon nanowires. | Parameswaran R, Carvalho-de-Souza JL, Jiang Y, Burke MJ, Zimmerman JF, Koehler K, Phillips AW, Yi J, Adams EJ, Bezanilla F, Tian B | Nature nanotechnology | 29459654 | Nat Nanotechnol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29459654 |
| Alloy-assisted deposition of three-dimensional arrays of atomic gold catalyst for crystal growth studies. | Fang Y, Jiang Y, Cherukara MJ, Shi F, Koehler K, Freyermuth G, Isheim D, Narayanan B, Nicholls AW, Seidman DN, Sankaranarayanan SKRS, Tian B | Nature communications | 29222439 | Nat Commun | 2017 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/29222439 |
| Silicon Nanowires for Intracellular Optical Interrogation with Subcellular Resolution. | Rotenberg MY, Elbaz B, Nair V, Schaumann EN, Yamamoto N, Sarma N, Matino L, Santoro F, Tian B | Nano letters | 31904975 | Nano Lett | 2020 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/31904975 |
| Nanowired Bioelectric Interfaces. | Tian B, Lieber CM | Chemical reviews | 30995019 | Chem Rev | 2019 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/30995019 |
| Soft-Hard Composites for Bioelectric Interfaces. | Lin Y, Fang Y, Yue J, Tian B | Trends in chemistry | 34296076 | Trends Chem | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34296076 |
| Biological Interfaces, Modulation, and Sensing with Inorganic Nano-Bioelectronic Materials. | Schaumann EN, Tian B | Small methods | 34295965 | Small Methods | 2020 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/34295965 |
| Talking to cells: semiconductor nanomaterials at the cellular interface. | Rotenberg MY, Tian B | Advanced biosystems | 30906852 | Adv Biosyst | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30906852 |
| Inorganic semiconductor biointerfaces. | Jiang Y, Tian B | Nature reviews. Materials | 31656635 | Nat Rev Mater | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31656635 |
| Recent advances in bioelectronics chemistry. | Fang Y , Meng L , Prominski A , Schaumann EN , Seebald M , Tian B | Chemical Society reviews | 32672777 | Chem Soc Rev | 2020 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/32672777 |
| Laser writing of nitrogen-doped silicon carbide for biological modulation. | Nair V, Yi J, Isheim D, Rotenberg M, Meng L, Shi F, Chen X, Gao X, Prominski A, Jiang Y, Yue J, Gallagher CT, Seidman DN, Tian B | Science advances | 32937377 | Sci Adv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32937377 |
| Optical stimulation of cardiac cells with a polymer-supported silicon nanowire matrix. | Parameswaran R, Koehler K, Rotenberg MY, Burke MJ, Kim J, Jeong KY, Hissa B, Paul MD, Moreno K, Sarma N, Hayes T, Sudzilovsky E, Park HG, Tian B | Proceedings of the National Academy of Sciences of the United States of America | 30538202 | Proc Natl Acad Sci U S A | 2019 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/30538202 |
| An atlas of nano-enabled neural interfaces. | Acarón Ledesma H, Li X, Carvalho-de-Souza JL, Wei W, Bezanilla F, Tian B | Nature nanotechnology | 31270446 | Nat Nanotechnol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31270446 |
| Rational design of silicon structures for optically controlled multiscale biointerfaces. | Jiang Y, Li X, Liu B, Yi J, Fang Y, Shi F, Gao X, Sudzilovsky E, Parameswaran R, Koehler K, Nair V, Yue J, Guo K, Fang Y, Tsai HM, Freyermuth G, Wong RCS, Kao CM, Chen CT, Nicholls AW, Wu X, Shepherd GMG, Tian B | Nature biomedical engineering | 30906646 | Nat Biomed Eng | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30906646 |
| Nongenetic optical neuromodulation with silicon-based materials. | Jiang Y, Parameswaran R, Li X, Carvalho-de-Souza JL, Gao X, Meng L, Bezanilla F, Shepherd GMG, Tian B | Nature protocols | 30980031 | Nat Protoc | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30980031 |
| Dissecting Biological and Synthetic Soft-Hard Interfaces for Tissue-Like Systems. | Fang Y, Yang X, Lin Y, Shi J, Prominski A, Clayton C, Ostroff E, Tian B | Chemical reviews | 34677943 | Chem Rev | 2022 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/34677943 |
| Nano-enabled cellular engineering for bioelectric studies. | Shi J, Clayton C, Tian B | Nano research | 34295455 | Nano Res | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/34295455 |
| Tracking Longitudinal Rotation of Silicon Nanowires for Biointerfaces. | Lee YV, Wu D, Fang Y, Peng Y, Tian B | Nano letters | 32208712 | Nano Lett | 2020 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/32208712 |
| Living myofibroblast-silicon composites for probing electrical coupling in cardiac systems. | Rotenberg MY, Yamamoto N, Schaumann EN, Matino L, Santoro F, Tian B | Proceedings of the National Academy of Sciences of the United States of America | 31624124 | Proc Natl Acad Sci U S A | 2019 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/31624124 |
| Micelle-enabled self-assembly of porous and monolithic carbon membranes for bioelectronic interfaces. | Fang Y, Prominski A, Rotenberg MY, Meng L, Acarón Ledesma H, Lv Y, Yue J, Schaumann E, Jeong J, Yamamoto N, Jiang Y, Elbaz B, Wei W, Tian B | Nature nanotechnology | 33288948 | Nat Nanotechnol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33288948 |
| Biomimetic Approaches Toward Smart Bio-hybrid Systems. | Luo Z, Weiss DE, Liu Q, Tian B | Nano research | 30906509 | Nano Res | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30906509 |
| Learning from Solar Energy Conversion: Biointerfaces for Artificial Photosynthesis and Biological Modulation. | Lee YV, Tian B | Nano letters | 30888185 | Nano Lett | 2019 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/30888185 |
| Electrical signals in the ER are cell type and stimulus specific with extreme spatial compartmentalization in neurons. | Campbell EP, Abushawish AA, Valdez LA, Bell MK, Haryono M, Rangamani P, Bloodgood BL | Cell reports | 36640310 | Cell Rep | 2023 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/36640310 |
| Sensorimotor Transformations Underlying Variability in Song Intensity during Drosophila Courtship. | Coen P, Xie M, Clemens J, Murthy M | Neuron | 26844835 | Neuron | 2016 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/26844835 |
| Neural network organization for courtship-song feature detection in Drosophila. | Baker CA, McKellar C, Pang R, Nern A, Dorkenwald S, Pacheco DA, Eckstein N, Funke J, Dickson BJ, Murthy M | Current biology : CB | 35793679 | Curr Biol | 2022 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/35793679 |
| Fast intensity adaptation enhances the encoding of sound in Drosophila. | Clemens J, Ozeri-Engelhard N, Murthy M | Nature communications | 29317624 | Nat Commun | 2018 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/29317624 |
| Acoustic Pattern Recognition and Courtship Songs: Insights from Insects. | Baker CA, Clemens J, Murthy M | Annual review of neuroscience | 30786225 | Annu Rev Neurosci | 2019 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/30786225 |
| Quantifying behavior to solve sensorimotor transformations: advances from worms and flies. | Calhoun AJ, Murthy M | Current opinion in neurobiology | 28850885 | Curr Opin Neurobiol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28850885 |
| Experimental and statistical reevaluation provides no evidence for Drosophila courtship song rhythms. | Stern DL, Clemens J, Coen P, Calhoun AJ, Hogenesch JB, Arthur BJ, Murthy M | Proceedings of the National Academy of Sciences of the United States of America | 28851830 | Proc Natl Acad Sci U S A | 2017 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/28851830 |
| Shared Song Detector Neurons in Drosophila Male and Female Brains Drive Sex-Specific Behaviors. | Deutsch D, Clemens J, Thiberge SY, Guan G, Murthy M | Current biology : CB | 31564492 | Curr Biol | 2019 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/31564492 |
| Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression. | Crocker A, Guan XJ, Murphy CT, Murthy M | Cell reports | 27160913 | Cell Rep | 2016 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/27160913 |
| Connecting Neural Codes with Behavior in the Auditory System of Drosophila. | Clemens J, Girardin CC, Coen P, Guan XJ, Dickson BJ, Murthy M | Neuron | 26365767 | Neuron | 2015 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/26365767 |
| Discovery of a New Song Mode in Drosophila Reveals Hidden Structure in the Sensory and Neural Drivers of Behavior. | Clemens J, Coen P, Roemschied FA, Pereira TD, Mazumder D, Aldarondo DE, Pacheco DA, Murthy M | Current biology : CB | 30057309 | Curr Biol | 2018 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/30057309 |
| Singing on the fly: sensorimotor integration and acoustic communication in Drosophila. | Coen P, Murthy M | Current opinion in neurobiology | 26874218 | Curr Opin Neurobiol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26874218 |
| Auditory activity is diverse and widespread throughout the central brain of Drosophila. | Pacheco DA, Thiberge SY, Pnevmatikakis E, Murthy M | Nature neuroscience | 33230320 | Nat Neurosci | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33230320 |
| Cre-dependent selection yields AAV variants for widespread gene transfer to the adult brain. | Deverman BE, Pravdo PL, Simpson BP, Kumar SR, Chan KY, Banerjee A, Wu WL, Yang B, Huber N, Pasca SP, Gradinaru V | Nature biotechnology | 26829320 | Nat Biotechnol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26829320 |
| Archaerhodopsin variants with enhanced voltage-sensitive fluorescence in mammalian and Caenorhabditis elegans neurons. | Flytzanis NC, Bedbrook CN, Chiu H, Engqvist MK, Xiao C, Chan KY, Sternberg PW, Arnold FH, Gradinaru V | Nature communications | 25222271 | Nat Commun | 2014 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/25222271 |
| Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. | Treweek JB, Chan KY, Flytzanis NC, Yang B, Deverman BE, Greenbaum A, Lignell A, Xiao C, Cai L, Ladinsky MS, Bjorkman PJ, Fowlkes CC, Gradinaru V | Nature protocols | 26492141 | Nat Protoc | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26492141 |
| AAV capsid variants with brain-wide transgene expression and decreased liver targeting after intravenous delivery in mouse and marmoset. | Goertsen D, Flytzanis NC, Goeden N, Chuapoco MR, Cummins A, Chen Y, Fan Y, Zhang Q, Sharma J, Duan Y, Wang L, Feng G, Chen Y, Ip NY, Pickel J, Gradinaru V | Nature neuroscience | 34887588 | Nat Neurosci | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34887588 |
| Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology? | Greenbaum A, Jang MJ, Challis C, Gradinaru V | BMC biology | 28946882 | BMC Biol | 2017 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/28946882 |
| Dopaminergic dysfunction in neurodevelopmental disorders: recent advances and synergistic technologies to aid basic research. | Robinson JE, Gradinaru V | Current opinion in neurobiology | 28850815 | Curr Opin Neurobiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28850815 |
| Cholinergic Mesopontine Signals Govern Locomotion and Reward through Dissociable Midbrain Pathways. | Xiao C, Cho JR, Zhou C, Treweek JB, Chan K, McKinney SL, Yang B, Gradinaru V | Neuron | 27100197 | Neuron | 2016 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/27100197 |
| The Jellyfish Cassiopea Exhibits a Sleep-like State. | Nath RD, Bedbrook CN, Abrams MJ, Basinger T, Bois JS, Prober DA, Sternberg PW, Gradinaru V, Goentoro L | Current biology : CB | 28943083 | Curr Biol | 2017 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/28943083 |
| Engineered AAVs for efficient noninvasive gene delivery to the central and peripheral nervous systems. | Chan KY, Jang MJ, Yoo BB, Greenbaum A, Ravi N, Wu WL, Sánchez-Guardado L, Lois C, Mazmanian SK, Deverman BE, Gradinaru V | Nature neuroscience | 28671695 | Nat Neurosci | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28671695 |
| Identification of peripheral neural circuits that regulate heart rate using optogenetic and viral vector strategies. | Rajendran PS, Challis RC, Fowlkes CC, Hanna P, Tompkins JD, Jordan MC, Hiyari S, Gabris-Weber BA, Greenbaum A, Chan KY, Deverman BE, Münzberg H, Ardell JL, Salama G, Gradinaru V, Shivkumar K | Nature communications | 31028266 | Nat Commun | 2019 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/31028266 |
| Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. | Ravindra Kumar S, Miles TF, Chen X, Brown D, Dobreva T, Huang Q, Ding X, Luo Y, Einarsson PH, Greenbaum A, Jang MJ, Deverman BE, Gradinaru V | Nature methods | 32313222 | Nat Methods | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32313222 |
| Use of high-content imaging to quantify transduction of AAV-PHP viruses in the brain following systemic delivery. | Smith EJ, Farshim PP, Flomen R, Jones ST, McAteer SJ, Deverman BE, Gradinaru V, Bates GP | Brain communications | 34131644 | Brain Commun | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34131644 |
| Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics. | Bedbrook CN, Yang KK, Robinson JE, Mackey ED, Gradinaru V, Arnold FH | Nature methods | 31611694 | Nat Methods | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31611694 |
| Directed evolution of a far-red fluorescent rhodopsin. | McIsaac RS, Engqvist MK, Wannier T, Rosenthal AZ, Herwig L, Flytzanis NC, Imasheva ES, Lanyi JK, Balashov SP, Gradinaru V, Arnold FH | Proceedings of the National Academy of Sciences of the United States of America | 25157169 | Proc Natl Acad Sci U S A | 2014 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/25157169 |
| Gut-seeded α-synuclein fibrils promote gut dysfunction and brain pathology specifically in aged mice. | Challis C, Hori A, Sampson TR, Yoo BB, Challis RC, Hamilton AM, Mazmanian SK, Volpicelli-Daley LA, Gradinaru V | Nature neuroscience | 32066981 | Nat Neurosci | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32066981 |
| Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates. | Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan E, Huang SF, Kumar SR, Arokiaraj CM, Plattner V, Campos LJ, Mich J, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore B, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V | bioRxiv : the preprint server for biology | 36711773 | bioRxiv | 2023 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/36711773 |
| Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates. | Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan EE, Huang SF, Ravindra Kumar S, Arokiaraj CM, Plattner VM, Campos LJ, Mich JK, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore BB, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V | Nature communications | 37291094 | Nat Commun | 2023 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/37291094 |
| Genetically Encoded Spy Peptide Fusion System to Detect Plasma Membrane-Localized Proteins In Vivo. | Bedbrook CN, Kato M, Ravindra Kumar S, Lakshmanan A, Nath RD, Sun F, Sternberg PW, Arnold FH, Gradinaru V | Chemistry & biology | 26211362 | Chem Biol | 2015 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26211362 |
| Single-cell phenotyping within transparent intact tissue through whole-body clearing. | Yang B, Treweek JB, Kulkarni RP, Deverman BE, Chen CK, Lubeck E, Shah S, Cai L, Gradinaru V | Cell | 25088144 | Cell | 2014 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/25088144 |
| Extracting structural and functional features of widely distributed biological circuits with single cell resolution via tissue clearing and delivery vectors. | Treweek JB, Gradinaru V | Current opinion in biotechnology | 27393829 | Curr Opin Biotechnol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27393829 |
| Light-guided sectioning for precise in situ localization and tissue interface analysis for brain-implanted optical fibers and GRIN lenses. | Kahan A, Greenbaum A, Jang MJ, Robinson JE, Cho JR, Chen X, Kassraian P, Wagenaar DA, Gradinaru V | Cell reports | 34592157 | Cell Rep | 2021 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/34592157 |
| Ultrafast neuronal imaging of dopamine dynamics with designed genetically encoded sensors. | Patriarchi T, Cho JR, Merten K, Howe MW, Marley A, Xiong WH, Folk RW, Broussard GJ, Liang R, Jang MJ, Zhong H, Dombeck D, von Zastrow M, Nimmerjahn A, Gradinaru V, Williams JT, Tian L | Science (New York, N.Y.) | 29853555 | Science | 2018 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/29853555 |
| Viral Strategies for Targeting the Central and Peripheral Nervous Systems. | Bedbrook CN, Deverman BE, Gradinaru V | Annual review of neuroscience | 29709207 | Annu Rev Neurosci | 2018 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/29709207 |
| Hydrogel-Tissue Chemistry: Principles and Applications. | Gradinaru V, Treweek J, Overton K, Deisseroth K | Annual review of biophysics | 29792820 | Annu Rev Biophys | 2018 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/29792820 |
| A Soluble Fluorescent Binding Assay Reveals PIP(2) Antagonism of TREK-1 Channels. | Cabanos C, Wang M, Han X, Hansen SB | Cell reports | 28793254 | Cell Rep | 2017 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/28793254 |
| Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D. | Petersen EN, Chung HW, Nayebosadri A, Hansen SB | Nature communications | 27976674 | Nat Commun | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27976674 |
| Disruption of palmitate-mediated localization; a shared pathway of force and anesthetic activation of TREK-1 channels. | Petersen EN, Pavel MA, Wang H, Hansen SB | Biochimica et biophysica acta. Biomembranes | 31672538 | Biochim Biophys Acta Biomembr | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31672538 |
| Tools for Understanding Nanoscale Lipid Regulation of Ion Channels. | Robinson CV, Rohacs T, Hansen SB | Trends in biochemical sciences | 31060927 | Trends Biochem Sci | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31060927 |
| Cholesterol Regulation of Membrane Proteins Revealed by Two-Color Super-Resolution Imaging. | Yuan Z, Hansen SB | Membranes | 36837753 | Membranes (Basel) | 2023 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/36837753 |
| Regulation of beta-amyloid production in neurons by astrocyte-derived cholesterol. | Wang H, Kulas JA, Wang C, Holtzman DM, Ferris HA, Hansen SB | Proceedings of the National Academy of Sciences of the United States of America | 34385305 | Proc Natl Acad Sci U S A | 2021 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/34385305 |
| A Molecular Target for an Alcohol Chain-Length Cutoff. | Chung HW, Petersen EN, Cabanos C, Murphy KR, Pavel MA, Hansen AS, Ja WW, Hansen SB | Journal of molecular biology | 30529033 | J Mol Biol | 2019 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/30529033 |
| Lipid agonism: The PIP2 paradigm of ligand-gated ion channels. | Hansen SB | Biochimica et biophysica acta | 25633344 | Biochim Biophys Acta | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25633344 |
| Studies on the mechanism of general anesthesia. | Pavel MA, Petersen EN, Wang H, Lerner RA, Hansen SB | Proceedings of the National Academy of Sciences of the United States of America | 32467161 | Proc Natl Acad Sci U S A | 2020 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/32467161 |
| Mechanical activation of TWIK-related potassium channel by nanoscopic movement and rapid second messenger signaling. | Petersen EN, Pavel MA, Hansen SS, Gudheti M, Wang H, Yuan Z, Murphy KR, Ja W, Ferris HA, Jorgensen E, Hansen SB | eLife | 38407149 | Elife | 2024 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/38407149 |
| Coordinated and Compartmentalized Neuromodulation Shapes Sensory Processing in Drosophila. | Cohn R, Morantte I, Ruta V | Cell | 26687359 | Cell | 2015 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/26687359 |
| A Taste Circuit that Regulates Ingestion by Integrating Food and Hunger Signals. | Yapici N, Cohn R, Schusterreiter C, Ruta V, Vosshall LB | Cell | 27040496 | Cell | 2016 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/27040496 |
| Evolution of a central neural circuit underlies Drosophila mate preferences. | Seeholzer LF, Seppo M, Stern DL, Ruta V | Nature | 29995860 | Nature | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29995860 |
| Multimodal Chemosensory Circuits Controlling Male Courtship in Drosophila. | Clowney EJ, Iguchi S, Bussell JJ, Scheer E, Ruta V | Neuron | 26279475 | Neuron | 2015 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/26279475 |
| Context-dependent representations of movement in Drosophila dopaminergic reinforcement pathways. | Zolin A, Cohn R, Pang R, Siliciano AF, Fairhall AL, Ruta V | Nature neuroscience | 34697455 | Nat Neurosci | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34697455 |
| Distinct Dopamine Receptor Pathways Underlie the Temporal Sensitivity of Associative Learning. | Handler A, Graham TGW, Cohn R, Morantte I, Siliciano AF, Zeng J, Li Y, Ruta V | Cell | 31230716 | Cell | 2019 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/31230716 |
| Three-dimensional scanless holographic optogenetics with temporal focusing (3D-SHOT). | Pégard NC, Mardinly AR, Oldenburg IA, Sridharan S, Waller L, Adesnik H | Nature communications | 29089483 | Nat Commun | 2017 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/29089483 |
| Layer-specific excitation/inhibition balances during neuronal synchronization in the visual cortex. | Adesnik H | The Journal of physiology | 29313982 | J Physiol | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29313982 |
| Cortical gamma band synchronization through somatostatin interneurons. | Veit J, Hakim R, Jadi MP, Sejnowski TJ, Adesnik H | Nature neuroscience | 28481348 | Nat Neurosci | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28481348 |
| Surround Integration Organizes a Spatial Map during Active Sensation. | Pluta SR, Lyall EH, Telian GI, Ryapolova-Webb E, Adesnik H | Neuron | 28504117 | Neuron | 2017 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/28504117 |
| Superficial Layers Suppress the Deep Layers to Fine-tune Cortical Coding. | Pluta SR, Telian GI, Naka A, Adesnik H | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30651326 | J Neurosci | 2019 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/30651326 |
| Cracking the Function of Layers in the Sensory Cortex. | Adesnik H, Naka A | Neuron | 30521778 | Neuron | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30521778 |
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| Complementary networks of cortical somatostatin interneurons enforce layer specific control. | Naka A, Veit J, Shababo B, Chance RK, Risso D, Stafford D, Snyder B, Egladyous A, Chu D, Sridharan S, Mossing DP, Paninski L, Ngai J, Adesnik H | eLife | 30883329 | Elife | 2019 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/30883329 |
| Spatial integration during active tactile sensation drives orientation perception. | Brown J, Oldenburg IA, Telian GI, Griffin S, Voges M, Jain V, Adesnik H | Neuron | 33826906 | Neuron | 2021 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/33826906 |
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| MicroRNA-based conversion of human fibroblasts into striatal medium spiny neurons. | Richner M, Victor MB, Liu Y, Abernathy D, Yoo AS | Nature protocols | 26379228 | Nat Protoc | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26379228 |
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| MicroRNAs Induce a Permissive Chromatin Environment that Enables Neuronal Subtype-Specific Reprogramming of Adult Human Fibroblasts. | Abernathy DG, Kim WK, McCoy MJ, Lake AM, Ouwenga R, Lee SW, Xing X, Li D, Lee HJ, Heuckeroth RO, Dougherty JD, Wang T, Yoo AS | Cell stem cell | 28886366 | Cell Stem Cell | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28886366 |
| Generation of human striatal neurons by microRNA-dependent direct conversion of fibroblasts. | Victor MB, Richner M, Hermanstyne TO, Ransdell JL, Sobieski C, Deng PY, Klyachko VA, Nerbonne JM, Yoo AS | Neuron | 25374357 | Neuron | 2014 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/25374357 |
| Maintenance of age in human neurons generated by microRNA-based neuronal conversion of fibroblasts. | Huh CJ, Zhang B, Victor MB, Dahiya S, Batista LF, Horvath S, Yoo AS | eLife | 27644593 | Elife | 2016 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/27644593 |
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| Redefining the BH3 Death Domain as a 'Short Linear Motif'. | Aouacheria A, Combet C, Tompa P, Hardwick JM | Trends in biochemical sciences | 26541461 | Trends Biochem Sci | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26541461 |
| MicroRNAs Overcome Cell Fate Barrier by Reducing EZH2-Controlled REST Stability during Neuronal Conversion of Human Adult Fibroblasts. | Lee SW, Oh YM, Lu YL, Kim WK, Yoo AS | Developmental cell | 29974865 | Dev Cell | 2018 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/29974865 |
| Mechanistic Insights Into MicroRNA-Induced Neuronal Reprogramming of Human Adult Fibroblasts. | Lu YL, Yoo AS | Frontiers in neuroscience | 30116172 | Front Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30116172 |
| Striatal neurons directly converted from Huntington's disease patient fibroblasts recapitulate age-associated disease phenotypes. | Victor MB, Richner M, Olsen HE, Lee SW, Monteys AM, Ma C, Huh CJ, Zhang B, Davidson BL, Yang XW, Yoo AS | Nature neuroscience | 29403030 | Nat Neurosci | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29403030 |
| MiR-124 synergism with ELAVL3 enhances target gene expression to promote neuronal maturity. | Lu YL, Liu Y, McCoy MJ, Yoo AS | Proceedings of the National Academy of Sciences of the United States of America | 34031238 | Proc Natl Acad Sci U S A | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/34031238 |
| Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. | Cates K, McCoy MJ, Kwon JS, Liu Y, Abernathy DG, Zhang B, Liu S, Gontarz P, Kim WK, Chen S, Kong W, Ho JN, Burbach KF, Gabel HW, Morris SA, Yoo AS | Cell stem cell | 32961143 | Cell Stem Cell | 2021 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/32961143 |
| Imaging large-scale cellular activity in spinal cord of freely behaving mice. | Sekiguchi KJ, Shekhtmeyster P, Merten K, Arena A, Cook D, Hoffman E, Ngo A, Nimmerjahn A | Nature communications | 27121084 | Nat Commun | 2016 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/27121084 |
| Microglia use TAM receptors to detect and engulf amyloid β plaques. | Huang Y, Happonen KE, Burrola PG, O'Connor C, Hah N, Huang L, Nimmerjahn A, Lemke G | Nature immunology | 33859405 | Nat Immunol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33859405 |
| Stepwise recruitment of transcellular and paracellular pathways underlies blood-brain barrier breakdown in stroke. | Knowland D, Arac A, Sekiguchi KJ, Hsu M, Lutz SE, Perrino J, Steinberg GK, Barres BA, Nimmerjahn A, Agalliu D | Neuron | 24746419 | Neuron | 2014 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/24746419 |
| TAM receptors regulate multiple features of microglial physiology. | Fourgeaud L, Través PG, Tufail Y, Leal-Bailey H, Lew ED, Burrola PG, Callaway P, Zagórska A, Rothlin CV, Nimmerjahn A, Lemke G | Nature | 27049947 | Nature | 2016 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/27049947 |
| Phosphatidylserine Exposure Controls Viral Innate Immune Responses by Microglia. | Tufail Y, Cook D, Fourgeaud L, Powers CJ, Merten K, Clark CL, Hoffman E, Ngo A, Sekiguchi KJ, O'Shea CC, Lemke G, Nimmerjahn A | Neuron | 28111081 | Neuron | 2017 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/28111081 |
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| Imaging neuromodulators with high spatiotemporal resolution using genetically encoded indicators. | Patriarchi T, Cho JR, Merten K, Marley A, Broussard GJ, Liang R, Williams J, Nimmerjahn A, von Zastrow M, Gradinaru V, Tian L | Nature protocols | 31732722 | Nat Protoc | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31732722 |
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| Neural dynamics in the orbitofrontal cortex reveal cognitive strategies. | Schiereck SS, Pérez-Rivera DT, Mah A, DeMaegd ML, Ward RM, Hocker D, Savin C, Constantinople CM | bioRxiv : the preprint server for biology | 39554155 | bioRxiv | 2024 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/39554155 |
| Dopamine transients encode reward prediction errors independent of learning rates. | Mah A, Golden CEM, Constantinople CM | Cell reports | 39395170 | Cell Rep | 2024 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/39395170 |
| Dopamine transients encode reward prediction errors independent of learning rates. | Mah A, Golden CEM, Constantinople CM | bioRxiv : the preprint server for biology | 38659861 | bioRxiv | 2024 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/38659861 |
| Distinct value computations support rapid sequential decisions. | Mah A, Schiereck SS, Bossio V, Constantinople CM | bioRxiv : the preprint server for biology | 36993514 | bioRxiv | 2023 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/36993514 |
| Distinct value computations support rapid sequential decisions. | Mah A, Schiereck SS, Bossio V, Constantinople CM | Nature communications | 37989741 | Nat Commun | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/37989741 |
| Independent inhibitory control mechanisms for aggressive motivation and action. | Minakuchi T, Guthman EM, Acharya P, Hinson J, Fleming W, Witten IB, Oline SN, Falkner AL | Nature neuroscience | 38347201 | Nat Neurosci | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38347201 |
| Aggression experience and observation promote shared behavioral and neural changes. | Iravedra-Garcia JM, Guthman EM, Cuturela L, Ocasio-Arce EJ, Pillow JW, Falkner AL | bioRxiv : the preprint server for biology | 39763843 | bioRxiv | 2024 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/39763843 |
| Behavioural and dopaminergic signatures of resilience. | Willmore L, Cameron C, Yang J, Witten IB, Falkner AL | Nature | 36261520 | Nature | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36261520 |
| Neural mechanisms of persistent aggression. | Guthman EM, Falkner AL | Current opinion in neurobiology | 35344844 | Curr Opin Neurobiol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35344844 |
| SLEAP: A deep learning system for multi-animal pose tracking. | Pereira TD, Tabris N, Matsliah A, Turner DM, Li J, Ravindranath S, Papadoyannis ES, Normand E, Deutsch DS, Wang ZY, McKenzie-Smith GC, Mitelut CC, Castro MD, D'Uva J, Kislin M, Sanes DH, Kocher SD, Wang SS, Falkner AL, Shaevitz JW, Murthy M | Nature methods | 35379947 | Nat Methods | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35379947 |
| Toward a neurobiological model of human performance under pressure. | Saikley A, Haroush K | Proceedings of the National Academy of Sciences of the United States of America | 34470823 | Proc Natl Acad Sci U S A | 2021 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/34470823 |
| The synaptic basis of activity-dependent eye-specific competition. | Zhang C, Yadav S, Speer CM | Cell reports | 36753422 | Cell Rep | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36753422 |
| Activity-dependent synapse clustering underlies eye-specific competition in the developing retinogeniculate system. | Zhang C, Vatan T, Speer CM | bioRxiv : the preprint server for biology | 39484601 | bioRxiv | 2024 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/39484601 |
| Volumetric super-resolution imaging by serial ultrasectioning and stochastic optical reconstruction microscopy in mouse neural tissue. | Vatan T, Minehart JA, Zhang C, Agarwal V, Yang J, Speer CM | STAR protocols | 34901889 | STAR Protoc | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34901889 |
| Microanalytical Mass Spectrometry with Super-Resolution Microscopy Reveals a Proteome Transition During Development of the Brain's Circadian Pacemaker. | Choi SB, Vatan T, Alexander TA, Zhang C, Mitchell SM, Speer CM, Nemes P | Analytical chemistry | 37792996 | Anal Chem | 2023 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/37792996 |
| A Picture Worth a Thousand Molecules-Integrative Technologies for Mapping Subcellular Molecular Organization and Plasticity in Developing Circuits. | Minehart JA, Speer CM | Frontiers in synaptic neuroscience | 33469427 | Front Synaptic Neurosci | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33469427 |
| Rapid 3D-STORM imaging of diverse molecular targets in tissue. | Albrecht NE, Jiang D, Akhanov V, Hobson R, Speer CM, Robichaux MA, Samuel MA | Cell reports methods | 35880013 | Cell Rep Methods | 2022 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/35880013 |
| A pheromone receptor in cichlid fish mediates attraction to females but inhibits male parental care. | Li CY, Bowers JM, Alexander TA, Behrens KA, Jackson P, Amini CJ, Juntti SA | Current biology : CB | 39094572 | Curr Biol | 2024 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/39094572 |
| Methods for correcting inference based on outcomes predicted by machine learning. | Wang S, McCormick TH, Leek JT | Proceedings of the National Academy of Sciences of the United States of America | 33208538 | Proc Natl Acad Sci U S A | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33208538 |
| Using Aggregated Relational Data to Feasibly Identify Network Structure without Network Data. | Breza E, Chandrasekhar AG, McCormick TH, Pan M | The American economic review | 34526729 | Am Econ Rev | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34526729 |
| Plasmodium falciparum infection in humans and mosquitoes influence natural Anopheline biting behavior and transmission. | Markwalter CF, Lapp Z, Abel L, Kimachas E, Omollo E, Freedman E, Chepkwony T, Amunga M, McCormick T, Bérubé S, Mangeni JN, Wesolowski A, Obala AA, Taylor SM, Prudhomme O'Meara W | Nature communications | 38816383 | Nat Commun | 2024 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/38816383 |
| Consistently estimating network statistics using aggregated relational data. | Breza E, Chandrasekhar AG, Lubold S, McCormick TH, Pan M | Proceedings of the National Academy of Sciences of the United States of America | 37192169 | Proc Natl Acad Sci U S A | 2023 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37192169 |
| ipd: an R package for conducting inference on predicted data. | Salerno S, Miao J, Afiaz A, Hoffman K, Neufeld A, Lu Q, McCormick TH, Leek JT | Bioinformatics (Oxford, England) | 39898809 | Bioinformatics | 2025 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/39898809 |
| Using Bayesian Latent Gaussian Graphical Models to Infer Symptom Associations in Verbal Autopsies. | Li ZR, McComick TH, Clark SJ | Bayesian analysis | 33273996 | Bayesian Anal | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33273996 |
| Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India. | Arinaminpathy N, Das J, McCormick TH, Mukhopadhyay P, Sircar N | Epidemics | 34171509 | Epidemics | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34171509 |
| Quantifying heterogeneity in SARS-CoV-2 transmission during the lockdown in India. | Arinaminpathy N, Das J, McCormick TH, Mukhopadhyay P, Sircar N | medRxiv : the preprint server for health sciences | 32995809 | medRxiv | 2020 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/32995809 |
| A FLEXIBLE BAYESIAN FRAMEWORK TO ESTIMATE AGE- AND CAUSE-SPECIFIC CHILD MORTALITY OVER TIME FROM SAMPLE REGISTRATION DATA. | Schumacher AE, McCormick TH, Wakefield J, Chu Y, Perin J, Villavicencio F, Simon N, Liu L | The annals of applied statistics | 37621750 | Ann Appl Stat | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/37621750 |
| Comparing the Robustness of Simple Network Scale-Up Method Estimators. | Kunke JP, Laga I, Niu X, McCormick TH | Sociological methodology | 39391075 | Sociol Methodol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39391075 |
| Simultaneous interneuron labeling reveals population-level interactions among parvalbumin, somatostatin, and pyramidal neurons in cortex. | Potter C, Bassi C, Runyan CA | bioRxiv : the preprint server for biology | 36711788 | bioRxiv | 2024 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/36711788 |
| The spatial scale of somatostatin subnetworks increases from sensory to association cortex. | Khoury CF, Fala NG, Runyan CA | Cell reports | 36070697 | Cell Rep | 2022 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/36070697 |
| Local Differences in Network Organization in the Auditory and Parietal Cortex, Revealed with Single Neuron Activation. | Khoury CF, Ferrone M, Runyan CA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39890466 | J Neurosci | 2025 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/39890466 |
| Different state-dependence of population codes across cortex. | Bandi AC, Runyan CA | bioRxiv : the preprint server for biology | 38826351 | bioRxiv | 2024 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/38826351 |
| Arousal and Locomotion Differently Modulate Activity of Somatostatin Neurons across Cortex. | Khoury CF, Fala NG, Runyan CA | eNeuro | 37169583 | eNeuro | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37169583 |
| Simultaneous interneuron labeling reveals cell type-specific, population-level interactions in cortex. | Potter CT, Bassi CD, Runyan CA | iScience | 39280622 | iScience | 2024 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/39280622 |
| Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism. | Ramaswami G, Won H, Gandal MJ, Haney J, Wang JC, Wong CCY, Sun W, Prabhakar S, Mill J, Geschwind DH | Nature communications | 32978376 | Nat Commun | 2020 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/32978376 |
| A computational tool (H-MAGMA) for improved prediction of brain-disorder risk genes by incorporating brain chromatin interaction profiles. | Sey NYA, Hu B, Mah W, Fauni H, McAfee JC, Rajarajan P, Brennand KJ, Akbarian S, Won H | Nature neuroscience | 32152537 | Nat Neurosci | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32152537 |
| Regulatory landscape in brain development and disease. | Spiess K, Won H | Current opinion in genetics & development | 32563855 | Curr Opin Genet Dev | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32563855 |
| Systematic investigation of allelic regulatory activity of schizophrenia-associated common variants. | McAfee JC, Lee S, Lee J, Bell JL, Krupa O, Davis J, Insigne K, Bond ML, Zhao N, Boyle AP, Phanstiel DH, Love MI, Stein JL, Ruzicka WB, Davila-Velderrain J, Kosuri S, Won H | Cell genomics | 37868037 | Cell Genom | 2023 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/37868037 |
| Focus on your locus with a massively parallel reporter assay. | McAfee JC, Bell JL, Krupa O, Matoba N, Stein JL, Won H | Journal of neurodevelopmental disorders | 36085003 | J Neurodev Disord | 2022 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/36085003 |
| Convergence and Divergence of Rare Genetic Disorders on Brain Phenotypes: A Review. | Raznahan A, Won H, Glahn DC, Jacquemont S | JAMA psychiatry | 35767289 | JAMA Psychiatry | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35767289 |
| Advances in profiling chromatin architecture shed light on the regulatory dynamics underlying brain disorders. | Pratt BM, Won H | Seminars in cell & developmental biology | 34483043 | Semin Cell Dev Biol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34483043 |
| Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits. | Sey NYA, Hu B, Iskhakova M, Lee S, Sun H, Shokrian N, Ben Hutta G, Marks JA, Quach BC, Johnson EO, Hancock DB, Akbarian S, Won H | Molecular psychiatry | 35422469 | Mol Psychiatry | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35422469 |
| Schizophrenia-Linked Protein tSNARE1 Regulates Endosomal Trafficking in Cortical Neurons. | Plooster M, Rossi G, Farrell MS, McAfee JC, Bell JL, Ye M, Diering GH, Won H, Gupton SL, Brennwald P | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34642214 | J Neurosci | 2021 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/34642214 |
| Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism. | Matoba N, Liang D, Sun H, Aygün N, McAfee JC, Davis JE, Raffield LM, Qian H, Piven J, Li Y, Kosuri S, Won H, Stein JL | Translational psychiatry | 32747698 | Transl Psychiatry | 2020 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/32747698 |
| Chromatin architecture provides a roadmap to improve our understanding of psychiatric disorders. | Hu B, Won H | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 32859998 | Neuropsychopharmacology | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32859998 |
| Annotating genetic variants to target genes using H-MAGMA. | Sey NYA, Pratt BM, Won H | Nature protocols | 36289406 | Nat Protoc | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36289406 |
| Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders. | Lee S, McAfee JC, Lee J, Gomez A, Ledford AT, Clarke D, Min H, Gerstein MB, Boyle AP, Sullivan PF, Beltran AS, Won H | Cell | 39848247 | Cell | 2025 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/39848247 |
| Limited Association between Schizophrenia Genetic Risk Factors and Transcriptomic Features. | Yu AW, Peery JD, Won H | Genes | 34356078 | Genes (Basel) | 2021 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/34356078 |
| Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. | Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, PsychENCODE Consortium, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH | Nature communications | 34172755 | Nat Commun | 2021 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/34172755 |
| Illuminating links between cis-regulators and trans-acting variants in the human prefrontal cortex. | Liu S, Won H, Clarke D, Matoba N, Khullar S, Mu Y, Wang D, Gerstein M | Genome medicine | 36424644 | Genome Med | 2022 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/36424644 |
| HIV integration in the human brain is linked to microglial activation and 3D genome remodeling. | Plaza-Jennings AL, Valada A, O'Shea C, Iskhakova M, Hu B, Javidfar B, Ben Hutta G, Lambert TY, Murray J, Kassim B, Chandrasekaran S, Chen BK, Morgello S, Won H, Akbarian S | Molecular cell | 36525955 | Mol Cell | 2022 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36525955 |
| Expanding the genetic architecture of nicotine dependence and its shared genetics with multiple traits. | Quach BC, Bray MJ, Gaddis NC, Liu M, Palviainen T, Minica CC, Zellers S, Sherva R, Aliev F, Nothnagel M, Young KA, Marks JA, Young H, Carnes MU, Guo Y, Waldrop A, Sey NYA, Landi MT, McNeil DW, Drichel D, Farrer LA, Markunas CA, Vink JM, Hottenga JJ, Iacono WG, Kranzler HR, Saccone NL, Neale MC, Madden P, Rietschel M, Marazita ML, McGue M, Won H, Winterer G, Grucza R, Dick DM, Gelernter J, Caporaso NE, Baker TB, Boomsma DI, Kaprio J, Hokanson JE, Vrieze S, Bierut LJ, Johnson EO, Hancock DB | Nature communications | 33144568 | Nat Commun | 2020 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/33144568 |
| Chromatin loop dynamics during cellular differentiation are associated with changes to both anchor and internal regulatory features. | Bond ML, Davis ES, Quiroga IY, Dey A, Kiran M, Love MI, Won H, Phanstiel DH | Genome research | 37699658 | Genome Res | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37699658 |
| Impact of schizophrenia GWAS loci converge onto distinct pathways in cortical interneurons vs glutamatergic neurons during development. | Liu D, Zinski A, Mishra A, Noh H, Park GH, Qin Y, Olorife O, Park JM, Abani CP, Park JS, Fung J, Sawaqed F, Coyle JT, Stahl E, Bendl J, Fullard JF, Roussos P, Zhang X, Stanton PK, Yin C, Huang W, Kim HY, Won H, Cho JH, Chung S | Molecular psychiatry | 35701597 | Mol Psychiatry | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35701597 |
| Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia. | Wen J, Trost B, Engchuan W, Halvorsen M, Pallotto LM, Mitina A, Ancalade N, Farrell M, Backstrom I, Guo K, Pellecchia G, Thiruvahindrapuram B, Giusti-Rodriguez P, Rosen JD, Li Y, Won H, Magnusson PKE, Gyllensten U, Bassett AS, Hultman CM, Sullivan PF, Yuen RKC, Szatkiewicz JP | Molecular psychiatry | 36380236 | Mol Psychiatry | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36380236 |
| Neuropod Cells: The Emerging Biology of Gut-Brain Sensory Transduction. | Kaelberer MM, Rupprecht LE, Liu WW, Weng P, Bohórquez DV | Annual review of neuroscience | 32101483 | Annu Rev Neurosci | 2020 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/32101483 |
| Deciphering visceral instincts: a scientific quest to unravel food choices from molecules to mind. | Alway E, Reicher N, Bohórquez DV | Genes & development | 39362782 | Genes Dev | 2024 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/39362782 |
| The nerve not taken. | Rupprecht LE, Bohórquez DV | Cell metabolism | 33657390 | Cell Metab | 2021 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/33657390 |
| Viscera affectum anno: the gut beyond eating behaviours. | Bohórquez DV | Nature reviews. Gastroenterology & hepatology | 33262502 | Nat Rev Gastroenterol Hepatol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33262502 |
| Multifunctional microelectronic fibers enable wireless modulation of gut and brain neural circuits. | Sahasrabudhe A, Rupprecht LE, Orguc S, Khudiyev T, Tanaka T, Sands J, Zhu W, Tabet A, Manthey M, Allen H, Loke G, Antonini MJ, Rosenfeld D, Park J, Garwood IC, Yan W, Niroui F, Fink Y, Chandrakasan A, Bohórquez DV, Anikeeva P | Nature biotechnology | 37349522 | Nat Biotechnol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37349522 |
| The preference for sugar over sweetener depends on a gut sensor cell. | Buchanan KL, Rupprecht LE, Kaelberer MM, Sahasrabudhe A, Klein ME, Villalobos JA, Liu WW, Yang A, Gelman J, Park S, Anikeeva P, Bohórquez DV | Nature neuroscience | 35027761 | Nat Neurosci | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35027761 |
| The neural basis of sugar preference. | Liu WW, Bohórquez DV | Nature reviews. Neuroscience | 35879409 | Nat Rev Neurosci | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35879409 |
| Interfacing behavioral and neural circuit models for habit formation. | Lerner TN | Journal of neuroscience research | 31916623 | J Neurosci Res | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31916623 |
| Chronically dysregulated corticosterone impairs dopaminergic transmission in the dorsomedial striatum by sex-divergent mechanisms. | Holloway AL, Schaid MD, Lerner TN | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 36810463 | Neuropsychopharmacology | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/36810463 |
| How Dopamine Enables Learning from Aversion. | Lopez GC, Lerner TN | Current opinion in behavioral sciences | 39719969 | Curr Opin Behav Sci | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39719969 |
| Region-specific nucleus accumbens dopamine signals encode distinct aspects of avoidance learning. | Lopez GC, Van Camp LD, Kovaleski RF, Schaid MD, Sherathiya VN, Cox JM, Lerner TN | Current biology : CB | 40267916 | Curr Biol | 2025 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/40267916 |
| Parvalbumin(+) and Npas1(+) Pallidal Neurons Have Distinct Circuit Topology and Function. | Pamukcu A, Cui Q, Xenias HS, Berceau BL, Augustine EC, Fan I, Chalasani S, Hantman AW, Lerner TN, Boca SM, Chan CS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 32868462 | J Neurosci | 2020 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/32868462 |
| GuPPy, a Python toolbox for the analysis of fiber photometry data. | Sherathiya VN, Schaid MD, Seiler JL, Lopez GC, Lerner TN | Scientific reports | 34930955 | Sci Rep | 2021 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/34930955 |
| Dopamine, Updated: Reward Prediction Error and Beyond. | Lerner TN, Holloway AL, Seiler JL | Current opinion in neurobiology | 33197709 | Curr Opin Neurobiol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33197709 |
| Editorial: Dopamine Neuron Diversity in Circuits and Diseases. | Poulin JF, Lerner TN, Howe MW | Frontiers in neural circuits | 35310549 | Front Neural Circuits | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35310549 |
| Hidden variables in stress neurobiology research. | Holloway AL, Lerner TN | Trends in neurosciences | 37985263 | Trends Neurosci | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37985263 |
| Dopamine signaling in the dorsomedial striatum promotes compulsive behavior. | Seiler JL, Cosme CV, Sherathiya VN, Schaid MD, Bianco JM, Bridgemohan AS, Lerner TN | Current biology : CB | 35134327 | Curr Biol | 2022 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/35134327 |
| UCSC Cell Browser: visualize your single-cell data. | Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M | Bioinformatics (Oxford, England) | 34244710 | Bioinformatics | 2021 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/34244710 |
| Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex. | Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS | bioRxiv : the preprint server for biology | 36824845 | bioRxiv | 2023 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/36824845 |
| Human-specific genetics: new tools to explore the molecular and cellular basis of human evolution. | Pollen AA, Kilik U, Lowe CB, Camp JG | Nature reviews. Genetics | 36737647 | Nat Rev Genet | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36737647 |
| Comparative landscape of genetic dependencies in human and chimpanzee stem cells. | She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA | bioRxiv : the preprint server for biology | 36993685 | bioRxiv | 2023 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/36993685 |
| Mapping cis- and trans-regulatory target genes of human-specific deletions. | Fair T, Pavlovic BJ, Swope D, Castillo OE, Schaefer NK, Pollen AA | bioRxiv : the preprint server for biology | 38234800 | bioRxiv | 2024 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/38234800 |
| Massively parallel characterization of regulatory elements in the developing human cortex. | Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, PsychENCODE Consortium‡, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS, PsychENCODE Consortium | Science (New York, N.Y.) | 38781390 | Science | 2024 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/38781390 |
| Conservation, alteration, and redistribution of mammalian striatal interneurons. | Corrigan EK, DeBerardine M, Poddar A, Turrero García M, Schmitz MT, Harwell CC, Paredes MF, Krienen FM, Pollen AA | bioRxiv : the preprint server for biology | 39131311 | bioRxiv | 2024 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/39131311 |
| Machine learning dissection of human accelerated regions in primate neurodevelopment. | Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, Ullian EM, Kriegstein A, Rubenstein JL, Shendure J, Pollen AA, Ahituv N, Pollard KS | Neuron | 36640767 | Neuron | 2023 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36640767 |
| Comparative landscape of genetic dependencies in human and chimpanzee stem cells. | She R, Fair T, Schaefer NK, Saunders RA, Pavlovic BJ, Weissman JS, Pollen AA | Cell | 37343560 | Cell | 2023 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/37343560 |
| CellBouncer, A Unified Toolkit for Single-Cell Demultiplexing and Ambient RNA Analysis, Reveals Hominid Mitochondrial Incompatibilities. | Schaefer NK, Pavlovic BJ, Pollen AA | bioRxiv : the preprint server for biology | 40166335 | bioRxiv | 2025 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/40166335 |
| Rethinking nomenclature for interspecies cell fusions. | Pavlovic BJ, Fox D, Schaefer NK, Pollen AA | Nature reviews. Genetics | 35082442 | Nat Rev Genet | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35082442 |
| Reverse engineering human brain evolution using organoid models. | Mostajo-Radji MA, Schmitz MT, Montoya ST, Pollen AA | Brain research | 31809699 | Brain Res | 2020 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/31809699 |
| Genetic architecture of human brain evolution. | Fair T, Pollen AA | Current opinion in neurobiology | 37003107 | Curr Opin Neurobiol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37003107 |
| Three-dimensional genome rewiring in loci with human accelerated regions. | Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium§, Nowakowski T, Ahituv N, Pollen A, Pollard KS | Science (New York, N.Y.) | 37104607 | Science | 2023 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/37104607 |
| INTERSPECIES ORGANOIDS REVEAL HUMAN-SPECIFIC MOLECULAR FEATURES OF DOPAMINERGIC NEURON DEVELOPMENT AND VULNERABILITY. | Nolbrant S, Wallace JL, Ding J, Zhu T, Sevetson JL, Kajtez J, Baldacci IA, Corrigan EK, Hoglin K, McMullen R, Schmitz MT, Breevoort A, Swope D, Wu F, Pavlovic BJ, Salama SR, Kirkeby A, Huang H, Schaefer NK, Pollen AA | bioRxiv : the preprint server for biology | 39605599 | bioRxiv | 2024 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/39605599 |
| The lab on lockdown: thinking back and looking ahead. | Poe GR, Cai DJ | Nature reviews. Neuroscience | 32699293 | Nat Rev Neurosci | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32699293 |
| The role of intrinsic excitability in the evolution of memory: Significance in memory allocation, consolidation, and updating. | Chen L, Cummings KA, Mau W, Zaki Y, Dong Z, Rabinowitz S, Clem RL, Shuman T, Cai DJ | Neurobiology of learning and memory | 32512183 | Neurobiol Learn Mem | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32512183 |
| Chronotate: An open-source tool for manual timestamping and quantification of animal behavior. | Philipsberg PA, Christenson Wick Z, Diego KS, Vaughan N, Galas A, Jurkowski A, Feng Y, Vetere LM, Chen L, Soler I, Cai DJ, Shuman T | Neuroscience letters | 37619698 | Neurosci Lett | 2023 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/37619698 |
| Minian, an open-source miniscope analysis pipeline. | Dong Z, Mau W, Feng Y, Pennington ZT, Chen L, Zaki Y, Rajan K, Shuman T, Aharoni D, Cai DJ | eLife | 35642786 | Elife | 2022 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/35642786 |
| Chemotagging: a chemogenetic approach for identifying cell types with in vivo calcium imaging. | Ko B, Bacon ME, Zaki Y, Cai DJ | bioRxiv : the preprint server for biology | 39651295 | bioRxiv | 2024 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/39651295 |
| Offline ensemble co-reactivation links memories across days. | Zaki Y, Pennington ZT, Morales-Rodriguez D, Bacon ME, Ko B, Francisco TR, LaBanca AR, Sompolpong P, Dong Z, Lamsifer S, Chen HT, Carrillo Segura S, Christenson Wick Z, Silva AJ, Rajan K, van der Meer M, Fenton A, Shuman T, Cai DJ | Nature | 39506117 | Nature | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39506117 |
| Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior. | Pennington ZT, LaBanca AR, Sompolpong P, Abdel-Raheim SD, Ko B, Christenson Wick Z, Feng Y, Dong Z, Francisco TR, Bacon ME, Chen L, Fulton SL, Maze I, Shuman T, Cai DJ | Cell reports | 39427320 | Cell Rep | 2024 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/39427320 |
| Progressive Excitability Changes in the Medial Entorhinal Cortex in the 3xTg Mouse Model of Alzheimer's Disease Pathology. | Chen L, Christenson Wick Z, Vetere LM, Vaughan N, Jurkowski A, Galas A, Diego KS, Philipsberg PA, Soler I, Feng Y, Cai DJ, Shuman T | The Journal of neuroscience : the official journal of the Society for Neuroscience | 37714705 | J Neurosci | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/37714705 |
| A distinct signaling pathway in parvalbumin-positive interneurons controls flexible memory updating. | Cai DJ, Shuman T | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 35236915 | Neuropsychopharmacology | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35236915 |
| ezTrack-A Step-by-Step Guide to Behavior Tracking. | Pennington ZT, Diego KS, Francisco TR, LaBanca AR, Lamsifer SI, Liobimova O, Shuman T, Cai DJ | Current protocols | 34610215 | Curr Protoc | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34610215 |
| The brain in motion: How ensemble fluidity drives memory-updating and flexibility. | Mau W, Hasselmo ME, Cai DJ | eLife | 33372892 | Elife | 2020 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/33372892 |
| Creating Space for Synaptic Formation-A New Role for Microglia in Synaptic Plasticity. | Zaki Y, Cai DJ | Cell | 32707091 | Cell | 2020 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/32707091 |
| Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior. | Pennington ZT, LaBanca AR, Sompolpong P, Abdel-Raheim SD, Ko B, Christenson Wick Z, Feng Y, Dong Z, Francisco TR, Bacon ME, Chen L, Fulton SL, Maze I, Shuman T, Cai DJ | bioRxiv : the preprint server for biology | 36945605 | bioRxiv | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/36945605 |
| Aversive experience drives offline ensemble reactivation to link memories across days. | Zaki Y, Pennington ZT, Morales-Rodriguez D, Francisco TR, LaBanca AR, Dong Z, Lamsifer S, Segura SC, Chen HT, Wick ZC, Silva AJ, van der Meer M, Shuman T, Fenton A, Rajan K, Cai DJ | bioRxiv : the preprint server for biology | 36993254 | bioRxiv | 2023 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/36993254 |
| Progressive excitability changes in the medial entorhinal cortex in the 3xTg mouse model of Alzheimer's disease pathology. | Chen L, Wick ZC, Vetere LM, Vaughan N, Jurkowski A, Galas A, Diego KS, Philipsberg P, Cai DJ, Shuman T | bioRxiv : the preprint server for biology | 37398359 | bioRxiv | 2023 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/37398359 |
| Drift of neural ensembles driven by slow fluctuations of intrinsic excitability. | Delamare G, Zaki Y, Cai DJ, Clopath C | eLife | 38712831 | Elife | 2024 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/38712831 |
| A Double Hit of Social and Economic Stress in Mice Precipitates Changes in Decision-Making Strategies. | Durand-de Cuttoli R, Martínez-Rivera FJ, Li L, Minier-Toribio A, Dong Z, Cai DJ, Russo SJ, Nestler EJ, Sweis BM | Biological psychiatry | 38141911 | Biol Psychiatry | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38141911 |
| Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy. | Feng Y, Diego KS, Dong Z, Wick ZC, Page-Harley L, Page-Harley V, Schnipper J, Lamsifer SI, Pennington ZT, Vetere LM, Philipsberg PA, Soler I, Jurkowski A, Rosado CJ, Khan NN, Cai DJ, Shuman T | bioRxiv : the preprint server for biology | 38559224 | bioRxiv | 2024 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/38559224 |
| Simultaneous dual-color calcium imaging in freely-behaving mice. | Dong Z, Feng Y, Diego K, Baggetta AM, Sweis BM, Pennington ZT, Lamsifer SI, Zaki Y, Sangiuliano F, Philipsberg PA, Morales-Rodriguez D, Kircher D, Slesinger P, Shuman T, Aharoni D, Cai DJ | bioRxiv : the preprint server for biology | 39005306 | bioRxiv | 2024 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/39005306 |
| Medial entorhinal-hippocampal desynchronization parallels the emergence of memory impairment in a mouse model of Alzheimer's disease pathology. | Vetere LM, Galas AM, Vaughan N, Feng Y, Wick ZC, Philipsberg PA, Liobimova O, Fernandez-Ruiz A, Cai DJ, Shuman T | bioRxiv : the preprint server for biology | 39868201 | bioRxiv | 2025 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/39868201 |
| Propranolol Inhibits Reactivation of Fear Memory. | Pennington ZT, Cai DJ | Biological psychiatry | 34082886 | Biol Psychiatry | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/34082886 |
| Ensemble-specific deficit in neuronal intrinsic excitability in aged mice. | Chen L, Francisco TR, Baggetta AM, Zaki Y, Ramirez S, Clem RL, Shuman T, Cai DJ | Neurobiology of aging | 36652783 | Neurobiol Aging | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36652783 |
| Memory engram stability and flexibility. | Zaki Y, Cai DJ | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 39300271 | Neuropsychopharmacology | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39300271 |
| An anterior hypothalamic circuit gates stress vulnerability. | Pennington ZT, LaBanca AR, Abdel-Raheim SD, Bacon ME, Mahmoud AN, Sompolpong P, Baggetta AM, Zaki Y, Ko B, Dong Z, Smith AC, Kenny PJ, Cai DJ | bioRxiv : the preprint server for biology | 39554090 | bioRxiv | 2024 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/39554090 |
| Dynamic and heterogeneous neural ensembles contribute to a memory engram. | Sweis BM, Mau W, Rabinowitz S, Cai DJ | Current opinion in neurobiology | 33388602 | Curr Opin Neurobiol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33388602 |
| ezTrack: An open-source video analysis pipeline for the investigation of animal behavior. | Pennington ZT, Dong Z, Feng Y, Vetere LM, Page-Harley L, Shuman T, Cai DJ | Scientific reports | 31882950 | Sci Rep | 2019 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/31882950 |
| Breakdown of spatial coding and interneuron synchronization in epileptic mice. | Shuman T, Aharoni D, Cai DJ, Lee CR, Chavlis S, Page-Harley L, Vetere LM, Feng Y, Yang CY, Mollinedo-Gajate I, Chen L, Pennington ZT, Taxidis J, Flores SE, Cheng K, Javaherian M, Kaba CC, Rao N, La-Vu M, Pandi I, Shtrahman M, Bakhurin KI, Masmanidis SC, Khakh BS, Poirazi P, Silva AJ, Golshani P | Nature neuroscience | 31907437 | Nat Neurosci | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31907437 |
| Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. | Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S | Nature communications | 34389722 | Nat Commun | 2021 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/34389722 |
| Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy. | Feng Y, Diego KS, Dong Z, Christenson Wick Z, Page-Harley L, Page-Harley V, Schnipper J, Lamsifer SI, Pennington ZT, Vetere LM, Philipsberg PA, Soler I, Jurkowski A, Rosado CJ, Khan NN, Cai DJ, Shuman T | Cell reports | 39847482 | Cell Rep | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39847482 |
| Region-Specific Phosphorylation Determines Neuroligin-3 Localization to Excitatory Versus Inhibitory Synapses. | Altas B, Tuffy LP, Patrizi A, Dimova K, Soykan T, Brandenburg C, Romanowski AJ, Whitten JR, Robertson CD, Khim SN, Crutcher GW, Ambrozkiewicz MC, Yagensky O, Krueger-Burg D, Hammer M, Hsiao HH, Laskowski PR, Dyck L, Puche AC, Sassoè-Pognetto M, Chua JJE, Urlaub H, Jahn O, Brose N, Poulopoulos A | Biological psychiatry | 38154503 | Biol Psychiatry | 2024 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/38154503 |
| NPRL3 loss alters neuronal morphology, mTOR localization, cortical lamination and seizure threshold. | Iffland PH, Everett ME, Cobb-Pitstick KM, Bowser LE, Barnes AE, Babus JK, Romanowski AJ, Baybis M, Elziny S, Puffenberger EG, Gonzaga-Jauregui C, Poulopoulos A, Carson VJ, Crino PB | Brain : a journal of neurology | 35136953 | Brain | 2022 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/35136953 |
| The brain's dark transcriptome: Sequencing RNA in distal compartments of neurons and glia. | Ament SA, Poulopoulos A | Current opinion in neurobiology | 37196598 | Curr Opin Neurobiol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37196598 |
| Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres. | Poulopoulos A, Davis P, Brandenburg C, Itoh Y, Galazo MJ, Greig LC, Romanowski AJ, Budnik B, Macklis JD | bioRxiv : the preprint server for biology | 38585721 | bioRxiv | 2024 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/38585721 |
| Enhancing Precision and Efficiency of Cas9-Mediated Knockin Through Combinatorial Fusions of DNA Repair Proteins. | Richardson RR, Steyert M, Khim SN, Crutcher GW, Brandenburg C, Robertson CD, Romanowski AJ, Inen J, Altas B, Poulopoulos A | The CRISPR journal | 37713292 | CRISPR J | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37713292 |
| Neuronal mTOR Outposts: Implications for Translation, Signaling, and Plasticity. | Altas B, Romanowski AJ, Bunce GW, Poulopoulos A | Frontiers in cellular neuroscience | 35465614 | Front Cell Neurosci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35465614 |
| India ink to 3D imaging: The legacy of Dr. Deepak "Dee" N. Pandya and his influence on generations of neuroanatomists. | Blatt GJ, Brandenburg C, Poulopoulos A | The Journal of comparative neurology | 37916788 | J Comp Neurol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37916788 |
| Rapid modeling of an ultra-rare epilepsy variant in wild-type mice by in utero prime editing. | Robertson CD, Davis P, Richardson RR, Iffland PH 2nd, Vieira DCO, Steyert M, McKeon PN, Romanowski AJ, Crutcher G, Jašarević E, Wolff SBE, Mathur BN, Crino PB, Bale TL, Dick IE, Poulopoulos A | bioRxiv : the preprint server for biology | 38106154 | bioRxiv | 2023 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/38106154 |
| Dysfunctional Cortical Gradient Topography in Treatment-Resistant Major Depressive Disorder. | Pasquini L, Fryer SL, Eisendrath SJ, Segal ZV, Lee AJ, Brown JA, Saggar M, Mathalon DH | Biological psychiatry. Cognitive neuroscience and neuroimaging | 36754677 | Biol Psychiatry Cogn Neurosci Neuroimaging | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36754677 |
| NeuMapper: A scalable computational framework for multiscale exploration of the brain's dynamical organization. | Geniesse C, Chowdhury S, Saggar M | Network neuroscience (Cambridge, Mass.) | 35733428 | Netw Neurosci | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35733428 |
| Spontaneous and deliberate modes of creativity: Multitask eigen-connectivity analysis captures latent cognitive modes during creative thinking. | Xie H, Beaty RE, Jahanikia S, Geniesse C, Sonalkar NS, Saggar M | NeuroImage | 34469816 | Neuroimage | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34469816 |
| Altered canonical and striatal-frontal resting state functional connectivity in children with pathogenic variants in the Ras/mitogen-activated protein kinase pathway. | Bruno JL, Shrestha SB, Reiss AL, Saggar M, Green T | Molecular psychiatry | 35087195 | Mol Psychiatry | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35087195 |
| Pushing the Boundaries of Psychiatric Neuroimaging to Ground Diagnosis in Biology. | Saggar M, Uddin LQ | eNeuro | 31685674 | eNeuro | 2019 Nov/Dec | https://www.ncbi.nlm.nih.gov/pubmed/31685674 |
| Brief intensive social gaze training reorganizes functional brain connectivity in boys with fragile X syndrome. | Saggar M, Bruno JL, Hall SS | Cerebral cortex (New York, N.Y. : 1991) | 36376964 | Cereb Cortex | 2023 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/36376964 |
| Deconstructing the Mapper algorithm to extract richer topological and temporal features from functional neuroimaging data. | Haşegan D, Geniesse C, Chowdhury S, Saggar M | bioRxiv : the preprint server for biology | 37904918 | bioRxiv | 2023 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/37904918 |
| Neural resources shift under Methylphenidate: A computational approach to examine anxiety-cognition interplay. | Saggar M, Bruno J, Gaillard C, Claudino L, Ernst M | NeuroImage | 36273770 | Neuroimage | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36273770 |
| Development of top-down cortical propagations in youth. | Pines A, Keller AS, Larsen B, Bertolero M, Ashourvan A, Bassett DS, Cieslak M, Covitz S, Fan Y, Feczko E, Houghton A, Rueter AR, Saggar M, Shafiei G, Tapera TM, Vogel J, Weinstein SM, Shinohara RT, Williams LM, Fair DA, Satterthwaite TD | Neuron | 36803653 | Neuron | 2023 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/36803653 |
| Brain mitochondrial diversity and network organization predict anxiety-like behavior in male mice. | Rosenberg AM, Saggar M, Monzel AS, Devine J, Rogu P, Limoges A, Junker A, Sandi C, Mosharov EV, Dumitriu D, Anacker C, Picard M | Nature communications | 37563104 | Nat Commun | 2023 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/37563104 |
| Increased anti-correlation between the left dorsolateral prefrontal cortex and the default mode network following Stanford Neuromodulation Therapy (SNT): analysis of a double-blinded, randomized, sham-controlled trial. | Gajawelli N, Geoly AD, Batail JM, Xiao X, Maron-Katz A, Cole E, Azeez A, Kratter IH, Saggar M, Williams NR | Npj mental health research | 38971869 | Npj Ment Health Res | 2024 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/38971869 |
| Densely sampled stimulus-response map of human cortex with single pulse TMS-EEG and its relation to whole brain neuroimaging measures. | Sun Y, Lucas MV, Cline CC, Menezes MC, Kim S, Badami FS, Narayan M, Wu W, Daskalakis ZJ, Etkin A, Saggar M | bioRxiv : the preprint server for biology | 38948696 | bioRxiv | 2024 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/38948696 |
| Cross-attractor repertoire provides new perspective on structure-function relationship in the brain. | Zhang M, Sun Y, Saggar M | NeuroImage | 35732244 | Neuroimage | 2022 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/35732244 |
| Thalamocortical connectivity is associated with autism symptoms in high-functioning adults with autism and typically developing adults. | Ayub R, Sun KL, Flores RE, Lam VT, Jo B, Saggar M, Fung LK | Translational psychiatry | 33536431 | Transl Psychiatry | 2021 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/33536431 |
| Generating dynamical neuroimaging spatiotemporal representations (DyNeuSR) using topological data analysis. | Geniesse C, Sporns O, Petri G, Saggar M | Network neuroscience (Cambridge, Mass.) | 31410378 | Netw Neurosci | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31410378 |
| Cross-attractor modeling of resting-state functional connectivity in psychiatric disorders. | Sun Y, Zhang M, Saggar M | NeuroImage | 37579998 | Neuroimage | 2023 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/37579998 |
| Precision dynamical mapping using topological data analysis reveals a hub-like transition state at rest. | Saggar M, Shine JM, Liégeois R, Dosenbach NUF, Fair D | Nature communications | 35970984 | Nat Commun | 2022 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/35970984 |
| Temporal Mapper: Transition networks in simulated and real neural dynamics. | Zhang M, Chowdhury S, Saggar M | Network neuroscience (Cambridge, Mass.) | 37397880 | Netw Neurosci | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37397880 |
| Network effects of Stanford Neuromodulation Therapy (SNT) in treatment-resistant major depressive disorder: a randomized, controlled trial. | Batail JM, Xiao X, Azeez A, Tischler C, Kratter IH, Bishop JH, Saggar M, Williams NR | Translational psychiatry | 37400432 | Transl Psychiatry | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/37400432 |
| How prior pair-bonding experience affects future bonding behavior in monogamous prairie voles. | Harbert KJ, Pellegrini M, Gordon KM, Donaldson ZR | Hormones and behavior | 32910950 | Horm Behav | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32910950 |
| PhAT: A Flexible Open-Source GUI-Driven Toolkit for Photometry Analysis. | Murphy KZ, Haile ED, McTigue AD, Pierce AF, Donaldson ZR | Current protocols | 37184156 | Curr Protoc | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37184156 |
| Neurobiology and treatment advances for prolonged grief disorder. | Donaldson ZR, Shear MK | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 37479860 | Neuropsychopharmacology | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37479860 |
| Nucleus accumbens dopamine release reflects the selective nature of pair bonds. | Pierce AF, Protter DSW, Watanabe YL, Chapel GD, Cameron RT, Donaldson ZR | Current biology : CB | 38218185 | Curr Biol | 2024 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/38218185 |
| Emergent intra-pair sex differences and organized behavior in pair bonded prairie voles (Microtus ochrogaster). | Brusman LE, Protter DSW, Fultz AC, Paulson MU, Chapel GD, Elges IO, Cameron RT, Beery AK, Donaldson ZR | Genes, brain, and behavior | 35044090 | Genes Brain Behav | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35044090 |
| Prairie voles as a model for adaptive reward remodeling following loss of a bonded partner. | Sadino JM, Donaldson ZR | Annals of the New York Academy of Sciences | 38594916 | Ann N Y Acad Sci | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38594916 |
| Exposure to novel females increases fecundity in adult male prairie voles. | Hurd JA, Watanabe YL, Toben GJ, Ford AK, Miller CA, Sergott CE, Kelley D, Donaldson ZR, McCullagh EA | bioRxiv : the preprint server for biology | 39763992 | bioRxiv | 2024 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/39763992 |
| Wireless multilateral devices for optogenetic studies of individual and social behaviors. | Yang Y, Wu M, Vázquez-Guardado A, Wegener AJ, Grajales-Reyes JG, Deng Y, Wang T, Avila R, Moreno JA, Minkowicz S, Dumrongprechachan V, Lee J, Zhang S, Legaria AA, Ma Y, Mehta S, Franklin D, Hartman L, Bai W, Han M, Zhao H, Lu W, Yu Y, Sheng X, Banks A, Yu X, Donaldson ZR, Gereau RW 4th, Good CH, Xie Z, Huang Y, Kozorovitskiy Y, Rogers JA | Nature neuroscience | 33972800 | Nat Neurosci | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33972800 |
| Sex differences in the reward value of familiar mates in prairie voles. | Vahaba DM, Halstead ER, Donaldson ZR, Ahern TH, Beery AK | Genes, brain, and behavior | 35044087 | Genes Brain Behav | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35044087 |
| PhAT: A flexible open-source GUI-driven toolkit for photometry analysis. | Murphy KZ, Haile E, McTigue A, Pierce AF, Donaldson ZR | bioRxiv : the preprint server for biology | 36993180 | bioRxiv | 2023 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/36993180 |
| A neuronal signature for monogamous reunion. | Scribner JL, Vance EA, Protter DSW, Sheeran WM, Saslow E, Cameron RT, Klein EM, Jimenez JC, Kheirbek MA, Donaldson ZR | Proceedings of the National Academy of Sciences of the United States of America | 32381740 | Proc Natl Acad Sci U S A | 2020 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/32381740 |
| Prairie vole pair bonding and plasticity of the social brain. | Hiura LC, Donaldson ZR | Trends in neurosciences | 36369029 | Trends Neurosci | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36369029 |
| Prolonged partner separation erodes nucleus accumbens transcriptional signatures of pair bonding in male prairie voles. | Sadino JM, Bradeen XG, Kelly CJ, Brusman LE, Walker DM, Donaldson ZR | eLife | 36852906 | Elife | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36852906 |
| Transcriptional profiling of mouse projection neurons with VECTORseq. | Cheung V, Chung P, Feinberg EH | STAR protocols | 36035788 | STAR Protoc | 2022 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/36035788 |
| Soma-Targeted Imaging of Neural Circuits by Ribosome Tethering. | Chen Y, Jang H, Spratt PWE, Kosar S, Taylor DE, Essner RA, Bai L, Leib DE, Kuo TW, Lin YC, Patel M, Subkhangulova A, Kato S, Feinberg EH, Bender KJ, Knight ZA, Garrison JL | Neuron | 32574560 | Neuron | 2020 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/32574560 |
| Hindbrain modules differentially transform activity of single collicular neurons to coordinate movements. | Zahler SH, Taylor DE, Wright BS, Wong JY, Shvareva VA, Park YA, Feinberg EH | Cell | 37343561 | Cell | 2023 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/37343561 |
| Superior colliculus drives stimulus-evoked directionally biased saccades and attempted head movements in head-fixed mice. | Zahler SH, Taylor DE, Wong JY, Adams JM, Feinberg EH | eLife | 34970968 | Elife | 2021 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/34970968 |
| Virally encoded connectivity transgenic overlay RNA sequencing (VECTORseq) defines projection neurons involved in sensorimotor integration. | Cheung V, Chung P, Bjorni M, Shvareva VA, Lopez YC, Feinberg EH | Cell reports | 34936877 | Cell Rep | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34936877 |
| Noradrenergic Signaling Disengages Feedforward Transmission in the Nucleus Accumbens Shell. | Manz KM, Coleman BC, Grueter CA, Shields BC, Tadross MR, Grueter BA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 33737458 | J Neurosci | 2021 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/33737458 |
| DART.2: bidirectional synaptic pharmacology with thousandfold cellular specificity. | Shields BC, Yan H, Lim SSX, Burwell SCV, Cammarata CM, Fleming EA, Yousefzadeh SA, Goldenshtein VZ, Kahuno EW, Vagadia PP, Loughran MH, Zhiquan L, McDonnell ME, Scalabrino ML, Thapa M, Hawley TM, Field GD, Hull C, Schiltz GE, Glickfeld LL, Reitz AB, Tadross MR | Nature methods | 38877316 | Nat Methods | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38877316 |
| Natural phasic inhibition of dopamine neurons signals cognitive rigidity. | Burwell SCV, Yan H, Lim SSX, Shields BC, Tadross MR | bioRxiv : the preprint server for biology | 38766037 | bioRxiv | 2024 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/38766037 |
| An open-source transparent microelectrode array. | Weaver IA, Li AW, Shields BC, Tadross MR | Journal of neural engineering | 35349992 | J Neural Eng | 2022 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/35349992 |
| Acute restraint stress redirects prefrontal cortex circuit function through mGlu(5) receptor plasticity on somatostatin-expressing interneurons. | Joffe ME, Maksymetz J, Luschinger JR, Dogra S, Ferranti AS, Luessen DJ, Gallinger IM, Xiang Z, Branthwaite H, Melugin PR, Williford KM, Centanni SW, Shields BC, Lindsley CW, Calipari ES, Siciliano CA, Niswender CM, Tadross MR, Winder DG, Conn PJ | Neuron | 35045338 | Neuron | 2022 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/35045338 |
| Local synaptic inhibition mediates cerebellar granule cell pattern separation and enables learned sensorimotor associations. | Fleming EA, Field GD, Tadross MR, Hull C | Nature neuroscience | 38321293 | Nat Neurosci | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38321293 |
| Genomic structural variation: A complex but important driver of human evolution. | Soto DC, Uribe-Salazar JM, Shew CJ, Sekar A, McGinty SP, Dennis MY | American journal of biological anthropology | 36794631 | Am J Biol Anthropol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/36794631 |
| FixItFelix: improving genomic analysis by fixing reference errors. | Behera S, LeFaive J, Orchard P, Mahmoud M, Paulin LF, Farek J, Soto DC, Parker SCJ, Smith AV, Dennis MY, Zook JM, Sedlazeck FJ | Genome biology | 36810122 | Genome Biol | 2023 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/36810122 |
| m(6)A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly. | Nishizaki SS, Haghani NK, La GN, Mariano NAF, Uribe-Salazar JM, Kaya G, Regester M, Andrews DS, Nordahl CW, Amaral DG, Dennis MY | Autism research : official journal of the International Society for Autism Research | 39887636 | Autism Res | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39887636 |
| Identification of Structural Variation in Chimpanzees Using Optical Mapping and Nanopore Sequencing. | Soto DC, Shew C, Mastoras M, Schmidt JM, Sahasrabudhe R, Kaya G, Andrés AM, Dennis MY | Genes | 32143403 | Genes (Basel) | 2020 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/32143403 |
| Diverse Molecular Mechanisms Contribute to Differential Expression of Human Duplicated Genes. | Shew CJ, Carmona-Mora P, Soto DC, Mastoras M, Roberts E, Rosas J, Jagannathan D, Kaya G, O'Geen H, Dennis MY | Molecular biology and evolution | 34009325 | Mol Biol Evol | 2021 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/34009325 |
| Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. | Zhu Y, Gomez JA, Laufer BI, Mordaunt CE, Mouat JS, Soto DC, Dennis MY, Benke KS, Bakulski KM, Dou J, Marathe R, Jianu JM, Williams LA, Gutierrez Fugón OJ, Walker CK, Ozonoff S, Daniels J, Grosvenor LP, Volk HE, Feinberg JI, Fallin MD, Hertz-Picciotto I, Schmidt RJ, Yasui DH, LaSalle JM | Genome biology | 35168652 | Genome Biol | 2022 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/35168652 |
| Telomere-to-telomere assembly of a complete human X chromosome. | Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM | Nature | 32663838 | Nature | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32663838 |
| Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform. | Colón-Rodríguez A, Uribe-Salazar JM, Weyenberg KB, Sriram A, Quezada A, Kaya G, Jao E, Radke B, Lein PJ, Dennis MY | Frontiers in cell and developmental biology | 33330465 | Front Cell Dev Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33330465 |
| Complete genomic and epigenetic maps of human centromeres. | Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH | Science (New York, N.Y.) | 35357911 | Science | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35357911 |
| The complete sequence of a human genome. | Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM | Science (New York, N.Y.) | 35357919 | Science | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35357919 |
| RapID Cell Counter: Semi-Automated and Mid-Throughput Estimation of Cell Density within Diverse Cortical Layers. | Sekar A, Sanches TM, Hino K, Kumar M, Wang J, Ha E, Durbin-Johnson B, Simó S, Dennis MY | eNeuro | 34725102 | eNeuro | 2021 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/34725102 |
| A complete reference genome improves analysis of human genetic variation. | Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC | Science (New York, N.Y.) | 35357935 | Science | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35357935 |
| Evaluation of CRISPR gene-editing tools in zebrafish. | Uribe-Salazar JM, Kaya G, Sekar A, Weyenberg K, Ingamells C, Dennis MY | BMC genomics | 34986794 | BMC Genomics | 2022 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/34986794 |
| LRRC37B is a human modifier of voltage-gated sodium channels and axon excitability in cortical neurons. | Libé-Philippot B, Lejeune A, Wierda K, Louros N, Erkol E, Vlaeminck I, Beckers S, Gaspariunaite V, Bilheu A, Konstantoulea K, Nyitrai H, De Vleeschouwer M, Vennekens KM, Vidal N, Bird TW, Soto DC, Jaspers T, Dewilde M, Dennis MY, Rousseau F, Comoletti D, Schymkowitz J, Theys T, de Wit J, Vanderhaeghen P | Cell | 38134874 | Cell | 2023 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/38134874 |
| Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development. | Uribe-Salazar JM, Kaya G, Weyenberg K, Radke B, Hino K, Soto DC, Shiu JL, Zhang W, Ingamells C, Haghani NK, Xu E, Rosas J, Simó S, Miesfeld J, Glaser T, Baraban SC, Jao LE, Dennis MY | bioRxiv : the preprint server for biology | 39314374 | bioRxiv | 2024 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/39314374 |
| Local genetic adaptation to habitat in wild chimpanzees. | Ostridge HJ, Fontsere C, Lizano E, Soto DC, Schmidt JM, Saxena V, Alvarez-Estape M, Barratt CD, Gratton P, Bocksberger G, Lester JD, Dieguez P, Agbor A, Angedakin S, Assumang AK, Bailey E, Barubiyo D, Bessone M, Brazzola G, Chancellor R, Cohen H, Coupland C, Danquah E, Deschner T, Dotras L, Dupain J, Egbe VE, Granjon AC, Head J, Hedwig D, Hermans V, Hernandez-Aguilar RA, Jeffery KJ, Jones S, Junker J, Kadam P, Kaiser M, Kalan AK, Kambere M, Kienast I, Kujirakwinja D, Langergraber KE, Lapuente J, Larson B, Laudisoit A, Lee KC, Llana M, Maretti G, Martín R, Meier A, Morgan D, Neil E, Nicholl S, Nixon S, Normand E, Orbell C, Ormsby LJ, Orume R, Pacheco L, Preece J, Regnaut S, Robbins MM, Rundus A, Sanz C, Sciaky L, Sommer V, Stewart FA, Tagg N, Tédonzong LR, van Schijndel J, Vendras E, Wessling EG, Willie J, Wittig RM, Yuh YG, Yurkiw K, Vigilant L, Piel A, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM | bioRxiv : the preprint server for biology | 39026872 | bioRxiv | 2024 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/39026872 |
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| Cellular arrangement impacts metabolic activity and antibiotic tolerance in Pseudomonas aeruginosa biofilms. | Dayton H, Kiss J, Wei M, Chauhan S, LaMarre E, Cornell WC, Morgan CJ, Janakiraman A, Min W, Tomer R, Price-Whelan A, Nirody JA, Dietrich LEP | PLoS biology | 38300958 | PLoS Biol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38300958 |
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| Astrocyte-derived interleukin-33 promotes microglial synapse engulfment and neural circuit development. | Vainchtein ID, Chin G, Cho FS, Kelley KW, Miller JG, Chien EC, Liddelow SA, Nguyen PT, Nakao-Inoue H, Dorman LC, Akil O, Joshita S, Barres BA, Paz JT, Molofsky AB, Molofsky AV | Science (New York, N.Y.) | 29420261 | Science | 2018 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/29420261 |
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| Location, Location, Location: Transcriptional Control of Astrocyte Heterogeneity. | Rosenberg MF, Molofsky AV | Trends in immunology | 32800455 | Trends Immunol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32800455 |
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| Type I interferon responsive microglia shape cortical development and behavior. | Escoubas CC, Dorman LC, Nguyen PT, Lagares-Linares C, Nakajo H, Anderson SR, Cuevas B, Vainchtein ID, Silva NJ, Xiao Y, Lidsky PV, Wang EY, Taloma SE, Nakao-Inoue H, Schwer B, Andino R, Nowakowski TJ, Molofsky AV | bioRxiv : the preprint server for biology | 35233577 | bioRxiv | 2023 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/35233577 |
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| Microglial Remodeling of the Extracellular Matrix Promotes Synapse Plasticity. | Nguyen PT, Dorman LC, Pan S, Vainchtein ID, Han RT, Nakao-Inoue H, Taloma SE, Barron JJ, Molofsky AB, Kheirbek MA, Molofsky AV | Cell | 32615087 | Cell | 2020 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/32615087 |
| Astrocytic β-catenin signaling via TCF7L2 regulates synapse development and social behavior. | Szewczyk LM, Lipiec MA, Liszewska E, Meyza K, Urban-Ciecko J, Kondrakiewicz L, Goncerzewicz A, Rafalko K, Krawczyk TG, Bogaj K, Vainchtein ID, Nakao-Inoue H, Puscian A, Knapska E, Sanders SJ, Jan Nowakowski T, Molofsky AV, Wisniewska MB | Molecular psychiatry | 37798419 | Mol Psychiatry | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37798419 |
| Dynamism of an Astrocyte In Vivo: Perspectives on Identity and Function. | Poskanzer KE, Molofsky AV | Annual review of physiology | 29166242 | Annu Rev Physiol | 2018 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/29166242 |
| Enhancing GAT-3 in thalamic astrocytes promotes resilience to brain injury in rodents. | Cho FS, Vainchtein ID, Voskobiynyk Y, Morningstar AR, Aparicio F, Higashikubo B, Ciesielska A, Broekaart DWM, Anink JJ, van Vliet EA, Yu X, Khakh BS, Aronica E, Molofsky AV, Paz JT | Science translational medicine | 35857628 | Sci Transl Med | 2022 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/35857628 |
| In situ and transcriptomic identification of microglia in synapse-rich regions of the developing zebrafish brain. | Silva NJ, Dorman LC, Vainchtein ID, Horneck NC, Molofsky AV | Nature communications | 34625548 | Nat Commun | 2021 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/34625548 |
| Regulatory T-cells inhibit microglia-induced pain hypersensitivity in female mice. | Kuhn JA, Vainchtein ID, Braz J, Hamel K, Bernstein M, Craik V, Dahlgren MW, Ortiz-Carpena J, Molofsky AB, Molofsky AV, Basbaum AI | eLife | 34652270 | Elife | 2021 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/34652270 |
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| scAAVengr, a transcriptome-based pipeline for quantitative ranking of engineered AAVs with single-cell resolution. | Öztürk BE, Johnson ME, Kleyman M, Turunç S, He J, Jabalameli S, Xi Z, Visel M, Dufour VL, Iwabe S, Pompeo Marinho LFL, Aguirre GD, Sahel JA, Schaffer DV, Pfenning AR, Flannery JG, Beltran WA, Stauffer WR, Byrne LC | eLife | 34664552 | Elife | 2021 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/34664552 |
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| 5C-ID: Increased resolution Chromosome-Conformation-Capture-Carbon-Copy with in situ 3C and double alternating primer design. | Kim JH, Titus KR, Gong W, Beagan JA, Cao Z, Phillips-Cremins JE | Methods (San Diego, Calif.) | 29772275 | Methods | 2018 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/29772275 |
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| Gamma and beta bursts during working memory readout suggest roles in its volitional control. | Lundqvist M, Herman P, Warden MR, Brincat SL, Miller EK | Nature communications | 29374153 | Nat Commun | 2018 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/29374153 |
| Daytime spikes in dopaminergic activity drive rapid mood-cycling in mice. | Sidor MM, Spencer SM, Dzirasa K, Parekh PK, Tye KM, Warden MR, Arey RN, Enwright JF, Jacobsen JP, Kumar S, Remillard EM, Caron MG, Deisseroth K, McClung CA | Molecular psychiatry | 25687774 | Mol Psychiatry | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25687774 |
| Intense threat switches dorsal raphe serotonin neurons to a paradoxical operational mode. | Seo C, Guru A, Jin M, Ito B, Sleezer BJ, Ho YY, Wang E, Boada C, Krupa NA, Kullakanda DS, Shen CX, Warden MR | Science (New York, N.Y.) | 30705194 | Science | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30705194 |
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| Nanodelivery of a functional membrane receptor to manipulate cellular phenotype. | Patriarchi T, Shen A, He W, Baikoghli M, Cheng RH, Xiang YK, Coleman MA, Tian L | Scientific reports | 29476125 | Sci Rep | 2018 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/29476125 |
| Imaging Neurotransmitter and Neuromodulator Dynamics In Vivo with Genetically Encoded Indicators. | Sabatini BL, Tian L | Neuron | 33058762 | Neuron | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/33058762 |
| Imaging voltage and brain chemistry with genetically encoded sensors and modulators. | Pal A, Tian L | Current opinion in chemical biology | 32823064 | Curr Opin Chem Biol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32823064 |
| Monitoring activity in neural circuits with genetically encoded indicators. | Broussard GJ, Liang R, Tian L | Frontiers in molecular neuroscience | 25538558 | Front Mol Neurosci | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25538558 |
| SynQuant: an automatic tool to quantify synapses from microscopy images. | Wang Y, Wang C, Ranefall P, Broussard GJ, Wang Y, Shi G, Lyu B, Wu CT, Wang Y, Tian L, Yu G | Bioinformatics (Oxford, England) | 31596456 | Bioinformatics | 2020 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/31596456 |
| Distinct temporal integration of noradrenaline signaling by astrocytic second messengers during vigilance. | Oe Y, Wang X, Patriarchi T, Konno A, Ozawa K, Yahagi K, Hirai H, Tsuboi T, Kitaguchi T, Tian L, McHugh TJ, Hirase H | Nature communications | 31980655 | Nat Commun | 2020 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/31980655 |
| Distinct sub-second dopamine signaling in dorsolateral striatum measured by a genetically-encoded fluorescent sensor. | Salinas AG, Lee JO, Augustin SM, Zhang S, Patriarchi T, Tian L, Morales M, Mateo Y, Lovinger DM | Nature communications | 37739964 | Nat Commun | 2023 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/37739964 |
| Aberrant Calcium Signaling in Astrocytes Inhibits Neuronal Excitability in a Human Down Syndrome Stem Cell Model. | Mizuno GO, Wang Y, Shi G, Wang Y, Sun J, Papadopoulos S, Broussard GJ, Unger EK, Deng W, Weick J, Bhattacharyya A, Chen CY, Yu G, Looger LL, Tian L | Cell reports | 29996097 | Cell Rep | 2018 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/29996097 |
| Optical dopamine monitoring with dLight1 reveals mesolimbic phenotypes in a mouse model of neurofibromatosis type 1. | Robinson JE, Coughlin GM, Hori AM, Cho JR, Mackey ED, Turan Z, Patriarchi T, Tian L, Gradinaru V | eLife | 31545171 | Elife | 2019 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/31545171 |
| A Neural Circuit Mechanism for Encoding Aversive Stimuli in the Mesolimbic Dopamine System. | de Jong JW, Afjei SA, Pollak Dorocic I, Peck JR, Liu C, Kim CK, Tian L, Deisseroth K, Lammel S | Neuron | 30503173 | Neuron | 2019 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/30503173 |
| Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning. | Unger EK, Keller JP, Altermatt M, Liang R, Matsui A, Dong C, Hon OJ, Yao Z, Sun J, Banala S, Flanigan ME, Jaffe DA, Hartanto S, Carlen J, Mizuno GO, Borden PM, Shivange AV, Cameron LP, Sinning S, Underhill SM, Olson DE, Amara SG, Temple Lang D, Rudnick G, Marvin JS, Lavis LD, Lester HA, Alvarez VA, Fisher AJ, Prescher JA, Kash TL, Yarov-Yarovoy V, Gradinaru V, Looger LL, Tian L | Cell | 33333022 | Cell | 2020 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/33333022 |
| Imaging chemical neurotransmission with genetically encoded fluorescent sensors. | Liang R, Broussard GJ, Tian L | ACS chemical neuroscience | 25565280 | ACS Chem Neurosci | 2015 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/25565280 |
| An ultrasensitive biosensor for high-resolution kinase activity imaging in awake mice. | Zhang JF, Liu B, Hong I, Mo A, Roth RH, Tenner B, Lin W, Zhang JZ, Molina RS, Drobizhev M, Hughes TE, Tian L, Huganir RL, Mehta S, Zhang J | Nature chemical biology | 32989297 | Nat Chem Biol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32989297 |
| An expanded palette of dopamine sensors for multiplex imaging in vivo. | Patriarchi T, Mohebi A, Sun J, Marley A, Liang R, Dong C, Puhger K, Mizuno GO, Davis CM, Wiltgen B, von Zastrow M, Berke JD, Tian L | Nature methods | 32895537 | Nat Methods | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32895537 |
| Psychedelic-inspired drug discovery using an engineered biosensor. | Dong C, Ly C, Dunlap LE, Vargas MV, Sun J, Hwang IW, Azinfar A, Oh WC, Wetsel WC, Olson DE, Tian L | Cell | 33915107 | Cell | 2021 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/33915107 |
| In vivo measurement of afferent activity with axon-specific calcium imaging. | Broussard GJ, Liang Y, Fridman M, Unger EK, Meng G, Xiao X, Ji N, Petreanu L, Tian L | Nature neuroscience | 30127424 | Nat Neurosci | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30127424 |
| Dopamine neurons projecting to medial shell of the nucleus accumbens drive heroin reinforcement. | Corre J, van Zessen R, Loureiro M, Patriarchi T, Tian L, Pascoli V, Lüscher C | eLife | 30373717 | Elife | 2018 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/30373717 |
| Maps of neuronal activity across the mouse brain. | Andreoni A, Tian L | Nature biomedical engineering | 31073176 | Nat Biomed Eng | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31073176 |
| Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus. | Simola DF, Graham RJ, Brady CM, Enzmann BL, Desplan C, Ray A, Zwiebel LJ, Bonasio R, Reinberg D, Liebig J, Berger SL | Science (New York, N.Y.) | 26722000 | Science | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26722000 |
| Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain. | Shields EJ, Sorida M, Sheng L, Sieriebriennikov B, Ding L, Bonasio R | BMC biology | 34838024 | BMC Biol | 2021 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/34838024 |
| Specialized odorant receptors in social insects that detect cuticular hydrocarbon cues and candidate pheromones. | Pask GM, Slone JD, Millar JG, Das P, Moreira JA, Zhou X, Bello J, Berger SL, Bonasio R, Desplan C, Reinberg D, Liebig J, Zwiebel LJ, Ray A | Nature communications | 28819196 | Nat Commun | 2017 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/28819196 |
| The expanding epigenetic landscape of non-model organisms. | Bonasio R | The Journal of experimental biology | 25568458 | J Exp Biol | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25568458 |
| Loss of KLHL6 promotes diffuse large B-cell lymphoma growth and survival by stabilizing the mRNA decay factor roquin2. | Choi J, Lee K, Ingvarsdottir K, Bonasio R, Saraf A, Florens L, Washburn MP, Tadros S, Green MR, Busino L | Nature cell biology | 29695787 | Nat Cell Biol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29695787 |
| Social reprogramming in ants induces longevity-associated glia remodeling. | Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R | Science advances | 32875108 | Sci Adv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32875108 |
| High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. | Shields EJ, Sheng L, Weiner AK, Garcia BA, Bonasio R | Cell reports | 29874592 | Cell Rep | 2018 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/29874592 |
| An Engineered orco Mutation Produces Aberrant Social Behavior and Defective Neural Development in Ants. | Yan H, Opachaloemphan C, Mancini G, Yang H, Gallitto M, Mlejnek J, Leibholz A, Haight K, Ghaninia M, Huo L, Perry M, Slone J, Zhou X, Traficante M, Penick CA, Dolezal K, Gokhale K, Stevens K, Fetter-Pruneda I, Bonasio R, Zwiebel LJ, Berger SL, Liebig J, Reinberg D, Desplan C | Cell | 28802043 | Cell | 2017 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/28802043 |
| The Neuropeptide Corazonin Controls Social Behavior and Caste Identity in Ants. | Gospocic J, Shields EJ, Glastad KM, Lin Y, Penick CA, Yan H, Mikheyev AS, Linksvayer TA, Garcia BA, Berger SL, Liebig J, Reinberg D, Bonasio R | Cell | 28802044 | Cell | 2017 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/28802044 |
| Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency. | Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, McWalter K, Telegrafi A, Baldridge D, Shinawi M, Leal SM, Schaefer GB, Stevenson RE, Banka S, Bonasio R, Fahrner JA | American journal of human genetics | 31928709 | Am J Hum Genet | 2020 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/31928709 |
| lncRedibly versatile: biochemical and biological functions of long noncoding RNAs. | Shields EJ, Petracovici AF, Bonasio R | The Biochemical journal | 30971458 | Biochem J | 2019 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/30971458 |
| Kr-h1 maintains distinct caste-specific neurotranscriptomes in response to socially regulated hormones. | Gospocic J, Glastad KM, Sheng L, Shields EJ, Berger SL, Bonasio R | Cell | 34739833 | Cell | 2021 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/34739833 |
| RNA Binding to CBP Stimulates Histone Acetylation and Transcription. | Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL | Cell | 28086087 | Cell | 2017 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/28086087 |
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| Sleep loss drives acetylcholine- and somatostatin interneuron-mediated gating of hippocampal activity to inhibit memory consolidation. | Delorme J, Wang L, Kuhn FR, Kodoth V, Ma J, Martinez JD, Raven F, Toth BA, Balendran V, Vega Medina A, Jiang S, Aton SJ | Proceedings of the National Academy of Sciences of the United States of America | 34344824 | Proc Natl Acad Sci U S A | 2021 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/34344824 |
| Linking Network Activity to Synaptic Plasticity during Sleep: Hypotheses and Recent Data. | Puentes-Mestril C, Aton SJ | Frontiers in neural circuits | 28932187 | Front Neural Circuits | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28932187 |
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| Sleep Promotes, and Sleep Loss Inhibits, Selective Changes in Firing Rate, Response Properties and Functional Connectivity of Primary Visual Cortex Neurons. | Clawson BC, Durkin J, Suresh AK, Pickup EJ, Broussard CG, Aton SJ | Frontiers in systems neuroscience | 30245617 | Front Syst Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30245617 |
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| Sleep Loss Drives Brain Region-Specific and Cell Type-Specific Alterations in Ribosome-Associated Transcripts Involved in Synaptic Plasticity and Cellular Timekeeping. | Puentes-Mestril C, Delorme J, Wang L, Donnelly M, Popke D, Jiang S, Aton SJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34001629 | J Neurosci | 2021 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/34001629 |
| Resonance with subthreshold oscillatory drive organizes activity and optimizes learning in neural networks. | Roach JP, Pidde A, Katz E, Wu J, Ognjanovski N, Aton SJ, Zochowski MR | Proceedings of the National Academy of Sciences of the United States of America | 29545273 | Proc Natl Acad Sci U S A | 2018 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/29545273 |
| Erratum: Parvalbumin-expressing interneurons coordinate hippocampal network dynamics required for memory consolidation. | Ognjanovski N, Schaeffer S, Wu J, Mofakham S, Maruyama D, Zochowski M, Aton SJ | Nature communications | 28681846 | Nat Commun | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28681846 |
| The role of clock genes in sleep, stress and memory. | Bolsius YG, Zurbriggen MD, Kim JK, Kas MJ, Meerlo P, Aton SJ, Havekes R | Biochemical pharmacology | 33647263 | Biochem Pharmacol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33647263 |
| Acetylcholine-gated current translates wake neuronal firing rate information into a spike timing-based code in Non-REM sleep, stabilizing neural network dynamics during memory consolidation. | Skilling QM, Eniwaye B, Clawson BC, Shaver J, Ognjanovski N, Aton SJ, Zochowski M | PLoS computational biology | 34543284 | PLoS Comput Biol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34543284 |
| Parvalbumin-expressing interneurons coordinate hippocampal network dynamics required for memory consolidation. | Ognjanovski N, Schaeffer S, Wu J, Mofakham S, Maruyama D, Zochowski M, Aton SJ | Nature communications | 28382952 | Nat Commun | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28382952 |
| Functional network stability and average minimal distance - A framework to rapidly assess dynamics of functional network representations. | Wu J, Skilling QM, Maruyama D, Li C, Ognjanovski N, Aton S, Zochowski M | Journal of neuroscience methods | 29294309 | J Neurosci Methods | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29294309 |
| Sleep deprivation during a specific 3-hour time window post-training impairs hippocampal synaptic plasticity and memory. | Prince TM, Wimmer M, Choi J, Havekes R, Aton S, Abel T | Neurobiology of learning and memory | 24380868 | Neurobiol Learn Mem | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24380868 |
| Editorial-Methods and models in sleep research. | Aton SJ, Di Giovanni G, Leresche N | Journal of neuroscience methods | 30576680 | J Neurosci Methods | 2019 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/30576680 |
| Sleep loss disrupts Arc expression in dentate gyrus neurons. | Delorme JE, Kodoth V, Aton SJ | Neurobiology of learning and memory | 29635031 | Neurobiol Learn Mem | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29635031 |
| Theta-gamma coupling emerges from spatially heterogeneous cholinergic neuromodulation. | Yang Y, Gritton H, Sarter M, Aton SJ, Booth V, Zochowski M | PLoS computational biology | 34329297 | PLoS Comput Biol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34329297 |
| Hippocampal Network Oscillations Rescue Memory Consolidation Deficits Caused by Sleep Loss. | Ognjanovski N, Broussard C, Zochowski M, Aton SJ | Cerebral cortex (New York, N.Y. : 1991) | 30060138 | Cereb Cortex | 2018 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/30060138 |
| Smartphone Global Positioning System (GPS) Data Enhances Recovery Assessment After Breast Cancer Surgery. | Panda N, Solsky I, Hawrusik B, Liu G, Reeder H, Lipsitz S, Desai EV, Lowery KW, Miller K, Gadd MA, Lubitz CC, Smith BL, Specht M, Onnela JP, Haynes AB | Annals of surgical oncology | 32812109 | Ann Surg Oncol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32812109 |
| Determining sample size and length of follow-up for smartphone-based digital phenotyping studies. | Barnett I, Torous J, Reeder HT, Baker J, Onnela JP | Journal of the American Medical Informatics Association : JAMIA | 33043370 | J Am Med Inform Assoc | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33043370 |
| Fluctuations in behavior and affect in college students measured using deep phenotyping. | Vidal Bustamante CM, Coombs G 3rd, Rahimi-Eichi H, Mair P, Onnela JP, Baker JT, Buckner RL | Scientific reports | 35121741 | Sci Rep | 2022 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/35121741 |
| The HOPE Pilot Study: Harnessing Patient-Reported Outcomes and Biometric Data to Enhance Cancer Care. | Wright AA, Raman N, Staples P, Schonholz S, Cronin A, Carlson K, Keating NL, Onnela JP | JCO clinical cancer informatics | 30652585 | JCO Clin Cancer Inform | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30652585 |
| New Tools for New Research in Psychiatry: A Scalable and Customizable Platform to Empower Data Driven Smartphone Research. | Torous J, Kiang MV, Lorme J, Onnela JP | JMIR mental health | 27150677 | JMIR Ment Health | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/27150677 |
| Characterizing the clinical relevance of digital phenotyping data quality with applications to a cohort with schizophrenia. | Torous J, Staples P, Barnett I, Sandoval LR, Keshavan M, Onnela JP | NPJ digital medicine | 31304300 | NPJ Digit Med | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/31304300 |
| Precision Assessment of Real-World Associations Between Stress and Sleep Duration Using Actigraphy Data Collected Continuously for an Academic Year: Individual-Level Modeling Study. | Vidal Bustamante CM, Coombs Iii G, Rahimi-Eichi H, Mair P, Onnela JP, Baker JT, Buckner RL | JMIR formative research | 38687600 | JMIR Form Res | 2024 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/38687600 |
| Utilizing a Personal Smartphone Custom App to Assess the Patient Health Questionnaire-9 (PHQ-9) Depressive Symptoms in Patients With Major Depressive Disorder. | Torous J, Staples P, Shanahan M, Lin C, Peck P, Keshavan M, Onnela JP | JMIR mental health | 26543914 | JMIR Ment Health | 2015 Jan-Mar | https://www.ncbi.nlm.nih.gov/pubmed/26543914 |
| Realizing the potential of mobile mental health: new methods for new data in psychiatry. | Torous J, Staples P, Onnela JP | Current psychiatry reports | 26073363 | Curr Psychiatry Rep | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26073363 |
| Beyond smartphones and sensors: choosing appropriate statistical methods for the analysis of longitudinal data. | Barnett I, Torous J, Staples P, Keshavan M, Onnela JP | Journal of the American Medical Informatics Association : JAMIA | 30272176 | J Am Med Inform Assoc | 2018 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/30272176 |
| Inferring mobility measures from GPS traces with missing data. | Barnett I, Onnela JP | Biostatistics (Oxford, England) | 30371736 | Biostatistics | 2020 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/30371736 |
| Sociodemographic characteristics of missing data in digital phenotyping. | Kiang MV, Chen JT, Krieger N, Buckee CO, Alexander MJ, Baker JT, Buckner RL, Coombs G 3rd, Rich-Edwards JW, Carlson KW, Onnela JP | Scientific reports | 34326370 | Sci Rep | 2021 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/34326370 |
| A comparison of passive and active estimates of sleep in a cohort with schizophrenia. | Staples P, Torous J, Barnett I, Carlson K, Sandoval L, Keshavan M, Onnela JP | NPJ schizophrenia | 29038553 | NPJ Schizophr | 2017 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/29038553 |
| Methodology and Reporting of Mobile Heath and Smartphone Application Studies for Schizophrenia. | Torous J, Firth J, Mueller N, Onnela JP, Baker JT | Harvard review of psychiatry | 28234658 | Harv Rev Psychiatry | 2017 May/Jun | https://www.ncbi.nlm.nih.gov/pubmed/28234658 |
| Digital Phenotyping to Quantify Psychosocial Well-Being Trajectories After Spinal Cord Injury. | Mercier HW, Hamner JW, Torous J, Onnela JP, Taylor JA | American journal of physical medicine & rehabilitation | 32576743 | Am J Phys Med Rehabil | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32576743 |
| Augmented Movelet Method for Activity Classification Using Smartphone Gyroscope and Accelerometer Data. | Huang EJ, Onnela JP | Sensors (Basel, Switzerland) | 32630752 | Sensors (Basel) | 2020 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/32630752 |
| Smartphone-based Assessment of Preoperative Decision Conflict and Postoperative Physical Activity Among Patients Undergoing Cancer Surgery: A Prospective Cohort Study. | Panda N, Solsky I, Cauley CE, Lipsitz S, Desai EV, Huang EJ, Benjamin EM, Lubitz CC, Onnela JP, Haynes AB | Annals of surgery | 32941270 | Ann Surg | 2022 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/32941270 |
| New dimensions and new tools to realize the potential of RDoC: digital phenotyping via smartphones and connected devices. | Torous J, Onnela JP, Keshavan M | Translational psychiatry | 28267146 | Transl Psychiatry | 2017 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/28267146 |
| Design and results of a smartphone-based digital phenotyping study to quantify ALS progression. | Berry JD, Paganoni S, Carlson K, Burke K, Weber H, Staples P, Salinas J, Chan J, Green JR, Connaghan K, Barback J, Onnela JP | Annals of clinical and translational neurology | 31139685 | Ann Clin Transl Neurol | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31139685 |
| Smartphone-Based Tracking of Sleep in Depression, Anxiety, and Psychotic Disorders. | Aledavood T, Torous J, Triana Hoyos AM, Naslund JA, Onnela JP, Keshavan M | Current psychiatry reports | 31161412 | Curr Psychiatry Rep | 2019 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/31161412 |
| Open-source Longitudinal Sleep Analysis From Accelerometer Data (DPSleep): Algorithm Development and Validation. | Rahimi-Eichi H, Coombs Iii G, Vidal Bustamante CM, Onnela JP, Baker JT, Buckner RL | JMIR mHealth and uHealth | 34612831 | JMIR Mhealth Uhealth | 2021 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/34612831 |
| High potential but limited evidence: Using voice data from smartphones to monitor and diagnose mood disorders. | Or F, Torous J, Onnela JP | Psychiatric rehabilitation journal | 28891659 | Psychiatr Rehabil J | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28891659 |
| Relapse prediction in schizophrenia through digital phenotyping: a pilot study. | Barnett I, Torous J, Staples P, Sandoval L, Keshavan M, Onnela JP | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 29511333 | Neuropsychopharmacology | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29511333 |
| Expected Versus Experienced Health-Related Quality of Life Among Patients Recovering From Cancer Surgery: A Prospective Cohort Study. | Panda N, Solsky I, Neal BJ, Hawrusik B, Lipsitz S, Lubitz CC, Gibbons C, Brindle M, Sinyard RD, Onnela JP, Cauley CE, Haynes AB | Annals of surgery open : perspectives of surgical history, education, and clinical approaches | 34179891 | Ann Surg Open | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34179891 |
| Estimating longitudinal depressive symptoms from smartphone data in a transdiagnostic cohort. | Pellegrini AM, Huang EJ, Staples PC, Hart KL, Lorme JM, Brown HE, Perlis RH, Onnela JJ | Brain and behavior | 35076166 | Brain Behav | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35076166 |
| Harnessing Smartphone-Based Digital Phenotyping to Enhance Behavioral and Mental Health. | Onnela JP, Rauch SL | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 26818126 | Neuropsychopharmacology | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26818126 |
| A crossroad for validating digital tools in schizophrenia and mental health. | Torous J, Staples P, Barnett I, Onnela JP, Keshavan M | NPJ schizophrenia | 29626190 | NPJ Schizophr | 2018 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/29626190 |
| Understanding the quality, effectiveness and attributes of top-rated smartphone health apps. | Wisniewski H, Liu G, Henson P, Vaidyam A, Hajratalli NK, Onnela JP, Torous J | Evidence-based mental health | 30635262 | Evid Based Ment Health | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30635262 |
| EndNote: Feature-based classification of networks. | Barnett I, Malik N, Kuijjer ML, Mucha PJ, Onnela JP | Network science (Cambridge University Press) | 31984135 | Netw Sci (Camb Univ Press) | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31984135 |
| The relationship of rate and pause features to the communicative participation of people living with ALS. | Connaghan KP, Green JR, Eshghi M, Haenssler AE, Scheier ZA, Clark A, Iyer A, Richburg BD, Rowe HP, Okada J, Johnson SA, Onnela JP, Burke KM, Berry JD | Muscle & nerve | 38837773 | Muscle Nerve | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38837773 |
| The Role of Epigenetic Mechanisms in the Regulation of Gene Expression in the Nervous System. | Cholewa-Waclaw J, Bird A, von Schimmelmann M, Schaefer A, Yu H, Song H, Madabhushi R, Tsai LH | The Journal of neuroscience : the official journal of the Society for Neuroscience | 27911745 | J Neurosci | 2016 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/27911745 |
| Polycomb repressive complex 2 (PRC2) silences genes responsible for neurodegeneration. | von Schimmelmann M, Feinberg PA, Sullivan JM, Ku SM, Badimon A, Duff MK, Wang Z, Lachmann A, Dewell S, Ma'ayan A, Han MH, Tarakhovsky A, Schaefer A | Nature neuroscience | 27526204 | Nat Neurosci | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27526204 |
| A comparative analysis of microglial inducible Cre lines. | Faust TE, Feinberg PA, O'Connor C, Kawaguchi R, Chan A, Strasburger H, Frosch M, Boyle MA, Masuda T, Amann L, Knobeloch KP, Prinz M, Schaefer A, Schafer DP | Cell reports | 37635351 | Cell Rep | 2023 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/37635351 |
| MicroRNA-128 governs neuronal excitability and motor behavior in mice. | Tan CL, Plotkin JL, Venø MT, von Schimmelmann M, Feinberg P, Mann S, Handler A, Kjems J, Surmeier DJ, O'Carroll D, Greengard P, Schaefer A | Science (New York, N.Y.) | 24311694 | Science | 2013 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/24311694 |
| Convergence of spectrums: neuronal gene network states in autism spectrum disorder. | Sullivan JM, De Rubeis S, Schaefer A | Current opinion in neurobiology | 31220745 | Curr Opin Neurobiol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31220745 |
| Microglia states and nomenclature: A field at its crossroads. | Paolicelli RC, Sierra A, Stevens B, Tremblay ME, Aguzzi A, Ajami B, Amit I, Audinat E, Bechmann I, Bennett M, Bennett F, Bessis A, Biber K, Bilbo S, Blurton-Jones M, Boddeke E, Brites D, Brône B, Brown GC, Butovsky O, Carson MJ, Castellano B, Colonna M, Cowley SA, Cunningham C, Davalos D, De Jager PL, de Strooper B, Denes A, Eggen BJL, Eyo U, Galea E, Garel S, Ginhoux F, Glass CK, Gokce O, Gomez-Nicola D, González B, Gordon S, Graeber MB, Greenhalgh AD, Gressens P, Greter M, Gutmann DH, Haass C, Heneka MT, Heppner FL, Hong S, Hume DA, Jung S, Kettenmann H, Kipnis J, Koyama R, Lemke G, Lynch M, Majewska A, Malcangio M, Malm T, Mancuso R, Masuda T, Matteoli M, McColl BW, Miron VE, Molofsky AV, Monje M, Mracsko E, Nadjar A, Neher JJ, Neniskyte U, Neumann H, Noda M, Peng B, Peri F, Perry VH, Popovich PG, Pridans C, Priller J, Prinz M, Ragozzino D, Ransohoff RM, Salter MW, Schaefer A, Schafer DP, Schwartz M, Simons M, Smith CJ, Streit WJ, Tay TL, Tsai LH, Verkhratsky A, von Bernhardi R, Wake H, Wittamer V, Wolf SA, Wu LJ, Wyss-Coray T | Neuron | 36327895 | Neuron | 2022 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/36327895 |
| Microglia enable cross-modal plasticity by removing inhibitory synapses. | Hashimoto A, Kawamura N, Tarusawa E, Takeda I, Aoyama Y, Ohno N, Inoue M, Kagamiuchi M, Kato D, Matsumoto M, Hasegawa Y, Nabekura J, Schaefer A, Moorhouse AJ, Yagi T, Wake H | Cell reports | 37086724 | Cell Rep | 2023 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/37086724 |
| Autism-like syndrome is induced by pharmacological suppression of BET proteins in young mice. | Sullivan JM, Badimon A, Schaefer U, Ayata P, Gray J, Chung CW, von Schimmelmann M, Zhang F, Garton N, Smithers N, Lewis H, Tarakhovsky A, Prinjha RK, Schaefer A | The Journal of experimental medicine | 26392221 | J Exp Med | 2015 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/26392221 |
| Argonaute-associated short introns are a novel class of gene regulators. | Hansen TB, Venø MT, Jensen TI, Schaefer A, Damgaard CK, Kjems J | Nature communications | 27173734 | Nat Commun | 2016 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/27173734 |
| CSF-1 controls cerebellar microglia and is required for motor function and social interaction. | Kana V, Desland FA, Casanova-Acebes M, Ayata P, Badimon A, Nabel E, Yamamuro K, Sneeboer M, Tan IL, Flanigan ME, Rose SA, Chang C, Leader A, Le Bourhis H, Sweet ES, Tung N, Wroblewska A, Lavin Y, See P, Baccarini A, Ginhoux F, Chitu V, Stanley ER, Russo SJ, Yue Z, Brown BD, Joyner AL, De Witte LD, Morishita H, Schaefer A, Merad M | The Journal of experimental medicine | 31350310 | J Exp Med | 2019 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/31350310 |
| G9a influences neuronal subtype specification in striatum. | Maze I, Chaudhury D, Dietz DM, Von Schimmelmann M, Kennedy PJ, Lobo MK, Daws SE, Miller ML, Bagot RC, Sun H, Turecki G, Neve RL, Hurd YL, Shen L, Han MH, Schaefer A, Nestler EJ | Nature neuroscience | 24584053 | Nat Neurosci | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24584053 |
| Negative feedback control of neuronal activity by microglia. | Badimon A, Strasburger HJ, Ayata P, Chen X, Nair A, Ikegami A, Hwang P, Chan AT, Graves SM, Uweru JO, Ledderose C, Kutlu MG, Wheeler MA, Kahan A, Ishikawa M, Wang YC, Loh YE, Jiang JX, Surmeier DJ, Robson SC, Junger WG, Sebra R, Calipari ES, Kenny PJ, Eyo UB, Colonna M, Quintana FJ, Wake H, Gradinaru V, Schaefer A | Nature | 32999463 | Nature | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32999463 |
| Epigenetic regulation of brain region-specific microglia clearance activity. | Ayata P, Badimon A, Strasburger HJ, Duff MK, Montgomery SE, Loh YE, Ebert A, Pimenova AA, Ramirez BR, Chan AT, Sullivan JM, Purushothaman I, Scarpa JR, Goate AM, Busslinger M, Shen L, Losic B, Schaefer A | Nature neuroscience | 30038282 | Nat Neurosci | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30038282 |
| An AUTS2-Polycomb complex activates gene expression in the CNS. | Gao Z, Lee P, Stafford JM, von Schimmelmann M, Schaefer A, Reinberg D | Nature | 25519132 | Nature | 2014 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/25519132 |
| Identifying specific prefrontal neurons that contribute to autism-associated abnormalities in physiology and social behavior. | Brumback AC, Ellwood IT, Kjaerby C, Iafrati J, Robinson S, Lee AT, Patel T, Nagaraj S, Davatolhagh F, Sohal VS | Molecular psychiatry | 29112191 | Mol Psychiatry | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29112191 |
| Interneuron Transplantation Rescues Social Behavior Deficits without Restoring Wild-Type Physiology in a Mouse Model of Autism with Excessive Synaptic Inhibition. | Southwell DG, Seifikar H, Malik R, Lavi K, Vogt D, Rubenstein JL, Sohal VS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 31988060 | J Neurosci | 2020 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/31988060 |
| Dynamic, Cell-Type-Specific Roles for GABAergic Interneurons in a Mouse Model of Optogenetically Inducible Seizures. | Khoshkhoo S, Vogt D, Sohal VS | Neuron | 28041880 | Neuron | 2017 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/28041880 |
| Gamma rhythms link prefrontal interneuron dysfunction with cognitive inflexibility in Dlx5/6(+/-) mice. | Cho KK, Hoch R, Lee AT, Patel T, Rubenstein JL, Sohal VS | Neuron | 25754826 | Neuron | 2015 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/25754826 |
| Roles of Prefrontal Cortex and Mediodorsal Thalamus in Task Engagement and Behavioral Flexibility. | Marton TF, Seifikar H, Luongo FJ, Lee AT, Sohal VS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 29437889 | J Neurosci | 2018 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/29437889 |
| Correlations between prefrontal neurons form a small-world network that optimizes the generation of multineuron sequences of activity. | Luongo FJ, Zimmerman CA, Horn ME, Sohal VS | Journal of neurophysiology | 26888108 | J Neurophysiol | 2016 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/26888108 |
| The parvalbumin/somatostatin ratio is increased in Pten mutant mice and by human PTEN ASD alleles. | Vogt D, Cho KKA, Lee AT, Sohal VS, Rubenstein JLR | Cell reports | 25937288 | Cell Rep | 2015 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/25937288 |
| Serotonin 1B Receptors Regulate Prefrontal Function by Gating Callosal and Hippocampal Inputs. | Kjaerby C, Athilingam J, Robinson SE, Iafrati J, Sohal VS | Cell reports | 27974203 | Cell Rep | 2016 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/27974203 |
| Tonic or Phasic Stimulation of Dopaminergic Projections to Prefrontal Cortex Causes Mice to Maintain or Deviate from Previously Learned Behavioral Strategies. | Ellwood IT, Patel T, Wadia V, Lee AT, Liptak AT, Bender KJ, Sohal VS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28739583 | J Neurosci | 2017 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/28739583 |
| Microcircuit Mechanisms through which Mediodorsal Thalamic Input to Anterior Cingulate Cortex Exacerbates Pain-Related Aversion. | Meda KS, Patel T, Braz JM, Malik R, Turner ML, Seifikar H, Basbaum AI, Sohal VS | Neuron | 31030955 | Neuron | 2019 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/31030955 |
| Pyramidal neurons in prefrontal cortex receive subtype-specific forms of excitation and inhibition. | Lee AT, Gee SM, Vogt D, Patel T, Rubenstein JL, Sohal VS | Neuron | 24361076 | Neuron | 2014 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/24361076 |
| Putative Microcircuit-Level Substrates for Attention Are Disrupted in Mouse Models of Autism. | Luongo FJ, Horn ME, Sohal VS | Biological psychiatry | 26022075 | Biol Psychiatry | 2016 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/26022075 |
| VIP Interneurons Contribute to Avoidance Behavior by Regulating Information Flow across Hippocampal-Prefrontal Networks. | Lee AT, Cunniff MM, See JZ, Wilke SA, Luongo FJ, Ellwood IT, Ponnavolu S, Sohal VS | Neuron | 31053407 | Neuron | 2019 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/31053407 |
| Network Effects of the 15q13.3 Microdeletion on the Transcriptome and Epigenome in Human-Induced Neurons. | Zhang S, Zhang X, Purmann C, Ma S, Shrestha A, Davis KN, Ho M, Huang Y, Pattni R, Wong WH, Bernstein JA, Hallmayer J, Urban AE | Biological psychiatry | 32919612 | Biol Psychiatry | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/32919612 |
| Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. | Zhang X, Zhang Y, Zhu X, Purmann C, Haney MS, Ward T, Khechaduri A, Yao J, Weissman SM, Urban AE | Nature communications | 30559385 | Nat Commun | 2018 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/30559385 |
| Mutations in human DNA methyltransferase DNMT1 induce specific genome-wide epigenomic and transcriptomic changes in neurodevelopment. | Davis KN, Qu PP, Ma S, Lin L, Plastini M, Dahl N, Plazzi G, Pizza F, O'Hara R, Wong WH, Hallmayer J, Mignot E, Zhang X, Urban AE | Human molecular genetics | 37584462 | Hum Mol Genet | 2023 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/37584462 |
| Cell-type specific global reprogramming of the transcriptome and epigenome in induced neurons with the 16p11.2 neuropsychiatric CNVs. | Ward TR, Qu PP, Leung LC, Zhou B, Muench KL, Khechaduri A, Plastini MJ, Charlton CA, Pattni R, Ho S, Ho M, Huang Y, Zhou P, Hallmayer JF, Mourrain P, Palmer TD, Zhang X, Urban AE | European journal of human genetics : EJHG | 40374944 | Eur J Hum Genet | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40374944 |
| Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. | Haraksingh RR, Abyzov A, Urban AE | BMC genomics | 28438122 | BMC Genomics | 2017 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/28438122 |
| Identification of Human Neuronal Protein Complexes Reveals Biochemical Activities and Convergent Mechanisms of Action in Autism Spectrum Disorders. | Li J, Ma Z, Shi M, Malty RH, Aoki H, Minic Z, Phanse S, Jin K, Wall DP, Zhang Z, Urban AE, Hallmayer J, Babu M, Snyder M | Cell systems | 26949739 | Cell Syst | 2015 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/26949739 |
| Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints. | Zhou B, Purmann C, Guo H, Shin G, Huang Y, Pattni R, Meng Q, Greer SU, Roychowdhury T, Wood RN, Ho M, Dohna HZ, Abyzov A, Hallmayer JF, Wong WH, Ji HP, Urban AE | Proceedings of the National Academy of Sciences of the United States of America | 39042694 | Proc Natl Acad Sci U S A | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39042694 |
| Seizure Action Plans Do Not Reduce Health Care Utilization in Pediatric Epilepsy Patients. | Roundy LM, Filloux FM, Kerr L, Rimer A, Bonkowsky JL | Journal of child neurology | 26245799 | J Child Neurol | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26245799 |
| Targeted leukodystrophy diagnosis based on charges and yields for testing. | Richards J, Korgenski EK, Taft RJ, Vanderver A, Bonkowsky JL | American journal of medical genetics. Part A | 26183797 | Am J Med Genet A | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26183797 |
| Microfluidic-aided genotyping of zebrafish in the first 48 h with 100% viability. | Samuel R, Stephenson R, Roy P, Pryor R, Zhou L, Bonkowsky JL, Gale BK | Biomedical microdevices | 25773537 | Biomed Microdevices | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25773537 |
| Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. | Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Quinlan AR | NPJ genomic medicine | 30109124 | NPJ Genom Med | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30109124 |
| Neonatal Magnesium Levels Between 24 and 48 Hours of Life and Outcomes for Epilepsy and Motor Impairment in Premature Infants. | Ostrander B, Bardsley T, Korgenski EK, Greene T, Bonkowsky JL | Pediatric neurology | 27025188 | Pediatr Neurol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27025188 |
| Live imaging of mitochondrial dynamics in CNS dopaminergic neurons in vivo demonstrates early reversal of mitochondrial transport following MPP(+) exposure. | Dukes AA, Bai Q, Van Laar VS, Zhou Y, Ilin V, David CN, Agim ZS, Bonkowsky JL, Cannon JR, Watkins SC, Croix CM, Burton EA, Berman SB | Neurobiology of disease | 27452482 | Neurobiol Dis | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27452482 |
| Chiari I Malformation Causing Developmental Regression in a 4 Month Old. | Doll ES, Bonkowsky JL, Brown LL, de Havenon AH, Brockmeyer DL, Glasgow TS, Morita DC | Global pediatric health.. | 27335920 | Glob Pediatr Health | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/27335920 |
| Costs of the diagnostic odyssey in children with inherited leukodystrophies. | Richards J, Korgenski EK, Srivastava R, Bonkowsky JL | Neurology | 26320197 | Neurology | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26320197 |
| A Serotonin Circuit Acts as an Environmental Sensor to Mediate Midline Axon Crossing through EphrinB2. | Xing L, Son JH, Stevenson TJ, Lillesaar C, Bally-Cuif L, Dahl T, Bonkowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26538650 | J Neurosci | 2015 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/26538650 |
| The Midline Axon Crossing Decision Is Regulated through an Activity-Dependent Mechanism by the NMDA Receptor. | Gao J, Stevenson TJ, Douglass AD, Barrios JP, Bonkowsky JL | eNeuro | 29766040 | eNeuro | 2018 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/29766040 |
| Intrapartum magnesium sulfate and the potential for cardiopulmonary drug-drug interactions. | Campbell SC, Stockmann C, Balch A, Clark EA, Kamyar M, Varner M, Korgenski EK, Bonkowsky JL, Spigarelli MG, Sherwin CM | Therapeutic drug monitoring | 24487252 | Ther Drug Monit | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24487252 |
| Determinants of health care use in a population-based leukodystrophy cohort. | Nelson C, Mundorff MB, Korgenski EK, Brimley CJ, Srivastava R, Bonkowsky JL | The Journal of pediatrics | 23069195 | J Pediatr | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23069195 |
| Expression of arginine vasotocin receptors in the developing zebrafish CNS. | Iwasaki K, Taguchi M, Bonkowsky JL, Kuwada JY | Gene expression patterns : GEP | 23830982 | Gene Expr Patterns | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23830982 |
| Temporal Dysynchrony in brain connectivity gene expression following hypoxia. | Milash B, Gao J, Stevenson TJ, Son JH, Dahl T, Bonkowsky JL | BMC genomics | 27146468 | BMC Genomics | 2016 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/27146468 |
| A Novel Developmental Role for Dopaminergic Signaling to Specify Hypothalamic Neurotransmitter Identity. | Chen YC, Semenova S, Rozov S, Sundvik M, Bonkowsky JL, Panula P | The Journal of biological chemistry | 27539857 | J Biol Chem | 2016 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/27539857 |
| Hypothalamic radial glia function as self-renewing neural progenitors in the absence of Wnt/β-catenin signaling. | Duncan RN, Xie Y, McPherson AD, Taibi AV, Bonkowsky JL, Douglass AD, Dorsky RI | Development (Cambridge, England) | 26603385 | Development | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26603385 |
| An automated system for rapid cellular extraction from live zebrafish embryos and larvae: Development and application to genotyping. | Lambert CJ, Freshner BC, Chung A, Stevenson TJ, Bowles DM, Samuel R, Gale BK, Bonkowsky JL | PloS one | 29543903 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29543903 |
| Motor Behavior Mediated by Continuously Generated Dopaminergic Neurons in the Zebrafish Hypothalamus Recovers after Cell Ablation. | McPherson AD, Barrios JP, Luks-Morgan SJ, Manfredi JP, Bonkowsky JL, Douglass AD, Dorsky RI | Current biology : CB | 26774784 | Curr Biol | 2016 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/26774784 |
| Rapid and efficient zebrafish genotyping using PCR with high-resolution melt analysis. | Xing L, Quist TS, Stevenson TJ, Dahlem TJ, Bonkowsky JL | Journal of visualized experiments : JoVE | 24561516 | J Vis Exp | 2014 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/24561516 |
| Maternal magnesium sulphate exposure predicts neonatal magnesium blood concentrations. | Sherwin CM, Balch A, Campbell SC, Fredrickson J, Clark EA, Varner M, Stockmann C, Korgenski EK, Bonkowsky JL, Spigarelli MG | Basic & clinical pharmacology & toxicology | 24164968 | Basic Clin Pharmacol Toxicol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24164968 |
| National variation in costs and mortality for leukodystrophy patients in US children's hospitals. | Brimley CJ, Lopez J, van Haren K, Wilkes J, Sheng X, Nelson C, Korgenski EK, Srivastava R, Bonkowsky JL | Pediatric neurology | 23953952 | Pediatr Neurol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23953952 |
| Dopaminergic Co-Regulation of Locomotor Development and Motor Neuron Synaptogenesis is Uncoupled by Hypoxia in Zebrafish. | Son JH, Stevenson TJ, Bowles MD, Scholl EA, Bonkowsky JL | eNeuro | 32001551 | eNeuro | 2020 Jan/Feb | https://www.ncbi.nlm.nih.gov/pubmed/32001551 |
| A zebrafish model of X-linked adrenoleukodystrophy recapitulates key disease features and demonstrates a developmental requirement for abcd1 in oligodendrocyte patterning and myelination. | Strachan LR, Stevenson TJ, Freshner B, Keefe MD, Miranda Bowles D, Bonkowsky JL | Human molecular genetics | 28911205 | Hum Mol Genet | 2017 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28911205 |
| Autism Spectrum Disorder and Neonatal Serum Magnesium Levels in Preterm Infants. | Bakian AV, Bilder DA, Korgenski EK, Bonkowsky JL | Child neurology open | 30246047 | Child Neurol Open | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30246047 |
| Sim1a and Arnt2 contribute to hypothalamo-spinal axon guidance by regulating Robo2 activity via a Robo3-dependent mechanism. | Schweitzer J, Löhr H, Bonkowsky JL, Hübscher K, Driever W | Development (Cambridge, England) | 23222439 | Development | 2013 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/23222439 |
| Preventable Infections in Children with Leukodystrophy. | Anderson HM, Wilkes J, Korgenski EK, Pulsipher MA, Blaschke AJ, Hersh AL, Srivastava R, Bonkowsky JL | Annals of clinical and translational neurology | 24955379 | Ann Clin Transl Neurol | 2014 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24955379 |
| Congenital lethal motor neuron disease with a novel defect in ribosome biogenesis. | Butterfield RJ, Stevenson TJ, Xing L, Newcomb TM, Nelson B, Zeng W, Li X, Lu HM, Lu H, Farwell Gonzalez KD, Wei JP, Chao EC, Prior TW, Snyder PJ, Bonkowsky JL, Swoboda KJ | Neurology | 24647030 | Neurology | 2014 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/24647030 |
| The conserved dopaminergic diencephalospinal tract mediates vertebrate locomotor development in zebrafish larvae. | Lambert AM, Bonkowsky JL, Masino MA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23015438 | J Neurosci | 2012 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/23015438 |
| Disease specific therapies in leukodystrophies and leukoencephalopathies. | Helman G, Van Haren K, Bonkowsky JL, Bernard G, Pizzino A, Braverman N, Suhr D, Patterson MC, Ali Fatemi S, Leonard J, van der Knaap MS, Back SA, Damiani S, Goldman SA, Takanohashi A, Petryniak M, Rowitch D, Messing A, Wrabetz L, Schiffmann R, Eichler F, Escolar ML, Vanderver A, GLIA Consortium | Molecular genetics and metabolism | 25684057 | Mol Genet Metab | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25684057 |
| Revised consensus statement on the preventive and symptomatic care of patients with leukodystrophies. | Adang LA, Sherbini O, Ball L, Bloom M, Darbari A, Amartino H, DiVito D, Eichler F, Escolar M, Evans SH, Fatemi A, Fraser J, Hollowell L, Jaffe N, Joseph C, Karpinski M, Keller S, Maddock R, Mancilla E, McClary B, Mertz J, Morgart K, Langan T, Leventer R, Parikh S, Pizzino A, Prange E, Renaud DL, Rizzo W, Shapiro J, Suhr D, Suhr T, Tonduti D, Waggoner J, Waldman A, Wolf NI, Zerem A, Bonkowsky JL, Bernard G, van Haren K, Vanderver A, Global Leukodystrophy Initiative (GLIA) Consortium | Molecular genetics and metabolism | 28863857 | Mol Genet Metab | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28863857 |
| Transgenic FingRs for Live Mapping of Synaptic Dynamics in Genetically-Defined Neurons. | Son JH, Keefe MD, Stevenson TJ, Barrios JP, Anjewierden S, Newton JB, Douglass AD, Bonkowsky JL | Scientific reports | 26728131 | Sci Rep | 2016 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/26728131 |
| Neurodegeneration in a Drosophila model of adrenoleukodystrophy: the roles of the Bubblegum and Double bubble acyl-CoA synthetases. | Sivachenko A, Gordon HB, Kimball SS, Gavin EJ, Bonkowsky JL, Letsou A | Disease models & mechanisms | 26893370 | Dis Model Mech | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26893370 |
| Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools. | Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, Ostrander B, Butterfield R, Bonkowsky JL, Dere W, Marth GT | Journal of clinical and translational science | 29707261 | J Clin Transl Sci | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29707261 |
| Clinical exome sequencing identifies a novel TUBB4A mutation in a child with static hypomyelinating leukodystrophy. | Purnell SM, Bleyl SB, Bonkowsky JL | Pediatric neurology | 24742798 | Pediatr Neurol | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24742798 |
| Neonatal magnesium levels correlate with motor outcomes in premature infants: a long-term retrospective cohort study. | Doll E, Wilkes J, Cook LJ, Korgenski EK, Faix RG, Yoder BA, Srivastava R, Sherwin CM, Spigarelli MG, Clark EA, Bonkowsky JL | Frontiers in pediatrics | 25414842 | Front Pediatr | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25414842 |
| Closing delivery gaps in the treatment of tuberculosis infection: Lessons from implementation research in Peru. | Yuen CM, Millones AK, Puma D, Jimenez J, Galea JT, Calderon R, Pages GS, Brooks MB, Lecca L, Nicholson T, Becerra MC, Keshavjee S | PloS one | 33606824 | PLoS One | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33606824 |
| Identifying barriers and facilitators to implementation of community-based tuberculosis active case finding with mobile X-ray units in Lima, Peru: a RE-AIM evaluation. | Yuen CM, Puma D, Millones AK, Galea JT, Tzelios C, Calderon RI, Brooks MB, Jimenez J, Contreras C, Nichols TC, Nicholson T, Lecca L, Becerra MC, Keshavjee S | BMJ open | 34234000 | BMJ Open | 2021 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/34234000 |
| The impact of the COVID-19 pandemic on patients' experiences obtaining a tuberculosis diagnosis in Peru: a mixed-methods study. | Millones AK, Lecca L, Acosta D, Campos H, Del Águila-Rojas E, Farroñay S, Morales G, Ramirez-Sandoval J, Torres I, Jimenez J, Yuen CM | BMC infectious diseases | 36352374 | BMC Infect Dis | 2022 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/36352374 |
| Barriers and facilitators to tuberculosis diagnosis in Lima, Peru: a mixed methods study. | Geadas C, Millones AK, Acosta D, Campos H, Del Aguila-Rojas E, Farroñay S, Morales G, Ramirez-Sandoval J, Torres I, Jimenez J, Lecca L, Yuen CM | BMC infectious diseases | 39118040 | BMC Infect Dis | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39118040 |
| A role for community-level socioeconomic indicators in targeting tuberculosis screening interventions. | Brooks MB, Jenkins HE, Puma D, Tzelios C, Millones AK, Jimenez J, Galea JT, Lecca L, Becerra MC, Keshavjee S, Yuen CM | Scientific reports | 35039612 | Sci Rep | 2022 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/35039612 |
| Geographic accessibility to health facilities predicts uptake of community-based tuberculosis screening in an urban setting. | Jenkins HE, Ayuk S, Puma D, Brooks MB, Millones AK, Jimenez J, Lecca L, Galea JT, Becerra M, Keshavjee S, Yuen CM | International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases | 35470023 | Int J Infect Dis | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35470023 |
| Mapping local hot spots with routine tuberculosis data: A pragmatic approach to identify spatial variability. | Brooks MB, Millones AK, Puma D, Contreras C, Jimenez J, Tzelios C, Jenkins HE, Yuen CM, Keshavjee S, Lecca L, Becerra MC | PloS one | 35324987 | PLoS One | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35324987 |
| Toward patient-centered tuberculosis preventive treatment: preferences for regimens and formulations in Lima, Peru. | Yuen CM, Millones AK, Galea JT, Puma D, Jimenez J, Lecca L, Becerra MC, Keshavjee S | BMC public health | 33430823 | BMC Public Health | 2021 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33430823 |
| Impact of the private sector on spatial accessibility to chest radiography services in Lima, Peru. | Xiong Y, Millones AK, Farroñay S, Torres I, Acosta D, Jordan DR, Jimenez J, Wippel C, Jenkins HE, Lecca L, Yuen CM | IJTLD open | 38698907 | IJTLD Open | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38698907 |
| Exploring the Role of the Private Sector in Tuberculosis Detection and Management in Lima, Peru: A Mixed-Methods Patient Pathway Analysis. | Wippel C, Farroñay S, Gilbert HN, Millones AK, Acosta D, Torres I, Jimenez J, Alarcón VA, Lecca L, Yuen CM | The American journal of tropical medicine and hygiene | 38744270 | Am J Trop Med Hyg | 2024 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/38744270 |
| Adapting a mobile TB screening unit to provide integrated screening services and linkage to primary care. | Millones AK, Cohen S, Acosta D, Campos H, Condeso A, Farroñay S, Torres I, Vargas C, Abanto K, Contreras C, Palomino S, Jimenez J, Lecca L, Yuen CM | Public health action | 39618835 | Public Health Action | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39618835 |
| Geospatial analysis of reported activity locations to identify sites for tuberculosis screening. | Yuen CM, Brooks MB, Millones AK, Acosta D, Del Águila-Rojas E, Campos H, Farroñay S, Morales G, Ramirez-Sandoval J, Nichols TC, Jimenez J, Jenkins HE, Lecca L | Scientific reports | 35982104 | Sci Rep | 2022 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/35982104 |
| Exploring the role of the private sector in tuberculosis detection and management in Lima, Peru: a mixed-methods patient pathway analysis. | Wippel C, Farroñay S, Gilbert HN, Millones AK, Acosta D, Torres I, Jimenez J, Lecca L, Yuen CM | medRxiv : the preprint server for health sciences | 37808756 | medRxiv | 2023 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/37808756 |
| Utility of Mycobacterium tuberculosis Genome Sequencing Snapshots to Assess Transmission Dynamics Over Time. | Yuen CM, Huang CC, Millones AK, Calderon RI, Manson AL, Jimenez J, Contreras C, Earl AM, Becerra MC, Lecca L, Murray MB | The Journal of infectious diseases | 37995298 | J Infect Dis | 2024 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/37995298 |
| Person-centered strategies for delivering TB diagnostic services in Lima, Peru. | Yuen CM, Millones AK, Acosta D, Torres I, Farroñay S, Jimenez J, Lecca L | Public health action | 37736576 | Public Health Action | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37736576 |
| A preliminary investigation of attachment style and inflammation in African-American young adults. | Ehrlich KB, Stern JA, Eccles J, Dinh JV, Hopper EA, Kemeny ME, Adam EK, Cassidy J | Attachment & human development | 30406721 | Attach Hum Dev | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30406721 |
| Maltreatment exposure across childhood and low-grade inflammation: Considerations of exposure type, timing, and sex differences. | Ehrlich KB, Miller GE, Rogosch FA, Cicchetti D | Developmental psychobiology | 32896910 | Dev Psychobiol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32896910 |
| Exposure to parental depression in adolescence and proinflammatory phenotypes 20 years later. | Ehrlich KB, Celia-Sanchez ML, Yu T, Heard-Garris N, Chen E, Miller GE, Brody GH | Brain, behavior, and immunity | 38242368 | Brain Behav Immun | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38242368 |
| The protective role of parental vigilance in the link between risky childhood environments and health. | Corallo KL, Carr CP, Lavner JA, Koss KJ, Ehrlich KB | Social science & medicine (1982) | 36527897 | Soc Sci Med | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36527897 |
| Preventive parenting intervention during childhood and young black adults' unhealthful behaviors: a randomized controlled trial. | Brody GH, Yu T, Miller GE, Ehrlich KB, Chen E | Journal of child psychology and psychiatry, and allied disciplines | 30203840 | J Child Psychol Psychiatry | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30203840 |
| Attachment and physical health: introduction to the special issue. | B Ehrlich K, Cassidy J | Attachment & human development | 30406722 | Attach Hum Dev | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30406722 |
| Emotional Distress, Targeted Rejection, and Antibody Production After Influenza Vaccination in Adolescence. | Corallo KL, Lyle SM, Carlock MA, Ross TM, Ehrlich KB | Psychosomatic medicine | 35100185 | Psychosom Med | 2022 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/35100185 |
| How does the social world shape health across the lifespan? Insights and new directions. | Ehrlich KB | The American psychologist | 33382288 | Am Psychol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33382288 |
| Changes in depressive symptoms and antibody production following influenza vaccination in adolescents and adults. | Ehrlich KB, Lyle SM, Corallo KL, Lavner JA, Ross TM | Vaccine | 38702230 | Vaccine | 2024 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/38702230 |
| Socioeconomic disadvantage and high-effort coping in childhood: evidence of skin-deep resilience. | Ehrlich KB, Lyle SM, Corallo KL, Brisson JM, Wiggins ER, Yu T, Chen E, Miller GE, Brody GH | Journal of child psychology and psychiatry, and allied disciplines | 37246563 | J Child Psychol Psychiatry | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/37246563 |
| Recalled Neighborhood Environments, Parental Control, and Cytokine-Mediated Response to Viral Challenge. | Corallo KL, Lyle SM, Murphy MLM, vanDellen MR, Ehrlich KB | Psychosomatic medicine | 34334728 | Psychosom Med | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34334728 |
| Neighborhood poverty, allostatic load, and changes in cellular aging in African American young adults: the moderating role of attachment. | Ehrlich KB, Yu T, Sadiq A, Brody GH | Attachment & human development | 34617499 | Attach Hum Dev | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34617499 |
| Beyond Early Adversity: The Role of Parenting in Infant Physical Health. | Stern JA, Beijers R, Ehrlich KB, Cassidy J, de Weerth C | Journal of developmental and behavioral pediatrics : JDBP | 32271266 | J Dev Behav Pediatr | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32271266 |
| Harsh parenting and youth systemic inflammation: Modulation by the autonomic nervous system. | Oshri A, Duprey EB, Liu S, Ehrlich KB | Health psychology : official journal of the Division of Health Psychology, American Psychological Association | 32202827 | Health Psychol | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32202827 |
| Attachment and psychoneuroimmunology. | Ehrlich KB | Current opinion in psychology | 29631123 | Curr Opin Psychol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29631123 |
| The Profundity of the Everyday: Family Routines in Adolescence Predict Development in Young Adulthood. | Barton AW, Brody GH, Yu T, Kogan SM, Chen E, Ehrlich KB | The Journal of adolescent health : official publication of the Society for Adolescent Medicine | 30392861 | J Adolesc Health | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30392861 |
| The benefits of nurturant-involved parenting for children's internalizing symptoms and cardiometabolic health in high-risk contexts. | Wiggins ER, Brisson JM, Lavner JA, Ehrlich KB | Development and psychopathology | 37386849 | Dev Psychopathol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37386849 |
| Ethical Machine Learning in Healthcare. | Chen IY, Pierson E, Rose S, Joshi S, Ferryman K, Ghassemi M | Annual review of biomedical data science | 34396058 | Annu Rev Biomed Data Sci | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34396058 |
| Improving the Performance of Risk Adjustment Systems: Constrained Regressions, Reinsurance, and Variable Selection. | McGuire TG, Zink AL, Rose S | American journal of health economics | 34869790 | Am J Health Econ | 2021 Fall | https://www.ncbi.nlm.nih.gov/pubmed/34869790 |
| Fair regression for health care spending. | Zink A, Rose S | Biometrics | 31860120 | Biometrics | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31860120 |
| Uncertainty in lung cancer stage for survival estimation via set-valued classification. | Bergquist S, Brooks GA, Landrum MB, Keating NL, Rose S | Statistics in medicine | 35675972 | Stat Med | 2022 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/35675972 |
| Data Source Concordance for Infectious Disease Epidemiology. | Majumder M, Cusick MM, Rose S | medRxiv : the preprint server for health sciences | 35677068 | medRxiv | 2022 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/35677068 |
| Causal inference in high dimensions: A marriage between Bayesian modeling and good frequentist properties. | Antonelli J, Papadogeorgou G, Dominici F | Biometrics | 33349923 | Biometrics | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33349923 |
| Measuring concordance of data sources used for infectious disease research in the USA: a retrospective data analysis. | Majumder MS, Cusick M, Rose S | BMJ open | 36854597 | BMJ Open | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36854597 |
| Conditional cross-design synthesis estimators for generalizability in Medicaid. | Degtiar I, Layton T, Wallace J, Rose S | Biometrics | 37018228 | Biometrics | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37018228 |
| CAUSAL INFERENCE IN THE CONTEXT OF AN ERROR PRONE EXPOSURE: AIR POLLUTION AND MORTALITY. | Wu X, Braun D, Kioumourtzoglou MA, Choirat C, Di Q, Dominici F | The annals of applied statistics | 31649797 | Ann Appl Stat | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31649797 |
| Considerations for outcome-dependent biased sampling in health databases. | Rose S | Statistics in medicine | 31489684 | Stat Med | 2019 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/31489684 |
| Air pollution exposure disparities across US population and income groups. | Jbaily A, Zhou X, Liu J, Lee TH, Kamareddine L, Verguet S, Dominici F | Nature | 35022594 | Nature | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35022594 |
| A generalizable data assembly algorithm for infectious disease outbreaks. | Majumder MS, Rose S | JAMIA open | 34350393 | JAMIA Open | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34350393 |
| Reflection on modern methods: when worlds collide-prediction, machine learning and causal inference. | Blakely T, Lynch J, Simons K, Bentley R, Rose S | International journal of epidemiology | 31298274 | Int J Epidemiol | 2021 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/31298274 |
| Intersections of machine learning and epidemiological methods for health services research. | Rose S | International journal of epidemiology | 32236476 | Int J Epidemiol | 2021 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/32236476 |
| High-Dimensional Confounding Adjustment Using Continuous Spike and Slab Priors. | Antonelli J, Parmigiani G, Dominici F | Bayesian analysis | 32431779 | Bayesian Anal | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32431779 |
| Machine Learning for Prediction in Electronic Health Data. | Rose S | JAMA network open | 30646089 | JAMA Netw Open | 2018 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/30646089 |
| Incidence, Persistence, and Steady-State Prevalence in Coding Intensity for Health Plan Payment. | McGuire TG, Enache OM, Chernew M, McWilliams JM, Nham T, Rose S | medRxiv : the preprint server for health sciences | 40321285 | medRxiv | 2025 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/40321285 |
| Limitations of P-Values and R-squared for Stepwise Regression Building: A Fairness Demonstration in Health Policy Risk Adjustment. | Rose S, McGuire TG | The American statistician | 31263291 | Am Stat | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31263291 |
| Discovering Heterogeneous Exposure Effects Using Randomization Inference in Air Pollution Studies. | Lee K, Small DS, Dominici F | Journal of the American Statistical Association | 36311902 | J Am Stat Assoc | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/36311902 |
| All Models are Wrong, but Many are Useful: Learning a Variable's Importance by Studying an Entire Class of Prediction Models Simultaneously. | Fisher A, Rudin C, Dominici F | Journal of machine learning research : JMLR | 34335110 | J Mach Learn Res | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/34335110 |
| A causal inference framework for cancer cluster investigations using publicly available data. | Nethery RC, Yang Y, Brown AJ, Dominici F | Journal of the Royal Statistical Society. Series A, (Statistics in Society) | 34262243 | J R Stat Soc Ser A Stat Soc | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34262243 |
| Considerations Across Three Cultures: Parametric Regressions, Interpretable Algorithms, and Complex Algorithms. | Eloyan A, Rose S | Observational studies.. | 34485997 | Obs Stud | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34485997 |
| Identifying undercompensated groups defined by multiple attributes in risk adjustment. | Zink A, Rose S | BMJ health & care informatics | 34535447 | BMJ Health Care Inform | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34535447 |
| Discussion on "Approval policies for modifications to machine learning-based software as a medical device: A study of biocreep" by Jean Feng, Scott Emerson, and Noah Simon. | Rose S | Biometrics | 33040334 | Biometrics | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33040334 |
| Evaluation of the health impacts of the 1990 Clean Air Act Amendments using causal inference and machine learning. | Nethery RC, Mealli F, Sacks JD, Dominici F | Journal of the American Statistical Association | 33424062 | J Am Stat Assoc | 2020 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/33424062 |
| Evaluating Federal Policies Using Bayesian Time Series Models: Estimating the Causal Impact of the Hospital Readmissions Reduction Program. | Papadogeorgou G, Menchetti F, Choirat C, Wasfy JH, Zigler CM, Mealli F | Health services & outcomes research methodology | 39866244 | Health Serv Outcomes Res Methodol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39866244 |
| Food Insecurity and Health Care Expenditures in the United States, 2011-2013. | Berkowitz SA, Basu S, Meigs JB, Seligman HK | Health services research | 28608473 | Health Serv Res | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28608473 |
| Characteristics Associated With Decreased or Increased Mortality Risk From Glycemic Therapy Among Patients With Type 2 Diabetes and High Cardiovascular Risk: Machine Learning Analysis of the ACCORD Trial. | Basu S, Raghavan S, Wexler DJ, Berkowitz SA | Diabetes care | 29279299 | Diabetes Care | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29279299 |
| Targeting weight loss interventions to reduce cardiovascular complications of type 2 diabetes: a machine learning-based post-hoc analysis of heterogeneous treatment effects in the Look AHEAD trial. | Baum A, Scarpa J, Bruzelius E, Tamler R, Basu S, Faghmous J | The lancet. Diabetes & endocrinology | 28711469 | Lancet Diabetes Endocrinol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28711469 |
| Preventing false discovery of heterogeneous treatment effect subgroups in randomized trials. | Rigdon J, Baiocchi M, Basu S | Trials | 30012181 | Trials | 2018 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/30012181 |
| Mother's education and late-life disparities in memory and dementia risk among US military veterans and non-veterans. | Vable AM, Eng CW, Mayeda ER, Basu S, Marden JR, Hamad R, Glymour MM | Journal of epidemiology and community health | 30082424 | J Epidemiol Community Health | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30082424 |
| Black-White Cardiovascular Disease Disparities After Target-Based Versus Personalized Benefit-Based Lipid and Blood Pressure Treatment. | Basu S, Sussman JB, Hayward RA | MDM policy & practice | 30288429 | MDM Policy Pract | 2017 Jul-Dec | https://www.ncbi.nlm.nih.gov/pubmed/30288429 |
| Moderation of the Relation of County-Level Cost of Living to Nutrition by the Supplemental Nutrition Assistance Program. | Basu S, Wimer C, Seligman H | American journal of public health | 27631742 | Am J Public Health | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27631742 |
| Comparative effectiveness and cost-effectiveness of treat-to-target versus benefit-based tailored treatment of type 2 diabetes in low-income and middle-income countries: a modelling analysis. | Basu S, Shankar V, Yudkin JS | The lancet. Diabetes & endocrinology | 27717768 | Lancet Diabetes Endocrinol | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27717768 |
| Detecting Heterogeneous Treatment Effects to Guide Personalized Blood Pressure Treatment: A Modeling Study of Randomized Clinical Trials. | Basu S, Sussman JB, Hayward RA | Annals of internal medicine | 28055048 | Ann Intern Med | 2017 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/28055048 |
| BOUNDS ON THE CONDITIONAL AND AVERAGE TREATMENT EFFECT WITH UNOBSERVED CONFOUNDING FACTORS. | Yadlowsky S, Namkoong H, Basu S, Duchi J, Tian L | Annals of statistics | 38050638 | Ann Stat | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38050638 |
| A New Tool for Case Studies in Epidemiology-the Synthetic Control Method. | Rehkopf DH, Basu S | Epidemiology (Cambridge, Mass.) | 29613871 | Epidemiology | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29613871 |
| Machine Learning Methods for Precision Medicine Research Designed to Reduce Health Disparities: A Structured Tutorial. | Basu S, Faghmous JH, Doupe P | Ethnicity & disease | 32269464 | Ethn Dis | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32269464 |
| Assessment of Changes in the Geographical Distribution of Opioid-Related Mortality Across the United States by Opioid Type, 1999-2016. | Kiang MV, Basu S, Chen J, Alexander MJ | JAMA network open | 30794299 | JAMA Netw Open | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30794299 |
| Clinical Implications of Revised Pooled Cohort Equations for Estimating Atherosclerotic Cardiovascular Disease Risk. | Yadlowsky S, Hayward RA, Sussman JB, McClelland RL, Min YI, Basu S | Annals of internal medicine | 29868850 | Ann Intern Med | 2018 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/29868850 |
| Generalizing Intensive Blood Pressure Treatment to Adults With Diabetes Mellitus. | Berkowitz SA, Sussman JB, Jonas DE, Basu S | Journal of the American College of Cardiology | 30189998 | J Am Coll Cardiol | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30189998 |
| Supplemental Nutrition Assistance Program (SNAP) Participation and Health Care Expenditures Among Low-Income Adults. | Berkowitz SA, Seligman HK, Rigdon J, Meigs JB, Basu S | JAMA internal medicine | 28973507 | JAMA Intern Med | 2017 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/28973507 |
| Re-evaluating associations between the Supplemental Nutrition Assistance Program participation and body mass index in the context of unmeasured confounders. | Rigdon J, Berkowitz SA, Seligman HK, Basu S | Social science & medicine (1982) | 28965002 | Soc Sci Med | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28965002 |
| Military Service, Childhood Socio-Economic Status, and Late-Life Lung Function: Korean War Era Military Service Associated with Smaller Disparities. | Vable AM, Kiang MV, Basu S, Rudolph KE, Kawachi I, Subramanian SV, Glymour MM | Military medicine | 29509934 | Mil Med | 2018 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/29509934 |
| Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil. | Mabud TS, de Lourdes Delgado Alves M, Ko AI, Basu S, Walter KS, Cohen T, Mathema B, Colijn C, Lemos E, Croda J, Andrews JR | PLoS medicine | 30677013 | PLoS Med | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30677013 |
| Opioid prescribing patterns among medical providers in the United States, 2003-17: retrospective, observational study. | Kiang MV, Humphreys K, Cullen MR, Basu S | BMJ (Clinical research ed.) | 31996352 | BMJ | 2020 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/31996352 |
| Development and validation of Risk Equations for Complications Of type 2 Diabetes (RECODe) using individual participant data from randomised trials. | Basu S, Sussman JB, Berkowitz SA, Hayward RA, Yudkin JS | The lancet. Diabetes & endocrinology | 28803840 | Lancet Diabetes Endocrinol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28803840 |
| The Monthly Cycle of Hypoglycemia: An Observational Claims-based Study of Emergency Room Visits, Hospital Admissions, and Costs in a Commercially Insured Population. | Basu S, Berkowitz SA, Seligman H | Medical care | 28481762 | Med Care | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28481762 |
| Food insecurity, healthcare utilization, and high cost: a longitudinal cohort study. | Berkowitz SA, Seligman HK, Meigs JB, Basu S | The American journal of managed care | 30222918 | Am J Manag Care | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30222918 |
| Cost Effectiveness of Subsidizing Fruit and Vegetable Purchases Through the Supplemental Nutrition Assistance Program. | Choi SE, Seligman H, Basu S | American journal of preventive medicine | 28153648 | Am J Prev Med | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28153648 |
| Machine learning with sparse nutrition data to improve cardiovascular mortality risk prediction in the USA using nationally randomly sampled data. | Rigdon J, Basu S | BMJ open | 31784446 | BMJ Open | 2019 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/31784446 |
| Personalizing Second-Line Type 2 Diabetes Treatment Selection: Combining Network Meta-analysis, Individualized Risk, and Patient Preferences for Unified Decision Support. | Choi SE, Berkowitz SA, Yudkin JS, Naci H, Basu S | Medical decision making : an international journal of the Society for Medical Decision Making | 30767632 | Med Decis Making | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30767632 |
| Evaluating the Health Impact of Large-Scale Public Policy Changes: Classical and Novel Approaches. | Basu S, Meghani A, Siddiqi A | Annual review of public health | 28384086 | Annu Rev Public Health | 2017 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/28384086 |
| Health and Economic Implications of National Treatment Coverage for Cardiovascular Disease in India: Cost-Effectiveness Analysis. | Basu S, Bendavid E, Sood N | Circulation. Cardiovascular quality and outcomes | 26555122 | Circ Cardiovasc Qual Outcomes | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26555122 |
| Illustrating a "consequential" shift in the study of health inequalities: a decomposition of racial differences in the distribution of body mass. | Siddiqi A, Shahidi FV, Hildebrand V, Hong A, Basu S | Annals of epidemiology | 29576050 | Ann Epidemiol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29576050 |
| Association between access to social service resources and cardiometabolic risk factors: a machine learning and multilevel modeling analysis. | Berkowitz SA, Basu S, Venkataramani A, Reznor G, Fleegler EW, Atlas SJ | BMJ open | 30862634 | BMJ Open | 2019 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/30862634 |
| Huntington's disease in the United States: Variation by demographic and socioeconomic factors. | Bruzelius E, Scarpa J, Zhao Y, Basu S, Faghmous JH, Baum A | Movement disorders : official journal of the Movement Disorder Society | 30868663 | Mov Disord | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30868663 |
| Health Behaviors, Mental Health, and Health Care Utilization Among Single Mothers After Welfare Reforms in the 1990s. | Basu S, Rehkopf DH, Siddiqi A, Glymour MM, Kawachi I | American journal of epidemiology | 26946395 | Am J Epidemiol | 2016 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/26946395 |
| Long-term effects of neighbourhood deprivation on diabetes risk: quasi-experimental evidence from a refugee dispersal policy in Sweden. | White JS, Hamad R, Li X, Basu S, Ohlsson H, Sundquist J, Sundquist K | The lancet. Diabetes & endocrinology | 27131930 | Lancet Diabetes Endocrinol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27131930 |
| Benefit and harm of intensive blood pressure treatment: Derivation and validation of risk models using data from the SPRINT and ACCORD trials. | Basu S, Sussman JB, Rigdon J, Steimle L, Denton BT, Hayward RA | PLoS medicine | 29040268 | PLoS Med | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29040268 |
| Validation of Risk Equations for Complications of Type 2 Diabetes (RECODe) Using Individual Participant Data From Diverse Longitudinal Cohorts in the U.S. | Basu S, Sussman JB, Berkowitz SA, Hayward RA, Bertoni AG, Correa A, Mwasongwe S, Yudkin JS | Diabetes care | 29269511 | Diabetes Care | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29269511 |
| Matching Microsimulation Risk Factor Correlations to Cross-sectional Data: The Shortest Distance Method. | Suen SC, Goldhaber-Fiebert JD, Basu S | Medical decision making : an international journal of the Society for Medical Decision Making | 29185378 | Med Decis Making | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29185378 |
| Impact of the North American Free Trade Agreement on high-fructose corn syrup supply in Canada: a natural experiment using synthetic control methods. | Barlow P, McKee M, Basu S, Stuckler D | CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne | 28676578 | CMAJ | 2017 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/28676578 |
| Machine Learning for Health Services Researchers. | Doupe P, Faghmous J, Basu S | Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research | 31277828 | Value Health | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31277828 |
| Association of Primary Care Physician Supply With Population Mortality in the United States, 2005-2015. | Basu S, Berkowitz SA, Phillips RL, Bitton A, Landon BE, Phillips RS | JAMA internal medicine | 30776056 | JAMA Intern Med | 2019 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/30776056 |
| Estimating the long-run relationship between state cigarette taxes and county life expectancy. | Baum A, Aguilar-Gomez S, Lightwood J, Bruzelius E, Glantz SA, Basu S | Tobacco control | 30705247 | Tob Control | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30705247 |
| Detecting Anomalies Among Practice Sites Within Multicenter Trials. | Berkowitz SA, Rudolph KE, Basu S | Circulation. Cardiovascular quality and outcomes | 30857413 | Circ Cardiovasc Qual Outcomes | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30857413 |
| Personalizing Medical Treatment Decisions: Integrating Meta-analytic Treatment Comparisons with Patient-Specific Risks and Preferences. | Weyant C, Brandeau ML, Basu S | Medical decision making : an international journal of the Society for Medical Decision Making | 31707910 | Med Decis Making | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31707910 |
| Alternative Strategies to Achieve Cardiovascular Mortality Goals in China and India: A Microsimulation of Target- Versus Risk-Based Blood Pressure Treatment. | Basu S, Yudkin JS, Sussman JB, Millett C, Hayward RA | Circulation | 26762520 | Circulation | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26762520 |
| Anticipated burden and mitigation of carbon-dioxide-induced nutritional deficiencies and related diseases: A simulation modeling study. | Weyant C, Brandeau ML, Burke M, Lobell DB, Bendavid E, Basu S | PLoS medicine | 29969442 | PLoS Med | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29969442 |
| Dynamic treatment selection and modification for personalised blood pressure therapy using a Markov decision process model: a cost-effectiveness analysis. | Choi SE, Brandeau ML, Basu S | BMJ open | 29146652 | BMJ Open | 2017 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/29146652 |
| Performance of Matching Methods as Compared With Unmatched Ordinary Least Squares Regression Under Constant Effects. | Vable AM, Kiang MV, Glymour MM, Rigdon J, Drabo EF, Basu S | American journal of epidemiology | 30995301 | Am J Epidemiol | 2019 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/30995301 |
| Near-Far Matching in R: The nearfar Package. | Rigdon J, Baiocchi M, Basu S | Journal of statistical software | 30386186 | J Stat Softw | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30386186 |
| Decomposition of the US black/white inequality in premature mortality, 2010-2015: an observational study. | Kiang MV, Krieger N, Buckee CO, Onnela JP, Chen JT | BMJ open | 31748287 | BMJ Open | 2019 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/31748287 |
| Basu et al. Respond to "Interdisciplinary Approach for Policy Evaluation". | Basu S, Rehkopf DH, Siddiqi A, Glymour MM, Kawachi I | American journal of epidemiology | 26946397 | Am J Epidemiol | 2016 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/26946397 |
| Are There Spillover Effects from the GI Bill? The Mental Health of Wives of Korean War Veterans. | Vable AM, Kawachi I, Canning D, Glymour MM, Jimenez MP, Subramanian SV | PloS one | 27186983 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27186983 |
| Gradient Descent Provably Solves Nonlinear Tomographic Reconstruction. | Fridovich-Keil S, Valdivia F, Wetzstein G, Recht B, Soltanolkotabi M | ArXiv | 37873016 | ArXiv | 2023 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/37873016 |
| Adapt and Diffuse: Sample-Adaptive Reconstruction Via Latent Diffusion Models. | Fabian Z, Tinaz B, Soltanolkotabi M | Proceedings of machine learning research | 39318400 | Proc Mach Learn Res | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39318400 |
| DiracDiffusion: Denoising and Incremental Reconstruction with Assured Data-Consistency. | Fabian Z, Tinaz B, Soltanolkotabi M | Proceedings of machine learning research | 39416230 | Proc Mach Learn Res | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39416230 |
| Provable Multi-Task Representation Learning by Two-Layer ReLU Neural Networks. | Collins L, Hassani H, Soltanolkotabi M, Mokhtari A, Shakkottai S | Proceedings of machine learning research | 39421278 | Proc Mach Learn Res | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39421278 |
| Towards aSmart Bionic Eye: AI-powered artificial vision for the treatment of incurable blindness. | Beyeler M, Sanchez-Garcia M | Journal of neural engineering | 36541463 | J Neural Eng | 2022 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/36541463 |
| Human-in-the-Loop Optimization for Deep Stimulus Encoding in Visual Prostheses. | Granley J, Fauvel T, Chalk M, Beyeler M | Advances in neural information processing systems | 38984104 | Adv Neural Inf Process Syst | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38984104 |
| Aligning Visual Prosthetic Development With Implantee Needs. | Nadolskis L, Turkstra LM, Larnyo E, Beyeler M | Translational vision science & technology | 39570616 | Transl Vis Sci Technol | 2024 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/39570616 |
| The Relative Importance of Depth Cues and Semantic Edges for Indoor Mobility Using Simulated Prosthetic Vision in Immersive Virtual Reality. | Rasla A, Beyeler M | Proceedings of the ACM Symposium on Virtual Reality Software and Technology. ACM Symposium on Virtual Reality Software and Technology | 40017497 | Proc ACM Symp Virtual Real Softw Technol | 2022 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/40017497 |
| Efficient Spatial Estimation of Perceptual Thresholds for Retinal Implants via Gaussian Process Regression. | Sadeghi R, Beyeler M | ArXiv | 39990794 | ArXiv | 2025 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/39990794 |
| A systematic review of extended reality (XR) for understanding and augmenting vision loss. | Kasowski J, Johnson BA, Neydavood R, Akkaraju A, Beyeler M | Journal of vision | 37140911 | J Vis | 2023 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/37140911 |
| Aligning visual prosthetic development with implantee needs. | Nadolskis LG, Turkstra LM, Larnyo E, Beyeler M | medRxiv : the preprint server for health sciences | 38559196 | medRxiv | 2024 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/38559196 |
| Performance Guarantees for Policy Learning. | Luedtke A, Chambaz A | Annales de l'I.H.P. Probabilites et statistiques | 35321441 | Ann I H P Probab Stat | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35321441 |
| Discussion of and : New Objectives for Policy Learning. | Li S, Li X, Luedtke A | Journal of the American Statistical Association | 36910906 | J Am Stat Assoc | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/36910906 |
| Adversarial Monte Carlo Meta-Learning of Optimal Prediction Procedures. | Luedtke A, Chung I, Sofrygin O | Journal of machine learning research : JMLR | 38476310 | J Mach Learn Res | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/38476310 |
| Inference for treatment-specific survival curves using machine learning. | Westling T, Luedtke A, Gilbert PB, Carone M | Journal of the American Statistical Association | 39184837 | J Am Stat Assoc | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39184837 |
| Rejoinder: Optimal individualized decision rules using instrumental variable methods. | Qiu H, Carone M, Sadikova E, Petukhova M, Kessler RC, Luedtke A | Journal of the American Statistical Association | 36092993 | J Am Stat Assoc | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/36092993 |
| Correction to: "Optimal Individualized Decision Rules Using Instrumental Variable Methods". | Qiu H, Carone M, Sadikova E, Petukhova M, Kessler RC, Luedtke A | Journal of the American Statistical Association | 35756162 | J Am Stat Assoc | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35756162 |
| Rejoinder: Improving precision and power in randomized trials for COVID-19 treatments using covariate adjustment, for binary, ordinal, and time-to-event outcomes. | Benkeser D, Díaz I, Luedtke A, Segal J, Scharfstein D, Rosenblum M | Biometrics | 34050931 | Biometrics | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34050931 |
| Improving precision and power in randomized trials for COVID-19 treatments using covariate adjustment, for binary, ordinal, and time-to-event outcomes. | Benkeser D, Díaz I, Luedtke A, Segal J, Scharfstein D, Rosenblum M | Biometrics | 32978962 | Biometrics | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32978962 |
| Causal isotonic calibration for heterogeneous treatment effects. | van der Laan L, Ulloa-Pérez E, Carone M, Luedtke A | Proceedings of machine learning research | 37575467 | Proc Mach Learn Res | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37575467 |
| EFFICIENT ESTIMATION OF THE MAXIMAL ASSOCIATION BETWEEN MULTIPLE PREDICTORS AND A SURVIVAL OUTCOME. | Huang TJ, Luedtke A, McKeague IW | Annals of statistics | 38405375 | Ann Stat | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38405375 |
| Improving Precision and Power in Randomized Trials for COVID-19 Treatments Using Covariate Adjustment, for Binary, Ordinal, and Time-to-Event Outcomes. | Benkeser D, Díaz I, Luedtke A, Segal J, Scharfstein D, Rosenblum M | medRxiv : the preprint server for health sciences | 32577668 | medRxiv | 2020 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/32577668 |
| Improved inference for vaccine-induced immune responses via shape-constrained methods. | Laha N, Moodie Z, Huang Y, Luedtke A | Electronic journal of statistics | 37974631 | Electron J Stat | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37974631 |
| Re. Selecting Optimal Subgroups for Treatment Using Many Covariates. | Penning de Vries BBL, Groenwold RHH, Luedtke A | Epidemiology (Cambridge, Mass.) | 32282408 | Epidemiology | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32282408 |
| Improved efficiency for cross-arm comparisons via platform designs. | Huang TJ, Luedtke A, AMP INVESTIGATOR GROUP | Biostatistics (Oxford, England) | 35939566 | Biostatistics | 2023 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/35939566 |
| Universal sieve-based strategies for efficient estimation using machine learning tools. | Qiu H, Luedtke A, Carone M | Bernoulli : official journal of the Bernoulli Society for Mathematical Statistics and Probability | 34733110 | Bernoulli (Andover) | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34733110 |
| Discussion on "Estimating vaccine efficacy over time after a randomized study is unblinded" by Anastasios A. Tsiatis and Marie Davidian. | Janes H, Gao F, Luedtke A | Biometrics | 34492117 | Biometrics | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34492117 |
| Optimal individualized decision rules using instrumental variable methods. | Qiu H, Carone M, Sadikova E, Petukhova M, Kessler RC, Luedtke A | Journal of the American Statistical Association | 33731969 | J Am Stat Assoc | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33731969 |
| Adversarial meta-learning of Gamma-minimax estimators that leverage prior knowledge. | Qiu H, Luedtke A | Electronic journal of statistics | 38463692 | Electron J Stat | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38463692 |
| Estimating the Efficiency Gain of Covariate-Adjusted Analyses in Future Clinical Trials Using External Data. | Li X, Li S, Luedtke A | Journal of the Royal Statistical Society. Series B, Statistical methodology | 37593690 | J R Stat Soc Series B Stat Methodol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37593690 |
| Efficient Estimation under Data Fusion. | Li S, Luedtke A | Biometrika | 37982010 | Biometrika | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37982010 |
| A systematic review of antibody mediated immunity to coronaviruses: antibody kinetics, correlates of protection, and association of antibody responses with severity of disease. | Huang AT, Garcia-Carreras B, Hitchings MDT, Yang B, Katzelnick LC, Rattigan SM, Borgert BA, Moreno CA, Solomon BD, Rodriguez-Barraquer I, Lessler J, Salje H, Burke D, Wesolowski A, Cummings DAT | medRxiv : the preprint server for health sciences | 32511434 | medRxiv | 2020 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/32511434 |
| Reconstructing unseen transmission events to infer dengue dynamics from viral sequences. | Salje H, Wesolowski A, Brown TS, Kiang MV, Berry IM, Lefrancq N, Fernandez S, Jarman RG, Ruchusatsawat K, Iamsirithaworn S, Vandepitte WP, Suntarattiwong P, Read JM, Klungthong C, Thaisomboonsuk B, Engø-Monsen K, Buckee C, Cauchemez S, Cummings DAT | Nature communications | 33753725 | Nat Commun | 2021 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/33753725 |
| A systematic review of antibody mediated immunity to coronaviruses: kinetics, correlates of protection, and association with severity. | Huang AT, Garcia-Carreras B, Hitchings MDT, Yang B, Katzelnick LC, Rattigan SM, Borgert BA, Moreno CA, Solomon BD, Trimmer-Smith L, Etienne V, Rodriguez-Barraquer I, Lessler J, Salje H, Burke DS, Wesolowski A, Cummings DAT | Nature communications | 32943637 | Nat Commun | 2020 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/32943637 |
| SARS-CoV-2 Testing in Florida, Illinois, and Maryland: Access and Barriers. | Clipman SJ, Wesolowski A, Mehta SH, Agarwal S, Cobey SE, Cummings DAT, Gibson DG, Labrique AB, Kirk GD, Solomon SS | medRxiv : the preprint server for health sciences | 33398298 | medRxiv | 2020 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/33398298 |
| Using geospatial models to map zero-dose children: factors associated with zero-dose vaccination status before and after a mass measles and rubella vaccination campaign in Southern province, Zambia. | Arambepola R, Yang Y, Hutchinson K, Mwansa FD, Doherty JA, Bwalya F, Ndubani P, Musukwa G, Moss WJ, Wesolowski A, Mutembo S | BMJ global health | 34969682 | BMJ Glob Health | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34969682 |
| Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar. | Ramiadantsoa T, Metcalf CJE, Raherinandrasana AH, Randrianarisoa S, Rice BL, Wesolowski A, Randriatsarafara FM, Rasambainarivo F | Epidemics | 34915300 | Epidemics | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34915300 |
| Infectious disease in an era of global change. | Baker RE, Mahmud AS, Miller IF, Rajeev M, Rasambainarivo F, Rice BL, Takahashi S, Tatem AJ, Wagner CE, Wang LF, Wesolowski A, Metcalf CJE | Nature reviews. Microbiology | 34646006 | Nat Rev Microbiol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34646006 |
| High Plasmodium falciparum genetic diversity and temporal stability despite control efforts in high transmission settings along the international border between Zambia and the Democratic Republic of the Congo. | Pringle JC, Wesolowski A, Berube S, Kobayashi T, Gebhardt ME, Mulenga M, Chaponda M, Bobanga T, Juliano JJ, Meshnick S, Moss WJ, Carpi G, Norris DE | Malaria journal | 31801548 | Malar J | 2019 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/31801548 |
| Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa. | Tessema S, Wesolowski A, Chen A, Murphy M, Wilheim J, Mupiri AR, Ruktanonchai NW, Alegana VA, Tatem AJ, Tambo M, Didier B, Cohen JM, Bennett A, Sturrock HJ, Gosling R, Hsiang MS, Smith DL, Mumbengegwi DR, Smith JL, Greenhouse B | eLife | 30938286 | Elife | 2019 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/30938286 |
| Mapping imported malaria in Bangladesh using parasite genetic and human mobility data. | Chang HH, Wesolowski A, Sinha I, Jacob CG, Mahmud A, Uddin D, Zaman SI, Hossain MA, Faiz MA, Ghose A, Sayeed AA, Rahman MR, Islam A, Karim MJ, Rezwan MK, Shamsuzzaman AKM, Jhora ST, Aktaruzzaman MM, Drury E, Gonçalves S, Kekre M, Dhorda M, Vongpromek R, Miotto O, Engø-Monsen K, Kwiatkowski D, Maude RJ, Buckee C | eLife | 30938289 | Elife | 2019 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/30938289 |
| Seasonal gaps in measles vaccination coverage in Madagascar. | Mensah K, Heraud JM, Takahashi S, Winter AK, Metcalf CJE, Wesolowski A | Vaccine | 30940486 | Vaccine | 2019 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/30940486 |
| Mapping the travel patterns of people with malaria in Bangladesh. | Sinha I, Sayeed AA, Uddin D, Wesolowski A, Zaman SI, Faiz MA, Ghose A, Rahman MR, Islam A, Karim MJ, Saha A, Rezwan MK, Shamsuzzaman AKM, Jhora ST, Aktaruzzaman MM, Chang HH, Miotto O, Kwiatkowski D, Dondorp AM, Day NPJ, Hossain MA, Buckee C, Maude RJ | BMC medicine | 32127002 | BMC Med | 2020 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/32127002 |
| Aggregated mobility data could help fight COVID-19. | Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A | Science (New York, N.Y.) | 32205458 | Science | 2020 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/32205458 |
| Seroprevalence of pertussis in Madagascar and implications for vaccination. | Razafimahatratra SL, Wesolowski A, Rafetrarivony L, Heraud JM, Jones FK, Cauchemez S, Razafindratsimandresy R, Raharinantoanina SJ, Harimanana A, Collard JM, Metcalf CJE | Epidemiology and infection | 33190665 | Epidemiol Infect | 2020 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/33190665 |
| Long-term dynamics of measles in London: Titrating the impact of wars, the 1918 pandemic, and vaccination. | Becker AD, Wesolowski A, Bjørnstad ON, Grenfell BT | PLoS computational biology | 31513578 | PLoS Comput Biol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31513578 |
| Characterizing mobility patterns and malaria risk factors in semi-nomadic populations of Northern Kenya. | Meredith HR, Wesolowski A, Okoth D, Maraga L, Ambani G, Chepkwony T, Abel L, Kipkoech J, Lokoel G, Esimit D, Lokemer S, Maragia J, Prudhomme O'Meara W, Obala AA | PLOS global public health | 38478562 | PLOS Glob Public Health | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38478562 |
| National-scale simulation of human movement in a spatially coupled individual-based model of malaria in Burkina Faso. | Zupko RJ, Nguyen TD, Wesolowski A, Gerardin J, Boni MF | Scientific reports | 36609584 | Sci Rep | 2023 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/36609584 |
| Long-term effects of increased adoption of artemisinin combination therapies in Burkina Faso. | Zupko RJ, Nguyen TD, Somé AF, Tran TN, Gerardin J, Dudas P, Giang DDH, Tran KT, Wesolowski A, Ouédraogo JB, Boni MF | PLOS global public health | 36962300 | PLOS Glob Public Health | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36962300 |
| Characterizing mobility patterns and malaria risk factors in semi-nomadic populations of Northern Kenya. | Meredith HR, Wesolowski A, Okoth D, Maraga L, Ambani G, Chepkwony T, Abel L, Kipkoech J, Lokoel G, Esimit D, Lokemer S, Maragia J, O'Meara WP, Obala AA | medRxiv : the preprint server for health sciences | 38106223 | medRxiv | 2023 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/38106223 |
| Who is missed in a community-based survey: Assessment and implications of biases due to incomplete sampling frame in a community-based serosurvey, Choma and Ndola Districts, Zambia, 2022. | Kostandova N, Mutembo S, Prosperi C, Mwansa FD, Nakazwe C, Namukoko H, Nachinga B, Chongwe G, Chilumba I, Matakala KH, Musukwa G, Hamahuwa M, Mufwambi W, Matoba J, Situtu K, Mutale I, Kong AC, Simulundu E, Ndubani P, Hasan AZ, Truelove SA, Winter AK, Carcelen AC, Lau B, Moss WJ, Wesolowski A | PLOS global public health | 38683820 | PLOS Glob Public Health | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38683820 |
| Geography versus sociodemographics as predictors of changes in daily mobility across the USA during the COVID-19 pandemic: a two-stage regression analysis across 26 metropolitan areas. | Schaber K, Arambepola R, Schluth C, Labrique AB, Mehta SH, Solomon SS, Cummings DAT, Wesolowski A | BMJ open | 38986558 | BMJ Open | 2024 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/38986558 |
| Fine scale human mobility changes within 26 US cities in 2020 in response to the COVID-19 pandemic were associated with distance and income. | Arambepola R, Schaber KL, Schluth C, Huang AT, Labrique AB, Mehta SH, Solomon SS, Cummings DAT, Wesolowski A | PLOS global public health | 37478056 | PLOS Glob Public Health | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37478056 |
| Coexisting attractors in the context of cross-scale population dynamics: measles in London as a case study. | Becker AD, Zhou SH, Wesolowski A, Grenfell BT | Proceedings. Biological sciences | 32315586 | Proc Biol Sci | 2020 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/32315586 |
| Genetic Evidence of Focal Plasmodium falciparum Transmission in a Pre-elimination Setting in Southern Province, Zambia. | Pringle JC, Tessema S, Wesolowski A, Chen A, Murphy M, Carpi G, Shields TM, Hamapumbu H, Searle KM, Kobayashi T, Katowa B, Musonda M, Stevenson JC, Thuma PE, Greenhouse B, Moss WJ, Norris DE | The Journal of infectious diseases | 30445612 | J Infect Dis | 2019 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/30445612 |
| A Mixture Model for Estimating SARS-CoV-2 Seroprevalence in Chennai, India. | Hitchings MDT, Patel EU, Khan R, Srikrishnan AK, Anderson M, Kumar KS, Wesolowski AP, Iqbal SH, Rodgers MA, Mehta SH, Cloherty G, Cummings DAT, Solomon SS | American journal of epidemiology | 37084085 | Am J Epidemiol | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37084085 |
| Impact of disruptions to routine vaccination programs, quantifying burden of measles, and mapping targeted supplementary immunization activities. | Kostandova N, Loisate S, Winter A, Moss WJ, Giles JR, Metcalf CJE, Mutembo S, Wesolowski A | Epidemics | 36343498 | Epidemics | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36343498 |
| Holiday gatherings, mobility and SARS-CoV-2 transmission: results from 10 US states following Thanksgiving. | Mehta SH, Clipman SJ, Wesolowski A, Solomon SS | Scientific reports | 34462499 | Sci Rep | 2021 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/34462499 |
| Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar. | Ramiadantsoa T, Metcalf CJE, Raherinandrasana AH, Randrianarisoa S, Rice BL, Wesolowski A, Randriatsarafara FM, Rasambainarivo F | medRxiv : the preprint server for health sciences | 34373863 | medRxiv | 2021 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/34373863 |
| Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread. | Giles JR, Cummings DAT, Grenfell BT, Tatem AJ, Erbach-Schoenberg EZ, Metcalf C, Wesolowski A | PLoS computational biology | 34375331 | PLoS Comput Biol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34375331 |
| The Challenge of Achieving Immunity Through Multiple-Dose Vaccines in Madagascar. | Jones FK, Mensah K, Heraud JM, Randriatsarafara FM, Metcalf CJE, Wesolowski A | American journal of epidemiology | 34023892 | Am J Epidemiol | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34023892 |
| The duration of travel impacts the spatial dynamics of infectious diseases. | Giles JR, Zu Erbach-Schoenberg E, Tatem AJ, Gardner L, Bjørnstad ON, Metcalf CJE, Wesolowski A | Proceedings of the National Academy of Sciences of the United States of America | 32839329 | Proc Natl Acad Sci U S A | 2020 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/32839329 |
| Using models to shape measles control and elimination strategies in low- and middle-income countries: A review of recent applications. | Cutts FT, Dansereau E, Ferrari MJ, Hanson M, McCarthy KA, Metcalf CJE, Takahashi S, Tatem AJ, Thakkar N, Truelove S, Utazi E, Wesolowski A, Winter AK | Vaccine | 31787412 | Vaccine | 2020 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/31787412 |
| Exploring how space, time, and sampling impact our ability to measure genetic structure across Plasmodium falciparum populations. | Arambepola R, Bérubé S, Freedman B, Taylor SM, Prudhomme O'Meara W, Obala AA, Wesolowski A | Frontiers in epidemiology | 38516334 | Front Epidemiol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38516334 |
| A systematic review of using population-level human mobility data to understand SARS-CoV-2 transmission. | Kostandova N, Schluth C, Arambepola R, Atuhaire F, Bérubé S, Chin T, Cleary E, Cortes-Azuero O, García-Carreras B, Grantz KH, Hitchings MDT, Huang AT, Kishore N, Lai S, Larsen SL, Loisate S, Martinez P, Meredith HR, Purbey R, Ramiadantsoa T, Read J, Rice BL, Rosman L, Ruktanonchai N, Salje H, Schaber KL, Tatem AJ, Wang J, Cummings DAT, Wesolowski A | Nature communications | 39627231 | Nat Commun | 2024 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/39627231 |
| Towards better targeting: lessons from a posthoneymoon measles outbreak in Madagascar, 2018-2019. | Raherindrasana A, Metcalf CJ, Heraud JM, Cauchemez S, Winter A, Wesolowski A, Razafindratsimandresy R, Randriamampionona L, Rafalimanantsoa SA, Masembe Y, Ndiaye C, Rakotonirina J | BMJ global health | 33082133 | BMJ Glob Health | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33082133 |
| Effect of non-pharmaceutical interventions to contain COVID-19 in China. | Lai S, Ruktanonchai NW, Zhou L, Prosper O, Luo W, Floyd JR, Wesolowski A, Santillana M, Zhang C, Du X, Yu H, Tatem AJ | Nature | 32365354 | Nature | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32365354 |
| Development and dissemination of infectious disease dynamic transmission models during the COVID-19 pandemic: what can we learn from other pathogens and how can we move forward? | Becker AD, Grantz KH, Hegde ST, Bérubé S, Cummings DAT, Wesolowski A | The Lancet. Digital health | 33735068 | Lancet Digit Health | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33735068 |
| Challenges in evaluating risks and policy options around endemic establishment or elimination of novel pathogens. | Metcalf CJE, Andriamandimby SF, Baker RE, Glennon EE, Hampson K, Hollingsworth TD, Klepac P, Wesolowski A | Epidemics | 34823222 | Epidemics | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34823222 |
| Rapid real-time tracking of non-pharmaceutical interventions and their association with SARS-CoV-2 positivity: The COVID-19 Pandemic Pulse Study. | Clipman SJ, Wesolowski AP, Gibson DG, Agarwal S, Lambrou AS, Kirk GD, Labrique AB, Mehta SH, Solomon SS | medRxiv : the preprint server for health sciences | 32766598 | medRxiv | 2020 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/32766598 |
| Rapid Real-time Tracking of Nonpharmaceutical Interventions and Their Association With Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Positivity: The Coronavirus Disease 2019 (COVID-19) Pandemic Pulse Study. | Clipman SJ, Wesolowski AP, Gibson DG, Agarwal S, Lambrou AS, Kirk GD, Labrique AB, Mehta SH, Solomon SS | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 32877921 | Clin Infect Dis | 2021 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/32877921 |
| The use of mobile phone data to inform analysis of COVID-19 pandemic epidemiology. | Grantz KH, Meredith HR, Cummings DAT, Metcalf CJE, Grenfell BT, Giles JR, Mehta S, Solomon S, Labrique A, Kishore N, Buckee CO, Wesolowski A | Nature communications | 32999287 | Nat Commun | 2020 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/32999287 |
| Prioritizing COVID-19 vaccination efforts and dose allocation within Madagascar. | Rasambainarivo F, Ramiadantsoa T, Raherinandrasana A, Randrianarisoa S, Rice BL, Evans MV, Roche B, Randriatsarafara FM, Wesolowski A, Metcalf JC | BMC public health | 35413894 | BMC Public Health | 2022 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/35413894 |
| Epidemiology of Plasmodium falciparum Infections in a Semi-Arid Rural African Setting: Evidence from Reactive Case Detection in Northwestern Kenya. | Meredith HR, Wesolowski A, Menya D, Esimit D, Lokoel G, Kipkoech J, Freedman B, Lokemer S, Maragia J, Ambani G, Taylor SM, Prudhomme-O'Meara W, Obala AA | The American journal of tropical medicine and hygiene | 34339387 | Am J Trop Med Hyg | 2021 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/34339387 |
| Improvements in Severe Acute Respiratory Syndrome Coronavirus 2 Testing Cascade in the United States: Data From Serial Cross-sectional Assessments. | Clipman SJ, Wesolowski A, Mehta SH, Cobey S, Cummings DAT, Solomon SS | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 34374758 | Clin Infect Dis | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/34374758 |
| Characterizing human mobility patterns in rural settings of sub-Saharan Africa. | Meredith HR, Giles JR, Perez-Saez J, Mande T, Rinaldo A, Mutembo S, Kabalo EN, Makungo K, Buckee CO, Tatem AJ, Metcalf CJE, Wesolowski A | eLife | 34533456 | Elife | 2021 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/34533456 |
| Mapping malaria by combining parasite genomic and epidemiologic data. | Wesolowski A, Taylor AR, Chang HH, Verity R, Tessema S, Bailey JA, Alex Perkins T, Neafsey DE, Greenhouse B, Buckee CO | BMC medicine | 30333020 | BMC Med | 2018 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/30333020 |
| Changes in mobility patterns during the COVID-19 pandemic in Zambia: Implications for the effectiveness of NPIs in Sub-Saharan Africa. | Loisate S, Mutembo S, Arambepola R, Makungo K, Kabalo EN, Sinyange NB, Kapata N, Liwewe M, Silumezi A, Chongwe G, Kostandova N, Truelove S, Wesolowski A | PLOS global public health | 37906535 | PLOS Glob Public Health | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37906535 |
| Adjusting mobile phone data to account for children's travel and the impact on measles dynamics in Zambia. | Kostandova N, Prosperi C, Mutembo S, Nakazwe C, Namukoko H, Nachinga B, Chongwe G, Chilumba I, Kabalo EN, Makungo K, Matakala KH, Musukwa G, Hamahuwa M, Mufwambi W, Matoba J, Mutale I, Simulundu E, Ndubani P, Hasan AZ, Truelove SA, Winter AK, Carcelen AC, Lau B, Moss WJ, Wesolowski A | American journal of epidemiology | 39191642 | Am J Epidemiol | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/39191642 |
| Clinician Testing and Treatment Thresholds for Management of Urinary Tract Infection. | Harris A, Pineles L, Baghdadiv JD, Magder L, Dhaliwal G, Korenstein D, Harris AD, Morgan DJ | Open forum infectious diseases | 37720701 | Open Forum Infect Dis | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37720701 |
| Clinician Attitudes and Beliefs Associated with More Aggressive Diagnostic Testing. | Korenstein D, Scherer LD, Foy A, Pineles L, Lydecker AD, Owczarzak J, Magder L, Brown JP, Pfeiffer CD, Terndrup C, Leykum L, Stevens D, Feldstein DA, Weisenberg SA, Baghdadi JD, Morgan DJ | The American journal of medicine | 35307357 | Am J Med | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35307357 |
| Medical overuse of therapies and diagnostics in rheumatology. | Khawaja MN, Alhassan E, Bilal J, Jatwani S, Mehta B, Bhalla V, Morgan DJ, Siaton BC, Hochberg MC | Clinical rheumatology | 33569709 | Clin Rheumatol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33569709 |
| Clinician Conceptualization of the Benefits of Treatments for Individual Patients. | Morgan DJ, Pineles L, Owczarzak J, Magder L, Scherer L, Brown JP, Pfeiffer C, Terndrup C, Leykum L, Feldstein D, Foy A, Stevens D, Koch C, Masnick M, Weisenberg S, Korenstein D | JAMA network open | 34287630 | JAMA Netw Open | 2021 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/34287630 |
| Accuracy of Practitioner Estimates of Probability of Diagnosis Before and After Testing. | Morgan DJ, Pineles L, Owczarzak J, Magder L, Scherer L, Brown JP, Pfeiffer C, Terndrup C, Leykum L, Feldstein D, Foy A, Stevens D, Koch C, Masnick M, Weisenberg S, Korenstein D | JAMA internal medicine | 33818595 | JAMA Intern Med | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/33818595 |
| Exploration of Primary Care Clinician Attitudes and Cognitive Characteristics Associated With Prescribing Antibiotics for Asymptomatic Bacteriuria. | Baghdadi JD, Korenstein D, Pineles L, Scherer LD, Lydecker AD, Magder L, Stevens DN, Morgan DJ | JAMA network open | 35622364 | JAMA Netw Open | 2022 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/35622364 |
| Reply to Fakih and Advani. | Trautner BW, Morgan DJ | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 33821997 | Clin Infect Dis | 2021 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/33821997 |
| Game-based learning to improve diagnostic accuracy: a pilot randomized-controlled trial. | Morgan DJ, Scherer L, Pineles L, Baghdadi J, Magder L, Thom K, Koch C, Wilkins N, LeGrand M, Stevens D, Walker R, Shirrell B, Harris AD, Korenstein D | Diagnosis (Berlin, Germany) | 38284830 | Diagnosis (Berl) | 2024 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38284830 |
| Efficacy of educational video game versus traditional educational apps at improving physician decision making in trauma triage: randomized controlled trial. | Mohan D, Farris C, Fischhoff B, Rosengart MR, Angus DC, Yealy DM, Wallace DJ, Barnato AE | BMJ (Clinical research ed.) | 29233854 | BMJ | 2017 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/29233854 |
| Selection bias, interventions and outcomes for survivors of cardiac arrest. | Wallace DJ, Coppler P, Callaway C, Rittenberger JC, Dezfulian C, Mohan D, Toma C, Elmer J | Heart (British Cardiac Society) | 29463613 | Heart | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29463613 |
| Serious games may improve physician heuristics in trauma triage. | Mohan D, Fischhoff B, Angus DC, Rosengart MR, Wallace DJ, Yealy DM, Farris C, Chang CH, Kerti S, Barnato AE | Proceedings of the National Academy of Sciences of the United States of America | 30150397 | Proc Natl Acad Sci U S A | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30150397 |
| Using Virtual Reality Simulation Environments to Assess Competence for Emergency Medicine Learners. | McGrath JL, Taekman JM, Dev P, Danforth DR, Mohan D, Kman N, Crichlow A, Bond WF | Academic emergency medicine : official journal of the Society for Academic Emergency Medicine | 28888070 | Acad Emerg Med | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28888070 |
| Testing the feasibility, acceptability, and preliminary effect of a novel deliberate practice intervention to reduce diagnostic error in trauma triage: a study protocol for a randomized pilot trial. | Mohan D, Elmer J, Arnold RM, Forsythe RM, Fischhoff B, Rak K, Barnes JL, White DB | Pilot and feasibility studies | 36510328 | Pilot Feasibility Stud | 2022 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/36510328 |
| Not Thinking Clearly? Play a Game, Seriously! | Mohan D, Schell J, Angus DC | JAMA | 27825014 | JAMA | 2016 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/27825014 |
| Using incentives to recruit physicians into behavioral trials: lessons learned from four studies. | Mohan D, Rosengart MR, Fischhoff B, Angus DC, Wallace DJ, Farris C, Yealy DM, Barnato AE | BMC research notes | 29282154 | BMC Res Notes | 2017 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/29282154 |
| Referral Regions for Time-Sensitive Acute Care Conditions in the United States. | Wallace DJ, Mohan D, Angus DC, Driessen JR, Seymour CM, Yealy DM, Roberts MM, Kurland KS, Kahn JM | Annals of emergency medicine | 29606286 | Ann Emerg Med | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29606286 |
| Using a theory-based, customized video game as an educational tool to improve physicians' trauma triage decisions: study protocol for a randomized cluster trial. | Mohan D, Angus DC, Chang CH, Elmer J, Fischhoff B, Rak KJ, Barnes JL, Peitzman AB, White DB | Trials | 38365758 | Trials | 2024 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/38365758 |
| Inner Deliberations of Surgeons Treating Critically-ill Emergency General Surgery Patients: A Qualitative Analysis. | Kulkarni SS, Briggs A, Sacks OA, Rosengart MR, White DB, Barnato AE, Peitzman AB, Mohan D | Annals of surgery | 31714316 | Ann Surg | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31714316 |
| Nudges in the Care of the Critically Ill. | Wallace DJ, Drake C, Mohan D | Critical care medicine | 31305299 | Crit Care Med | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31305299 |
| Testing a videogame intervention to recalibrate physician heuristics in trauma triage: study protocol for a randomized controlled trial. | Mohan D, Rosengart MR, Fischhoff B, Angus DC, Farris C, Yealy DM, Wallace DJ, Barnato AE | BMC emergency medicine | 27835981 | BMC Emerg Med | 2016 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/27835981 |
| Testing a Novel Deliberate Practice Intervention to Improve Diagnostic Reasoning in Trauma Triage: A Pilot Randomized Clinical Trial. | Mohan D, Elmer J, Arnold RM, Forsythe RM, Fischhoff B, Rak K, Barnes JL, White DB | JAMA network open | 37195666 | JAMA Netw Open | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/37195666 |
| Defining the representativeness heuristic in trauma triage: A retrospective observational cohort study. | Kulkarni SS, Dewitt B, Fischhoff B, Rosengart MR, Angus DC, Saul M, Yealy DM, Mohan D | PloS one | 30735553 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30735553 |
| Videogame intervention to increase advance care planning conversations by hospitalists with older adults: study protocol for a stepped-wedge clinical trial. | Mohan D, O'Malley AJ, Chelen J, MacMartin M, Murphy M, Rudolph M, Barnato A | BMJ open | 33753443 | BMJ Open | 2021 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/33753443 |
| Does Preexisting Practice Modify How Video Games Recalibrate Physician Heuristics in Trauma Triage? | Kulkarni SS, Barnato AE, Rosengart MR, Fischhoff B, Angus DC, Yealy DM, Wallace DJ, Mohan D | The Journal of surgical research | 31071605 | J Surg Res | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31071605 |
| Development of a theory-based video-game intervention to increase advance care planning conversations by healthcare providers. | Mohan D, MacMartin MA, Chelen JSC, Maezes CB, Barnato AE | Implementation science communications | 34645515 | Implement Sci Commun | 2021 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/34645515 |
| Outcomes after a Digital Behavior Change Intervention to Improve Trauma Triage: An Analysis of Medicare Claims. | Mohan D, Chang CC, Fischhoff B, Rosengart MR, Angus DC, Yealy DM, Barnato AE | The Journal of surgical research | 34464890 | J Surg Res | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34464890 |
| Association of Practitioner Interfacility Triage Performance With Outcomes for Severely Injured Patients With Fee-for-Service Medicare Insurance. | Mohan D, Wallace DJ, Kerti SJ, Angus DC, Rosengart MR, Barnato AE, Yealy DM, Fischhoff B, Chang CC, Kahn JM | JAMA surgery | 31642889 | JAMA Surg | 2019 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31642889 |
| Constructing within and between hospital physician social networks for modeling physician research participation. | Bobak CA, Mohan D, Murphy MA, Barnato AE, O'Malley AJ | BMC medical research methodology | 37898745 | BMC Med Res Methodol | 2023 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/37898745 |
| Using a Video Game Intervention to Increase Hospitalists' Advance Care Planning Conversations with Older Adults: a Stepped Wedge Randomized Clinical Trial. | Mohan D, O'Malley AJ, Chelen J, MacMartin M, Murphy M, Rudolph M, Engel JA, Barnato AE | Journal of general internal medicine | 37429972 | J Gen Intern Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37429972 |
| Influence of Stress and Antibiotic Resistance on Cell-Length Distribution in Mycobacterium tuberculosis Clinical Isolates. | Vijay S, Vinh DN, Hai HT, Ha VTN, Dung VTM, Dinh TD, Nhung HN, Tram TTB, Aldridge BB, Hanh NT, Thu DDA, Phu NH, Thwaites GE, Thuong NTT | Frontiers in microbiology | 29209302 | Front Microbiol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29209302 |
| Stress-Induced Reorganization of the Mycobacterial Membrane Domain. | Hayashi JM, Richardson K, Melzer ES, Sandler SJ, Aldridge BB, Siegrist MS, Morita YS | mBio | 29362232 | mBio | 2018 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/29362232 |
| Identification of cell wall synthesis inhibitors active against Mycobacterium tuberculosis by competitive activity-based protein profiling. | Li M, Patel HV, Cognetta AB 3rd, Smith TC 2nd, Mallick I, Cavalier JF, Previti ML, Canaan S, Aldridge BB, Cravatt BF, Seeliger JC | Cell chemical biology | 34599873 | Cell Chem Biol | 2022 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/34599873 |
| Spatially distinct and metabolically active membrane domain in mycobacteria. | Hayashi JM, Luo CY, Mayfield JA, Hsu T, Fukuda T, Walfield AL, Giffen SR, Leszyk JD, Baer CE, Bennion OT, Madduri A, Shaffer SA, Aldridge BB, Sassetti CM, Sandler SJ, Kinoshita T, Moody DB, Morita YS | Proceedings of the National Academy of Sciences of the United States of America | 27114527 | Proc Natl Acad Sci U S A | 2016 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/27114527 |
| Accelerating Early Antituberculosis Drug Discovery by Creating Mycobacterial Indicator Strains That Predict Mode of Action. | Boot M, Commandeur S, Subudhi AK, Bahira M, Smith TC 2nd, Abdallah AM, van Gemert M, Lelièvre J, Ballell L, Aldridge BB, Pain A, Speer A, Bitter W | Antimicrobial agents and chemotherapy | 29661879 | Antimicrob Agents Chemother | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29661879 |
| Temporal and intrinsic factors of rifampicin tolerance in mycobacteria. | Richardson K, Bennion OT, Tan S, Hoang AN, Cokol M, Aldridge BB | Proceedings of the National Academy of Sciences of the United States of America | 27357669 | Proc Natl Acad Sci U S A | 2016 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/27357669 |
| Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis. | Ma S, Jaipalli S, Larkins-Ford J, Lohmiller J, Aldridge BB, Sherman DR, Chandrasekaran S | mBio | 31719182 | mBio | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31719182 |
| Morphological profiling of tubercle bacilli identifies drug pathways of action. | Smith TC 2nd, Pullen KM, Olson MC, McNellis ME, Richardson I, Hu S, Larkins-Ford J, Wang X, Freundlich JS, Ando DM, Aldridge BB | Proceedings of the National Academy of Sciences of the United States of America | 32680963 | Proc Natl Acad Sci U S A | 2020 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/32680963 |
| Exploitation of Mycobacterium tuberculosis reporter strains to probe the impact of vaccination at sites of infection. | Sukumar N, Tan S, Aldridge BB, Russell DG | PLoS pathogens | 25233380 | PLoS Pathog | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25233380 |
| Stable Regulation of Cell Cycle Events in Mycobacteria: Insights From Inherently Heterogeneous Bacterial Populations. | Logsdon MM, Aldridge BB | Frontiers in microbiology | 29619019 | Front Microbiol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29619019 |
| Prediction of ultra-high-order antibiotic combinations based on pairwise interactions. | Katzir I, Cokol M, Aldridge BB, Alon U | PLoS computational biology | 30699106 | PLoS Comput Biol | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30699106 |
| Efficient measurement and factorization of high-order drug interactions in Mycobacterium tuberculosis. | Cokol M, Kuru N, Bicak E, Larkins-Ford J, Aldridge BB | Science advances | 29026882 | Sci Adv | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29026882 |
| Rv0004 is a new essential member of the mycobacterial DNA replication machinery. | Mann KM, Huang DL, Hooppaw AJ, Logsdon MM, Richardson K, Lee HJ, Kimmey JM, Aldridge BB, Stallings CL | PLoS genetics | 29176877 | PLoS Genet | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29176877 |
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| Intravital measurements of solid stresses in tumours reveal length-scale and microenvironmentally dependent force transmission. | Zhang S, Grifno G, Passaro R, Regan K, Zheng S, Hadzipasic M, Banerji R, O'Connor L, Chu V, Kim SY, Yang J, Shi L, Karrobi K, Roblyer D, Grinstaff MW, Nia HT | Nature biomedical engineering | 37640900 | Nat Biomed Eng | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37640900 |
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| B cells in the pneumococcus-infected lung are heterogeneous and require CD4(+) T cell help including CD40L to become resident memory B cells. | Etesami NS, Barker KA, Shenoy AT, De Ana CL, Arafa EI, Grifno GN, Matschulat AM, Vannini ME, Pihl RMF, Breen MP, Soucy AM, Goltry WN, Ha CT, Betsuyaku H, Browning JL, Varelas X, Traber KE, Jones MR, Quinton LJ, Maglione PJ, Nia HT, Belkina AC, Mizgerd JP | Frontiers in immunology | 38715601 | Front Immunol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38715601 |
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| Mapping the strain-stiffening behavior of the lung and lung cancer at microscale resolution using the crystal ribcage. | LeBourdais R, Grifno GN, Banerji R, Regan K, Suki B, Nia HT | Frontiers in network physiology | 39050550 | Front Netw Physiol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39050550 |
| A CAR enhancer increases the activity and persistence of CAR T cells. | Rakhshandehroo T, Mantri SR, Moravej H, Louis BBV, Salehi Farid A, Munaretto L, Regan K, Khan RMM, Wolff A, Farkash Z, Cong M, Kuhnast A, Nili A, Lee UJ, Allen HH, Berland L, Simkova E, Uslu SC, Tavakolpour S, Rowley JE, Codet E, Shahbazian H, Baral J, Pyrdol J, Jacobson CA, Nadeem O, Nia HT, Wucherpfennig KW, Rashidian M | Nature biotechnology | 39079964 | Nat Biotechnol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/39079964 |
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| Paralysis by analysis: Overcoming cardiac contraction with computer vision. | Christoph J, Ripplinger CM | Proceedings of the National Academy of Sciences of the United States of America | 37792520 | Proc Natl Acad Sci U S A | 2023 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/37792520 |
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| O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology. | Balana AT, Mahul-Mellier AL, Nguyen BA, Horvath M, Javed A, Hard ER, Jasiqi Y, Singh P, Afrin S, Pedretti R, Singh V, Lee VM, Luk KC, Saelices L, Lashuel HA, Pratt MR | Nature chemical biology | 38347213 | Nat Chem Biol | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38347213 |
| Structure-Based Probe Reveals the Presence of Large Transthyretin Aggregates in Plasma of ATTR Amyloidosis Patients. | Pedretti R, Wang L, Yakubovska A, Zhang QS, Nguyen B, Grodin JL, Masri A, Saelices L | JACC. Basic to translational science | 39444930 | JACC Basic Transl Sci | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39444930 |
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| Detection of Circulating Transthyretin Amyloid Aggregates in Plasma: A Novel Biomarker for Transthyretin Amyloidosis. | Pedretti R, Wang L, Hanna M, Benson MD, Grodin JL, Tang WHW, Masri A, Saelices L | Circulation | 38768274 | Circulation | 2024 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/38768274 |
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| Cryo-EM structures of hIAPP fibrils seeded by patient-extracted fibrils reveal new polymorphs and conserved fibril cores. | Cao Q, Boyer DR, Sawaya MR, Abskharon R, Saelices L, Nguyen BA, Lu J, Murray KA, Kandeel F, Eisenberg DS | Nature structural & molecular biology | 34518699 | Nat Struct Mol Biol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34518699 |
| Structural polymorphism of amyloid fibrils in ATTR amyloidosis revealed by cryo-electron microscopy. | Nguyen BA, Singh V, Afrin S, Yakubovska A, Wang L, Ahmed Y, Pedretti R, Fernandez-Ramirez MDC, Singh P, Pękała M, Cabrera Hernandez LO, Kumar S, Lemoff A, Gonzalez-Prieto R, Sawaya MR, Eisenberg DS, Benson MD, Saelices L | Nature communications | 38233397 | Nat Commun | 2024 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/38233397 |
| ATTRv-V30M Type A amyloid fibrils from heart and nerves exhibit structural homogeneity. | Nguyen BA, Afrin S, Yakubovska A, Singh V, Alicea JV, Kunach P, Singh P, Pekala M, Ahmed Y, Fernandez-Ramirez MDC, Hernandez LOC, Pedretti R, Bassett P, Wang L, Lemoff A, Villalon L, Kluve-Beckerman B, Saelices L | bioRxiv : the preprint server for biology | 38798361 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798361 |
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| ATTRv-V30M amyloid fibrils from heart and nerves exhibit structural homogeneity. | Nguyen BA, Afrin S, Yakubovska A, Singh V, Pedretti R, Bassett P, Pekala M, Alicea JV, Kunach P, Wang L, Lemoff A, Kluve-Beckerman B, Saelices L | Structure (London, England : 1993) | 39423808 | Structure | 2024 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/39423808 |
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| Amyloid fibril polymorphism in the heart of an ATTR amyloidosis patient with polyneuropathy attributed to the V122Δ variant. | Ahmed Y, Nguyen BA, Afrin S, Singh V, Evers B, Singh P, Pedretti R, Wang L, Bassett P, Del Carmen Fernandez-Ramirez M, Pekala M, Kluve-Beckerman B, Saelices L | bioRxiv : the preprint server for biology | 38766262 | bioRxiv | 2024 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/38766262 |
| Multi-organ structural homogeneity of amyloid fibrils in ATTRv-T60A amyloidosis patients, revealed by Cryo-EM. | Fernandez-Ramirez MDC, Nguyen BA, Singh V, Afrin S, Evers B, Basset P, Wang L, Pękała M, Ahmed Y, Singh P, Canepa J, Wosztyl A, Li Y, Saelices L | bioRxiv : the preprint server for biology | 38798519 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798519 |
| Cryo-EM confirms a common fibril fold in the heart of four patients with ATTRwt amyloidosis. | Nguyen BA, Singh V, Afrin S, Singh P, Pekala M, Ahmed Y, Pedretti R, Canepa J, Lemoff A, Kluve-Beckerman B, Wydorski PM, Chhapra F, Saelices L | Communications biology | 39068302 | Commun Biol | 2024 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/39068302 |
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| Reply: Pathophysiology of Takotsubo Syndrome Explored in the Cardiac Electrophysiology Laboratory. | DeMazumder D, Thirumal R, Wittstein IS, Calkins H | JACC. Clinical electrophysiology | 35589185 | JACC Clin Electrophysiol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35589185 |
| Neurocardiac Changes Preceding and During the Onset of Takotsubo Cardiomyopathy in the Cardiac Electrophysiology Laboratory. | Thirumal R, Wittstein IS, Calkins H, DeMazumder D | JACC. Clinical electrophysiology | 35210091 | JACC Clin Electrophysiol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35210091 |
| Impaired Right Ventricular Calcium Cycling Is an Early Risk Factor in R14del-Phospholamban Arrhythmias. | Haghighi K, Gardner G, Vafiadaki E, Kumar M, Green LC, Ma J, Crocker JS, Koch S, Arvanitis DA, Bidwell P, Rubinstein J, van de Leur R, Doevendans PA, Akar FG, Tranter M, Wang HS, Sadayappan S, DeMazumder D, Sanoudou D, Hajjar RJ, Stillitano F, Kranias EG | Journal of personalized medicine | 34204946 | J Pers Med | 2021 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/34204946 |
| Artificial Intelligence, Wearables and Remote Monitoring for Heart Failure: Current and Future Applications. | Gautam N, Ghanta SN, Mueller J, Mansour M, Chen Z, Puente C, Ha YM, Tarun T, Dhar G, Sivakumar K, Zhang Y, Halimeh AA, Nakarmi U, Al-Kindi S, DeMazumder D, Al'Aref SJ | Diagnostics (Basel, Switzerland) | 36552971 | Diagnostics (Basel) | 2022 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/36552971 |
| Ryanodine receptor 2 inhibition reduces dispersion of cardiac repolarization, improves contractile function, and prevents sudden arrhythmic death in failing hearts. | Joshi P, Estes S, DeMazumder D, Knollmann BC, Dey S | eLife | 38078905 | Elife | 2023 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/38078905 |
| Cardiac sympathetic denervation prevents sudden cardiac arrest and improves cardiac function by enhancing mitochondrial-antioxidant capacity. | Dey S, Joshi P, O'Rourke B, Estes S, DeMazumder D | bioRxiv : the preprint server for biology | 36778270 | bioRxiv | 2023 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/36778270 |
| Contemporary Applications of Machine Learning for Device Therapy in Heart Failure. | Gautam N, Ghanta SN, Clausen A, Saluja P, Sivakumar K, Dhar G, Chang Q, DeMazumder D, Rabbat MG, Greene SJ, Fudim M, Al'Aref SJ | JACC. Heart failure | 36049812 | JACC Heart Fail | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36049812 |
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| Birth Weight Is Associated With Clonal Hematopoiesis of Indeterminate Potential and Cardiovascular Outcomes in Adulthood. | Schuermans A, Nakao T, Ruan Y, Koyama S, Yu Z, Uddin MM, Haidermota S, Hornsby W, Lewandowski AJ, Bick AG, Niroula A, Jaiswal S, Ebert BL, Natarajan P, Honigberg MC | Journal of the American Heart Association | 37345823 | J Am Heart Assoc | 2023 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/37345823 |
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| Dnmt3a-mutated clonal hematopoiesis promotes osteoporosis. | Kim PG, Niroula A, Shkolnik V, McConkey M, Lin AE, Słabicki M, Kemp JP, Bick A, Gibson CJ, Griffin G, Sekar A, Brooks DJ, Wong WJ, Cohen DN, Uddin MM, Shin WJ, Pirruccello J, Tsai JM, Agrawal M, Kiel DP, Bouxsein ML, Richards JB, Evans DM, Wein MN, Charles JF, Jaiswal S, Natarajan P, Ebert BL | The Journal of experimental medicine | 34698806 | J Exp Med | 2021 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/34698806 |
| Clonal haematopoiesis of indeterminate potential predicts incident cardiac arrhythmias. | Schuermans A, Vlasschaert C, Nauffal V, Cho SMJ, Uddin MM, Nakao T, Niroula A, Klarqvist MDR, Weeks LD, Lin AE, Saadatagah S, Lannery K, Wong M, Hornsby W, Lubitz SA, Ballantyne C, Jaiswal S, Libby P, Ebert BL, Bick AG, Ellinor PT, Natarajan P, Honigberg MC | European heart journal | 37952204 | Eur Heart J | 2024 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/37952204 |
| Clonal Hematopoiesis of Indeterminate Potential Predicts Adverse Outcomes in Patients With Atherosclerotic Cardiovascular Disease. | Gumuser ED, Schuermans A, Cho SMJ, Sporn ZA, Uddin MM, Paruchuri K, Nakao T, Yu Z, Haidermota S, Hornsby W, Weeks LD, Niroula A, Jaiswal S, Libby P, Ebert BL, Bick AG, Natarajan P, Honigberg MC | Journal of the American College of Cardiology | 37197843 | J Am Coll Cardiol | 2023 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37197843 |
| TET2-mutant clonal hematopoiesis and risk of gout. | Agrawal M, Niroula A, Cunin P, McConkey M, Shkolnik V, Kim PG, Wong WJ, Weeks LD, Lin AE, Miller PG, Gibson CJ, Sekar A, Schaefer IM, Neuberg D, Stone RM, Bick AG, Uddin MM, Griffin GK, Jaiswal S, Natarajan P, Nigrovic PA, Rao DA, Ebert BL | Blood | 35714308 | Blood | 2022 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/35714308 |
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| ZBTB33 is mutated in clonal hematopoiesis and myelodysplastic syndromes and impacts RNA splicing. | Beauchamp EM, Leventhal M, Bernard E, Hoppe ER, Todisco G, Creignou M, Gallì A, Castellano CA, McConkey M, Tarun A, Wong W, Schenone M, Stanclift C, Tanenbaum B, Malolepsza E, Nilsson B, Bick AG, Weinstock JS, Miller M, Niroula A, Dunford A, Taylor-Weiner A, Wood T, Barbera A, Anand S, Psaty BM, Desai P, Cho MH, Johnson AD, Loos R, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, MacArthur DG, Lek M, Exome Aggregation Consortium, Neuberg DS, Lage K, Carr SA, Hellstrom-Lindberg E, Malcovati L, Papaemmanuil E, Stewart C, Getz G, Bradley RK, Jaiswal S, Ebert BL | Blood cancer discovery | 34568833 | Blood Cancer Discov | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34568833 |
| Inherited causes of clonal haematopoiesis in 97,691 whole genomes. | Bick AG, Weinstock JS, Nandakumar SK, Fulco CP, Bao EL, Zekavat SM, Szeto MD, Liao X, Leventhal MJ, Nasser J, Chang K, Laurie C, Burugula BB, Gibson CJ, Lin AE, Taub MA, Aguet F, Ardlie K, Mitchell BD, Barnes KC, Moscati A, Fornage M, Redline S, Psaty BM, Silverman EK, Weiss ST, Palmer ND, Vasan RS, Burchard EG, Kardia SLR, He J, Kaplan RC, Smith NL, Arnett DK, Schwartz DA, Correa A, de Andrade M, Guo X, Konkle BA, Custer B, Peralta JM, Gui H, Meyers DA, McGarvey ST, Chen IY, Shoemaker MB, Peyser PA, Broome JG, Gogarten SM, Wang FF, Wong Q, Montasser ME, Daya M, Kenny EE, North KE, Launer LJ, Cade BE, Bis JC, Cho MH, Lasky-Su J, Bowden DW, Cupples LA, Mak ACY, Becker LC, Smith JA, Kelly TN, Aslibekyan S, Heckbert SR, Tiwari HK, Yang IV, Heit JA, Lubitz SA, Johnsen JM, Curran JE, Wenzel SE, Weeks DE, Rao DC, Darbar D, Moon JY, Tracy RP, Buth EJ, Rafaels N, Loos RJF, Durda P, Liu Y, Hou L, Lee J, Kachroo P, Freedman BI, Levy D, Bielak LF, Hixson JE, Floyd JS, Whitsel EA, Ellinor PT, Irvin MR, Fingerlin TE, Raffield LM, Armasu SM, Wheeler MM, Sabino EC, Blangero J, Williams LK, Levy BD, Sheu WH, Roden DM, Boerwinkle E, Manson JE, Mathias RA, Desai P, Taylor KD, Johnson AD, NHLBI Trans-Omics for Precision Medicine Consortium, Auer PL, Kooperberg C, Laurie CC, Blackwell TW, Smith AV, Zhao H, Lange E, Lange L, Rich SS, Rotter JI, Wilson JG, Scheet P, Kitzman JO, Lander ES, Engreitz JM, Ebert BL, Reiner AP, Jaiswal S, Abecasis G, Sankaran VG, Kathiresan S, Natarajan P | Nature | 33057201 | Nature | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33057201 |
| Mendelian randomization supports bidirectional causality between telomere length and clonal hematopoiesis of indeterminate potential. | Nakao T, Bick AG, Taub MA, Zekavat SM, Uddin MM, Niroula A, Carty CL, Lane J, Honigberg MC, Weinstock JS, Pampana A, Gibson CJ, Griffin GK, Clarke SL, Bhattacharya R, Assimes TL, Emery LS, Stilp AM, Wong Q, Broome J, Laurie CA, Khan AT, Smith AV, Blackwell TW, Codd V, Nelson CP, Yoneda ZT, Peralta JM, Bowden DW, Irvin MR, Boorgula M, Zhao W, Yanek LR, Wiggins KL, Hixson JE, Gu CC, Peloso GM, Roden DM, Reupena MS, Hwu CM, DeMeo DL, North KE, Kelly S, Musani SK, Bis JC, Lloyd-Jones DM, Johnsen JM, Preuss M, Tracy RP, Peyser PA, Qiao D, Desai P, Curran JE, Freedman BI, Tiwari HK, Chavan S, Smith JA, Smith NL, Kelly TN, Hidalgo B, Cupples LA, Weeks DE, Hawley NL, Minster RL, Samoan Obesity, Lifestyle and Genetic Adaptations Study (OLaGA) Group, Deka R, Naseri TT, de las Fuentes L, Raffield LM, Morrison AC, Vries PS, Ballantyne CM, Kenny EE, Rich SS, Whitsel EA, Cho MH, Shoemaker MB, Pace BS, Blangero J, Palmer ND, Mitchell BD, Shuldiner AR, Barnes KC, Redline S, Kardia SLR, Abecasis GR, Becker LC, Heckbert SR, He J, Post W, Arnett DK, Vasan RS, Darbar D, Weiss ST, McGarvey ST, de Andrade M, Chen YI, Kaplan RC, Meyers DA, Custer BS, Correa A, Psaty BM, Fornage M, Manson JE, Boerwinkle E, Konkle BA, Loos RJF, Rotter JI, Silverman EK, Kooperberg C, Danesh J, Samani NJ, Jaiswal S, Libby P, Ellinor PT, Pankratz N, Ebert BL, Reiner AP, Mathias RA, Do R, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Natarajan P | Science advances | 35385311 | Sci Adv | 2022 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/35385311 |
| Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self. | Chowdhury RR, D'Addabbo J, Huang X, Veizades S, Sasagawa K, Louis DM, Cheng P, Sokol J, Jensen A, Tso A, Shankar V, Wendel BS, Bakerman I, Liang G, Koyano T, Fong R, Nau AN, Ahmad H, Gopakumar J, Wirka R, Lee AS, Boyd J, Woo YJ, Quertermous T, Gulati GS, Jaiswal S, Chien YH, Chan CKF, Davis MM, Nguyen PK | Circulation research | 35430876 | Circ Res | 2022 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/35430876 |
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| Prediction of risk for myeloid malignancy in clonal hematopoiesis. | Weeks LD, Niroula A, Neuberg D, Wong W, Lindsley RC, Luskin M, Berliner N, Stone RM, DeAngelo DJ, Soiffer R, Uddin MM, Griffin G, Vlasschaert C, Gibson CJ, Jaiswal S, Bick AG, Malcovati L, Natarajan P, Ebert BL | NEJM evidence | 37483562 | NEJM Evid | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37483562 |
| Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk. | Yu Z, Fidler TP, Ruan Y, Vlasschaert C, Nakao T, Uddin MM, Mack T, Niroula A, Heimlich JB, Zekavat SM, Gibson CJ, Griffin GK, Wang Y, Peloso GM, Heard-Costa N, Levy D, Vasan RS, Aguet F, Ardlie KG, Taylor KD, Rich SS, Rotter JI, Libby P, Jaiswal S, Ebert BL, Bick AG, Tall AR, Natarajan P | The Journal of clinical investigation | 37498674 | J Clin Invest | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37498674 |
| A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets. | Vlasschaert C, Mack T, Heimlich JB, Niroula A, Uddin MM, Weinstock J, Sharber B, Silver AJ, Xu Y, Savona M, Gibson C, Lanktree MB, Rauh MJ, Ebert BL, Natarajan P, Jaiswal S, Bick AG | Blood | 36652671 | Blood | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/36652671 |
| Longitudinal profiling of clonal hematopoiesis provides insight into clonal dynamics. | Uddin MM, Zhou Y, Bick AG, Burugula BB, Jaiswal S, Desai P, Honigberg MC, Love SA, Barac A, Hayden KM, Manson JE, Whitsel EA, Kooperberg C, Natarajan P, Reiner AP, Kitzman JO | Immunity & ageing : I & A | 35610705 | Immun Ageing | 2022 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/35610705 |
| Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. | Duncavage EJ, Bagg A, Hasserjian RP, DiNardo CD, Godley LA, Iacobucci I, Jaiswal S, Malcovati L, Vannucchi AM, Patel KP, Arber DA, Arcila ME, Bejar R, Berliner N, Borowitz MJ, Branford S, Brown AL, Cargo CA, Döhner H, Falini B, Garcia-Manero G, Haferlach T, Hellström-Lindberg E, Kim AS, Klco JM, Komrokji R, Lee-Cheun Loh M, Loghavi S, Mullighan CG, Ogawa S, Orazi A, Papaemmanuil E, Reiter A, Ross DM, Savona M, Shimamura A, Skoda RC, Solé F, Stone RM, Tefferi A, Walter MJ, Wu D, Ebert BL, Cazzola M | Blood | 36130297 | Blood | 2022 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/36130297 |
| Clonal hematopoiesis is associated with protection from Alzheimer's disease. | Bouzid H, Belk JA, Jan M, Qi Y, Sarnowski C, Wirth S, Ma L, Chrostek MR, Ahmad H, Nachun D, Yao W, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Beiser A, Bick AG, Bis JC, Fornage M, Longstreth WT Jr, Lopez OL, Natarajan P, Psaty BM, Satizabal CL, Weinstock J, Larson EB, Crane PK, Keene CD, Seshadri S, Satpathy AT, Montine TJ, Jaiswal S | Nature medicine | 37322115 | Nat Med | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37322115 |
| In utero adenine base editing corrects multi-organ pathology in a lethal lysosomal storage disease. | Bose SK, White BM, Kashyap MV, Dave A, De Bie FR, Li H, Singh K, Menon P, Wang T, Teerdhala S, Swaminathan V, Hartman HA, Jayachandran S, Chandrasekaran P, Musunuru K, Jain R, Frank DB, Zoltick P, Peranteau WH | Nature communications | 34257302 | Nat Commun | 2021 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/34257302 |
| In utero hematopoietic cell transplantation leads to sustained engraftment in a mouse model of Fanconi anemia. | Dave A, Liu S, Riley JS, Bose S, Luks V, Berkowitz C, Menon P, Jung S, Li H, Kurre P, Peranteau WH | Blood advances | 37906519 | Blood Adv | 2024 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/37906519 |
| Improved specificity and efficiency of in vivo adenine base editing therapies with hybrid guide RNAs. | Whittaker MN, Testa LC, Brooks DL, Quigley A, Said H, Dwivedi G, Jindal I, Volpp D, Qu P, Wang JZ, Levine MA, Ahrens-Nicklas RC, Li Q, Musunuru K, Alameh MG, Peranteau WH, Wang X | bioRxiv : the preprint server for biology | 38712058 | bioRxiv | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/38712058 |
| InUtero Gene Therapy: Progress and Challenges. | Bose SK, Menon P, Peranteau WH | Trends in molecular medicine | 34176774 | Trends Mol Med | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34176774 |
| Fetal and Maternal Safety Considerations for In Utero Therapy Clinical Trials: iFeTiS Consensus Statement. | Sagar R, Almeida-Porada G, Blakemore K, Chan JKY, Choolani M, Götherström C, Jaulent A, MacKenzie TC, Mattar C, Porada CD, Peranteau WH, Schneider H, Shaw SW, Waddington SN, Westgren M, David AL | Molecular therapy : the journal of the American Society of Gene Therapy | 33069884 | Mol Ther | 2020 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/33069884 |
| Molecular and Cellular In Utero Therapy. | Berkowitz CL, Luks VL, Puc M, Peranteau WH | Clinics in perinatology | 36328600 | Clin Perinatol | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36328600 |
| Comment on: Premature delivery in the domestic sow in response to in utero delivery of AAV9 to fetal piglets. | Dave A, Berkowitz CL, Luks VL, White BM, Palanki R, Carpenter MD, Riley JS, Bose SK, Li H, Li L, Menon PV, Teerdhala S, Ebrahimi M, Zoltick PW, Peranteau WH | Gene therapy | 36918654 | Gene Ther | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36918654 |
| Fetal allotransplant recipients are resistant to graft-versus-host disease. | Riley JS, McClain LE, Stratigis JD, Coons BE, Bose SK, Dave A, White BM, Li H, Loukogeorgakis SP, Fachin CG, Dias AIBS, Flake AW, Peranteau WH | Experimental hematology | 36535408 | Exp Hematol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36535408 |
| In utero pulse injection of isotopic amino acids quantifies protein turnover rates during murine fetal development. | Baeza J, Coons BE, Lin Z, Riley J, Mendoza M, Peranteau WH, Garcia BA | bioRxiv : the preprint server for biology | 37293076 | bioRxiv | 2023 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/37293076 |
| Immune modulation permits tolerance and engraftment in a murine model of late-gestation transplantation. | Riley JS, Berkowitz CL, Luks VL, Dave A, Cyril-Olutayo MC, Pogoriler J, Flake AW, Abdulmalik O, Peranteau WH | Blood advances | 38941538 | Blood Adv | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/38941538 |
| Preexisting maternal immunity to AAV but not Cas9 impairs in utero gene editing in mice. | Riley JS, Luks VL, Berkowitz CL, Dumitru AM, Kus NJ, Dave A, Menon P, De Paepe ME, Jain R, Li L, Dugoff L, Teefey CP, Alameh MG, Zoltick PW, Peranteau WH | The Journal of clinical investigation | 38950310 | J Clin Invest | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38950310 |
| Prenatal Gene Therapy for Metabolic Disorders. | Coons B, Peranteau WH | Clinical obstetrics and gynecology | 34652302 | Clin Obstet Gynecol | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/34652302 |
| The Future of In Utero Gene Therapy. | Peranteau WH, Flake AW | Molecular diagnosis & therapy | 32020561 | Mol Diagn Ther | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32020561 |
| Foetal genome editing. | Bose SK, Kennedy K, Peranteau WH | Current opinion in obstetrics & gynecology | 36924409 | Curr Opin Obstet Gynecol | 2023 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/36924409 |
| Fetal gene therapy. | Waddington SN, Peranteau WH, Rahim AA, Boyle AK, Kurian MA, Gissen P, Chan JKY, David AL | Journal of inherited metabolic disease | 37470194 | J Inherit Metab Dis | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37470194 |
| The emerging role of extracellular vesicles in bronchopulmonary dysplasia. | Ransom MA, Blatt AM, Pua HH, Sucre JMS | American journal of physiology. Lung cellular and molecular physiology | 38469633 | Am J Physiol Lung Cell Mol Physiol | 2024 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38469633 |
| Secret messengers: Extracellular RNA communication in the immune system. | Nation GK, Saffold CE, Pua HH | Immunological reviews | 34542176 | Immunol Rev | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34542176 |
| Developmental trajectory of extracellular vesicle characteristics from the lungs of preterm infants. | Ransom MA, Bunn KE, Negretti NM, Jetter CS, Bressman ZJ, Sucre JMS, Pua HH | American journal of physiology. Lung cellular and molecular physiology | 36719083 | Am J Physiol Lung Cell Mol Physiol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36719083 |
| Transcriptome Complexity Disentangled: A Regulatory Molecules Approach. | Asiaee A, Abrams ZB, Pua HH, Coombes KR | bioRxiv : the preprint server for biology | 37131792 | bioRxiv | 2025 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/37131792 |
| Lipid kinase PIK3C3 maintains healthy brown and white adipose tissues to prevent metabolic diseases. | Song W, Postoak JL, Yang G, Guo X, Pua HH, Bader J, Rathmell JC, Kobayashi H, Haase VH, Leaptrot KL, Schrimpe-Rutledge AC, Sherrod SD, McLean JA, Zhang J, Wu L, Van Kaer L | Proceedings of the National Academy of Sciences of the United States of America | 36574710 | Proc Natl Acad Sci U S A | 2023 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/36574710 |
| RNA regulation in immunity. | Pua H, Ansel KM | Immunological reviews | 34816450 | Immunol Rev | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34816450 |
| Multiparametric Single-Vesicle Flow Cytometry Resolves Extracellular Vesicle Heterogeneity and Reveals Selective Regulation of Biogenesis and Cargo Distribution. | von Lersner AK, Fernandes F, Ozawa PMM, Jackson M, Masureel M, Ho H, Lima SM, Vagner T, Sung BH, Wehbe M, Franze K, Pua H, Wilson JT, Irish JM, Weaver AM, Di Vizio D, Zijlstra A | ACS nano | 38578701 | ACS Nano | 2024 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/38578701 |
| Extracellular RNA in oncogenesis, metastasis and drug resistance. | Nelson H, Qu S, Franklin JL, Liu Q, Pua HH, Vickers KC, Weaver AM, Coffey RJ, Patton JG | RNA biology | 39107918 | RNA Biol | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39107918 |
| Extracellular vesicles: mediators of intercellular communication in tissue injury and disease. | Berumen Sánchez G, Bunn KE, Pua HH, Rafat M | Cell communication and signaling : CCS | 34656117 | Cell Commun Signal | 2021 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/34656117 |
| MicroRNAs in Macrophages: Regulators of Activation and Function. | Sprenkle NT, Serezani CH, Pua HH | Journal of immunology (Baltimore, Md. : 1950) | 36724439 | J Immunol | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36724439 |
| Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. | Welsh JA, Goberdhan DCI, O'Driscoll L, Buzas EI, Blenkiron C, Bussolati B, Cai H, Di Vizio D, Driedonks TAP, Erdbrügger U, Falcon-Perez JM, Fu QL, Hill AF, Lenassi M, Lim SK, Mahoney MG, Mohanty S, Möller A, Nieuwland R, Ochiya T, Sahoo S, Torrecilhas AC, Zheng L, Zijlstra A, Abuelreich S, Bagabas R, Bergese P, Bridges EM, Brucale M, Burger D, Carney RP, Cocucci E, Crescitelli R, Hanser E, Harris AL, Haughey NJ, Hendrix A, Ivanov AR, Jovanovic-Talisman T, Kruh-Garcia NA, Ku'ulei-Lyn Faustino V, Kyburz D, Lässer C, Lennon KM, Lötvall J, Maddox AL, Martens-Uzunova ES, Mizenko RR, Newman LA, Ridolfi A, Rohde E, Rojalin T, Rowland A, Saftics A, Sandau US, Saugstad JA, Shekari F, Swift S, Ter-Ovanesyan D, Tosar JP, Useckaite Z, Valle F, Varga Z, van der Pol E, van Herwijnen MJC, Wauben MHM, Wehman AM, Williams S, Zendrini A, Zimmerman AJ, MISEV Consortium, Théry C, Witwer KW | Journal of extracellular vesicles | 38326288 | J Extracell Vesicles | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38326288 |
| Cholecystokinin-A signaling regulates automaticity of pacemaker cardiomyocytes. | Ruan H, Mandla R, Ravi N, Galang G, Soe AW, Olgin JE, Lang D, Vedantham V | Frontiers in physiology | 38179138 | Front Physiol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38179138 |
| ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function. | Galang G, Mandla R, Ruan H, Jung C, Sinha T, Stone NR, Wu RS, Mannion BJ, Allu PKR, Chang K, Rammohan A, Shi MB, Pennacchio LA, Black BL, Vedantham V | Circulation research | 33044128 | Circ Res | 2020 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/33044128 |
| Single Cell Multi-Omics of an iPSC Model of Human Sinoatrial Node Development Reveals Genetic Determinants of Heart Rate and Arrhythmia Susceptibility. | Engel JL, Zhang X, Lu DR, Vila OF, Arias V, Lee J, Hale C, Hsu YH, Li CM, Wu RS, Vedantham V, Ang YS | bioRxiv : the preprint server for biology | 37425707 | bioRxiv | 2023 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/37425707 |
| Transcriptional and Epigenetic Landscape of Cardiac Pacemaker Cells: Insights Into Cellular Specialization in the Sinoatrial Node. | Mandla R, Jung C, Vedantham V | Frontiers in physiology | 34335313 | Front Physiol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34335313 |
| Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. | Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel JG, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D | Circulation | 35938400 | Circulation | 2022 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/35938400 |
| Cholecystokinin-A Signaling Regulates Automaticity of Pacemaker Cardiomyocytes. | Ruan H, Mandla R, Ravi N, Galang G, Soe AW, Olgin JE, Lang D, Vedantham V | bioRxiv : the preprint server for biology | 36747643 | bioRxiv | 2023 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/36747643 |
| Epigenetic Regulation of Cardiomyocyte Maturation by Arginine Methyltransferase CARM1. | Garbutt TA, Wang Z, Wang H, Ma H, Ruan H, Dong Y, Xie Y, Tan L, Phookan R, Stouffer JA, Vedantham V, Yang Y, Qian L, Liu J | Circulation | 38223978 | Circulation | 2024 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/38223978 |
| Combining simulations and experiments for the molecular engineering of multifunctional collagen mimetic peptide-based materials. | Hilderbrand AM, Taylor PA, Stanzione F, LaRue M, Guo C, Jayaraman A, Kloxin AM | Soft matter | 33434255 | Soft Matter | 2021 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/33434255 |
| Effects of solvent conditions on the self-assembly of heterotrimeric collagen-like peptide (CLP) triple helices: a coarse-grained simulation study. | Taylor PA, Kronenberger S, Kloxin AM, Jayaraman A | Soft matter | 37340986 | Soft Matter | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37340986 |
| Engineered hydrogels for mechanobiology. | Blache U, Ford EM, Ha B, Rijns L, Chaudhuri O, Dankers PYW, Kloxin AM, Snedeker JG, Gentleman E | Nature reviews. Methods primers | 37461429 | Nat Rev Methods Primers | 2022 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/37461429 |
| Dynamic bioinspired coculture model for probing ER(+) breast cancer dormancy in the bone marrow niche. | Pradhan L, Moore D, Ovadia EM, Swedzinski SL, Cossette T, Sikes RA, van Golen K, Kloxin AM | Science advances | 36888709 | Sci Adv | 2023 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/36888709 |
| Biomaterials-Based Opportunities to Engineer the Pulmonary Host Immune Response in COVID-19. | Jarai BM, Stillman Z, Bomb K, Kloxin AM, Fromen CA | ACS biomaterials science & engineering | 33356134 | ACS Biomater Sci Eng | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/33356134 |
| Sequence-defined vinyl sulfonamide click nucleic acids (VS-CNAs) and their assembly into dynamically responsive materials. | Sutherland BP, LeValley PJ, Bischoff DJ, Kloxin AM, Kloxin CJ | Chemical communications (Cambridge, England) | 32820777 | Chem Commun (Camb) | 2020 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/32820777 |
| On the path to predicting immune responses in the lung: Modeling the pulmonary innate immune system at the air-liquid interface (ALI). | Graf J, Trautmann-Rodriguez M, Sabnis S, Kloxin AM, Fromen CA | European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences | 37770004 | Eur J Pharm Sci | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/37770004 |
| Bridging the gender gap in autoimmunity with T-cell-targeted biomaterials. | López Ruiz A, Slaughter ED, Kloxin AM, Fromen CA | Current opinion in biotechnology | 38377884 | Curr Opin Biotechnol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38377884 |
| Dynamic reporters for probing real-time activation of human fibroblasts from single cells to populations. | Cassel SE, Huntington BM, Chen W, Lei P, Andreadis ST, Kloxin AM | APL bioengineering | 38938687 | APL Bioeng | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38938687 |
| Rational Design of Hydrogel Networks with Dynamic Mechanical Properties to Mimic Matrix Remodeling. | Wiley KL, Sutherland BP, Ogunnaike BA, Kloxin AM | Advanced healthcare materials | 34936227 | Adv Healthc Mater | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34936227 |
| Harnessing multifunctional collagen mimetic peptides to create bioinspired stimuli responsive hydrogels for controlled cell culture. | Ford EM, Hilderbrand AM, Kloxin AM | Journal of materials chemistry. B | 39211975 | J Mater Chem B | 2024 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/39211975 |
| Rapid Production of Multifunctional Self-Assembling Peptides for Incorporation and Visualization within Hydrogel Biomaterials. | Ford EM, Kloxin AM | ACS biomaterials science & engineering | 34283566 | ACS Biomater Sci Eng | 2021 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/34283566 |
| Tools for probing host-bacteria interactions in the gut microenvironment: From molecular to cellular levels. | Wodzanowski KA, Cassel SE, Grimes CL, Kloxin AM | Bioorganic & medicinal chemistry letters | 32223923 | Bioorg Med Chem Lett | 2020 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/32223923 |
| On-demand and tunable dual wavelength release of antibody using light-responsive hydrogels. | LeValley PJ, Sutherland BP, Jaje J, Gibbs S, Jones M, Gala R, Kloxin CJ, Kiick KL, Kloxin AM | ACS applied bio materials | 34327309 | ACS Appl Bio Mater | 2020 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/34327309 |
| Multiscale Invasion Assay for Probing Macrophage Response to Gram-Negative Bacteria. | Wodzanowski KA, Caplan JL, Kloxin AM, Grimes CL | Frontiers in chemistry | 35242744 | Front Chem | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35242744 |
| Systematic d-Amino Acid Substitutions to Control Peptide and Hydrogel Degradation in Cellular Microenvironments. | Bomb K, Zhang Q, Ford EM, Fromen CA, Kloxin AM | ACS macro letters | 37195203 | ACS Macro Lett | 2023 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/37195203 |
| Impact of collagen-like peptide (CLP) heterotrimeric triple helix design on helical thermal stability and hierarchical assembly: a coarse-grained molecular dynamics simulation study. | Taylor PA, Kloxin AM, Jayaraman A | Soft matter | 35380571 | Soft Matter | 2022 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/35380571 |
| Destructive fibrotic teamwork: how both microenvironment stiffness and profibrotic interleukin 13 impair alveolar macrophage phenotype and function. | Bomb K, Pradhan L, Zhang Q, Jarai BM, Bhattacharjee A, Burris DL, Kloxin AM, Fromen CA | Biomaterials science | 36018297 | Biomater Sci | 2022 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/36018297 |
| Microgels Formed by Spontaneous Click Chemistries Utilizing Microfluidic Flow Focusing for Cargo Release in Response to Endogenous or Exogenous Stimuli. | LeValley PJ, Parsons AL, Sutherland BP, Kiick KL, Oakey JS, Kloxin AM | Pharmaceutics | 35631649 | Pharmaceutics | 2022 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/35631649 |
| Multiomic Analysis and CRISPR Perturbation Screens Identify Endothelial Cell Programs and Novel Therapeutic Targets for Coronary Artery Disease. | Gupta RM, Schnitzler GR, Fang S, Lee-Kim VS, Barry A | Arteriosclerosis, thrombosis, and vascular biology | 36994731 | Arterioscler Thromb Vasc Biol | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36994731 |
| The Aging Aorta: Are We Only as Old as Our Endothelium? | Gupta RM, Plutzky J | Arteriosclerosis, thrombosis, and vascular biology | 35080899 | Arterioscler Thromb Vasc Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35080899 |
| The Role of Endothelial Cells in Atherosclerosis: Insights from Genetic Association Studies. | Pepin ME, Gupta RM | The American journal of pathology | 37827214 | Am J Pathol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37827214 |
| Protein interaction networks in the vasculature prioritize genes and pathways underlying coronary artery disease. | Zhu QM, Hsu YH, Lassen FH, MacDonald BT, Stead S, Malolepsza E, Kim A, Li T, Mizoguchi T, Schenone M, Guzman G, Tanenbaum B, Fornelos N, Carr SA, Gupta RM, Ellinor PT, Lage K | Communications biology | 38216744 | Commun Biol | 2024 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/38216744 |
| Rare, Damaging DNA Variants in CORIN and Risk of Coronary Artery Disease: Insights From Functional Genomics and Large-Scale Sequencing Analyses. | Wang M, Lee-Kim VS, Atri DS, Elowe NH, Yu J, Garvie CW, Won HH, Hadaya JE, MacDonald BT, Trindade K, Melander O, Rader DJ, Natarajan P, Kathiresan S, Kaushik VK, Khera AV, Gupta RM | Circulation. Genomic and precision medicine | 34592835 | Circ Genom Precis Med | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34592835 |
| Causal Gene Confusion: The Complicated EDN1/PHACTR1 Locus for Coronary Artery Disease. | Gupta RM | Arteriosclerosis, thrombosis, and vascular biology | 35387481 | Arterioscler Thromb Vasc Biol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35387481 |
| Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases. | Weeks EM, Ulirsch JC, Cheng NY, Trippe BL, Fine RS, Miao J, Patwardhan TA, Kanai M, Nasser J, Fulco CP, Tashman KC, Aguet F, Li T, Ordovas-Montanes J, Smillie CS, Biton M, Shalek AK, Ananthakrishnan AN, Xavier RJ, Regev A, Gupta RM, Lage K, Ardlie KG, Hirschhorn JN, Lander ES, Engreitz JM, Finucane HK | Nature genetics | 37443254 | Nat Genet | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37443254 |
| Missing Regulation Between Genetic Association and Transcriptional Abundance for Hypercholesterolemia Genes. | Hakim A, Connally NJ, Schnitzler GR, Cho MH, Jiang ZG, Sunyaev SR, Gupta RM | Genes | 39858631 | Genes (Basel) | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39858631 |
| Linking regulation of nitric oxide to endothelin-1: The Yin and Yang of vascular tone in the atherosclerotic plaque. | Gupta RM, Libby P, Barton M | Atherosclerosis | 31810569 | Atherosclerosis | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31810569 |
| The March of Monocytes in Atherosclerosis: One Cell at a Time. | Gupta RM, Lee-Kim VS, Libby P | Circulation research | 32379573 | Circ Res | 2020 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/32379573 |
| CRISPR-Cas9 Genome Editing of Primary Human Vascular Cells In Vitro. | Atri DS, Lee-Kim VS, Vellarikkal SK, Sias-Garcia O, Yanamandala M, Schniztler GR, Gupta RM | Current protocols | 34748284 | Curr Protoc | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34748284 |
| Convergence of coronary artery disease genes onto endothelial cell programs. | Schnitzler GR, Kang H, Fang S, Angom RS, Lee-Kim VS, Ma XR, Zhou R, Zeng T, Guo K, Taylor MS, Vellarikkal SK, Barry AE, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Hinshaw S, Cheng N, Cleary B, Aragam K, Lander ES, Finucane HK, Mukhopadhyay D, Gupta RM, Engreitz JM | Nature | 38326615 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38326615 |
| Polygenic prediction of preeclampsia and gestational hypertension. | Honigberg MC, Truong B, Khan RR, Xiao B, Bhatta L, Vy HMT, Guerrero RF, Schuermans A, Selvaraj MS, Patel AP, Koyama S, Cho SMJ, Vellarikkal SK, Trinder M, Urbut SM, Gray KJ, Brumpton BM, Patil S, Zöllner S, Antopia MC, Saxena R, Nadkarni GN, Do R, Yan Q, Pe'er I, Verma SS, Gupta RM, Haas DM, Martin HC, van Heel DA, Laisk T, Natarajan P | Nature medicine | 37248299 | Nat Med | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37248299 |
| Vagal sensory neurons and gut-brain signaling. | Yu CD, Xu QJ, Chang RB | Current opinion in neurobiology | 32380360 | Curr Opin Neurobiol | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32380360 |
| The Coding Logic of Interoception. | Wang RL, Chang RB | Annual review of physiology | 38061018 | Annu Rev Physiol | 2024 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/38061018 |
| A multidimensional coding architecture of the vagal interoceptive system. | Zhao Q, Yu CD, Wang R, Xu QJ, Dai Pra R, Zhang L, Chang RB | Nature | 35296859 | Nature | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35296859 |
| Differential developmental blueprints of organ-intrinsic nervous systems. | Hsu IU, Lin Y, Guo Y, Xu QJ, Shao Y, Wang RL, Yin D, Zhao J, Young LH, Zhao H, Zhang L, Chang RB | bioRxiv : the preprint server for biology | 38168446 | bioRxiv | 2023 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/38168446 |
| Cardiovascular Brain Circuits. | Mohanta SK, Yin C, Weber C, Godinho-Silva C, Veiga-Fernandes H, Xu QJ, Chang RB, Habenicht AJR | Circulation research | 37228235 | Circ Res | 2023 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/37228235 |
| The vagus nerve in cardiovascular physiology and pathophysiology: From evolutionary insights to clinical medicine. | Rajendran PS, Hadaya J, Khalsa SS, Yu C, Chang R, Shivkumar K | Seminars in cell & developmental biology | 36641366 | Semin Cell Dev Biol | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36641366 |
| Regulation of Cardiac Function by the Autonomic Nervous System. | Hafez OA, Chang RB | Physiology (Bethesda, Md.) | 39585760 | Physiology (Bethesda) | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/39585760 |
| Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin. | Ma S, Zhang B, LaFave LM, Earl AS, Chiang Z, Hu Y, Ding J, Brack A, Kartha VK, Tay T, Law T, Lareau C, Hsu YC, Regev A, Buenrostro JD | Cell | 33098772 | Cell | 2020 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/33098772 |
| Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. | Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD | bioRxiv : the preprint server for biology | 37034577 | bioRxiv | 2023 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/37034577 |
| A transcription factor atlas of directed differentiation. | Joung J, Ma S, Tay T, Geiger-Schuller KR, Kirchgatterer PC, Verdine VK, Guo B, Arias-Garcia MA, Allen WE, Singh A, Kuksenko O, Abudayyeh OO, Gootenberg JS, Fu Z, Macrae RK, Buenrostro JD, Regev A, Zhang F | Cell | 36608654 | Cell | 2023 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/36608654 |
| scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution. | Hingerl JC, Martens LD, Karollus A, Manz T, Buenrostro JD, Theis FJ, Gagneur J | bioRxiv : the preprint server for biology | 39345504 | bioRxiv | 2025 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/39345504 |
| Spatial genomics enables multi-modal study of clonal heterogeneity in tissues. | Zhao T, Chiang ZD, Morriss JW, LaFave LM, Murray EM, Del Priore I, Meli K, Lareau CA, Nadaf NM, Li J, Earl AS, Macosko EZ, Jacks T, Buenrostro JD, Chen F | Nature | 34912115 | Nature | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34912115 |
| Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma. | LaFave LM, Kartha VK, Ma S, Meli K, Del Priore I, Lareau C, Naranjo S, Westcott PMK, Duarte FM, Sankar V, Chiang Z, Brack A, Law T, Hauck H, Okimoto A, Regev A, Buenrostro JD, Jacks T | Cancer cell | 32707078 | Cancer Cell | 2020 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/32707078 |
| Functional inference of gene regulation using single-cell multi-omics. | Kartha VK, Duarte FM, Hu Y, Ma S, Chew JG, Lareau CA, Earl A, Burkett ZD, Kohlway AS, Lebofsky R, Buenrostro JD | Cell genomics | 36204155 | Cell Genom | 2022 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/36204155 |
| Multiscale footprints reveal the organization of cis-regulatory elements. | Hu Y, Horlbeck MA, Zhang R, Ma S, Shrestha R, Kartha VK, Duarte FM, Hock C, Savage RE, Labade A, Kletzien H, Meliki A, Castillo A, Durand NC, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers AJ, Buenrostro JD | Nature | 39843737 | Nature | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39843737 |
| A microRNA expression and regulatory element activity atlas of the mouse immune system. | Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD, Immunological Genome Consortium | Nature immunology | 34099919 | Nat Immunol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34099919 |
| Reprogramming identifies functionally distinct stages of clonal evolution in myelodysplastic syndromes. | Hsu J, Reilly A, Hayes BJ, Clough CA, Konnick EQ, Torok-Storb B, Gulsuner S, Wu D, Becker PS, Keel SB, Abkowitz JL, Doulatov S | Blood | 31010849 | Blood | 2019 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/31010849 |
| Lamin B1 deletion in myeloid neoplasms causes nuclear anomaly and altered hematopoietic stem cell function. | Reilly A, Philip Creamer J, Stewart S, Stolla MC, Wang Y, Du J, Wellington R, Busch S, Estey EH, Becker PS, Fang M, Keel SB, Abkowitz JL, Soma LA, Ma J, Duan Z, Doulatov S | Cell stem cell | 35278369 | Cell Stem Cell | 2022 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/35278369 |
| R-Loop Accumulation in Spliceosome Mutant Leukemias Confers Sensitivity to PARP1 Inhibition by Triggering Transcription-Replication Conflicts. | Liu ZS, Sinha S, Bannister M, Song A, Arriaga-Gomez E, McKeeken AJ, Bonner EA, Hanson BK, Sarchi M, Takashima K, Zong D, Corral VM, Nguyen E, Yoo J, Chiraphapphaiboon W, Leibson C, McMahon MC, Rai S, Swisher EM, Sachs Z, Chatla S, Stirewalt DL, Deeg HJ, Skorski T, Papapetrou EP, Walter MJ, Graubert TA, Doulatov S, Lee SC, Nguyen HD | Cancer research | 37967363 | Cancer Res | 2024 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/37967363 |
| Induced pluripotent stem cell models of myeloid malignancies and clonal evolution. | Reilly A, Doulatov S | Stem cell research | 33592565 | Stem Cell Res | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33592565 |
| ATG4A regulates human erythroid maturation and mitochondrial clearance. | Stolla MC, Reilly A, Bergantinos R, Stewart S, Thom N, Clough CA, Wellington RC, Stolitenko R, Abkowitz JL, Doulatov S | Blood advances | 35443024 | Blood Adv | 2022 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/35443024 |
| Coordinated missplicing of TMEM14C and ABCB7 causes ring sideroblast formation in SF3B1-mutant myelodysplastic syndrome. | Clough CA, Pangallo J, Sarchi M, Ilagan JO, North K, Bergantinos R, Stolla MC, Naru J, Nugent P, Kim E, Stirewalt DL, Subramaniam AR, Abdel-Wahab O, Abkowitz JL, Bradley RK, Doulatov S | Blood | 34861039 | Blood | 2022 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/34861039 |
| Induced pluripotent stem cell line (SDQLCHi041-A) from a male patient with mucopolysaccharidosis type IIIB. | Guan J, Tian G, Dong R, Zhang H, Yang X, Li Y, Gai Z, Liu Y | Stem cell research | 33550137 | Stem Cell Res | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33550137 |
| Studying clonal evolution of myeloid malignancies using induced pluripotent stem cells. | Doulatov S, Papapetrou EP | Current opinion in hematology | 33264225 | Curr Opin Hematol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33264225 |
| Mis-splicing of Mitotic Regulators Sensitizes SF3B1-Mutated Human HSCs to CHK1 Inhibition. | Sarchi M, Clough CA, Crosse EI, Kim J, Baquero Galvis LD, Aydinyan N, Wellington R, Yang F, Gallì A, Creamer JP, Stewart S, Bradley RK, Malcovati L, Doulatov S | Blood cancer discovery | 38856693 | Blood Cancer Discov | 2024 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/38856693 |
| Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells. | Wellington R, Cheng X, Campbell CA, Trapnell C, Espin-Palazon R, Hadland B, Doulatov S | bioRxiv : the preprint server for biology | 39386462 | bioRxiv | 2024 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/39386462 |
| Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. | Jiang CL, Goyal Y, Jain N, Wang Q, Truitt RE, Coté AJ, Emert B, Mellis IA, Kiani K, Yang W, Jain R, Raj A | Genome biology | 35382863 | Genome Biol | 2022 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/35382863 |
| A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva. | Warneford-Thomson R, Shah PP, Lundgren P, Lerner J, Morgan J, Davila A, Abella BS, Zaret K, Schug J, Jain R, Thaiss CA, Bonasio R | eLife | 35532013 | Elife | 2022 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/35532013 |
| Early lineage specification defines alveolar epithelial ontogeny in the murine lung. | Frank DB, Penkala IJ, Zepp JA, Sivakumar A, Linares-Saldana R, Zacharias WJ, Stolz KG, Pankin J, Lu M, Wang Q, Babu A, Li L, Zhou S, Morley MP, Jain R, Morrisey EE | Proceedings of the National Academy of Sciences of the United States of America | 30782824 | Proc Natl Acad Sci U S A | 2019 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/30782824 |
| A Balance Between Intermediate Filaments and Microtubules Maintains Nuclear Architecture in the Cardiomyocyte. | Heffler J, Shah PP, Robison P, Phyo S, Veliz K, Uchida K, Bogush A, Rhoades J, Jain R, Prosser BL | Circulation research | 31822208 | Circ Res | 2020 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/31822208 |
| Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors. | Smith CL, Lan Y, Jain R, Epstein JA, Poleshko A | Science advances | 34559565 | Sci Adv | 2021 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/34559565 |
| Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains. | See K, Lan Y, Rhoades J, Jain R, Smith CL, Epstein JA | Development (Cambridge, England) | 30723106 | Development | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30723106 |
| Picking Winners and Losers: Cell Competition in Tissue Development and Homeostasis. | Kim W, Jain R | Trends in genetics : TIG | 32418713 | Trends Genet | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32418713 |
| InterLINCing Chromatin Organization and Mechanobiology in Laminopathies. | Shah PP, Santini GT, Shen KM, Jain R | Current cardiology reports | 37052760 | Curr Cardiol Rep | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37052760 |
| Core Components of the Nuclear Pore Bind Distinct States of Chromatin and Contribute to Polycomb Repression. | Gozalo A, Duke A, Lan Y, Pascual-Garcia P, Talamas JA, Nguyen SC, Shah PP, Jain R, Joyce EF, Capelson M | Molecular cell | 31784359 | Mol Cell | 2020 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/31784359 |
| PRR14 organizes H3K9me3-modified heterochromatin at the nuclear lamina. | Kiseleva AA, Cheng YC, Smith CL, Katz RA, Poleshko A | Nucleus (Austin, Tex.) | 36633363 | Nucleus | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36633363 |
| Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. | Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R | Cell stem cell | 33529599 | Cell Stem Cell | 2021 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/33529599 |
| H3K9me2 orchestrates inheritance of spatial positioning of peripheral heterochromatin through mitosis. | Poleshko A, Smith CL, Nguyen SC, Sivaramakrishnan P, Wong KG, Murray JI, Lakadamyali M, Joyce EF, Jain R, Epstein JA | eLife | 31573510 | Elife | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31573510 |
| A Common Embryonic Origin of Stem Cells Drives Developmental and Adult Neurogenesis. | Berg DA, Su Y, Jimenez-Cyrus D, Patel A, Huang N, Morizet D, Lee S, Shah R, Ringeling FR, Jain R, Epstein JA, Wu QF, Canzar S, Ming GL, Song H, Bond AM | Cell | 30929900 | Cell | 2019 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/30929900 |
| Biophysical forces mediated by respiration maintain lung alveolar epithelial cell fate. | Shiraishi K, Shah PP, Morley MP, Loebel C, Santini GT, Katzen J, Basil MC, Lin SM, Planer JD, Cantu E, Jones DL, Nottingham AN, Li S, Cardenas-Diaz FL, Zhou S, Burdick JA, Jain R, Morrisey EE | Cell | 36870331 | Cell | 2023 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/36870331 |
| Aberrant chromatin organization at the nexus of laminopathy disease pathways. | Santini GT, Shah PP, Karnay A, Jain R | Nucleus (Austin, Tex.) | 36503349 | Nucleus | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36503349 |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R | Genome biology | 36691074 | Genome Biol | 2023 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/36691074 |
| Advanced Human BBB-on-a-Chip: A New Platform for Alzheimer's Disease Studies. | Yoon JK, Kim J, Shah Z, Awasthi A, Mahajan A, Kim Y | Advanced healthcare materials | 34075728 | Adv Healthc Mater | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34075728 |
| Detecting the functional complexities between high-density lipoprotein mimetics. | Sei YJ, Ahn J, Kim T, Shin E, Santiago-Lopez AJ, Jang SS, Jeon NL, Jang YC, Kim Y | Biomaterials | 29653287 | Biomaterials | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29653287 |
| Nanotherapeutics Engineered to Cross the Blood-Brain Barrier for Advanced Drug Delivery to the Central Nervous System. | Kim J, Ahn SI, Kim Y | Journal of industrial and engineering chemistry (Seoul, Korea) | 31588177 | J Ind Eng Chem | 2019 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/31588177 |
| Microvascularized tumor organoids-on-chips: advancing preclinical drug screening with pathophysiological relevance. | Lim J, Ching H, Yoon JK, Jeon NL, Kim Y | Nano convergence | 33846849 | Nano Converg | 2021 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/33846849 |
| Engineered biomimetic nanoparticle for dual targeting of the cancer stem-like cell population in sonic hedgehog medulloblastoma. | Kim J, Dey A, Malhotra A, Liu J, Ahn SI, Sei YJ, Kenney AM, MacDonald TJ, Kim Y | Proceedings of the National Academy of Sciences of the United States of America | 32934143 | Proc Natl Acad Sci U S A | 2020 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/32934143 |
| Engineered Heterochronic Parabiosis in 3D Microphysiological System for Identification of Muscle Rejuvenating Factors. | Lee Y, Choi JJ, Ahn SI, Lee NH, Han WM, Mohiuddin M, Shin EJ, Wood L, Park KD, Kim Y, Jang YC | Advanced functional materials | 38053980 | Adv Funct Mater | 2020 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/38053980 |
| Polymeric Nanoparticles Controlled by On-Chip Self-Assembly Enhance Cancer Treatment Effectiveness. | Jung S, Lee J, Lim J, Suh J, Kim T, Ahn J, Kim WJ, Kim Y | Advanced healthcare materials | 33073526 | Adv Healthc Mater | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33073526 |
| Phosphodiesterase 2A as a therapeutic target to restore cardiac neurotransmission during sympathetic hyperactivity. | Liu K, Li D, Hao G, McCaffary D, Neely O, Woodward L, Ioannides D, Lu CJ, Brescia M, Zaccolo M, Tandri H, Ajijola OA, Ardell JL, Shivkumar K, Paterson DJ | JCI insight | 29720569 | JCI Insight | 2018 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/29720569 |
| Managing ventricular arrhythmias after failed catheter ablation: Interrupting the reentrant loop of repeat ablation. | Yoshie K, Ajijola OA | Heart rhythm | 28958931 | Heart Rhythm | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28958931 |
| Estimating Cardiac Sympathetic Activity From Subcutaneous Nerve Recordings: More Than Skin Deep? | Dusi V, Ajijola OA | JACC. Clinical electrophysiology | 29798800 | JACC Clin Electrophysiol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29798800 |
| Coronary Sinus Neuropeptide Y Levels and Adverse Outcomes in Patients With Stable Chronic Heart Failure. | Ajijola OA, Chatterjee NA, Gonzales MJ, Gornbein J, Liu K, Li D, Paterson DJ, Shivkumar K, Singh JP, Herring N | JAMA cardiology | 31876927 | JAMA Cardiol | 2020 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/31876927 |
| Cardiac TRPV1 afferent signaling promotes arrhythmogenic ventricular remodeling after myocardial infarction. | Yoshie K, Rajendran PS, Massoud L, Mistry J, Swid MA, Wu X, Sallam T, Zhang R, Goldhaber JI, Salavatian S, Ajijola OA | JCI insight | 31846438 | JCI Insight | 2020 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/31846438 |
| Aorticorenal ganglion as a novel target for renal neuromodulation. | Hori Y, Temma T, Wooten C, Sobowale C, Tahmasian S, Chan C, Swid MA, Zuckerman JE, Peacock W, Ajijola OA | Heart rhythm | 34182169 | Heart Rhythm | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34182169 |
| Cardiac vanilloid receptor-1 afferent depletion enhances stellate ganglion neuronal activity and efferent sympathetic response to cardiac stress. | Yoshie K, Rajendran PS, Massoud L, Kwon O, Tadimeti V, Salavatian S, Ardell JL, Shivkumar K, Ajijola OA | American journal of physiology. Heart and circulatory physiology | 29351450 | Am J Physiol Heart Circ Physiol | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29351450 |
| Inflammation, oxidative stress, and glial cell activation characterize stellate ganglia from humans with electrical storm. | Ajijola OA, Hoover DB, Simerly TM, Brown TC, Yanagawa J, Biniwale RM, Lee JM, Sadeghi A, Khanlou N, Ardell JL, Shivkumar K | JCI insight | 28931760 | JCI Insight | 2017 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/28931760 |
| The cardiac sympathetic co-transmitter neuropeptide Y is pro-arrhythmic following ST-elevation myocardial infarction despite beta-blockade. | Kalla M, Hao G, Tapoulal N, Tomek J, Liu K, Woodward L, ‘Oxford Acute Myocardial Infarction (OxAMI) Study’, Dall'Armellina E, Banning AP, Choudhury RP, Neubauer S, Kharbanda RK, Channon KM, Ajijola OA, Shivkumar K, Paterson DJ, Herring N | European heart journal | 31834357 | Eur Heart J | 2020 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/31834357 |
| Cardiac sympathetic denervation and mental health. | Khalsa SS, Clausen AN, Shahabi L, Sorg J, Gonzalez SE, Naliboff B, Shivkumar K, Ajijola OA | Autonomic neuroscience : basic & clinical | 33631539 | Auton Neurosci | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33631539 |
| RNA Sequencing Reveals Novel Transcripts from Sympathetic Stellate Ganglia During Cardiac Sympathetic Hyperactivity. | Bardsley EN, Davis H, Ajijola OA, Buckler KJ, Ardell JL, Shivkumar K, Paterson DJ | Scientific reports | 29872217 | Sci Rep | 2018 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/29872217 |
| Single-cell transcriptomic profiling of satellite glial cells in stellate ganglia reveals developmental and functional axial dynamics. | van Weperen VYH, Littman RJ, Arneson DV, Contreras J, Yang X, Ajijola OA | Glia | 33432730 | Glia | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33432730 |
| 3D-Printed Coronary Implants Are Effective for Percutaneous Creation of Swine Models with Focal Coronary Stenosis. | Colbert CM, Shao J, Hollowed JJ, Currier JW, Ajijola OA, Fishbein GA, Duarte-Vogel SM, Dharmakumar R, Hu P, Nguyen KL | Journal of cardiovascular translational research | 32394352 | J Cardiovasc Transl Res | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32394352 |
| Transcriptional profiling of stellate ganglia from normotensive and spontaneously hypertensive rat strains. | Davis H, Bardsley EN, Paterson DJ | Scientific data | 29944142 | Sci Data | 2018 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/29944142 |
| Efficacy of Stellate Ganglion Blockade in Managing Electrical Storm: A Systematic Review. | Meng L, Tseng CH, Shivkumar K, Ajijola O | JACC. Clinical electrophysiology | 29270467 | JACC Clin Electrophysiol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29270467 |
| Neuromodulation Approaches for Cardiac Arrhythmias: Recent Advances. | Dusi V, Zhu C, Ajijola OA | Current cardiology reports | 30887264 | Curr Cardiol Rep | 2019 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/30887264 |
| A novel metric linking stellate ganglion neuronal population dynamics to cardiopulmonary physiology. | Sudarshan KB, Hori Y, Swid MA, Karavos AC, Wooten C, Armour JA, Kember G, Ajijola OA | American journal of physiology. Heart and circulatory physiology | 34213390 | Am J Physiol Heart Circ Physiol | 2021 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/34213390 |
| Cardiac afferent signaling partially underlies premature ventricular contraction-induced cardiomyopathy. | Hori Y, Temma T, Wooten C, Sobowale C, Chan C, Swid M, Ajijola OA | Heart rhythm | 33845214 | Heart Rhythm | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33845214 |
| Tiered sympathetic control of cardiac function revealed by viral tracing and single cell transcriptome profiling. | Sharma S, Littman R, Tompkins JD, Arneson D, Contreras J, Dajani AH, Ang K, Tsanhani A, Sun X, Jay PY, Herzog H, Yang X, Ajijola OA | eLife | 37162194 | Elife | 2023 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/37162194 |
| Circulating Neuropeptide Y as a Biomarker for Neuromodulation in Atrial Fibrillation. | Stavrakis S, Morris L, Takashima AD, Elkholey K, Van Wagoner DR, Ajijola OA | JACC. Clinical electrophysiology | 33213819 | JACC Clin Electrophysiol | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33213819 |
| Prognostic impact of atrial rhythm and dimension in patients with structural heart disease undergoing cardiac sympathetic denervation for ventricular arrhythmias. | Dusi V, Sorg JM, Gornbein J, Gima J, Yanagawa J, Lee JM, Vecerek N, Vaseghi M, Bradfield JS, De Ferrari GM, Shivkumar K, Ajijola OA | Heart rhythm | 31837474 | Heart Rhythm | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/31837474 |
| Cardiovascular autonomic reflex function after bilateral cardiac sympathetic denervation for ventricular arrhythmias. | Dusi V, Shahabi L, Lapidus RC, Sorg JM, Naliboff BD, Shivkumar K, Khalsa SS, Ajijola OA | Heart rhythm | 32325196 | Heart Rhythm | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32325196 |
| Chronic Kidney Disease: A Nerve-Racking Situation for the Heart. | Ajijola OA | Circulation research | 35209720 | Circ Res | 2022 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/35209720 |
| The derivative of tissue activation as a marker of arrhythmogenic myocardium. | Temma T, Lux RL, Yoshie K, Hayase J, Bradfield JS, Shivkumar K, Ajijola OA | Heart rhythm | 36270579 | Heart Rhythm | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36270579 |
| Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase. | Schutsky EK, DeNizio JE, Hu P, Liu MY, Nabel CS, Fabyanic EB, Hwang Y, Bushman FD, Wu H, Kohli RM | Nature biotechnology | 30295673 | Nat Biotechnol | 2018 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/30295673 |
| Single-cell transcriptomic analysis of adult mouse pituitary reveals sexual dimorphism and physiologic demand-induced cellular plasticity. | Ho Y, Hu P, Peel MT, Chen S, Camara PG, Epstein DJ, Wu H, Liebhaber SA | Protein & cell | 32193873 | Protein Cell | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32193873 |
| Single-cell multiomics reveals increased plasticity, resistant populations, and stem-cell-like blasts in KMT2A-rearranged leukemia. | Chen C, Yu W, Alikarami F, Qiu Q, Chen CH, Flournoy J, Gao P, Uzun Y, Fang L, Davenport JW, Hu Y, Zhu Q, Wang K, Libbrecht C, Felmeister A, Rozich I, Ding YY, Hunger SP, Felix CA, Wu H, Brown PA, Guest EM, Barrett DM, Bernt KM, Tan K | Blood | 34864916 | Blood | 2022 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/34864916 |
| Single-nucleus transcriptomic survey of cell diversity and functional maturation in postnatal mammalian hearts. | Hu P, Liu J, Zhao J, Wilkins BJ, Lupino K, Wu H, Pei L | Genes & development | 30254108 | Genes Dev | 2018 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/30254108 |
| Mammalian DNA methylome dynamics: mechanisms, functions and new frontiers. | Wei A, Wu H | Development (Cambridge, England) | 36519514 | Development | 2022 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36519514 |
| Massively parallel and time-resolved RNA sequencing in single cells with scNT-seq. | Qiu Q, Hu P, Qiu X, Govek KW, Cámara PG, Wu H | Nature methods | 32868927 | Nat Methods | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32868927 |
| Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects. | Fabyanic EB, Hu P, Qiu Q, Berríos KN, Connolly DR, Wang T, Flournoy J, Zhou Z, Kohli RM, Wu H | Nature biotechnology | 37640946 | Nat Biotechnol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37640946 |
| Dissecting Cell-Type Composition and Activity-Dependent Transcriptional State in Mammalian Brains by Massively Parallel Single-Nucleus RNA-Seq. | Hu P, Fabyanic E, Kwon DY, Tang S, Zhou Z, Wu H | Molecular cell | 29220646 | Mol Cell | 2017 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/29220646 |
| Tet2-mediated epigenetic drive for astrocyte differentiation from embryonic neural stem cells. | He F, Wu H, Zhou L, Lin Q, Cheng Y, Sun YE | Cell death discovery | 32377393 | Cell Death Discov | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32377393 |
| Highly multiplexed spatial mapping of microbial communities. | Shi H, Shi Q, Grodner B, Lenz JS, Zipfel WR, Brito IL, De Vlaminck I | Nature | 33268897 | Nature | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33268897 |
| Examining horizontal gene transfer in microbial communities. | Brito IL | Nature reviews. Microbiology | 33846600 | Nat Rev Microbiol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33846600 |
| Structural host immune-microbiota interactions. | Brito IL, Kriegel MA | Current opinion in structural biology | 36063760 | Curr Opin Struct Biol | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36063760 |
| Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix. | Porras AM, Zhou H, Shi Q, Xiao X, JRI Live Cell Bank, Longman R, Brito IL | mBio | 36445085 | mBio | 2022 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/36445085 |
| Host-microbiome protein-protein interactions capture disease-relevant pathways. | Zhou H, Beltrán JF, Brito IL | Genome biology | 35246229 | Genome Biol | 2022 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/35246229 |
| Segatella clades adopt distinct roles within a single individual's gut. | Xiao X, Singh A, Giometto A, Brito IL | NPJ biofilms and microbiomes | 39465298 | NPJ Biofilms Microbiomes | 2024 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/39465298 |
| Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders. | Zhou H, Balint D, Shi Q, Vartanian T, Kriegel MA, Brito I | Annals of the rheumatic diseases | 39874239 | Ann Rheum Dis | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39874239 |
| Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide. | Diebold PJ, Rhee MW, Shi Q, Trung NV, Umrani F, Ahmed S, Kulkarni V, Deshpande P, Alexander M, Thi Hoa N, Christakis NA, Iqbal NT, Ali SA, Mathad JS, Brito IL | Nature communications | 37963868 | Nat Commun | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/37963868 |
| Linking plasmid-based beta-lactamases to their bacterial hosts using single-cell fusion PCR. | Diebold PJ, New FN, Hovan M, Satlin MJ, Brito IL | eLife | 34282723 | Elife | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/34282723 |
| Functions predict horizontal gene transfer and the emergence of antibiotic resistance. | Zhou H, Beltrán JF, Brito IL | Science advances | 34678056 | Sci Adv | 2021 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/34678056 |
| Collective effects of human genomic variation on microbiome function. | New FN, Baer BR, Clark AG, Wells MT, Brito IL | Scientific reports | 35264618 | Sci Rep | 2022 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/35264618 |
| Prevotella copri variants among a single host diverge in sphingolipid production. | Xiao X, Le HH, Lee M-T, Lamm D, Johnson EL, Brito IL | mBio | 38236049 | mBio | 2024 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/38236049 |
| Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming. | Jones J, Shi Q, Nath RR, Brito IL | bioRxiv : the preprint server for biology | 37066368 | bioRxiv | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/37066368 |
| Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C. | Kent AG, Vill AC, Shi Q, Satlin MJ, Brito IL | Nature communications | 32873785 | Nat Commun | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32873785 |
| Structural insight into protein-protein interactions between intestinal microbiome and host. | Post SE, Brito IL | Current opinion in structural biology | 35390637 | Curr Opin Struct Biol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35390637 |
| Keystone pathobionts associated with colorectal cancer promote oncogenic reprograming. | Jones J, Shi Q, Nath RR, Brito IL | PloS one | 38363784 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38363784 |
| The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells. | Kabir S, Cidado J, Andersen C, Dick C, Lin PC, Mitros T, Ma H, Baik SH, Belmonte MA, Drew L, Corn JE | eLife | 31294695 | Elife | 2019 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/31294695 |
| Advances in genome editing through control of DNA repair pathways. | Yeh CD, Richardson CD, Corn JE | Nature cell biology | 31792376 | Nat Cell Biol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31792376 |
| Double stranded DNA breaks and genome editing trigger loss of ribosomal protein RPS27A. | Riepe C, Zelin E, Frankino PA, Meacham ZA, Fernandez SG, Ingolia NT, Corn JE | The FEBS journal | 34914197 | FEBS J | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34914197 |
| In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway. | Wienert B, Shin J, Zelin E, Pestal K, Corn JE | PLoS biology | 30011268 | PLoS Biol | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30011268 |
| Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. | Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P, Porritt MJ, Morlock M, Vu JT, Kazane KR, Watry HL, Judge LM, Conklin BR, Maresca M, Corn JE | Science (New York, N.Y.) | 31000663 | Science | 2019 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/31000663 |
| Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. | Shin JJ, Schröder MS, Caiado F, Wyman SK, Bray NL, Bordi M, Dewitt MA, Vu JT, Kim WT, Hockemeyer D, Manz MG, Corn JE | Cell reports | 32877675 | Cell Rep | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32877675 |
| Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. | Wienert B, Nguyen DN, Guenther A, Feng SJ, Locke MN, Wyman SK, Shin J, Kazane KR, Gregory GL, Carter MAM, Wright F, Conklin BR, Marson A, Richardson CD, Corn JE | Nature communications | 32355159 | Nat Commun | 2020 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/32355159 |
| SLC19A1 transports immunoreactive cyclic dinucleotides. | Luteijn RD, Zaver SA, Gowen BG, Wyman SK, Garelis NE, Onia L, McWhirter SM, Katibah GE, Corn JE, Woodward JJ, Raulet DH | Nature | 31511694 | Nature | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31511694 |
| A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. | Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE | Cell | 32160526 | Cell | 2020 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/32160526 |
| Genome editing to model and reverse a prevalent mutation associated with myeloproliferative neoplasms. | Baik R, Wyman SK, Kabir S, Corn JE | PloS one | 33661998 | PLoS One | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33661998 |
| Atlastins remodel the endoplasmic reticulum for selective autophagy. | Liang JR, Lingeman E, Ahmed S, Corn JE | The Journal of cell biology | 30143524 | J Cell Biol | 2018 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/30143524 |
| DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution. | Elacqua JJ, Ranu N, DiIorio SE, Blainey PC | Genome research | 33355294 | Genome Res | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33355294 |
| Quantification of somatic mutation flow across individual cell division events by lineage sequencing. | Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC | Genome research | 30459213 | Genome Res | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30459213 |
| Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing. | Borrajo J, Javanmardi K, Griffin J, St Martin SJ, Yao D, Hill K, Blainey PC, Al-Shayeb B | bioRxiv : the preprint server for biology | 37645763 | bioRxiv | 2023 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/37645763 |
| Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers. | Najia MA, Jha DK, Zhang C, Laurent B, Kubaczka C, Markel A, Li C, Morris V, Tompkins A, Hensch L, Qin Y, Chapuy B, Huang YC, Morse M, Marunde MR, Vaidya A, Gillespie ZB, Howard SA, North TE, Dominguez D, Keogh MC, Schlaeger TM, Shi Y, Li H, Shipp MM, Blainey PC, Daley GQ | bioRxiv : the preprint server for biology | 39975048 | bioRxiv | 2025 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/39975048 |
| CRISPResso2 provides accurate and rapid genome editing sequence analysis. | Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L | Nature biotechnology | 30809026 | Nat Biotechnol | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30809026 |
| Functional interrogation of non-coding DNA through CRISPR genome editing. | Canver MC, Bauer DE, Orkin SH | Methods (San Diego, Calif.) | 28288828 | Methods | 2017 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/28288828 |
| 14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts. | Lessard S, Beaudoin M, Orkin SH, Bauer DE, Lettre G | Human molecular genetics | 29432581 | Hum Mol Genet | 2018 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/29432581 |
| Genome-wide CRISPR-Cas9 Screen Identifies Leukemia-Specific Dependence on a Pre-mRNA Metabolic Pathway Regulated by DCPS. | Yamauchi T, Masuda T, Canver MC, Seiler M, Semba Y, Shboul M, Al-Raqad M, Maeda M, Schoonenberg VAC, Cole MA, Macias-Trevino C, Ishikawa Y, Yao Q, Nakano M, Arai F, Orkin SH, Reversade B, Buonamici S, Pinello L, Akashi K, Bauer DE, Maeda T | Cancer cell | 29478914 | Cancer Cell | 2018 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/29478914 |
| DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens. | Canver MC, Bauer DE, Maeda T, Pinello L | Bioinformatics (Oxford, England) | 30395160 | Bioinformatics | 2019 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/30395160 |
| CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. | Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L | Nature methods | 30504875 | Nat Methods | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30504875 |
| Editing aberrant splice sites efficiently restores β-globin expression in β-thalassemia. | Xu S, Luk K, Yao Q, Shen AH, Zeng J, Wu Y, Luo HY, Brendel C, Pinello L, Chui DHK, Wolfe SA, Bauer DE | Blood | 30704988 | Blood | 2019 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/30704988 |
| Technical considerations for the use of CRISPR/Cas9 in hematology research. | Gundry MC, Dever DP, Yudovich D, Bauer DE, Haas S, Wilkinson AC, Singbrant S | Experimental hematology | 28757433 | Exp Hematol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28757433 |
| An erythroid-specific ATP2B4 enhancer mediates red blood cell hydration and malaria susceptibility. | Lessard S, Gatof ES, Beaudoin M, Schupp PG, Sher F, Ali A, Prehar S, Kurita R, Nakamura Y, Baena E, Ledoux J, Oceandy D, Bauer DE, Lettre G | The Journal of clinical investigation | 28714864 | J Clin Invest | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28714864 |
| Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci. | Canver MC, Lessard S, Pinello L, Wu Y, Ilboudo Y, Stern EN, Needleman AJ, Galactéros F, Brugnara C, Kutlar A, McKenzie C, Reid M, Chen DD, Das PP, A Cole M, Zeng J, Kurita R, Nakamura Y, Yuan GC, Lettre G, Bauer DE, Orkin SH | Nature genetics | 28218758 | Nat Genet | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28218758 |
| Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM. | Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan GC, Pinello L | Nature communications | 31015418 | Nat Commun | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/31015418 |
| Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells. | Nagpal N, Wang J, Zeng J, Lo E, Moon DH, Luk K, Braun RO, Burroughs LM, Keel SB, Reilly C, Lindsley RC, Wolfe SA, Tai AK, Cahan P, Bauer DE, Fong YW, Agarwal S | Cell stem cell | 32320679 | Cell Stem Cell | 2020 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/32320679 |
| Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation. | Rao S, Yao Y, Bauer DE | Genome medicine | 33691767 | Genome Med | 2021 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/33691767 |
| AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing. | Clement K, Farouni R, Bauer DE, Pinello L | Bioinformatics (Oxford, England) | 29949956 | Bioinformatics | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29949956 |
| Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. | Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI | Nature genetics | 33230299 | Nat Genet | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33230299 |
| Author Correction: Transcription factor competition at the γ-globin promoters controls hemoglobin switching. | Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH | Nature genetics | 33731942 | Nat Genet | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33731942 |
| Highly efficient therapeutic gene editing of human hematopoietic stem cells. | Wu Y, Zeng J, Roscoe BP, Liu P, Yao Q, Lazzarotto CR, Clement K, Cole MA, Luk K, Baricordi C, Shen AH, Ren C, Esrick EB, Manis JP, Dorfman DM, Williams DA, Biffi A, Brugnara C, Biasco L, Brendel C, Pinello L, Tsai SQ, Wolfe SA, Bauer DE | Nature medicine | 30911135 | Nat Med | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30911135 |
| Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis. | Sher F, Hossain M, Seruggia D, Schoonenberg VAC, Yao Q, Cifani P, Dassama LMK, Cole MA, Ren C, Vinjamur DS, Macias-Trevino C, Luk K, McGuckin C, Schupp PG, Canver MC, Kurita R, Nakamura Y, Fujiwara Y, Wolfe SA, Pinello L, Maeda T, Kentsis A, Orkin SH, Bauer DE | Nature genetics | 31253978 | Nat Genet | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31253978 |
| ZNF410 represses fetal globin by singular control of CHD4. | Vinjamur DS, Yao Q, Cole MA, McGuckin C, Ren C, Zeng J, Hossain M, Luk K, Wolfe SA, Pinello L, Bauer DE | Nature genetics | 33859416 | Nat Genet | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33859416 |
| Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. | Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S | Blood advances | 33938942 | Blood Adv | 2021 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33938942 |
| Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program. | Wheeler MM, Stilp AM, Rao S, Halldórsson BV, Beyter D, Wen J, Mihkaylova AV, McHugh CP, Lane J, Jiang MZ, Raffield LM, Jun G, Sedlazeck FJ, Metcalf G, Yao Y, Bis JB, Chami N, de Vries PS, Desai P, Floyd JS, Gao Y, Kammers K, Kim W, Moon JY, Ratan A, Yanek LR, Almasy L, Becker LC, Blangero J, Cho MH, Curran JE, Fornage M, Kaplan RC, Lewis JP, Loos RJF, Mitchell BD, Morrison AC, Preuss M, Psaty BM, Rich SS, Rotter JI, Tang H, Tracy RP, Boerwinkle E, Abecasis GR, Blackwell TW, Smith AV, Johnson AD, Mathias RA, Nickerson DA, Conomos MP, Li Y, Þorsteinsdóttir U, Magnússon MK, Stefansson K, Pankratz ND, Bauer DE, Auer PL, Reiner AP | Nature communications | 36481753 | Nat Commun | 2022 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/36481753 |
| Whole-genome sequencing association analysis of quantitative red blood cell phenotypes: The NHLBI TOPMed program. | Hu Y, Stilp AM, McHugh CP, Rao S, Jain D, Zheng X, Lane J, Méric de Bellefon S, Raffield LM, Chen MH, Yanek LR, Wheeler M, Yao Y, Ren C, Broome J, Moon JY, de Vries PS, Hobbs BD, Sun Q, Surendran P, Brody JA, Blackwell TW, Choquet H, Ryan K, Duggirala R, Heard-Costa N, Wang Z, Chami N, Preuss MH, Min N, Ekunwe L, Lange LA, Cushman M, Faraday N, Curran JE, Almasy L, Kundu K, Smith AV, Gabriel S, Rotter JI, Fornage M, Lloyd-Jones DM, Vasan RS, Smith NL, North KE, Boerwinkle E, Becker LC, Lewis JP, Abecasis GR, Hou L, O'Connell JR, Morrison AC, Beaty TH, Kaplan R, Correa A, Blangero J, Jorgenson E, Psaty BM, Kooperberg C, Walton RT, Kleinstiver BP, Tang H, Loos RJF, Soranzo N, Butterworth AS, Nickerson D, Rich SS, Mitchell BD, Johnson AD, Auer PL, Li Y, Mathias RA, Lettre G, Pankratz N, Laurie CC, Laurie CA, Bauer DE, Conomos MP, Reiner AP, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium | American journal of human genetics | 33887194 | Am J Hum Genet | 2021 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/33887194 |
| Motif-Raptor: a cell type-specific and transcription factor centric approach for post-GWAS prioritization of causal regulators. | Yao Q, Ferragina P, Reshef Y, Lettre G, Bauer DE, Pinello L | Bioinformatics (Oxford, England) | 33532840 | Bioinformatics | 2021 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/33532840 |
| An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. | Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK | Nature biotechnology | 30059493 | Nat Biotechnol | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30059493 |
| CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis. | Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE | Genome biology | 30340514 | Genome Biol | 2018 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/30340514 |
| Transcription factor competition at the γ-globin promoters controls hemoglobin switching. | Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH | Nature genetics | 33649594 | Nat Genet | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33649594 |
| Spatial presentation of biological molecules to cells by localized diffusive transfer. | Regier MC, Olszewski E, Carter CC, Aitchison JD, Kaushansky A, Davis J, Berthier E, Beebe DJ, Stevens KR | Lab on a chip | 31111131 | Lab Chip | 2019 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/31111131 |
| User-defined morphogen patterning for directing human cell fate stratification. | Regier MC, Tokar JJ, Warrick JW, Pabon L, Berthier E, Beebe DJ, Stevens KR | Scientific reports | 31015521 | Sci Rep | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/31015521 |
| Human Organ-Specific Endothelial Cell Heterogeneity. | Marcu R, Choi YJ, Xue J, Fortin CL, Wang Y, Nagao RJ, Xu J, MacDonald JW, Bammler TK, Murry CE, Muczynski K, Stevens KR, Himmelfarb J, Schwartz SM, Zheng Y | iScience | 30240741 | iScience | 2018 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/30240741 |
| Photopatterned biomolecule immobilization to guide three-dimensional cell fate in natural protein-based hydrogels. | Batalov I, Stevens KR, DeForest CA | Proceedings of the National Academy of Sciences of the United States of America | 33468675 | Proc Natl Acad Sci U S A | 2021 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/33468675 |
| Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates. | Kinstlinger IS, Saxton SH, Calderon GA, Ruiz KV, Yalacki DR, Deme PR, Rosenkrantz JE, Louis-Rosenberg JD, Johansson F, Janson KD, Sazer DW, Panchavati SS, Bissig KD, Stevens KR, Miller JS | Nature biomedical engineering | 32601395 | Nat Biomed Eng | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32601395 |
| Author Correction: Generation of model tissues with dendritic vascular networks via sacrificial laser-sintered carbohydrate templates. | Kinstlinger IS, Saxton SH, Calderon GA, Ruiz KV, Yalacki DR, Deme PR, Rosenkrantz JE, Louis-Rosenberg JD, Johansson F, Janson KD, Sazer DW, Panchavati SS, Bissig KD, Stevens KR, Miller JS | Nature biomedical engineering | 34135476 | Nat Biomed Eng | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34135476 |
| Thermofluidic heat exchangers for actuation of transcription in artificial tissues. | Corbett DC, Fabyan WB, Grigoryan B, O'Connor CE, Johansson F, Batalov I, Regier MC, DeForest CA, Miller JS, Stevens KR | Science advances | 32998880 | Sci Adv | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32998880 |
| Infarct Collagen Topography Regulates Fibroblast Fate via p38-Yes-Associated Protein Transcriptional Enhanced Associate Domain Signals. | Bugg D, Bretherton R, Kim P, Olszewski E, Nagle A, Schumacher AE, Chu N, Gunaje J, DeForest CA, Stevens K, Kim DH, Davis J | Circulation research | 32883176 | Circ Res | 2020 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/32883176 |
| Human Pluripotent Stem Cell-Derived Engineered Tissues: Clinical Considerations. | Stevens KR, Murry CE | Cell stem cell | 29499147 | Cell Stem Cell | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29499147 |
| Multivascular networks and functional intravascular topologies within biocompatible hydrogels. | Grigoryan B, Paulsen SJ, Corbett DC, Sazer DW, Fortin CL, Zaita AJ, Greenfield PT, Calafat NJ, Gounley JP, Ta AH, Johansson F, Randles A, Rosenkrantz JE, Louis-Rosenberg JD, Galie PA, Stevens KR, Miller JS | Science (New York, N.Y.) | 31048486 | Science | 2019 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/31048486 |
| A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives. | El-Nachef D, Shi K, Beussman KM, Martinez R, Regier MC, Everett GW, Murry CE, Stevens KR, Young JE, Sniadecki NJ, Davis J | Stem cell reports | 32619493 | Stem Cell Reports | 2020 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/32619493 |
| Engineering Heart Morphogenesis. | Mandrycky CJ, Williams NP, Batalov I, El-Nachef D, de Bakker BS, Davis J, Kim DH, DeForest CA, Zheng Y, Stevens KR, Sniadecki NJ | Trends in biotechnology | 32673587 | Trends Biotechnol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32673587 |
| Embryo-scale, single-cell spatial transcriptomics. | Srivatsan SR, Regier MC, Barkan E, Franks JM, Packer JS, Grosjean P, Duran M, Saxton S, Ladd JJ, Spielmann M, Lois C, Lampe PD, Shendure J, Stevens KR, Trapnell C | Science (New York, N.Y.) | 34210887 | Science | 2021 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/34210887 |
| A FRESH Take on Resolution in 3D Bioprinting. | Corbett DC, Olszewski E, Stevens K | Trends in biotechnology | 31623960 | Trends Biotechnol | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31623960 |
| Guided vascularization in the rat heart leads to transient vessel patterning. | Brady EL, Kirby MA, Olszewski E, Grosjean P, Johansson F, Davis J, Wang RK, Stevens KR | APL bioengineering | 32161835 | APL Bioeng | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32161835 |
| Engineered tissue vascularization and engraftment depends on host model. | Brady EL, Prado O, Johansson F, Mitchell SN, Martinson AM, Karbassi E, Reinecke H, Murry CE, Davis J, Stevens KR | Scientific reports | 36737618 | Sci Rep | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/36737618 |
| Assessing the Physiological Relevance of Cough Simulators for Respiratory Droplet Dispersion. | Patel SH, Yim W, Garg AK, Shah SH, Jokerst JV, Chao DL | Journal of clinical medicine | 32957639 | J Clin Med | 2020 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/32957639 |
| Multispectral Nanoparticle Tracking Analysis for the Real-Time and Label-Free Characterization of Amyloid-β Self-Assembly In Vitro. | Moore C, Wing R, Pham T, Jokerst JV | Analytical chemistry | 32786456 | Anal Chem | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32786456 |
| Smart-Dust-Nanorice for Enhancement of Endogenous Raman Signal, Contrast in Photoacoustic Imaging, and T2-Shortening in Magnetic Resonance Imaging. | Pohling C, Campbell JL, Larson TA, Van de Sompel D, Levi J, Bachmann MH, Bohndiek SE, Jokerst JV, Gambhir SS | Small (Weinheim an der Bergstrasse, Germany) | 29635739 | Small | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29635739 |
| Photoacoustic Imaging for Noninvasive Periodontal Probing Depth Measurements. | Lin CY, Chen F, Hariri A, Chen CJ, Wilder-Smith P, Takesh T, Jokerst JV | Journal of dental research | 28880116 | J Dent Res | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28880116 |
| Enhanced Performance of a Molecular Photoacoustic Imaging Agent by Encapsulation in Mesoporous Silicon Nanoparticles. | Kang J, Kim D, Wang J, Han Y, Zuidema JM, Hariri A, Park JH, Jokerst JV, Sailor MJ | Advanced materials (Deerfield Beach, Fla.) | 29782671 | Adv Mater | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29782671 |
| A Mechanistic Investigation of Methylene Blue and Heparin Interactions and Their Photoacoustic Enhancement. | Wang J, Jeevarathinam AS, Humphries K, Jhunjhunwala A, Chen F, Hariri A, Miller BR 3rd, Jokerst JV | Bioconjugate chemistry | 30281976 | Bioconjug Chem | 2018 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/30281976 |
| Switchable Photoacoustic Intensity of Methylene Blue via Sodium Dodecyl Sulfate Micellization. | Wang J, Lin CY, Moore C, Jhunjhunwala A, Jokerst JV | Langmuir : the ACS journal of surfaces and colloids | 29232146 | Langmuir | 2018 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/29232146 |
| A cellulose-based photoacoustic sensor to measure heparin concentration and activity in human blood samples. | Jeevarathinam AS, Pai N, Huang K, Hariri A, Wang J, Bai Y, Wang L, Hancock T, Keys S, Penny W, Jokerst JV | Biosensors & bioelectronics | 30602265 | Biosens Bioelectron | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30602265 |
| Development of a Trimodal Contrast Agent for Acoustic and Magnetic Particle Imaging of Stem Cells. | Lemaster JE, Chen F, Kim T, Hariri A, Jokerst JV | ACS applied nano materials | 33860154 | ACS Appl Nano Mater | 2018 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/33860154 |
| A Wearable Colorimetric Dosimeter to Monitor Sunlight Exposure. | Wang J, Jeevarathinam AS, Jhunjhunwala A, Ren H, Lemaster J, Luo Y, Fenning DP, Fullerton EE, Jokerst JV | Advanced materials technologies | 33928184 | Adv Mater Technol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33928184 |
| Ultrasmall gold nanorod-polydopamine hybrids for enhanced photoacoustic imaging and photothermal therapy in second near-infrared window. | Yim W, Borum RM, Zhou J, Mantri Y, Wu Z, Zhou J, Jin Z, Creyer M, Jokerst JV | Nanotheranostics | 34976582 | Nanotheranostics | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34976582 |
| A Photoacoustic-Fluorescent Imaging Probe for Proteolytic Gingipains Expressed by Porphyromonas gingivalis. | Moore C, Cheng Y, Tjokro N, Zhang B, Kerr M, Hayati M, Chang KCJ, Shah N, Chen C, Jokerst JV | Angewandte Chemie (International ed. in English) | 35583940 | Angew Chem Int Ed Engl | 2022 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/35583940 |
| A fiber optic photoacoustic sensor for real-time heparin monitoring. | Zhou J, Yim W, Zhou J, Jin Z, Xu M, Mantri Y, He T, Cheng Y, Fu L, Wu Z, Hancock T, Penny W, Jokerst JV | Biosensors & bioelectronics | 34653712 | Biosens Bioelectron | 2022 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/34653712 |
| Enhanced Photoacoustic Detection of Heparin in Whole Blood via Melanin Nanocapsules Carrying Molecular Agents. | Yim W, Takemura K, Zhou J, Zhou J, Jin Z, Borum RM, Xu M, Cheng Y, He T, Penny W, Miller BR 3rd, Jokerst JV | ACS nano | 34962765 | ACS Nano | 2022 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/34962765 |
| Optics-Free, Non-Contact Measurements of Fluids, Bubbles, and Particles in Microchannels Using Metallic Nano-Islands on Graphene. | Dhong C, Edmunds SJ, Ramírez J, Kayser LV, Chen F, Jokerst JV, Lipomi DJ | Nano letters | 30024767 | Nano Lett | 2018 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/30024767 |
| Photoacoustic imaging for monitoring periodontal health: A first human study. | Moore C, Bai Y, Hariri A, Sanchez JB, Lin CY, Koka S, Sedghizadeh P, Chen C, Jokerst JV | Photoacoustics | 30450281 | Photoacoustics | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30450281 |
| Photoacoustic Imaging of Human Mesenchymal Stem Cells Labeled with Prussian Blue-Poly(l-lysine) Nanocomplexes. | Kim T, Lemaster JE, Chen F, Li J, Jokerst JV | ACS nano | 28759195 | ACS Nano | 2017 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/28759195 |
| Listening for the therapeutic window: Advances in drug delivery utilizing photoacoustic imaging. | Moore C, Chen F, Wang J, Jokerst JV | Advanced drug delivery reviews | 31295522 | Adv Drug Deliv Rev | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31295522 |
| Noninvasive staging of pressure ulcers using photoacoustic imaging. | Hariri A, Chen F, Moore C, Jokerst JV | Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society | 31301258 | Wound Repair Regen | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31301258 |
| Tuning the ultrasonic and photoacoustic response of polydopamine-stabilized perfluorocarbon contrast agents. | Xie Y, Wang J, Wang J, Hu Z, Hariri A, Tu N, Krug KA, Burkart MD, Gianneschi NC, Jokerst JV, Rinehart JD | Journal of materials chemistry. B | 31389967 | J Mater Chem B | 2019 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/31389967 |
| Strategies for Image-Guided Therapy, Surgery, and Drug Delivery Using Photoacoustic Imaging. | Moore C, Jokerst JV | Theranostics | 31037123 | Theranostics | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31037123 |
| Stem Cell Tracking with Nanoparticle-Based Ultrasound Contrast Agents. | Chen F, Jokerst JV | Methods in molecular biology (Clifton, N.J.) | 32112386 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32112386 |
| Synthesis of Ultrasmall Synthetic Melanin Nanoparticles by UV Irradiation in Acidic and Neutral Conditions. | Lemaster JE, Jeevarathinam AS, Kumar A, Chandrasekar B, Chen F, Jokerst JV | ACS applied bio materials | 31930189 | ACS Appl Bio Mater | 2019 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/31930189 |
| Photoacoustic Imaging Quantifies Drug Release from Nanocarriers via Redox Chemistry of Dye-Labeled Cargo. | Jeevarathinam AS, Lemaster JE, Chen F, Zhao E, Jokerst JV | Angewandte Chemie (International ed. in English) | 31840357 | Angew Chem Int Ed Engl | 2020 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/31840357 |
| Activatable Carbocyanine Dimers for Photoacoustic and Fluorescent Detection of Protease Activity. | Moore C, Borum RM, Mantri Y, Xu M, Fajtová P, O'Donoghue AJ, Jokerst JV | ACS sensors | 34038103 | ACS Sens | 2021 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/34038103 |
| Gadolinium Doping Enhances the Photoacoustic Signal of Synthetic Melanin Nanoparticles: A Dual Modality Contrast Agent for Stem Cell Imaging. | Lemaster JE, Wang Z, Hariri A, Chen F, Hu Z, Huang Y, Barback CV, Cochran R, Gianneschi NC, Jokerst JV | Chemistry of materials : a publication of the American Chemical Society | 33859455 | Chem Mater | 2019 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/33859455 |
| Gold Nanorod-Melanin Hybrids for Enhanced and Prolonged Photoacoustic Imaging in the Near-Infrared-II Window. | Yim W, Zhou J, Mantri Y, Creyer MN, Moore CA, Jokerst JV | ACS applied materials & interfaces | 33761255 | ACS Appl Mater Interfaces | 2021 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/33761255 |
| Motion-compensated noninvasive periodontal health monitoring using handheld and motor-based photoacoustic-ultrasound imaging systems. | Mozaffarzadeh M, Moore C, Golmoghani EB, Mantri Y, Hariri A, Jorns A, Fu L, Verweij MD, Orooji M, de Jong N, Jokerst JV | Biomedical optics express | 33796371 | Biomed Opt Express | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/33796371 |
| Silicon Carbide Nanoparticles as a Photoacoustic and Photoluminescent Dual-Imaging Contrast Agent for Long-Term Cell Tracking. | Chen F, Zhao ER, Hu T, Shi Y, Sirbuly DJ, Jokerst JV | Nanoscale advances | 33313479 | Nanoscale Adv | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/33313479 |
| Increasing the Efficacy of Stem Cell Therapy via Triple-Function Inorganic Nanoparticles. | Chen F, Zhao ER, Hableel G, Hu T, Kim T, Li J, Gonzalez-Pech NI, Cheng DJ, Lemaster JE, Xie Y, Grassian VH, Sen GL, Jokerst JV | ACS nano | 31188564 | ACS Nano | 2019 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/31188564 |
| Photoacoustic imaging with fiber optic technology: A review. | Zhou J, Jokerst JV | Photoacoustics | 33163358 | Photoacoustics | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33163358 |
| Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging. | Borum RM , Jokerst JV | Biomaterials science | 32734995 | Biomater Sci | 2021 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/32734995 |
| Assessment of Respiratory Droplet Transmission During the Ophthalmic Slit-Lamp Exam: A Particle Tracking Analysis. | Shah SH, Garg AK, Patel S, Yim W, Jokerst JV, Chao DL | American journal of ophthalmology | 32980331 | Am J Ophthalmol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32980331 |
| Supramolecular Loading of DNA Hydrogels with Dye-Drug Conjugates for Real-Time Photoacoustic Monitoring of Chemotherapy. | Borum RM, Moore C, Mantri Y, Xu M, Jokerst JV | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 36403233 | Adv Sci (Weinh) | 2022 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/36403233 |
| Exosome-like silica nanoparticles: a novel ultrasound contrast agent for stem cell imaging. | Chen F, Ma M, Wang J, Wang F, Chern SX, Zhao ER, Jhunjhunwala A, Darmadi S, Chen H, Jokerst JV | Nanoscale | 27924340 | Nanoscale | 2017 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/27924340 |
| The characterization of an economic and portable LED-based photoacoustic imaging system to facilitate molecular imaging. | Hariri A, Lemaster J, Wang J, Jeevarathinam AS, Chao DL, Jokerst JV | Photoacoustics | 29234601 | Photoacoustics | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29234601 |
| The development and characterization of a novel yet simple 3D printed tool to facilitate phantom imaging of photoacoustic contrast agents. | Arconada-Alvarez SJ, Lemaster JE, Wang J, Jokerst JV | Photoacoustics | 28239554 | Photoacoustics | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28239554 |
| A Nanoscale Tool for Photoacoustic-Based Measurements of Clotting Time and Therapeutic Drug Monitoring of Heparin. | Wang J, Chen F, Arconada-Alvarez SJ, Hartanto J, Yap LP, Park R, Wang F, Vorobyova I, Dagliyan G, Conti PS, Jokerst JV | Nano letters | 27668964 | Nano Lett | 2016 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/27668964 |
| KN95 and N95 Respirators Retain Filtration Efficiency despite a Loss of Dipole Charge during Decontamination. | Yim W, Cheng D, Patel SH, Kou R, Meng YS, Jokerst JV | ACS applied materials & interfaces | 33253527 | ACS Appl Mater Interfaces | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33253527 |
| Copper Sulfide Nanodisks and Nanoprisms for Photoacoustic Ovarian Tumor Imaging. | Wang J, Hsu SW, Gonzalez-Pech N, Jhunjhunwala A, Chen F, Hariri A, Grassian V, Tao A, Jokerst JV | Particle & particle systems characterization : measurement and description of particle properties and behavior in powders and other disperse systems | 32863594 | Part Part Syst Charact | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32863594 |
| Cellular toxicity of silicon carbide nanomaterials as a function of morphology. | Chen F, Li G, Zhao ER, Li J, Hableel G, Lemaster JE, Bai Y, Sen GL, Jokerst JV | Biomaterials | 29980075 | Biomaterials | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29980075 |
| Molecular imaging of oxidative stress using an LED-based photoacoustic imaging system. | Hariri A, Zhao E, Jeevarathinam AS, Lemaster J, Zhang J, Jokerst JV | Scientific reports | 31388020 | Sci Rep | 2019 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/31388020 |
| Dictionary learning technique enhances signal in LED-based photoacoustic imaging. | Farnia P, Najafzadeh E, Hariri A, Lavasani SN, Makkiabadi B, Ahmadian A, Jokerst JV | Biomedical optics express | 32499941 | Biomed Opt Express | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32499941 |
| Deep learning improves contrast in low-fluence photoacoustic imaging. | Hariri A, Alipour K, Mantri Y, Schulze JP, Jokerst JV | Biomedical optics express | 32637260 | Biomed Opt Express | 2020 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/32637260 |
| A Photoacoustic Contrast Agent for miR-21 via NIR Fluorescent Hybridization Chain Reaction. | Borum RM, Moore C, Chan SK, Steinmetz NF, Jokerst JV | Bioconjugate chemistry | 34406744 | Bioconjug Chem | 2022 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/34406744 |
| Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers. | Retout M, Mantri Y, Jin Z, Zhou J, Noël G, Donovan B, Yim W, Jokerst JV | ACS nano | 35377141 | ACS Nano | 2022 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/35377141 |
| Organosilica Nanoparticles with an Intrinsic Secondary Amine: An Efficient and Reusable Adsorbent for Dyes. | Chen F, Zhao E, Kim T, Wang J, Hableel G, Reardon PJT, Ananthakrishna SJ, Wang T, Arconada-Alvarez S, Knowles JC, Jokerst JV | ACS applied materials & interfaces | 28422482 | ACS Appl Mater Interfaces | 2017 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/28422482 |
| Versatile Polymer Nanocapsules via Redox Competition. | Zhou J, Xu M, Jin Z, Borum RM, Avakyan N, Cheng Y, Yim W, He T, Zhou J, Wu Z, Mantri Y, Jokerst JV | Angewandte Chemie (International ed. in English) | 34580967 | Angew Chem Int Ed Engl | 2021 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/34580967 |
| The in vivo fate of tobacco mosaic virus nanoparticle theranostic agents modified by the addition of a polydopamine coat. | Nkanga CI, Chung YH, Shukla S, Zhou J, Jokerst JV, Steinmetz NF | Biomaterials science | 34591046 | Biomater Sci | 2021 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/34591046 |
| Engineering Plasmonic Nanoparticles for Enhanced Photoacoustic Imaging. | Mantri Y, Jokerst JV | ACS nano | 32806027 | ACS Nano | 2020 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/32806027 |
| Iodide-doped precious metal nanoparticles: measuring oxidative stress in vivo via photoacoustic imaging. | Mantri Y, Davidi B, Lemaster JE, Hariri A, Jokerst JV | Nanoscale | 32396928 | Nanoscale | 2020 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/32396928 |
| Robust and Versatile Coatings Engineered via Simultaneous Covalent and Noncovalent Interactions. | Zhou J, Penna M, Lin Z, Han Y, Lafleur RPM, Qu Y, Richardson JJ, Yarovsky I, Jokerst JV, Caruso F | Angewandte Chemie (International ed. in English) | 34258845 | Angew Chem Int Ed Engl | 2021 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/34258845 |
| Stereoselective Growth of Small Molecule Patches on Nanoparticles. | Zhou J, Creyer MN, Chen A, Yim W, Lafleur RPM, He T, Lin Z, Xu M, Abbasi P, Wu J, Pascal TA, Caruso F, Jokerst JV | Journal of the American Chemical Society | 34270250 | J Am Chem Soc | 2021 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/34270250 |
| Multifunctional nanomedicine with silica: Role of silica in nanoparticles for theranostic, imaging, and drug monitoring. | Chen F, Hableel G, Zhao ER, Jokerst JV | Journal of colloid and interface science | 29510868 | J Colloid Interface Sci | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29510868 |
| A Gold/Silver Hybrid Nanoparticle for Treatment and Photoacoustic Imaging of Bacterial Infection. | Kim T, Zhang Q, Li J, Zhang L, Jokerst JV | ACS nano | 29746090 | ACS Nano | 2018 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/29746090 |
| Simultaneous Enhancement of Photoluminescence, MRI Relaxivity, and CT Contrast by Tuning the Interfacial Layer of Lanthanide Heteroepitaxial Nanoparticles. | He S, Johnson NJJ, Nguyen Huu VA, Cory E, Huang Y, Sah RL, Jokerst JV, Almutairi A | Nano letters | 28657755 | Nano Lett | 2017 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/28657755 |
| Gold nanoparticles to enhance ophthalmic imaging. | Chen F , Si P , de la Zerda A , Jokerst JV , Myung D | Biomaterials science | 33057463 | Biomater Sci | 2021 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/33057463 |
| In vivo photoacoustic imaging of chorioretinal oxygen gradients. | Hariri A, Wang J, Kim Y, Jhunjhunwala A, Chao DL, Jokerst JV | Journal of biomedical optics | 29524321 | J Biomed Opt | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29524321 |
| Synchronization of RF Data in Ultrasound Open Platforms (UOPs) for High-Accuracy and High-Resolution Photoacoustic Tomography Using the "Scissors" Programming Method. | Fu L, Jin Z, Qi B, Yim W, Wu Z, He T, Jokerst JV | IEEE transactions on ultrasonics, ferroelectrics, and frequency control | 35377843 | IEEE Trans Ultrason Ferroelectr Freq Control | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35377843 |
| Phenolic-enabled nanotechnology: versatile particle engineering for biomedicine. | Wu D , Zhou J , Creyer MN , Yim W , Chen Z , Messersmith PB , Jokerst JV | Chemical Society reviews | 33595004 | Chem Soc Rev | 2021 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/33595004 |
| A Protease-Responsive Polymer/Peptide Conjugate and Reversible Assembly of Silver Clusters for the Detection of Porphyromonas gingivalis Enzymatic Activity. | Retout M, Amer L, Yim W, Creyer MN, Lam B, Trujillo DF, Potempa J, O'Donoghue AJ, Chen C, Jokerst JV | ACS nano | 37602819 | ACS Nano | 2023 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/37602819 |
| Polyphenol-stabilized coacervates for enzyme-triggered drug delivery. | Yim W, Jin Z, Chang YC, Brambila C, Creyer MN, Ling C, He T, Li Y, Retout M, Penny WF, Zhou J, Jokerst JV | Nature communications | 39181884 | Nat Commun | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39181884 |
| Activatable Photoacoustic Probe for Imaging Infection: Gold Nanorod Dissociation In Vivo Reports Bacterial Protease Activity. | Retout M, Lepeintre V, Amer L, Yim W, Jokerst JV | ACS nano | 40116426 | ACS Nano | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40116426 |
| Erythrocytes lacking the Langereis blood group protein ABCB6 are resistant to the malaria parasite Plasmodium falciparum. | Egan ES, Weekes MP, Kanjee U, Manzo J, Srinivasan A, Lomas-Francis C, Westhoff C, Takahashi J, Tanaka M, Watanabe S, Brugnara C, Gygi SP, Tani Y, Duraisingh MT | Communications biology | 30271928 | Commun Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30271928 |
| Cryo-electron tomography with mixed-scale dense neural networks reveals key steps in deployment of Toxoplasma invasion machinery. | Segev-Zarko LA, Dahlberg PD, Sun SY, Pelt DM, Kim CY, Egan ES, Sethian JA, Chiu W, Boothroyd JC | PNAS nexus | 36329726 | PNAS Nexus | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36329726 |
| Cryogenic electron tomography reveals novel structures in the apical complex of Plasmodium falciparum. | Sun SY, Segev-Zarko L-a, Pintilie GD, Kim CY, Staggers SR, Schmid MF, Egan ES, Chiu W, Boothroyd JC | mBio | 38456679 | mBio | 2024 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/38456679 |
| Beyond Hemoglobin: Screening for Malaria Host Factors. | Egan ES | Trends in genetics : TIG | 29249333 | Trends Genet | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29249333 |
| Erythrocyte CD55 mediates the internalization of Plasmodium falciparum parasites. | Shakya B, Patel SD, Tani Y, Egan ES | eLife | 34028351 | Elife | 2021 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/34028351 |
| Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy. | Ebel ER, Uricchio LH, Petrov DA, Egan ES | Trends in parasitology | 35065882 | Trends Parasitol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35065882 |
| A common polymorphism in the mechanosensitive ion channel PIEZO1 is associated with protection from severe malaria in humans. | Nguetse CN, Purington N, Ebel ER, Shakya B, Tetard M, Kremsner PG, Velavan TP, Egan ES | Proceedings of the National Academy of Sciences of the United States of America | 32265284 | Proc Natl Acad Sci U S A | 2020 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/32265284 |
| Plasmodium falciparum exploits CD44 as a coreceptor for erythrocyte invasion. | Baro B, Kim CY, Lin C, Kongsomboonvech AK, Tetard M, Peterson NA, Salinas ND, Tolia NH, Egan ES | Blood | 37832027 | Blood | 2023 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/37832027 |
| Uncovering a Cryptic Site of Malaria Pathogenesis: Models to Study Interactions Between Plasmodium and the Bone Marrow. | Feldman TP, Egan ES | Frontiers in cellular and infection microbiology | 35719356 | Front Cell Infect Microbiol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35719356 |
| Understanding and repurposing CRISPR-mediated alternative splicing. | Smith JL, Mou H, Xue W | Genome biology | 30400804 | Genome Biol | 2018 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/30400804 |
| Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. | Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG | Nature chemical biology | 29377001 | Nat Chem Biol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29377001 |
| Combinatorial design of nanoparticles for pulmonary mRNA delivery and genome editing. | Li B, Manan RS, Liang SQ, Gordon A, Jiang A, Varley A, Gao G, Langer R, Xue W, Anderson D | Nature biotechnology | 36997680 | Nat Biotechnol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36997680 |
| Targeted genome editing with a DNA-dependent DNA polymerase and exogenous DNA-containing templates. | Liu B, Dong X, Zheng C, Keener D, Chen Z, Cheng H, Watts JK, Xue W, Sontheimer EJ | Nature biotechnology | 37709915 | Nat Biotechnol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37709915 |
| Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. | Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA | Nature methods | 37156841 | Nat Methods | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37156841 |
| Template-jumping prime editing enables large insertion and exon rewriting in vivo. | Zheng C, Liu B, Dong X, Gaston N, Sontheimer EJ, Xue W | Nature communications | 37291100 | Nat Commun | 2023 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/37291100 |
| AAV5 Delivery of CRISPR/Cas9 Mediates Genome Editing in the Lungs of Young Rhesus Monkeys. | Liang SQ, Navia AW, Ramseier M, Zhou X, Martinez M, Lee C, Zhou C, Wu J, Xie J, Su Q, Wang D, Flotte TR, Anderson DG, Tarantal AF, Shalek AK, Gao G, Xue W | Human gene therapy | 38767512 | Hum Gene Ther | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38767512 |
| A Compact, High-Accuracy Cas9 with a Dinucleotide PAM for In Vivo Genome Editing. | Edraki A, Mir A, Ibraheim R, Gainetdinov I, Yoon Y, Song CQ, Cao Y, Gallant J, Xue W, Rivera-Pérez JA, Sontheimer EJ | Molecular cell | 30581144 | Mol Cell | 2019 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/30581144 |
| Genome-Wide CRISPR Screen Identifies Regulators of Mitogen-Activated Protein Kinase as Suppressors of Liver Tumors in Mice. | Song CQ, Li Y, Mou H, Moore J, Park A, Pomyen Y, Hough S, Kennedy Z, Fischer A, Yin H, Anderson DG, Conte D Jr, Zender L, Wang XW, Thorgeirsson S, Weng Z, Xue W | Gastroenterology | 27956228 | Gastroenterology | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27956228 |
| Tissue-restricted genome editing in vivo specified by microRNA-repressible anti-CRISPR proteins. | Lee J, Mou H, Ibraheim R, Liang SQ, Liu P, Xue W, Sontheimer EJ | RNA (New York, N.Y.) | 31439808 | RNA | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31439808 |
| Deletion and replacement of long genomic sequences using prime editing. | Jiang T, Zhang XO, Weng Z, Xue W | Nature biotechnology | 34650270 | Nat Biotechnol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34650270 |
| Adenine base editing in an adult mouse model of tyrosinaemia. | Song CQ, Jiang T, Richter M, Rhym LH, Koblan LW, Zafra MP, Schatoff EM, Doman JL, Cao Y, Dow LE, Zhu LJ, Anderson DG, Liu DR, Yin H, Xue W | Nature biomedical engineering | 31740768 | Nat Biomed Eng | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31740768 |
| CRISPR-Cas-related technologies in basic and translational liver research. | Song CQ, Xue W | Nature reviews. Gastroenterology & hepatology | 29443117 | Nat Rev Gastroenterol Hepatol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29443117 |
| Targeting the De Novo Purine Synthesis Pathway Through Adenylosuccinate Lyase Depletion Impairs Liver Cancer Growth by Perturbing Mitochondrial Function. | Jiang T, Sánchez-Rivera FJ, Soto-Feliciano YM, Yang Q, Song CQ, Bhuatkar A, Haynes CM, Hemann MT, Xue W | Hepatology (Baltimore, Md.) | 33336367 | Hepatology | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33336367 |
| YAP1 Withdrawal in Hepatoblastoma Drives Therapeutic Differentiation of Tumor Cells to Functional Hepatocyte-Like Cells. | Smith JL, Rodríguez TC, Mou H, Kwan SY, Pratt H, Zhang XO, Cao Y, Liang S, Ozata DM, Yu T, Yin Q, Hazeltine M, Weng Z, Sontheimer EJ, Xue W | Hepatology (Baltimore, Md.) | 32452550 | Hepatology | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32452550 |
| All-in-one adeno-associated virus delivery and genome editing by Neisseria meningitidis Cas9 in vivo. | Ibraheim R, Song CQ, Mir A, Amrani N, Xue W, Sontheimer EJ | Genome biology | 30231914 | Genome Biol | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/30231914 |
| Advances in CRISPR/Cas-based Gene Therapy in Human Genetic Diseases. | Wu SS, Li QC, Yin CQ, Xue W, Song CQ | Theranostics | 32292501 | Theranostics | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32292501 |
| Depletion of TRRAP Induces p53-Independent Senescence in Liver Cancer by Down-Regulating Mitotic Genes. | Kwan SY, Sheel A, Song CQ, Zhang XO, Jiang T, Dang H, Cao Y, Ozata DM, Mou H, Yin H, Weng Z, Wang XW, Xue W | Hepatology (Baltimore, Md.) | 31188495 | Hepatology | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31188495 |
| AAV5 delivery of CRISPR-Cas9 supports effective genome editing in mouse lung airway. | Liang SQ, Walkey CJ, Martinez AE, Su Q, Dickinson ME, Wang D, Lagor WR, Heaney JD, Gao G, Xue W | Molecular therapy : the journal of the American Society of Gene Therapy | 34695545 | Mol Ther | 2022 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/34695545 |
| Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. | Liang SQ, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, Yang Q, Lee J, Haynes CM, Zhu LJ, Watts JK, Sontheimer EJ, Wolfe SA, Xue W | Nature communications | 35064134 | Nat Commun | 2022 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/35064134 |
| Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice. | Liu P, Liang SQ, Zheng C, Mintzer E, Zhao YG, Ponnienselvan K, Mir A, Sontheimer EJ, Gao G, Flotte TR, Wolfe SA, Xue W | Nature communications | 33837189 | Nat Commun | 2021 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/33837189 |
| A flexible split prime editor using truncated reverse transcriptase improves dual-AAV delivery in mouse liver. | Zheng C, Liang SQ, Liu B, Liu P, Kwan SY, Wolfe SA, Xue W | Molecular therapy : the journal of the American Society of Gene Therapy | 34998953 | Mol Ther | 2022 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/34998953 |
| Multiomics characterization of mouse hepatoblastoma identifies yes-associated protein 1 target genes. | Rodríguez TC, Kwan SY, Smith JL, Dadafarin S, Wu CH, Sontheimer EJ, Xue W | Hepatology (Baltimore, Md.) | 35932276 | Hepatology | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/35932276 |
| CRISPR/Cas9-mediated genome editing induces exon skipping by alternative splicing or exon deletion. | Mou H, Smith JL, Peng L, Yin H, Moore J, Zhang XO, Song CQ, Sheel A, Wu Q, Ozata DM, Li Y, Anderson DG, Emerson CP, Sontheimer EJ, Moore MJ, Weng Z, Xue W | Genome biology | 28615073 | Genome Biol | 2017 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/28615073 |
| Genetic disruption of oncogenic Kras sensitizes lung cancer cells to Fas receptor-mediated apoptosis. | Mou H, Moore J, Malonia SK, Li Y, Ozata DM, Hough S, Song CQ, Smith JL, Fischer A, Weng Z, Green MR, Xue W | Proceedings of the National Academy of Sciences of the United States of America | 28320962 | Proc Natl Acad Sci U S A | 2017 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/28320962 |
| Self-inactivating, all-in-one AAV vectors for precision Cas9 genome editing via homology-directed repair in vivo. | Ibraheim R, Tai PWL, Mir A, Javeed N, Wang J, Rodríguez TC, Namkung S, Nelson S, Khokhar ES, Mintzer E, Maitland S, Chen Z, Cao Y, Tsagkaraki E, Wolfe SA, Wang D, Pai AA, Xue W, Gao G, Sontheimer EJ | Nature communications | 34725353 | Nat Commun | 2021 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/34725353 |
| Cas9-mediated allelic exchange repairs compound heterozygous recessive mutations in mice. | Wang D, Li J, Song CQ, Tran K, Mou H, Wu PH, Tai PWL, Mendonca CA, Ren L, Wang BY, Su Q, Gessler DJ, Zamore PD, Xue W, Gao G | Nature biotechnology | 30102296 | Nat Biotechnol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30102296 |
| The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. | Zhang XO, Fu Y, Mou H, Xue W, Weng Z | PLoS genetics | 30148885 | PLoS Genet | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30148885 |
| In Vivo Genome Editing Partially Restores Alpha1-Antitrypsin in a Murine Model of AAT Deficiency. | Song CQ, Wang D, Jiang T, O'Connor K, Tang Q, Cai L, Li X, Weng Z, Yin H, Gao G, Mueller C, Flotte TR, Xue W | Human gene therapy | 29597895 | Hum Gene Ther | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29597895 |
| Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. | Yin H, Song CQ, Suresh S, Wu Q, Walsh S, Rhym LH, Mintzer E, Bolukbasi MF, Zhu LJ, Kauffman K, Mou H, Oberholzer A, Ding J, Kwan SY, Bogorad RL, Zatsepin T, Koteliansky V, Wolfe SA, Xue W, Langer R, Anderson DG | Nature biotechnology | 29131148 | Nat Biotechnol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29131148 |
| Chemical modifications of adenine base editor mRNA and guide RNA expand its application scope. | Jiang T, Henderson JM, Coote K, Cheng Y, Valley HC, Zhang XO, Wang Q, Rhym LH, Cao Y, Newby GA, Bihler H, Mense M, Weng Z, Anderson DG, McCaffrey AP, Liu DR, Xue W | Nature communications | 32332735 | Nat Commun | 2020 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/32332735 |
| CRISPR-SONIC: targeted somatic oncogene knock-in enables rapid in vivo cancer modeling. | Mou H, Ozata DM, Smith JL, Sheel A, Kwan SY, Hough S, Kucukural A, Kennedy Z, Cao Y, Xue W | Genome medicine | 30987660 | Genome Med | 2019 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/30987660 |
| A split prime editor with untethered reverse transcriptase and circular RNA template. | Liu B, Dong X, Cheng H, Zheng C, Chen Z, Rodríguez TC, Liang SQ, Xue W, Sontheimer EJ | Nature biotechnology | 35379962 | Nat Biotechnol | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35379962 |
| Human monocyte transcriptional profiling identifies IL-18 receptor accessory protein and lactoferrin as novel immune targets in hypertension. | Alexander MR, Norlander AE, Elijovich F, Atreya RV, Gaye A, Gnecco JS, Laffer CL, Galindo CL, Madhur MS | British journal of pharmacology | 29774543 | Br J Pharmacol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29774543 |
| Status of Early-Career Academic Cardiology: A Global Perspective. | Tong CW, Madhur MS, Rzeszut AK, Abdalla M, Abudayyeh I, Alexanderson E, Buber J, Feldman DN, Gopinathannair R, Hira RS, Kates AM, Kessler T, Leung S, Raj SR, Spatz ES, Turner MB, Valente AM, West K, Sivaram CA, Hill JA, Mann DL, Freeman AM | Journal of the American College of Cardiology | 29073958 | J Am Coll Cardiol | 2017 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/29073958 |
| Adaptive immune cells in calcific aortic valve disease. | Raddatz MA, Madhur MS, Merryman WD | American journal of physiology. Heart and circulatory physiology | 31050556 | Am J Physiol Heart Circ Physiol | 2019 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/31050556 |
| Class switching and high-affinity immunoglobulin G production by B cells is dispensable for the development of hypertension in mice. | Chen Y, Dale BL, Alexander MR, Xiao L, Ao M, Pandey AK, Smart CD, Davis GK, Madhur MS | Cardiovascular research | 32609312 | Cardiovasc Res | 2021 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/32609312 |
| LNK deficiency promotes acute aortic dissection and rupture. | Laroumanie F, Korneva A, Bersi MR, Alexander MR, Xiao L, Zhong X, Van Beusecum JP, Chen Y, Saleh MA, McMaster WG, Gavulic KA, Dale BL, Zhao S, Guo Y, Shyr Y, Perrien DS, Cox NJ, Curci JA, Humphrey JD, Madhur MS | JCI insight | 30333305 | JCI Insight | 2018 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/30333305 |
| Evidence for a Causal Role of the SH2B3-β(2)M Axis in Blood Pressure Regulation. | Keefe JA, Hwang SJ, Huan T, Mendelson M, Yao C, Courchesne P, Saleh MA, Madhur MS, Levy D | Hypertension (Dallas, Tex. : 1979) | 30624993 | Hypertension | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30624993 |
| A Single Nucleotide Polymorphism in SH2B3/LNK Promotes Hypertension Development and Renal Damage. | Alexander MR, Hank S, Dale BL, Himmel L, Zhong X, Smart CD, Fehrenbach DJ, Chen Y, Prabakaran N, Tirado B, Centrella M, Ao M, Du L, Shyr Y, Levy D, Madhur MS | Circulation research | 36169218 | Circ Res | 2022 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/36169218 |
| Hypertension: Do Inflammation and Immunity Hold the Key to Solving this Epidemic? | Madhur MS, Elijovich F, Alexander MR, Pitzer A, Ishimwe J, Van Beusecum JP, Patrick DM, Smart CD, Kleyman TR, Kingery J, Peck RN, Laffer CL, Kirabo A | Circulation research | 33793336 | Circ Res | 2021 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/33793336 |
| Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species. | Alexander MR, Schoeder CT, Brown JA, Smart CD, Moth C, Wikswo JP, Capra JA, Meiler J, Chen W, Madhur MS | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 33015868 | FASEB J | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33015868 |
| Critical role of Interleukin 21 and T follicular helper cells in hypertension and vascular dysfunction. | Dale BL, Pandey AK, Chen Y, Smart CD, Laroumanie F, Ao M, Xiao L, Dikalova AE, Dikalov SI, Elijovich F, Foss JD, Barbaro NR, Van Beusecum JP, Deger SM, Alsouqi A, Itani HA, Norlander AE, Alexander MR, Zhao S, Ikizler TA, Algood HMS, Madhur MS | JCI insight | 31013256 | JCI Insight | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/31013256 |
| From Rags to Riches: Moving Beyond RAG1 in Studies of Hypertension. | Madhur MS, Kirabo A, Guzik TJ, Harrison DG | Hypertension (Dallas, Tex. : 1979) | 32078385 | Hypertension | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32078385 |
| Immune profiling of murine cardiac leukocytes identifies triggering receptor expressed on myeloid cells 2 as a novel mediator of hypertensive heart failure. | Smart CD, Fehrenbach DJ, Wassenaar JW, Agrawal V, Fortune NL, Dixon DD, Cottam MA, Hasty AH, Hemnes AR, Doran AC, Gupta DK, Madhur MS | Cardiovascular research | 37314125 | Cardiovasc Res | 2023 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/37314125 |
| A salt-sensing kinase in T lymphocytes, SGK1, drives hypertension and hypertensive end-organ damage. | Norlander AE, Saleh MA, Pandey AK, Itani HA, Wu J, Xiao L, Kang J, Dale BL, Goleva SB, Laroumanie F, Du L, Harrison DG, Madhur MS | JCI insight | 28679951 | JCI Insight | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28679951 |
| Coordinate adaptations of skeletal muscle and kidney to maintain extracellular [K(+)] during K(+)-deficient diet. | McFarlin BE, Chen Y, Priver TS, Ralph DL, Mercado A, Gamba G, Madhur MS, McDonough AA | American journal of physiology. Cell physiology | 32845718 | Am J Physiol Cell Physiol | 2020 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/32845718 |
| COVID-19 and the cardiovascular system: implications for risk assessment, diagnosis, and treatment options. | Guzik TJ, Mohiddin SA, Dimarco A, Patel V, Savvatis K, Marelli-Berg FM, Madhur MS, Tomaszewski M, Maffia P, D'Acquisto F, Nicklin SA, Marian AJ, Nosalski R, Murray EC, Guzik B, Berry C, Touyz RM, Kreutz R, Wang DW, Bhella D, Sagliocco O, Crea F, Thomson EC, McInnes IB | Cardiovascular research | 32352535 | Cardiovasc Res | 2020 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/32352535 |
| Interleukin 17A: Key Player in the Pathogenesis of Hypertension and a Potential Therapeutic Target. | Davis GK, Fehrenbach DJ, Madhur MS | Current hypertension reports | 33666761 | Curr Hypertens Rep | 2021 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/33666761 |
| The immunology of hypertension. | Norlander AE, Madhur MS, Harrison DG | The Journal of experimental medicine | 29247045 | J Exp Med | 2018 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/29247045 |
| Inflammation Resolution in the Cardiovascular System: Arterial Hypertension, Atherosclerosis, and Ischemic Heart Disease. | Gonzalez AL, Dungan MM, Smart CD, Madhur MS, Doran AC | Antioxidants & redox signaling | 37125445 | Antioxid Redox Signal | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37125445 |
| Targeting IL-33/ST2 Signaling Alters Cardiac Structure and Function in Hypertensive Heart Disease. | Wassenaar JW, Smart CD, Fehrenbach DJ, Agrawal V, Dungan MM, Fortune NL, Zhong L, Hemnes AR, Peebles RS Jr, Miller FJ Jr, Doran AC, Madhur MS | JACC. Basic to translational science | 39958476 | JACC Basic Transl Sci | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39958476 |
| Targeted Delivery of Cell Softening Micelles to Schlemm's Canal Endothelial Cells for Treatment of Glaucoma. | Stack T, Vincent M, Vahabikashi A, Li G, Perkumas KM, Stamer WD, Johnson M, Scott E | Small (Weinheim an der Bergstrasse, Germany) | 33015961 | Small | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33015961 |
| Rapid, Scalable Assembly and Loading of Bioactive Proteins and Immunostimulants into Diverse Synthetic Nanocarriers Via Flash Nanoprecipitation. | Allen S, Vincent M, Scott E | Journal of visualized experiments : JoVE | 30148497 | J Vis Exp | 2018 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/30148497 |
| Tailoring Nanostructure Morphology for Enhanced Targeting of Dendritic Cells in Atherosclerosis. | Yi S, Allen SD, Liu YG, Ouyang BZ, Li X, Augsornworawat P, Thorp EB, Scott EA | ACS nano | 27935698 | ACS Nano | 2016 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/27935698 |
| Just add water: hydratable, morphologically diverse nanocarrier powders for targeted delivery. | Bobbala S, Vincent MP, Scott EA | Nanoscale | 34160529 | Nanoscale | 2021 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/34160529 |
| Surface Engineering of FLT4-Targeted Nanocarriers Enhances Cell-Softening Glaucoma Therapy. | Vincent MP, Stack T, Vahabikashi A, Li G, Perkumas KM, Ren R, Gong H, Stamer WD, Johnson M, Scott EA | ACS applied materials & interfaces | 34232612 | ACS Appl Mater Interfaces | 2021 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/34232612 |
| Enhancing subcutaneous injection and target tissue accumulation of nanoparticles via co-administration with macropinocytosis inhibitory nanoparticles (MiNP). | Stack T, Liu Y, Frey M, Bobbala S, Vincent M, Scott E | Nanoscale horizons | 33884386 | Nanoscale Horiz | 2021 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/33884386 |
| On the advancement of polymeric bicontinuous nanospheres toward biomedical applications. | Allen SD, Bobbala S, Karabin NB, Scott EA | Nanoscale horizons | 32254084 | Nanoscale Horiz | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/32254084 |
| Employing bicontinuous-to-micellar transitions in nanostructure morphology for on-demand photo-oxidation responsive cytosolic delivery and off-on cytotoxicity. | Bobbala S, Allen SD, Yi S, Vincent M, Frey M, Karabin NB, Scott EA | Nanoscale | 32090217 | Nanoscale | 2020 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/32090217 |
| Efficacy of benznidazole delivery during Chagas disease nanotherapy is dependent on the nanocarrier morphology. | Scariot DB, Staneviciute A, Machado RRB, Yuk SA, Liu YG, Sharma S, Almunif S, Arona Mbaye EH, Nakamura CV, Engman DM, Scott EA | Biomaterials | 40318604 | Biomaterials | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40318604 |
| Sequential intracellular release of water-soluble cargos from Shell-crosslinked polymersomes. | Du F, Bobbala S, Yi S, Scott EA | Journal of controlled release : official journal of the Controlled Release Society | 29601932 | J Control Release | 2018 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/29601932 |
| Nanocarrier-enhanced intracellular delivery of benznidazole for treatment of Trypanosoma cruzi infection. | Li X, Yi S, Scariot DB, Martinez SJ, Falk BA, Olson CL, Romano PS, Scott EA, Engman DM | JCI insight | 33986194 | JCI Insight | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/33986194 |
| Surface engineered polymersomes for enhanced modulation of dendritic cells during cardiovascular immunotherapy. | Yi S, Zhang X, Sangji H, Liu Y, Allen SD, Xiao B, Bobbala S, Braverman CL, Cai L, Hecker PI, DeBerge M, Thorp EB, Temel RE, Stupp SI, Scott EA | Advanced functional materials | 34335131 | Adv Funct Mater | 2019 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/34335131 |
| An Injectable Hydrogel Platform for Sustained Delivery of Anti-inflammatory Nanocarriers and Induction of Regulatory T Cells in Atherosclerosis. | Yi S, Karabin NB, Zhu J, Bobbala S, Lyu H, Li S, Liu Y, Frey M, Vincent M, Scott EA | Frontiers in bioengineering and biotechnology | 32582667 | Front Bioeng Biotechnol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32582667 |
| Immunotheranostic Polymersomes Modularly Assembled from Tetrablock and Diblock Copolymers with Oxidation-Responsive Fluorescence. | Du F, Liu YG, Scott EA | Cellular and molecular bioengineering | 28989540 | Cell Mol Bioeng | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28989540 |
| Celastrol-loaded PEG-b-PPS nanocarriers as an anti-inflammatory treatment for atherosclerosis. | Allen SD , Liu YG , Kim T , Bobbala S , Yi S , Zhang X , Choi J , Scott EA | Biomaterials science | 30601470 | Biomater Sci | 2019 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/30601470 |
| Induction of Mycobacterium Tuberculosis Lipid-Specific T Cell Responses by Pulmonary Delivery of Mycolic Acid-Loaded Polymeric Micellar Nanocarriers. | Shang S, Kats D, Cao L, Morgun E, Velluto D, He Y, Xu Q, Wang CR, Scott EA | Frontiers in immunology | 30538700 | Front Immunol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30538700 |
| Engineering nanomaterials to address cell-mediated inflammation in atherosclerosis. | Allen S, Liu YG, Scott E | Regenerative engineering and translational medicine | 27135051 | Regen Eng Transl Med | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27135051 |
| Facile assembly and loading of theranostic polymersomes via multi-impingement flash nanoprecipitation. | Allen S, Osorio O, Liu YG, Scott E | Journal of controlled release : official journal of the Controlled Release Society | 28736263 | J Control Release | 2017 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/28736263 |
| Sustained micellar delivery via inducible transitions in nanostructure morphology. | Karabin NB, Allen S, Kwon HK, Bobbala S, Firlar E, Shokuhfar T, Shull KR, Scott EA | Nature communications | 29434200 | Nat Commun | 2018 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/29434200 |
| Super-Resolution Imaging of Self-Assembled Nanocarriers Using Quantitative Spectroscopic Analysis for Cluster Extraction. | Davis JL, Zhang Y, Yi S, Du F, Song KH, Scott EA, Sun C, Zhang HF | Langmuir : the ACS journal of surfaces and colloids | 32069413 | Langmuir | 2020 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/32069413 |
| Dendritic peptide-conjugated polymeric nanovectors for non-toxic delivery of plasmid DNA and enhanced non-viral transfection of immune cells. | Yi S, Kim SY, Vincent MP, Yuk SA, Bobbala S, Du F, Scott EA | iScience | 35769884 | iScience | 2022 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/35769884 |
| Acute CD47 Blockade During Ischemic Myocardial Reperfusion Enhances Phagocytosis-Associated Cardiac Repair. | Zhang S, Yeap XY, DeBerge M, Naresh NK, Wang K, Jiang Z, Wilcox JE, White SM, Morrow JP, Burridge PW, Procissi D, Scott EA, Frazier W, Thorp EB | JACC. Basic to translational science | 28920097 | JACC Basic Transl Sci | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28920097 |
| The Combination of Morphology and Surface Chemistry Defines the Immunological Identity of Nanocarriers in Human Blood. | Vincent MP, Karabin NB, Allen SD, Bobbala S, Frey MA, Yi S, Yang Y, Scott EA | Advanced therapeutics | 34485684 | Adv Ther (Weinh) | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34485684 |
| Pi-stacking Enhances Stability, Scalability of Formation, Control over Flexibility and Circulation Time of Polymeric Filaments. | Li S, Bobbala S, Vincent MP, Modak M, Liu Y, Scott EA | Advanced nanobiomed research | 34870281 | Adv Nanobiomed Res | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34870281 |
| Subcutaneous nanotherapy repurposes the immunosuppressive mechanism of rapamycin to enhance allogeneic islet graft viability. | Burke JA, Zhang X, Bobbala S, Frey MA, Bohorquez Fuentes C, Freire Haddad H, Allen SD, Richardson RAK, Ameer GA, Scott EA | Nature nanotechnology | 35039683 | Nat Nanotechnol | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35039683 |
| Surface chemistry-mediated modulation of adsorbed albumin folding state specifies nanocarrier clearance by distinct macrophage subsets. | Vincent MP, Bobbala S, Karabin NB, Frey M, Liu Y, Navidzadeh JO, Stack T, Scott EA | Nature communications | 33510170 | Nat Commun | 2021 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/33510170 |
| Influences of nanocarrier morphology on therapeutic immunomodulation. | Frey M, Bobbala S, Karabin N, Scott E | Nanomedicine (London, England) | 30084296 | Nanomedicine (Lond) | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/30084296 |
| Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding. | Du F, Qiao B, Nguyen TD, Vincent MP, Bobbala S, Yi S, Lescott C, Dravid VP, Olvera de la Cruz M, Scott EA | Nature communications | 32994414 | Nat Commun | 2020 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/32994414 |
| Flash nanoprecipitation permits versatile assembly and loading of polymeric bicontinuous cubic nanospheres. | Bobbala S , Allen SD , Scott EA | Nanoscale | 29255814 | Nanoscale | 2018 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/29255814 |
| Modulation of Schlemm's canal endothelial cell stiffness via latrunculin loaded block copolymer micelles. | Stack T, Vahabikashi A, Johnson M, Scott E | Journal of biomedical materials research. Part A | 29468812 | J Biomed Mater Res A | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29468812 |
| Employment of targeted nanoparticles for imaging of cellular processes in cardiovascular disease. | Modak M, Frey MA, Yi S, Liu Y, Scott EA | Current opinion in biotechnology | 32682272 | Curr Opin Biotechnol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32682272 |
| Leveraging self-assembled nanobiomaterials for improved cancer immunotherapy. | Vincent MP, Navidzadeh JO, Bobbala S, Scott EA | Cancer cell | 35148814 | Cancer Cell | 2022 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/35148814 |
| Minimizing Molecular Misidentification in Imaging Low-Abundance Protein Interactions Using Spectroscopic Single-Molecule Localization Microscopy. | Zhang Y, Wang G, Huang P, Sun E, Kweon J, Li Q, Zhe J, Ying LL, Zhang HF | Analytical chemistry | 36165784 | Anal Chem | 2022 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/36165784 |
| Dual Treatment of Chronic Chagasic Cardiomyopathy and Parasitic Burden via Combination Nanotherapy. | Staneviciute A, B Scariot D, Liu YG, Qian Y, Sharma S, Mbaye EHA, Almunif S, Engman DM, Scott EA | ACS nano | 40279477 | ACS Nano | 2025 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/40279477 |
| No sympathy for the hypoxic: the role of fetal oxygenation in autonomic dysfunction. | Hoang JD, Vaseghi M | The Journal of physiology | 29774552 | J Physiol | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29774552 |
| Risk Stratification and Sudden Cardiac Death: Is It Time to Include Autonomic Variables? | Khakpour H, Vaseghi M | Circulation. Cardiovascular imaging | 28794140 | Circ Cardiovasc Imaging | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28794140 |
| Cardiac Sympathetic Denervation for Refractory Ventricular Arrhythmias. | Vaseghi M, Barwad P, Malavassi Corrales FJ, Tandri H, Mathuria N, Shah R, Sorg JM, Gima J, Mandal K, Sàenz Morales LC, Lokhandwala Y, Shivkumar K | Journal of the American College of Cardiology | 28641796 | J Am Coll Cardiol | 2017 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/28641796 |
| Thoracic Epidural Anesthesia Can Be Effective for the Short-Term Management of Ventricular Tachycardia Storm. | Do DH, Bradfield J, Ajijola OA, Vaseghi M, Le J, Rahman S, Mahajan A, Nogami A, Boyle NG, Shivkumar K | Journal of the American Heart Association | 29079570 | J Am Heart Assoc | 2017 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/29079570 |
| A novel mechanism for regulation of cardiac Ca(2+) current by estradiol: cAMP-ing out at the basal epicardium. | Hoang JD, Vaseghi M | Heart rhythm | 29382545 | Heart Rhythm | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29382545 |
| Outcomes of Catheter Ablation of Ventricular Tachycardia Based on Etiology in Nonischemic Heart Disease: An International Ventricular Tachycardia Ablation Center Collaborative Study. | Vaseghi M, Hu TY, Tung R, Vergara P, Frankel DS, Di Biase L, Tedrow UB, Gornbein JA, Yu R, Mathuria N, Nakahara S, Tzou WS, Sauer WH, Burkhardt JD, Tholakanahalli VN, Dickfeld TM, Weiss JP, Bunch TJ, Reddy M, Callans DJ, Lakkireddy DR, Natale A, Marchlinski FE, Stevenson WG, Della Bella P, Shivkumar K | JACC. Clinical electrophysiology | 30236386 | JACC Clin Electrophysiol | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30236386 |
| Update on prevention and treatment of sudden cardiac arrest. | Krokhaleva Y, Vaseghi M | Trends in cardiovascular medicine | 30449537 | Trends Cardiovasc Med | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30449537 |
| Liver Disease as a Predictor of New-Onset Atrial Fibrillation. | Huang WA, Dunipace EA, Sorg JM, Vaseghi M | Journal of the American Heart Association | 30371253 | J Am Heart Assoc | 2018 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/30371253 |
| Cardiac neuroanatomy - Imaging nerves to define functional control. | Hanna P, Rajendran PS, Ajijola OA, Vaseghi M, Andrew Armour J, Ardell JL, Shivkumar K | Autonomic neuroscience : basic & clinical | 28802636 | Auton Neurosci | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28802636 |
| Premature ventricular contractions activate vagal afferents and alter autonomic tone: implications for premature ventricular contraction-induced cardiomyopathy. | Salavatian S, Yamaguchi N, Hoang J, Lin N, Patel S, Ardell JL, Armour JA, Vaseghi M | American journal of physiology. Heart and circulatory physiology | 31322427 | Am J Physiol Heart Circ Physiol | 2019 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/31322427 |
| Cardiac sympathetic denervation for intractable ventricular arrhythmias in Chagas disease. | Saenz LC, Corrales FM, Bautista W, Traina M, Meymandi S, Rodriguez DA, Tellez LJ, Vaseghi M, Garcia F, Shivkumar K, Bradfield JS | Heart rhythm | 26969783 | Heart Rhythm | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26969783 |
| Antiarrhythmic effects of vagal nerve stimulation after cardiac sympathetic denervation in the setting of chronic myocardial infarction. | Yamaguchi N, Yamakawa K, Rajendran PS, Takamiya T, Vaseghi M | Heart rhythm | 29530832 | Heart Rhythm | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29530832 |
| Sex and Race/Ethnicity Differences in Atrial Fibrillation. | Volgman AS, Bairey Merz CN, Benjamin EJ, Curtis AB, Fang MC, Lindley KJ, Pepine CJ, Vaseghi M, Waldo AL, Wenger NK, Russo AM | Journal of the American College of Cardiology | 31779796 | J Am Coll Cardiol | 2019 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/31779796 |
| Cardiac sympathetic activation circumvents high-dose beta blocker therapy in part through release of neuropeptide Y. | Hoang JD, Salavatian S, Yamaguchi N, Swid MA, David H, Vaseghi M | JCI insight | 32493842 | JCI Insight | 2020 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/32493842 |
| European Heart Rhythm Association (EHRA)/Heart Rhythm Society (HRS)/Asia Pacific Heart Rhythm Society (APHRS)/Latin American Heart Rhythm Society (LAHRS) expert consensus on risk assessment in cardiac arrhythmias: use the right tool for the right outcome, in the right population. | Nielsen JC, Lin YJ, de Oliveira Figueiredo MJ, Sepehri Shamloo A, Alfie A, Boveda S, Dagres N, Di Toro D, Eckhardt LL, Ellenbogen K, Hardy C, Ikeda T, Jaswal A, Kaufman E, Krahn A, Kusano K, Kutyifa V, Lim HS, Lip GYH, Nava-Townsend S, Pak HN, Rodríguez Diez G, Sauer W, Saxena A, Svendsen JH, Vanegas D, Vaseghi M, Wilde A, Bunch TJ, ESC Scientific Document Group, Buxton AE, Calvimontes G, Chao TF, Eckardt L, Estner H, Gillis AM, Isa R, Kautzner J, Maury P, Moss JD, Nam GB, Olshansky B, Pava Molano LF, Pimentel M, Prabhu M, Tzou WS, Sommer P, Swampillai J, Vidal A, Deneke T, Hindricks G, Leclercq C | Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology | 32538434 | Europace | 2020 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/32538434 |
| Recurrent ventricular tachycardia after cardiac sympathetic denervation: Prolonged cycle length with improved hemodynamic tolerance and ablation outcomes. | Hayase J, Dusi V, Do D, Ajijola OA, Vaseghi M, Lee JM, Yanagawa J, Hoftman N, Revels S, Buch EF, Khakpour H, Fujimura O, Krokhaleva Y, Macias C, Sorg J, Gima J, Pavez G, Boyle NG, Shivkumar K, Bradfield JS | Journal of cardiovascular electrophysiology | 32558054 | J Cardiovasc Electrophysiol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32558054 |
| Looking Beyond Storm: Forecast Remains Gloomy for Clustered Ventricular Arrhythmias. | Khakpour H, Vaseghi M | JACC. Clinical electrophysiology | 32192685 | JACC Clin Electrophysiol | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32192685 |
| Cardiac sympathetic innervation via middle cervical and stellate ganglia and antiarrhythmic mechanism of bilateral stellectomy. | Irie T, Yamakawa K, Hamon D, Nakamura K, Shivkumar K, Vaseghi M | American journal of physiology. Heart and circulatory physiology | 28011590 | Am J Physiol Heart Circ Physiol | 2017 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/28011590 |
| Parasympathetic dysfunction and antiarrhythmic effect of vagal nerve stimulation following myocardial infarction. | Vaseghi M, Salavatian S, Rajendran PS, Yagishita D, Woodward WR, Hamon D, Yamakawa K, Irie T, Habecker BA, Shivkumar K | JCI insight | 28814663 | JCI Insight | 2017 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/28814663 |
| Arrhythmogenic Right Ventricular Cardiomyopathy: Electroarchitecture of the Substrate. | Watanabe A, Seki A, Fishbein MC, Shivkumar K, Vaseghi M | HeartRhythm case reports | 26955520 | HeartRhythm Case Rep | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26955520 |
| Arrhythmic Risk Profile and Outcomes of Patients Undergoing Cardiac Sympathetic Denervation for Recurrent Monomorphic Ventricular Tachycardia After Ablation. | Dusi V, Gornbein J, Do DH, Sorg JM, Khakpour H, Krokhaleva Y, Ajijola OA, Macias C, Bradfield JS, Buch E, Fujimura OA, Boyle NG, Yanagawa J, Lee JM, Shivkumar K, Vaseghi M | Journal of the American Heart Association | 33441022 | J Am Heart Assoc | 2021 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/33441022 |
| The autonomic nervous system and ventricular arrhythmias in myocardial infarction and heart failure. | Wu P, Vaseghi M | Pacing and clinical electrophysiology : PACE | 31823401 | Pacing Clin Electrophysiol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31823401 |
| Myocardial infarction reduces cardiac nociceptive neurotransmission through the vagal ganglia. | Salavatian S, Hoang JD, Yamaguchi N, Lokhandwala ZA, Swid MA, Armour JA, Ardell JL, Vaseghi M | JCI insight | 35015733 | JCI Insight | 2022 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/35015733 |
| Editorial Commentary: Chronic obstructive pulmonary disease and sudden cardiac death: Cause and effect or simply an association? | Hoffman J, Vaseghi M | Trends in cardiovascular medicine | 27238054 | Trends Cardiovasc Med | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27238054 |
| Microstructural Infarct Border Zone Remodeling in the Post-infarct Swine Heart Measured by Diffusion Tensor MRI. | Kung GL, Vaseghi M, Gahm JK, Shevtsov J, Garfinkel A, Shivkumar K, Ennis DB | Frontiers in physiology | 30246802 | Front Physiol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30246802 |
| Clinical neurocardiology defining the value of neuroscience-based cardiovascular therapeutics. | Shivkumar K, Ajijola OA, Anand I, Armour JA, Chen PS, Esler M, De Ferrari GM, Fishbein MC, Goldberger JJ, Harper RM, Joyner MJ, Khalsa SS, Kumar R, Lane R, Mahajan A, Po S, Schwartz PJ, Somers VK, Valderrabano M, Vaseghi M, Zipes DP | The Journal of physiology | 27114333 | J Physiol | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27114333 |
| Relationship between sinus rhythm late activation zones and critical sites for scar-related ventricular tachycardia: systematic analysis of isochronal late activation mapping. | Irie T, Yu R, Bradfield JS, Vaseghi M, Buch EF, Ajijola O, Macias C, Fujimura O, Mandapati R, Boyle NG, Shivkumar K, Tung R | Circulation. Arrhythmia and electrophysiology | 25740836 | Circ Arrhythm Electrophysiol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25740836 |
| Cardiac Innervation and the Autonomic Nervous System in Sudden Cardiac Death. | Huang WA, Boyle NG, Vaseghi M | Cardiac electrophysiology clinics | 29173409 | Card Electrophysiol Clin | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29173409 |
| Ventricular Tachycardia in Dilated Cardiomyopathy: Is it Time for Genetic Testing in All Patients? | Nguyen HL, Vaseghi M | JACC. Clinical electrophysiology | 32972545 | JACC Clin Electrophysiol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32972545 |
| Chip-based frequency comb sources for optical coherence tomography. | Ji X, Yao X, Klenner A, Gan Y, Gaeta AL, Hendon CP, Lipson M | Optics express | 31503744 | Opt Express | 2019 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/31503744 |
| Compressed sensing-enabled phase-sensitive swept-source optical coherence tomography. | Ling Y, Meiniel W, Singh-Moon R, Angelini E, Olivo-Marin JC, Hendon CP | Optics express | 30696165 | Opt Express | 2019 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/30696165 |
| Optical coherence tomography imaging of cardiac substrates. | Hendon CP, Lye TH, Yao X, Gan Y, Marboe CC | Quantitative imaging in medicine and surgery | 31281782 | Quant Imaging Med Surg | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31281782 |
| Multicontrast endomyocardial imaging by single-channel high-resolution cross-polarization optical coherence tomography. | Yao X, Gan Y, Ling Y, Marboe CC, Hendon CP | Journal of biophotonics | 29165902 | J Biophotonics | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29165902 |
| Automated classification of optical coherence tomography images of human atrial tissue. | Gan Y, Tsay D, Amir SB, Marboe CC, Hendon CP | Journal of biomedical optics | 26926869 | J Biomed Opt | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26926869 |
| Optical coherence tomography holds promise to transform the diagnostic anatomic pathology gross evaluation process. | Mojahed D, Applegate M, Guo H, Taback B, Ha R, Hibshoosh H, Hendon C | Journal of biomedical optics | 36050827 | J Biomed Opt | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36050827 |
| Cardiac endocardial left atrial substrate and lesion depth mapping using near-infrared spectroscopy. | Park SY, Yang H, Marboe C, Ziv O, Laurita K, Rollins A, Saluja D, Hendon CP | Biomedical optics express | 35519253 | Biomed Opt Express | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35519253 |
| Optical coherence tomography-enabled classification of the human venoatrial junction. | Joasil AS, Therien AM, Hendon CP | Journal of biomedical optics | 39840147 | J Biomed Opt | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39840147 |
| Compressed sensing of human breast optical coherence 3-D image volume data using predictive coding. | Song Cho DM, Jerome MJ, Hendon CP | Biomedical optics express | 38021138 | Biomed Opt Express | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/38021138 |
| Monitoring of irrigated lesion formation with single fiber based multispectral system using machine learning. | Park SY, Singh-Moon RP, Yang H, Hendon CP | Journal of biophotonics | 35666015 | J Biophotonics | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35666015 |
| Phase-noise analysis of swept-source optical coherence tomography systems. | Ling Y, Gan Y, Yao X, Hendon CP | Optics letters | 28362762 | Opt Lett | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28362762 |
| Fully Automated Postlumpectomy Breast Margin Assessment Utilizing Convolutional Neural Network Based Optical Coherence Tomography Image Classification Method. | Mojahed D, Ha RS, Chang P, Gan Y, Yao X, Angelini B, Hibshoosh H, Taback B, Hendon CP | Academic radiology | 31324579 | Acad Radiol | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/31324579 |
| Imaging of subendocardial adipose tissue and fiber orientation distributions in the human left atrium using optical coherence tomography. | Lye TH, Marboe CC, Hendon CP | Journal of cardiovascular electrophysiology | 31661178 | J Cardiovasc Electrophysiol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31661178 |
| Collagen Fiber Orientation and Dispersion in the Upper Cervix of Non-Pregnant and Pregnant Women. | Yao W, Gan Y, Myers KM, Vink JY, Wapner RJ, Hendon CP | PloS one | 27898677 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27898677 |
| Cardiac Adipose Tissue Segmentation via Image-Level Annotations. | Huang Z, Gan Y, Lye T, Liu Y, Zhang H, Laine A, Angelini E, Hendon C | IEEE journal of biomedical and health informatics | 37023157 | IEEE J Biomed Health Inform | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37023157 |
| Ex vivo visualization of human ciliated epithelium and quantitative analysis of induced flow dynamics by using optical coherence tomography. | Ling Y, Yao X, Gamm UA, Arteaga-Solis E, Emala CW, Choma MA, Hendon CP | Lasers in surgery and medicine | 28231402 | Lasers Surg Med | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28231402 |
| Myocardial imaging using ultrahigh-resolution spectral domain optical coherence tomography. | Yao X, Gan Y, Marboe CC, Hendon CP | Journal of biomedical optics | 27001162 | J Biomed Opt | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27001162 |
| Analyzing three-dimensional ultrastructure of human cervical tissue using optical coherence tomography. | Gan Y, Yao W, Myers KM, Vink JY, Wapner RJ, Hendon CP | Biomedical optics express | 25908997 | Biomed Opt Express | 2015 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/25908997 |
| Visualization and tissue classification of human breast cancer images using ultrahigh-resolution OCT. | Yao X, Gan Y, Chang E, Hibshoosh H, Feldman S, Hendon C | Lasers in surgery and medicine | 28264146 | Lasers Surg Med | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28264146 |
| An automated 3D registration method for optical coherence tomography volumes. | Gan Y, Yao W, Myers KM, Hendon CP | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 25570837 | Annu Int Conf IEEE Eng Med Biol Soc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25570837 |
| Three-dimensional collagen fiber mapping and tractography of human uterine tissue using OCT. | McLean JP, Fang S, Gallos G, Myers KM, Hendon CP | Biomedical optics express | 33149968 | Biomed Opt Express | 2020 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/33149968 |
| Characterization of the human myocardium by optical coherence tomography. | Gan Y, Lye TH, Marboe CC, Hendon CP | Journal of biophotonics | 31400074 | J Biophotonics | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31400074 |
| Mapping the human pulmonary venoatrial junction with optical coherence tomography. | Lye TH, Iyer V, Marboe CC, Hendon CP | Biomedical optics express | 30800491 | Biomed Opt Express | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30800491 |
| Quantification of irrigated lesion morphology using near-infrared spectroscopy. | Park SY, Singh-Moon R, Yang H, Saluja D, Hendon C | Scientific reports | 34635764 | Sci Rep | 2021 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/34635764 |
| Comparative study of texture features in OCT images at different scales for human breast tissue classification. | Yu Gan, Xinwen Yao, Chang E, Bin Amir S, Hibshoosh H, Feldman S, Hendon CP | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 28269144 | Annu Int Conf IEEE Eng Med Biol Soc | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28269144 |
| Millimeter-scale chip-based supercontinuum generation for optical coherence tomography. | Ji X, Mojahed D, Okawachi Y, Gaeta AL, Hendon CP, Lipson M | Science advances | 34533990 | Sci Adv | 2021 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/34533990 |
| Real-time optical spectroscopic monitoring of nonirrigated lesion progression within atrial and ventricular tissues. | Singh-Moon RP, Yao X, Iyer V, Marboe C, Whang W, Hendon CP | Journal of biophotonics | 30058239 | J Biophotonics | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30058239 |
| Frequency-constrained robust principal component analysis: a sparse representation approach to segmentation of dynamic features in optical coherence tomography imaging. | McLean JP, Ling Y, Hendon CP | Optics express | 29041245 | Opt Express | 2017 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/29041245 |
| Near-infrared spectroscopy integrated catheter for characterization of myocardial tissues: preliminary demonstrations to radiofrequency ablation therapy for atrial fibrillation. | Singh-Moon RP, Marboe CC, Hendon CP | Biomedical optics express | 26203376 | Biomed Opt Express | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/26203376 |
| A continuous fiber distribution material model for human cervical tissue. | Myers KM, Hendon CP, Gan Y, Yao W, Yoshida K, Fernandez M, Vink J, Wapner RJ | Journal of biomechanics | 25817474 | J Biomech | 2015 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/25817474 |
| Highly phase-stable 200 kHz swept-source optical coherence tomography based on KTN electro-optic deflector. | Ling Y, Yao X, Hendon CP | Biomedical optics express | 29082103 | Biomed Opt Express | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/29082103 |
| Heterogeneity Measurement of Cardiac Tissues Leveraging Uncertainty Information from Image Segmentation. | Huang Z, Gan Y, Lye T, Zhang H, Laine A, Angelini ED, Hendon C | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 34169298 | Med Image Comput Comput Assist Interv | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34169298 |
| 3-D compressed sensing optical coherence tomography using predictive coding. | McLean JP, Hendon CP | Biomedical optics express | 33996246 | Biomed Opt Express | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33996246 |
| Tissue-Specific Optical Mapping Models of Swine Atria Informed by Optical Coherence Tomography. | Lye TH, Vincent KP, McCulloch AD, Hendon CP | Biophysical journal | 29590604 | Biophys J | 2018 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/29590604 |
| Feasibility of near-infrared spectroscopy as a tool for anatomical mapping of the human epicardium. | Singh-Moon RP, Park SY, Song Cho DM, Vaidya A, Marboe CC, Wan EY, Hendon CP | Biomedical optics express | 32923031 | Biomed Opt Express | 2020 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/32923031 |
| In Vivo Clonal Analysis of Cardiomyocytes. | Nguyen NB, Fernandez GE, Ding Y, Hsiai T, Ardehali R | Methods in molecular biology (Clifton, N.J.) | 32857378 | Methods Mol Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/32857378 |
| Biomarkers of Human Pluripotent Stem Cell-Derived Cardiac Lineages. | Skelton RJP, Kamp TJ, Elliott DA, Ardehali R | Trends in molecular medicine | 28576602 | Trends Mol Med | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28576602 |
| Arrhythmia in stem cell transplantation. | Almeida SO, Skelton RJ, Adigopula S, Ardehali R | Cardiac electrophysiology clinics | 26002399 | Card Electrophysiol Clin | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26002399 |
| Translational aspects of cardiac cell therapy. | Chen CH, Sereti KI, Wu BM, Ardehali R | Journal of cellular and molecular medicine | 26119413 | J Cell Mol Med | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26119413 |
| Direct cardiac reprogramming: A new frontier in heart regeneration. | Ardehali R | Seminars in cell & developmental biology | 34538519 | Semin Cell Dev Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34538519 |
| Cardiac Light-Sheet Fluorescent Microscopy for Multi-Scale and Rapid Imaging of Architecture and Function. | Fei P, Lee J, Packard RR, Sereti KI, Xu H, Ma J, Ding Y, Kang H, Chen H, Sung K, Kulkarni R, Ardehali R, Kuo CC, Xu X, Ho CM, Hsiai TK | Scientific reports | 26935567 | Sci Rep | 2016 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/26935567 |
| Harnessing the versatility of PLGA nanoparticles for targeted Cre-mediated recombination. | Nguyen NB, Chen CH, Zhang Y, Zhao P, Wu BM, Ardehali R | Nanomedicine : nanotechnology, biology, and medicine | 31026512 | Nanomedicine | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31026512 |
| Genetic Regulation of Fibroblast Activation and Proliferation in Cardiac Fibrosis. | Park S, Ranjbarvaziri S, Lay FD, Zhao P, Miller MJ, Dhaliwal JS, Huertas-Vazquez A, Wu X, Qiao R, Soffer JM, Rau C, Wang Y, Mikkola HKA, Lusis AJ, Ardehali R | Circulation | 29950403 | Circulation | 2018 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/29950403 |
| Direct Cardiac Reprogramming: Progress and Promise. | Engel JL, Ardehali R | Stem cells international | 29731772 | Stem Cells Int | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29731772 |
| Generation of Nkx2-5/CreER transgenic mice for inducible Cre expression in developing hearts. | Ranjbarvaziri S, Park S, Nguyen NB, Gilmore WB, Zhao P, Ardehali R | Genesis (New York, N.Y. : 2000) | 28589709 | Genesis | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28589709 |
| Cardiac fibrosis: potential therapeutic targets. | Park S, Nguyen NB, Pezhouman A, Ardehali R | Translational research : the journal of laboratory and clinical medicine | 30930180 | Transl Res | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30930180 |
| Environmental factors influence somatic cell reprogramming to cardiomyocyte-like cells. | Van Handel B, Wang L, Ardehali R | Seminars in cell & developmental biology | 34083115 | Semin Cell Dev Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34083115 |
| Cardiac Fibrosis Is Associated With Decreased Circulating Levels of Full-Length CILP in Heart Failure. | Park S, Ranjbarvaziri S, Zhao P, Ardehali R | JACC. Basic to translational science | 32478206 | JACC Basic Transl Sci | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32478206 |
| Analysis of cardiomyocyte clonal expansion during mouse heart development and injury. | Sereti KI, Nguyen NB, Kamran P, Zhao P, Ranjbarvaziri S, Park S, Sabri S, Engel JL, Sung K, Kulkarni RP, Ding Y, Hsiai TK, Plath K, Ernst J, Sahoo D, Mikkola HKA, Iruela-Arispe ML, Ardehali R | Nature communications | 29467410 | Nat Commun | 2018 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/29467410 |
| Sendai virus based direct cardiac reprogramming: what lies ahead? | Engel JL, Ardehali R | Stem cell investigation | 30498748 | Stem Cell Investig | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30498748 |
| Heart Regeneration by Endogenous Stem Cells and Cardiomyocyte Proliferation: Controversy, Fallacy, and Progress. | He L, Nguyen NB, Ardehali R, Zhou B | Circulation | 32687441 | Circulation | 2020 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/32687441 |
| HBL1 Is a Human Long Noncoding RNA that Modulates Cardiomyocyte Development from Pluripotent Stem Cells by Counteracting MIR1. | Liu J, Li Y, Lin B, Sheng Y, Yang L | Developmental cell | 28829943 | Dev Cell | 2017 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/28829943 |
| Mechanism of automaticity in cardiomyocytes derived from human induced pluripotent stem cells. | Kim JJ, Yang L, Lin B, Zhu X, Sun B, Kaplan AD, Bett GC, Rasmusson RL, London B, Salama G | Journal of molecular and cellular cardiology | 25644533 | J Mol Cell Cardiol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25644533 |
| HBL1 Is a Human Long Noncoding RNA that Modulates Cardiomyocyte Development from Pluripotent Stem Cells by Counteracting MIR1. | Liu J, Li Y, Lin B, Sheng Y, Yang L | Developmental cell | 29112854 | Dev Cell | 2017 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/29112854 |
| Genome-wide studies reveal the essential and opposite roles of ARID1A in controlling human cardiogenesis and neurogenesis from pluripotent stem cells. | Liu J, Liu S, Gao H, Han L, Chu X, Sheng Y, Shou W, Wang Y, Liu Y, Wan J, Yang L | Genome biology | 32646524 | Genome Biol | 2020 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/32646524 |
| Comparative transcriptomic analysis of multiple cardiovascular fates from embryonic stem cells predicts novel regulators in human cardiogenesis. | Li Y, Lin B, Yang L | Scientific reports | 25997157 | Sci Rep | 2015 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/25997157 |
| Modeling and study of the mechanism of dilated cardiomyopathy using induced pluripotent stem cells derived from individuals with Duchenne muscular dystrophy. | Lin B, Li Y, Han L, Kaplan AD, Ao Y, Kalra S, Bett GC, Rasmusson RL, Denning C, Yang L | Disease models & mechanisms | 25791035 | Dis Model Mech | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25791035 |
| A microphysiological model of the human placental barrier. | Blundell C, Tess ER, Schanzer AS, Coutifaris C, Su EJ, Parry S, Huh D | Lab on a chip | 27229450 | Lab Chip | 2016 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/27229450 |
| Organoids-on-a-chip. | Park SE, Georgescu A, Huh D | Science (New York, N.Y.) | 31171693 | Science | 2019 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/31171693 |
| A microengineered model of RBC transfusion-induced pulmonary vascular injury. | Seo J, Conegliano D, Farrell M, Cho M, Ding X, Seykora T, Qing D, Mangalmurti NS, Huh D | Scientific reports | 28611413 | Sci Rep | 2017 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/28611413 |
| Placental Drug Transport-on-a-Chip: A Microengineered In Vitro Model of Transporter-Mediated Drug Efflux in the Human Placental Barrier. | Blundell C, Yi YS, Ma L, Tess ER, Farrell MJ, Georgescu A, Aleksunes LM, Huh D | Advanced healthcare materials | 29121458 | Adv Healthc Mater | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29121458 |
| Soft robotic constrictor for in vitro modeling of dynamic tissue compression. | Paek J, Song JW, Ban E, Morimitsu Y, Osuji CO, Shenoy VB, Huh DD | Scientific reports | 34389738 | Sci Rep | 2021 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/34389738 |
| In Vitro Granuloma Models of Tuberculosis: Potential and Challenges. | Elkington P, Lerm M, Kapoor N, Mahon R, Pienaar E, Huh D, Kaushal D, Schlesinger LS | The Journal of infectious diseases | 30929010 | J Infect Dis | 2019 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/30929010 |
| Multiscale reverse engineering of the human ocular surface. | Seo J, Byun WY, Alisafaei F, Georgescu A, Yi YS, Massaro-Giordano M, Shenoy VB, Lee V, Bunya VY, Huh D | Nature medicine | 31384041 | Nat Med | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31384041 |
| Placenta-on-a-chip: a novel platform to study the biology of the human placenta. | Lee JS, Romero R, Han YM, Kim HC, Kim CJ, Hong JS, Huh D | The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians | 26075842 | J Matern Fetal Neonatal Med | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26075842 |
| A bioinspired microfluidic model of liquid plug-induced mechanical airway injury. | Song JW, Paek J, Park KT, Seo J, Huh D | Biomicrofluidics | 29887935 | Biomicrofluidics | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29887935 |
| A Human Vascular Injury-on-a-Chip Model of Hemostasis. | Poventud-Fuentes I, Kwon KW, Seo J, Tomaiuolo M, Stalker TJ, Brass LF, Huh D | Small (Weinheim an der Bergstrasse, Germany) | 33150735 | Small | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33150735 |
| Organs-on-chips at the frontiers of drug discovery. | Esch EW, Bahinski A, Huh D | Nature reviews. Drug discovery | 25792263 | Nat Rev Drug Discov | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25792263 |
| Native extracellular matrix-derived semipermeable, optically transparent, and inexpensive membrane inserts for microfluidic cell culture. | Mondrinos MJ, Yi YS, Wu NK, Ding X, Huh D | Lab on a chip | 28809418 | Lab Chip | 2017 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/28809418 |
| Polydopamine-Based Interfacial Engineering of Extracellular Matrix Hydrogels for the Construction and Long-Term Maintenance of Living Three-Dimensional Tissues. | Park SE, Georgescu A, Oh JM, Kwon KW, Huh D | ACS applied materials & interfaces | 31199616 | ACS Appl Mater Interfaces | 2019 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/31199616 |
| Geometric engineering of organoid culture for enhanced organogenesis in a dish. | Park SE, Kang S, Paek J, Georgescu A, Chang J, Yi AY, Wilkins BJ, Karakasheva TA, Hamilton KE, Huh DD | Nature methods | 36280722 | Nat Methods | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36280722 |
| Self-organization of the hematopoietic vascular niche and emergent innate immunity on a chip. | Georgescu A, Oved JH, Galarraga JH, Cantrell T, Mehta S, Dulmovits BM, Olson TS, Fattahi P, Wang A, Candarlioglu PL, Muvaffak A, Kim MM, Aydin SA, Seo J, Diffenderfer ES, Lynch A, Worthen GS, Huh DD | Cell stem cell | 39642865 | Cell Stem Cell | 2024 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/39642865 |
| Surface-directed engineering of tissue anisotropy in microphysiological models of musculoskeletal tissue. | Mondrinos MJ, Alisafaei F, Yi AY, Ahmadzadeh H, Lee I, Blundell C, Seo J, Osborn M, Jeon TJ, Kim SM, Shenoy VB, Huh D | Science advances | 33712463 | Sci Adv | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33712463 |
| A microengineered pathophysiological model of early-stage breast cancer. | Choi Y, Hyun E, Seo J, Blundell C, Kim HC, Lee E, Lee SH, Moon A, Moon WK, Huh D | Lab on a chip | 26158500 | Lab Chip | 2015 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/26158500 |
| Microphysiological Engineering of Self-Assembled and Perfusable Microvascular Beds for the Production of Vascularized Three-Dimensional Human Microtissues. | Paek J, Park SE, Lu Q, Park KT, Cho M, Oh JM, Kwon KW, Yi YS, Song JW, Edelstein HI, Ishibashi J, Yang W, Myerson JW, Kiseleva RY, Aprelev P, Hood ED, Stambolian D, Seale P, Muzykantov VR, Huh D | ACS nano | 31194909 | ACS Nano | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31194909 |
| Immune Modulation to Improve Survival of Viral Pneumonia in Mice. | Wali S, Flores JR, Jaramillo AM, Goldblatt DL, Pantaleón García J, Tuvim MJ, Dickey BF, Evans SE | American journal of respiratory cell and molecular biology | 32853024 | Am J Respir Cell Mol Biol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32853024 |
| Bacterial Pneumonia in Patients with Cancer: Novel Risk Factors and Management. | Wong JL, Evans SE | Clinics in chest medicine | 28477638 | Clin Chest Med | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28477638 |
| Lung epithelial cells: therapeutically inducible effectors of antimicrobial defense. | Leiva-Juárez MM, Kolls JK, Evans SE | Mucosal immunology | 28812547 | Mucosal Immunol | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28812547 |
| Muc5b is required for airway defence. | Roy MG, Livraghi-Butrico A, Fletcher AA, McElwee MM, Evans SE, Boerner RM, Alexander SN, Bellinghausen LK, Song AS, Petrova YM, Tuvim MJ, Adachi R, Romo I, Bordt AS, Bowden MG, Sisson JH, Woodruff PG, Thornton DJ, Rousseau K, De la Garza MM, Moghaddam SJ, Karmouty-Quintana H, Blackburn MR, Drouin SM, Davis CW, Terrell KA, Grubb BR, O'Neal WK, Flores SC, Cota-Gomez A, Lozupone CA, Donnelly JM, Watson AM, Hennessy CE, Keith RC, Yang IV, Barthel L, Henson PM, Janssen WJ, Schwartz DA, Boucher RC, Dickey BF, Evans CM | Nature | 24317696 | Nature | 2014 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/24317696 |
| Viral Pneumonia in Patients with Hematologic Malignancy or Hematopoietic Stem Cell Transplantation. | Vakil E, Evans SE | Clinics in chest medicine | 28159165 | Clin Chest Med | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28159165 |
| Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial metabolic reprogramming. | Wang Y, Kulkarni VV, Pantaleón García J, Leiva-Juárez MM, Goldblatt DL, Gulraiz F, Chen J, Donepudi SR, Lorenzi PL, Wang H, Wong LJ, Tuvim MJ, Evans SE | bioRxiv : the preprint server for biology | 36711510 | bioRxiv | 2023 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/36711510 |
| Epithelial immunomodulation by aerosolized Toll-like receptor agonists prevents allergic inflammation in airway mucosa in mice. | Goldblatt DL, Valverde Ha G, Wali S, Kulkarni VV, Longmire MK, Jaramillo AM, Chittuluru RP, Fouts A, Martinez-Moczygemba M, Lei JT, Huston DP, Tuvim MJ, Dickey BF, Evans SE | Frontiers in pharmacology | 36105216 | Front Pharmacol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36105216 |
| Minimizing caging effects in murine lung microbiome studies. | Pantaleón García J, Dickson RP, Evans SE | American journal of physiology. Lung cellular and molecular physiology | 35944140 | Am J Physiol Lung Cell Mol Physiol | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35944140 |
| Combined aerosolized Toll-like receptor ligands are an effective therapeutic agent against influenza pneumonia when co-administered with oseltamivir. | Leiva-Juarez MM, Kirkpatrick CT, Gilbert BE, Scott B, Tuvim MJ, Dickey BF, Evans SE, Markesich D | European journal of pharmacology | 29066417 | Eur J Pharmacol | 2018 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/29066417 |
| Future Research Directions in Pneumonia. NHLBI Working Group Report. | Dela Cruz CS, Wunderink RG, Christiani DC, Cormier SA, Crothers K, Doerschuk CM, Evans SE, Goldstein DR, Khatri P, Kobzik L, Kolls JK, Levy BD, Metersky ML, Niederman MS, Nusrat R, Orihuela CJ, Peyrani P, Prince AS, Ramírez JA, Ridge KM, Sethi S, Suratt BT, Sznajder JI, Tsalik EL, Walkey AJ, Yende S, Aggarwal NR, Caler EV, Mizgerd JP | American journal of respiratory and critical care medicine | 29546996 | Am J Respir Crit Care Med | 2018 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/29546996 |
| Inducible Lung Epithelial Resistance Requires Multisource Reactive Oxygen Species Generation To Protect against Viral Infections. | Kirkpatrick CT, Wang Y, Leiva Juarez MM, Shivshankar P, Pantaleón García J, Plumer AK, Kulkarni VV, Ware HH, Gulraiz F, Chavez Cavasos MA, Martinez Zayas G, Wali S, Rice AP, Liu H, Tour JM, Sikkema WKA, Cruz Solbes AS, Youker KA, Tuvim MJ, Dickey BF, Evans SE | mBio | 29764948 | mBio | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29764948 |
| Fungal Pneumonia in Patients with Hematologic Malignancy and Hematopoietic Stem Cell Transplantation. | Young AY, Leiva Juarez MM, Evans SE | Clinics in chest medicine | 28797490 | Clin Chest Med | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28797490 |
| Porous silicon microparticle potentiates anti-tumor immunity by enhancing cross-presentation and inducing type I interferon response. | Xia X, Mai J, Xu R, Perez JET, Guevara ML, Shen Q, Mu C, Tung HY, Corry DB, Evans SE, Liu X, Ferrari M, Zhang Z, Li XC, Wang RF, Shen H | Cell reports | 25937283 | Cell Rep | 2015 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/25937283 |
| Safety, tolerability, and biomarkers of the treatment of mice with aerosolized Toll-like receptor ligands. | Alfaro VY, Goldblatt DL, Valverde GR, Munsell MF, Quinton LJ, Walker AK, Dantzer R, Varadhachary A, Scott BL, Evans SE, Tuvim MJ, Dickey BF | Frontiers in pharmacology | 24567720 | Front Pharmacol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24567720 |
| Selective Modulation of the Pulmonary Innate Immune Response Does Not Change Lung Microbiota in Healthy Mice. | Pantaleón García J, Hinkle KJ, Falkowski NR, Evans SE, Dickson RP | American journal of respiratory and critical care medicine | 34153197 | Am J Respir Crit Care Med | 2021 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/34153197 |
| Repetitive aeroallergen challenges elucidate maladaptive epithelial and inflammatory traits that underpin allergic airway diseases. | Smith AM, Harper N, Meunier JA, Branum AP, Jimenez F, Pandranki L, Carrillo A, Dela Cruz CS, Restrepo MI, Maselli DJ, Rather CG, Heisser AH, Ramirez DA, He W, Clark RA, Andrews CP, Evans SE, Pugh JA, Zhang N, Lee GC, Moreira AG, Segal LN, Ramirez RM, Jacobs RL, Manoharan MS, Okulicz JF, Ahuja SK | The Journal of allergy and clinical immunology | 33493557 | J Allergy Clin Immunol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33493557 |
| Pneumonia in the neutropenic cancer patient. | Evans SE, Ost DE | Current opinion in pulmonary medicine | 25784246 | Curr Opin Pulm Med | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25784246 |
| The development and plasticity of alveolar type 1 cells. | Yang J, Hernandez BJ, Martinez Alanis D, Narvaez del Pilar O, Vila-Ellis L, Akiyama H, Evans SE, Ostrin EJ, Chen J | Development (Cambridge, England) | 26586225 | Development | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26586225 |
| MAGI1 as a link between endothelial activation and ER stress drives atherosclerosis. | Abe JI, Ko KA, Kotla S, Wang Y, Paez-Mayorga J, Shin IJ, Imanishi M, Vu HT, Tao Y, Leiva-Juarez MM, Thomas TN, Medina JL, Won JH, Fujii Y, Giancursio CJ, McBeath E, Shin JH, Guzman L, Abe RJ, Taunton J, Mochizuki N, Faubion W, Cooke JP, Fujiwara K, Evans SE, Le NT | JCI insight | 30944250 | JCI Insight | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30944250 |
| Inducible epithelial resistance against acute Sendai virus infection prevents chronic asthma-like lung disease in mice. | Goldblatt DL, Flores JR, Valverde Ha G, Jaramillo AM, Tkachman S, Kirkpatrick CT, Wali S, Hernandez B, Ost DE, Scott BL, Chen J, Evans SE, Tuvim MJ, Dickey BF | British journal of pharmacology | 31968123 | Br J Pharmacol | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/31968123 |
| Inducible lung epithelial resistance requires multisource reactive oxygen species generation to protect against bacterial infections. | Ware HH, Kulkarni VV, Wang Y, Pantaleón García J, Leiva Juarez M, Kirkpatrick CT, Wali S, Syed S, Kontoyiannis AD, Sikkema WKA, Tour JM, Evans SE | PloS one | 30794556 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30794556 |
| Editorial: Purinergic Signaling and Inflammation. | Yuan X, Ferrari D, Mills T, Wang Y, Czopik A, Doursout MF, Evans SE, Idzko M, Eltzschig HK | Frontiers in immunology | 34093597 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34093597 |
| Targeting the Hypoxia-Adenosine Link for Controlling Excessive Inflammation. | Czopik A, Yuan X, Evans SE, Eltzschig HK | Anesthesiology | 34046661 | Anesthesiology | 2021 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/34046661 |
| Antimicrobial mitochondrial reactive oxygen species induction by lung epithelial immunometabolic modulation. | Wang Y, Kulkarni VV, Pantaleón García J, Leiva-Juárez MM, Goldblatt DL, Gulraiz F, Vila Ellis L, Chen J, Longmire MK, Donepudi SR, Lorenzi PL, Wang H, Wong LJ, Tuvim MJ, Evans SE | PLoS pathogens | 37695784 | PLoS Pathog | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37695784 |
| OBIF: an omics-based interaction framework to reveal molecular drivers of synergy. | Pantaleón García J, Kulkarni VV, Reese TC, Wali S, Wase SJ, Zhang J, Singh R, Caetano MS, Kadara H, Moghaddam SJ, Johnson FM, Wang J, Wang Y, Evans SE | NAR genomics and bioinformatics | 35387383 | NAR Genom Bioinform | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35387383 |
| Redox-Dependent Activation of Lung Epithelial STAT3 Is Required for Inducible Protection against Bacterial Pneumonia. | Kulkarni VV, Wang Y, Pantaleon Garcia J, Evans SE | American journal of respiratory cell and molecular biology | 36826841 | Am J Respir Cell Mol Biol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36826841 |
| Inducible epithelial resistance protects mice against leukemia-associated pneumonia. | Leiva-Juárez MM, Ware HH, Kulkarni VV, Zweidler-McKay PA, Tuvim MJ, Evans SE | Blood | 27317793 | Blood | 2016 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/27317793 |
| Progression of the Radiologic Severity Index predicts mortality in patients with parainfluenza virus-associated lower respiratory infections. | Sheshadri A, Shah DP, Godoy M, Erasmus JJ, Song J, Li L, Evans SE, Chemaly RF, Dickey BF, Ost DE | PloS one | 29771962 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29771962 |
| Lung epithelial cells are essential effectors of inducible resistance to pneumonia. | Cleaver JO, You D, Michaud DR, Pruneda FA, Juarez MM, Zhang J, Weill PM, Adachi R, Gong L, Moghaddam SJ, Poynter ME, Tuvim MJ, Evans SE | Mucosal immunology | 23632328 | Mucosal Immunol | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23632328 |
| Toll-like receptor-2/6 and Toll-like receptor-9 agonists suppress viral replication but not airway hyperreactivity in guinea pigs. | Drake MG, Evans SE, Dickey BF, Fryer AD, Jacoby DB | American journal of respiratory cell and molecular biology | 23449736 | Am J Respir Cell Mol Biol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23449736 |
| A molecularly engineered antiviral banana lectin inhibits fusion and is efficacious against influenza virus infection in vivo. | Covés-Datson EM, King SR, Legendre M, Gupta A, Chan SM, Gitlin E, Kulkarni VV, Pantaleón García J, Smee DF, Lipka E, Evans SE, Tarbet EB, Ono A, Markovitz DM | Proceedings of the National Academy of Sciences of the United States of America | 31932446 | Proc Natl Acad Sci U S A | 2020 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/31932446 |
| The RNA receptor RIG-I binding synthetic oligodeoxynucleotide promotes pneumonia survival. | Wang Y, Kulkarni VV, PantaleónGarcía J, Longmire MK, Lethier M, Cusack S, Evans SE | JCI insight | 39352770 | JCI Insight | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39352770 |
| Machine Learning in Medicine. | Deo RC | Circulation | 26572668 | Circulation | 2015 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/26572668 |
| The structure of a calsequestrin filament reveals mechanisms of familial arrhythmia. | Titus EW, Deiter FH, Shi C, Wojciak J, Scheinman M, Jura N, Deo RC | Nature structural & molecular biology | 33046906 | Nat Struct Mol Biol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33046906 |
| An International Multicenter Evaluation of Inheritance Patterns, Arrhythmic Risks, and Underlying Mechanisms of CASQ2-Catecholaminergic Polymorphic Ventricular Tachycardia. | Ng K, Titus EW, Lieve KV, Roston TM, Mazzanti A, Deiter FH, Denjoy I, Ingles J, Till J, Robyns T, Connors SP, Steinberg C, Abrams DJ, Pang B, Scheinman MM, Bos JM, Duffett SA, van der Werf C, Maltret A, Green MS, Rutberg J, Balaji S, Cadrin-Tourigny J, Orland KM, Knight LM, Brateng C, Wu J, Tang AS, Skanes AC, Manlucu J, Healey JS, January CT, Krahn AD, Collins KK, Maginot KR, Fischbach P, Etheridge SP, Eckhardt LL, Hamilton RM, Ackerman MJ, Noguer FRI, Semsarian C, Jura N, Leenhardt A, Gollob MH, Priori SG, Sanatani S, Wilde AAM, Deo RC, Roberts JD | Circulation | 32693635 | Circulation | 2020 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/32693635 |
| Phenomapping for novel classification of heart failure with preserved ejection fraction. | Shah SJ, Katz DH, Selvaraj S, Burke MA, Yancy CW, Gheorghiade M, Bonow RO, Huang CC, Deo RC | Circulation | 25398313 | Circulation | 2015 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/25398313 |
| Learning About Machine Learning: The Promise and Pitfalls of Big Data and the Electronic Health Record. | Deo RC, Nallamothu BK | Circulation. Cardiovascular quality and outcomes | 28263936 | Circ Cardiovasc Qual Outcomes | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28263936 |
| Research Priorities for Heart Failure With Preserved Ejection Fraction: National Heart, Lung, and Blood Institute Working Group Summary. | Shah SJ, Borlaug BA, Kitzman DW, McCulloch AD, Blaxall BC, Agarwal R, Chirinos JA, Collins S, Deo RC, Gladwin MT, Granzier H, Hummel SL, Kass DA, Redfield MM, Sam F, Wang TJ, Desvigne-Nickens P, Adhikari BB | Circulation | 32202936 | Circulation | 2020 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/32202936 |
| RNA sequencing of mouse sinoatrial node reveals an upstream regulatory role for Islet-1 in cardiac pacemaker cells. | Vedantham V, Galang G, Evangelista M, Deo RC, Srivastava D | Circulation research | 25623957 | Circ Res | 2015 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/25623957 |
| Automated and Interpretable Patient ECG Profiles for Disease Detection, Tracking, and Discovery. | Tison GH, Zhang J, Delling FN, Deo RC | Circulation. Cardiovascular quality and outcomes | 31525078 | Circ Cardiovasc Qual Outcomes | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31525078 |
| Response by Zhang and Deo to Letter Regarding Article, "Fully Automated Echocardiogram Interpretation in Clinical Practice: Feasibility and Diagnostic Accuracy". | Zhang J, Deo RC | Circulation | 30908098 | Circulation | 2019 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/30908098 |
| Precision Phenotyping of Dilated Cardiomyopathy Using Multidimensional Data. | Tayal U, Verdonschot JAJ, Hazebroek MR, Howard J, Gregson J, Newsome S, Gulati A, Pua CJ, Halliday BP, Lota AS, Buchan RJ, Whiffin N, Kanapeckaite L, Baruah R, Jarman JWE, O'Regan DP, Barton PJR, Ware JS, Pennell DJ, Adriaans BP, Bekkers SCAM, Donovan J, Frenneaux M, Cooper LT, Januzzi JL Jr, Cleland JGF, Cook SA, Deo RC, Heymans SRB, Prasad SK | Journal of the American College of Cardiology | 35654493 | J Am Coll Cardiol | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35654493 |
| Alternative Splicing, Internal Promoter, Nonsense-Mediated Decay, or All Three: Explaining the Distribution of Truncation Variants in Titin. | Deo RC | Circulation. Cardiovascular genetics | 27625338 | Circ Cardiovasc Genet | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27625338 |
| Targeted deep sequencing reveals no definitive evidence for somatic mosaicism in atrial fibrillation. | Roberts JD, Longoria J, Poon A, Gollob MH, Dewland TA, Kwok PY, Olgin JE, Deo RC, Marcus GM | Circulation. Cardiovascular genetics | 25406240 | Circ Cardiovasc Genet | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25406240 |
| An internal promoter underlies the difference in disease severity between N- and C-terminal truncation mutations of Titin in zebrafish. | Zou J, Tran D, Baalbaki M, Tang LF, Poon A, Pelonero A, Titus EW, Yuan C, Shi C, Patchava S, Halper E, Garg J, Movsesyan I, Yin C, Wu R, Wilsbacher LD, Liu J, Hager RL, Coughlin SR, Jinek M, Pullinger CR, Kane JP, Hart DO, Kwok PY, Deo RC | eLife | 26473617 | Elife | 2015 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/26473617 |
| Prioritizing causal disease genes using unbiased genomic features. | Deo RC, Musso G, Tasan M, Tang P, Poon A, Yuan C, Felix JF, Vasan RS, Beroukhim R, De Marco T, Kwok PY, MacRae CA, Roth FP | Genome biology | 25633252 | Genome Biol | 2014 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/25633252 |
| A case of mistaken identity: The MAR-1 antibody to mouse FcεRIα cross-reacts with FcγRI and FcγRIV. | Tang XZ, Jung JB, Allen CDC | The Journal of allergy and clinical immunology | 30639345 | J Allergy Clin Immunol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30639345 |
| Bronchus-associated macrophages efficiently capture and present soluble inhaled antigens and are capable of local Th2 cell activation. | Tang XZ, Kreuk LSM, Cho C, Metzger RJ, Allen CDC | eLife | 36173678 | Elife | 2022 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/36173678 |
| Macrophage Cx43 Is Necessary for Fibroblast Cytosolic Calcium and Lung Fibrosis After Injury. | Bhattacharyya A, Torre P, Yadav P, Boostanpour K, Chen TY, Tsukui T, Sheppard D, Muramatsu R, Seed RI, Nishimura SL, Jung JB, Tang XZ, Allen CDC, Bhattacharya M | Frontiers in immunology | 35634278 | Front Immunol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35634278 |
| Expression of Exogenous Genes in Murine Primary B Cells and B Cell Lines Using Retroviral Vectors. | Yang Z, Allen CDC | Methods in molecular biology (Clifton, N.J.) | 29388098 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29388098 |
| Integrin α2β1 regulates collagen I tethering to modulate hyperresponsiveness in reactive airway disease models. | Liu S, Ngo U, Tang XZ, Ren X, Qiu W, Huang X, DeGrado W, Allen CD, Jo H, Sheppard D, Sundaram AB | The Journal of clinical investigation | 33956668 | J Clin Invest | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/33956668 |
| Regulatory constraints in the generation and differentiation of IgE-expressing B cells. | Yang Z, Robinson MJ, Allen CD | Current opinion in immunology | 24632082 | Curr Opin Immunol | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24632082 |
| Study of IgE-Producing B Cells Using the Verigem Fluorescent Reporter Mouse. | Yang Z, Jung JB, Allen CDC | Methods in molecular biology (Clifton, N.J.) | 29956157 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29956157 |
| Spontaneous Helical Structure Formation in Laminin Nanofibers. | Szymanski JM, Ba M, Feinberg AW | Journal of materials chemistry. B | 26693018 | J Mater Chem B | 2015 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/26693018 |
| Engineered Basement Membranes for Regenerating the Corneal Endothelium. | Palchesko RN, Funderburgh JL, Feinberg AW | Advanced healthcare materials | 27723276 | Adv Healthc Mater | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27723276 |
| Stretch-dependent changes in molecular conformation in fibronectin nanofibers. | Szymanski JM, Sevcik EN, Zhang K, Feinberg AW | Biomaterials science | 28612067 | Biomater Sci | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28612067 |
| Measuring the Poisson's Ratio of Fibronectin Using Engineered Nanofibers. | Szymanski JM, Zhang K, Feinberg AW | Scientific reports | 29042643 | Sci Rep | 2017 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/29042643 |
| Shrink Wrapping Cells in a Defined Extracellular Matrix to Modulate the Chemo-Mechanical Microenvironment. | Palchesko RN, Szymanski JM, Sahu A, Feinberg AW | Cellular and molecular bioengineering | 25530816 | Cell Mol Bioeng | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25530816 |
| In vitro expansion of corneal endothelial cells on biomimetic substrates. | Palchesko RN, Lathrop KL, Funderburgh JL, Feinberg AW | Scientific reports | 25609008 | Sci Rep | 2015 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/25609008 |
| Fabrication of freestanding alginate microfibers and microstructures for tissue engineering applications. | Szymanski JM, Feinberg AW | Biofabrication | 24695323 | Biofabrication | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24695323 |
| Cryopreserved cell-laden alginate microgel bioink for 3D bioprinting of living tissues. | Jeon O, Bin Lee Y, Hinton TJ, Feinberg AW, Alsberg E | Materials today. Chemistry | 30778400 | Mater Today Chem | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30778400 |
| Conformal nanopatterning of extracellular matrix proteins onto topographically complex surfaces. | Sun Y, Jallerat Q, Szymanski JM, Feinberg AW | Nature methods | 25506720 | Nat Methods | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25506720 |
| Engineering aligned human cardiac muscle using developmentally inspired fibronectin micropatterns. | Batalov I, Jallerat Q, Kim S, Bliley J, Feinberg AW | Scientific reports | 34075068 | Sci Rep | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/34075068 |
| Engineering Aligned Skeletal Muscle Tissue Using Decellularized Plant-Derived Scaffolds. | Cheng YW, Shiwarski DJ, Ball RL, Whitehead KA, Feinberg AW | ACS biomaterials science & engineering | 33463300 | ACS Biomater Sci Eng | 2020 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33463300 |
| ECM protein nanofibers and nanostructures engineered using surface-initiated assembly. | Szymanski JM, Jallerat Q, Feinberg AW | Journal of visualized experiments : JoVE | 24799041 | J Vis Exp | 2014 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/24799041 |
| Fibronectin-based nanomechanical biosensors to map 3D surface strains in live cells and tissue. | Shiwarski DJ, Tashman JW, Tsamis A, Bliley JM, Blundon MA, Aranda-Michel E, Jallerat Q, Szymanski JM, McCartney BM, Feinberg AW | Nature communications | 33208732 | Nat Commun | 2020 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/33208732 |
| Large volume syringe pump extruder for desktop 3D printers. | Pusch K, Hinton TJ, Feinberg AW | HardwareX | 30498799 | HardwareX | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30498799 |
| 3D Printing PDMS Elastomer in a Hydrophilic Support Bath via Freeform Reversible Embedding. | Hinton TJ, Hudson A, Pusch K, Lee A, Feinberg AW | ACS biomaterials science & engineering | 27747289 | ACS Biomater Sci Eng | 2016 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/27747289 |
| Understanding the Role of ECM Protein Composition and Geometric Micropatterning for Engineering Human Skeletal Muscle. | Duffy RM, Sun Y, Feinberg AW | Annals of biomedical engineering | 26983843 | Ann Biomed Eng | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26983843 |
| Three-dimensional printing of complex biological structures by freeform reversible embedding of suspended hydrogels. | Hinton TJ, Jallerat Q, Palchesko RN, Park JH, Grodzicki MS, Shue HJ, Ramadan MH, Hudson AR, Feinberg AW | Science advances | 26601312 | Sci Adv | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26601312 |
| Patterning on Topography for Generation of Cell Culture Substrates with Independent Nanoscale Control of Chemical and Topographical Extracellular Matrix Cues. | Sevcik EN, Szymanski JM, Jallerat Q, Feinberg AW | Current protocols in cell biology | 28627752 | Curr Protoc Cell Biol | 2017 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/28627752 |
| Extracellular Matrix Structure and Composition in the Early Four-Chambered Embryonic Heart. | Jallerat Q, Feinberg AW | Cells | 31991580 | Cells | 2020 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/31991580 |
| 3D bioprinting of collagen to rebuild components of the human heart. | Lee A, Hudson AR, Shiwarski DJ, Tashman JW, Hinton TJ, Yerneni S, Bliley JM, Campbell PG, Feinberg AW | Science (New York, N.Y.) | 31371612 | Science | 2019 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/31371612 |
| Dynamic loading of human engineered heart tissue enhances contractile function and drives a desmosome-linked disease phenotype. | Bliley JM, Vermeer MCSC, Duffy RM, Batalov I, Kramer D, Tashman JW, Shiwarski DJ, Lee A, Teplenin AS, Volkers L, Coffin B, Hoes MF, Kalmykov A, Palchesko RN, Sun Y, Jongbloed JDH, Bomer N, de Boer RA, Suurmeijer AJH, Pijnappels DA, Bolling MC, van der Meer P, Feinberg AW | Science translational medicine | 34290054 | Sci Transl Med | 2021 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/34290054 |
| Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. | Caschera F, Lee JW, Ho KK, Liu AP, Jewett MC | Chemical communications (Cambridge, England) | 27019994 | Chem Commun (Camb) | 2016 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/27019994 |
| Cofactoring and dimerization of proteinase-activated receptors. | Lin H, Liu AP, Smith TH, Trejo J | Pharmacological reviews | 24064459 | Pharmacol Rev | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24064459 |
| Cell-sized mechanosensitive and biosensing compartment programmed with DNA. | Majumder S, Garamella J, Wang YL, DeNies M, Noireaux V, Liu AP | Chemical communications (Cambridge, England) | 28524182 | Chem Commun (Camb) | 2017 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/28524182 |
| Lipid bilayer vesicle generation using microfluidic jetting. | Coyne CW, Patel K, Heureaux J, Stachowiak J, Fletcher DA, Liu AP | Journal of visualized experiments : JoVE | 24637415 | J Vis Exp | 2014 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/24637415 |
| Activation of a bacterial mechanosensitive channel in mammalian cells by cytoskeletal stress. | Heureaux J, Chen D, Murray VL, Deng CX, Liu AP | Cellular and molecular bioengineering | 25606062 | Cell Mol Bioeng | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25606062 |
| Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets. | Wang S, Majumder S, Emery NJ, Liu AP | Synthetic biology (Oxford, England) | 30003145 | Synth Biol (Oxf) | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30003145 |
| The rise of bottom-up synthetic biology and cell-free biology. | Liu AP | Physical biology | 31018188 | Phys Biol | 2019 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/31018188 |
| Development of an advanced microfluidic micropipette aspiration device for single cell mechanics studies. | Lee LM, Lee JW, Chase D, Gebrezgiabhier D, Liu AP | Biomicrofluidics | 27703591 | Biomicrofluidics | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27703591 |
| Protein aggregation with poly(vinyl) alcohol surfactant reduces double emulsion-encapsulated mammalian cell-free expression. | Ho KK, Lee JW, Durand G, Majumder S, Liu AP | PloS one | 28358875 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28358875 |
| Bottom-up synthetic biology: modular design for making artificial platelets. | Majumder S, Liu AP | Physical biology | 29091050 | Phys Biol | 2017 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/29091050 |
| The Application of Micropipette Aspiration in Molecular Mechanics of Single Cells. | Lee LM, Liu AP | Journal of nanotechnology in engineering and medicine | 26155329 | J Nanotechnol Eng Med | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26155329 |
| Biophysical Tools for Cellular and Subcellular Mechanical Actuation of Cell Signaling. | Liu AP | Biophysical journal | 27456131 | Biophys J | 2016 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/27456131 |
| Engineering artificial cells by combining HeLa-based cell-free expression and ultrathin double emulsion template. | Ho KK, Murray VL, Liu AP | Methods in cell biology | 25997354 | Methods Cell Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25997354 |
| Uniaxial cell stretching device for live-cell imaging of mechanosensitive cellular functions. | Shao Y, Tan X, Novitski R, Muqaddam M, List P, Williamson L, Fu J, Liu AP | The Review of scientific instruments | 24289415 | Rev Sci Instrum | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24289415 |
| Mechanically activated artificial cell by using microfluidics. | Ho KK, Lee LM, Liu AP | Scientific reports | 27610921 | Sci Rep | 2016 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/27610921 |
| A microfluidic pipette array for mechanophenotyping of cancer cells and mechanical gating of mechanosensitive channels. | Lee LM, Liu AP | Lab on a chip | 25361042 | Lab Chip | 2015 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/25361042 |
| Synergistic and non-specific nucleic acid production by T7 RNA polymerase and Bsu DNA polymerase catalyzed by single-stranded polynucleotides. | Emery NJ, Majumder S, Liu AP | Synthetic and systems biotechnology | 29900426 | Synth Syst Biotechnol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29900426 |
| Multiplex detection of homo- and heterodimerization of g protein-coupled receptors by proximity biotinylation. | Steel E, Murray VL, Liu AP | PloS one | 24691126 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24691126 |
| Advanced Microfluidic Device Designed for Cyclic Compression of Single Adherent Cells. | Ho KKY, Wang YL, Wu J, Liu AP | Frontiers in bioengineering and biotechnology | 30386779 | Front Bioeng Biotechnol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30386779 |
| Gel-forming mucins form distinct morphologic structures in airways. | Ostedgaard LS, Moninger TO, McMenimen JD, Sawin NM, Parker CP, Thornell IM, Powers LS, Gansemer ND, Bouzek DC, Cook DP, Meyerholz DK, Abou Alaiwa MH, Stoltz DA, Welsh MJ | Proceedings of the National Academy of Sciences of the United States of America | 28607090 | Proc Natl Acad Sci U S A | 2017 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/28607090 |
| Mucociliary Transport in Healthy and Cystic Fibrosis Pig Airways. | Xie Y, Ostedgaard L, Abou Alaiwa MH, Lu L, Fischer AJ, Stoltz DA | Annals of the American Thoracic Society | 30431346 | Ann Am Thorac Soc | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30431346 |
| Impaired mucus detachment disrupts mucociliary transport in a piglet model of cystic fibrosis. | Hoegger MJ, Fischer AJ, McMenimen JD, Ostedgaard LS, Tucker AJ, Awadalla MA, Moninger TO, Michalski AS, Hoffman EA, Zabner J, Stoltz DA, Welsh MJ | Science (New York, N.Y.) | 25124441 | Science | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/25124441 |
| Assessing mucociliary transport of single particles in vivo shows variable speed and preference for the ventral trachea in newborn pigs. | Hoegger MJ, Awadalla M, Namati E, Itani OA, Fischer AJ, Tucker AJ, Adam RJ, McLennan G, Hoffman EA, Stoltz DA, Welsh MJ | Proceedings of the National Academy of Sciences of the United States of America | 24474805 | Proc Natl Acad Sci U S A | 2014 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/24474805 |
| Sonographic evidence of abnormal tracheal cartilage ring structure in cystic fibrosis. | Diwakar A, Adam RJ, Michalski AS, Tamegnon MM, Fischer AJ, Launspach JL, Horan RA, Kao SC, Chaloner K, Meyerholz DK, Stoltz DA | The Laryngoscope | 25827636 | Laryngoscope | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25827636 |
| Intestinal CFTR expression alleviates meconium ileus in cystic fibrosis pigs. | Stoltz DA, Rokhlina T, Ernst SE, Pezzulo AA, Ostedgaard LS, Karp PH, Samuel MS, Reznikov LR, Rector MV, Gansemer ND, Bouzek DC, Abou Alaiwa MH, Hoegger MJ, Ludwig PS, Taft PJ, Wallen TJ, Wohlford-Lenane C, McMenimen JD, Chen JH, Bogan KL, Adam RJ, Hornick EE, Nelson GA 4th, Hoffman EA, Chang EH, Zabner J, McCray PB Jr, Prather RS, Meyerholz DK, Welsh MJ | The Journal of clinical investigation | 23676501 | J Clin Invest | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23676501 |
| Air trapping and airflow obstruction in newborn cystic fibrosis piglets. | Adam RJ, Michalski AS, Bauer C, Abou Alaiwa MH, Gross TJ, Awadalla MS, Bouzek DC, Gansemer ND, Taft PJ, Hoegger MJ, Diwakar A, Ochs M, Reinhardt JM, Hoffman EA, Beichel RR, Meyerholz DK, Stoltz DA | American journal of respiratory and critical care medicine | 24168209 | Am J Respir Crit Care Med | 2013 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/24168209 |
| Airway acidification initiates host defense abnormalities in cystic fibrosis mice. | Shah VS, Meyerholz DK, Tang XX, Reznikov L, Abou Alaiwa M, Ernst SE, Karp PH, Wohlford-Lenane CL, Heilmann KP, Leidinger MR, Allen PD, Zabner J, McCray PB Jr, Ostedgaard LS, Stoltz DA, Randak CO, Welsh MJ | Science (New York, N.Y.) | 26823428 | Science | 2016 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/26823428 |
| Immunohistochemical Detection of Markers for Translational Studies of Lung Disease in Pigs and Humans. | Meyerholz DK, Lambertz AM, Reznikov LR, Ofori-Amanfo GK, Karp PH, McCray PB Jr, Welsh MJ, Stoltz DA | Toxicologic pathology | 26511846 | Toxicol Pathol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26511846 |
| CF airway smooth muscle transcriptome reveals a role for PYK2. | Cook DP, Adam RJ, Zarei K, Deonovic B, Stroik MR, Gansemer ND, Meyerholz DK, Au KF, Stoltz DA | JCI insight | 28878137 | JCI Insight | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28878137 |
| Cystic Fibrosis Transmembrane Conductance Regulator in Sarcoplasmic Reticulum of Airway Smooth Muscle. Implications for Airway Contractility. | Cook DP, Rector MV, Bouzek DC, Michalski AS, Gansemer ND, Reznikov LR, Li X, Stroik MR, Ostedgaard LS, Abou Alaiwa MH, Thompson MA, Prakash YS, Krishnan R, Meyerholz DK, Seow CY, Stoltz DA | American journal of respiratory and critical care medicine | 26488271 | Am J Respir Crit Care Med | 2016 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/26488271 |
| Acidic pH increases airway surface liquid viscosity in cystic fibrosis. | Tang XX, Ostedgaard LS, Hoegger MJ, Moninger TO, Karp PH, McMenimen JD, Choudhury B, Varki A, Stoltz DA, Welsh MJ | The Journal of clinical investigation | 26808501 | J Clin Invest | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26808501 |
| Origins of cystic fibrosis lung disease. | Stoltz DA, Meyerholz DK, Welsh MJ | The New England journal of medicine | 25607428 | N Engl J Med | 2015 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/25607428 |
| Single-cell resolution of morphological changes in hemogenic endothelium. | Bos FL, Hawkins JS, Zovein AC | Development (Cambridge, England) | 26243871 | Development | 2015 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/26243871 |
| Cell cycle dynamics and complement expression distinguishes mature haematopoietic subsets arising from hemogenic endothelium. | Zape JP, Lizama CO, Cautivo KM, Zovein AC | Cell cycle (Georgetown, Tex.) | 28820341 | Cell Cycle | 2017 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/28820341 |
| Polarizing pathways: balancing endothelial polarity, permeability, and lumen formation. | Lizama CO, Zovein AC | Experimental cell research | 23567183 | Exp Cell Res | 2013 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/23567183 |
| Repression of arterial genes in hemogenic endothelium is sufficient for haematopoietic fate acquisition. | Lizama CO, Hawkins JS, Schmitt CE, Bos FL, Zape JP, Cautivo KM, Borges Pinto H, Rhyner AM, Yu H, Donohoe ME, Wythe JD, Zovein AC | Nature communications | 26204127 | Nat Commun | 2015 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/26204127 |
| Let-7 microRNA-dependent control of leukotriene signaling regulates the transition of hematopoietic niche in mice. | Jiang X, Hawkins JS, Lee J, Lizama CO, Bos FL, Zape JP, Ghatpande P, Peng Y, Louie J, Lagna G, Zovein AC, Hata A | Nature communications | 28743859 | Nat Commun | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28743859 |
| Molecular convergence of risk variants for congenital heart defects leveraging a regulatory map of the human fetal heart. | Ma XR, Conley SD, Kosicki M, Bredikhin D, Cui R, Tran S, Sheth MU, Qiu WL, Chen S, Kundu S, Kang HY, Amgalan D, Munger CJ, Duan L, Dang K, Rubio OM, Kany S, Zamirpour S, DePaolo J, Padmanabhan A, Birth Defects Research Laboratory, Olgin J, Damrauer S, Andersson R, Gu M, Priest JR, Quertermous T, Qiu X, Rabinovitch M, Visel A, Pennacchio L, Kundaje A, Glass IA, Gifford CA, Pirruccello JP, Goodyer WR, Engreitz JM | medRxiv : the preprint server for health sciences | 39606363 | medRxiv | 2024 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/39606363 |
| Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. | Xu Z, Sziraki A, Lee J, Zhou W, Cao J | Nature biotechnology | 37749268 | Nat Biotechnol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37749268 |
| Optics-free Spatial Genomics for Mapping Mouse Brain Aging. | Abdulraouf A, Jiang W, Xu Z, Zhang Z, Isakov S, Raihan T, Zhou W, Cao J | bioRxiv : the preprint server for biology | 39149282 | bioRxiv | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39149282 |
| Single-cell, whole-embryo phenotyping of mammalian developmental disorders. | Huang X, Henck J, Qiu C, Sreenivasan VKA, Balachandran S, Amarie OV, Hrabě de Angelis M, Behncke RY, Chan WL, Despang A, Dickel DE, Duran M, Feuchtinger A, Fuchs H, Gailus-Durner V, Haag N, Hägerling R, Hansmeier N, Hennig F, Marshall C, Rajderkar S, Ringel A, Robson M, Saunders LM, da Silva-Buttkus P, Spielmann N, Srivatsan SR, Ulferts S, Wittler L, Zhu Y, Kalscheuer VM, Ibrahim DM, Kurth I, Kornak U, Visel A, Pennacchio LA, Beier DR, Trapnell C, Cao J, Shendure J, Spielmann M | Nature | 37968388 | Nature | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37968388 |
| Tracking cell-type-specific temporal dynamics in human and mouse brains. | Lu Z, Zhang M, Lee J, Sziraki A, Anderson S, Zhang Z, Xu Z, Jiang W, Ge S, Nelson PT, Zhou W, Cao J | Cell | 37774676 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774676 |
| A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains. | Sziraki A, Lu Z, Lee J, Banyai G, Anderson S, Abdulraouf A, Metzner E, Liao A, Banfelder J, Epstein A, Schaefer C, Xu Z, Zhang Z, Gan L, Nelson PT, Zhou W, Cao J | Nature genetics | 38036784 | Nat Genet | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38036784 |
| A Panoramic View of Cell Population Dynamics in Mammalian Aging. | Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J | bioRxiv : the preprint server for biology | 38496474 | bioRxiv | 2024 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/38496474 |
| A panoramic view of cell population dynamics in mammalian aging. | Zhang Z, Schaefer C, Jiang W, Lu Z, Lee J, Sziraki A, Abdulraouf A, Wick B, Haeussler M, Li Z, Molla G, Satija R, Zhou W, Cao J | Science (New York, N.Y.) | 39607904 | Science | 2025 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/39607904 |
| Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging. | Lu Z, Zhang Z, Xu Z, Abdulraouf A, Zhou W, Cao J | bioRxiv : the preprint server for biology | 40463164 | bioRxiv | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40463164 |
| Early peanut introduction wins over the HLA-DQA1*01:02 allele in the interplay between environment and genetics. | Manohar M, Nadeau KC, Kasowski M | The Journal of clinical investigation | 34981779 | J Clin Invest | 2022 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/34981779 |
| Mutant NPM1 Hijacks Transcriptional Hubs to Maintain Pathogenic Gene Programs in Acute Myeloid Leukemia. | Wang XQD, Fan D, Han Q, Liu Y, Miao H, Wang X, Li Q, Chen D, Gore H, Himadewi P, Pfeifer GP, Cierpicki T, Grembecka J, Su J, Chong S, Wan L, Zhang X | Cancer discovery | 36455589 | Cancer Discov | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36455589 |
| Hotspot mutations in the structured ENL YEATS domain link aberrant transcriptional condensates and cancer. | Song L, Yao X, Li H, Peng B, Boka AP, Liu Y, Chen G, Liu Z, Mathias KM, Xia L, Li Q, Mir M, Li Y, Li H, Wan L | Molecular cell | 36272410 | Mol Cell | 2022 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/36272410 |
| Small-Molecule Inhibition of the Acyl-Lysine Reader ENL as a Strategy against Acute Myeloid Leukemia. | Liu Y, Li Q, Alikarami F, Barrett DR, Mahdavi L, Li H, Tang S, Khan TA, Michino M, Hill C, Song L, Yang L, Li Y, Pokharel SP, Stamford AW, Liverton N, Renzetti LM, Taylor S, Watt GF, Ladduwahetty T, Kargman S, Meinke PT, Foley MA, Shi J, Li H, Carroll M, Chen CW, Gardini A, Maillard I, Huggins DJ, Bernt KM, Wan L | Cancer discovery | 36053276 | Cancer Discov | 2022 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/36053276 |
| DLBCL-associated NOTCH2 mutations escape ubiquitin-dependent degradation and promote chemoresistance. | Zhou N, Choi J, Grothusen G, Kim BJ, Ren D, Cao Z, Liu Y, Li Q, Inamdar A, Beer T, Tang HY, Perkey E, Maillard I, Bonasio R, Shi J, Ruella M, Wan L, Busino L | Blood | 37235754 | Blood | 2023 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/37235754 |
| Dysregulation of transcriptional condensates in human disease: mechanisms, biological functions, and open questions. | Mathias KM, Liu Y, Wan L | Current opinion in genetics & development | 38788489 | Curr Opin Genet Dev | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38788489 |
| Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. | Song L, Li Q, Xia L, Sahay AE, Qiu Q, Li Y, Li H, Sasaki K, Susztak K, Wu H, Wan L | Nature communications | 39009564 | Nat Commun | 2024 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/39009564 |
| Condensate-Promoting ENL Mutation Drives Tumorigenesis In Vivo Through Dynamic Regulation of Histone Modifications and Gene Expression. | Liu Y, Li Q, Song L, Gong C, Tang S, Budinich KA, Vanderbeck A, Mathias KM, Wertheim GB, Nguyen SC, Outen R, Joyce EF, Maillard I, Wan L | Cancer discovery | 38655899 | Cancer Discov | 2024 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/38655899 |
| HMGB1 restores a dynamic chromatin environment in the presence of linker histone by deforming nucleosomal DNA. | Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ | bioRxiv : the preprint server for biology | 39229246 | bioRxiv | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39229246 |
| A Germline Point Mutation in the MYC-FBW7 Phosphodegron Initiates Hematopoietic Malignancies. | Freie B, Carroll PA, Varnum-Finney BJ, Ramani V, Bernstein I, Eisenman RN | bioRxiv : the preprint server for biology | 37961183 | bioRxiv | 2023 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/37961183 |
| Direct transposition of native DNA for sensitive multimodal single-molecule sequencing. | Nanda AS, Wu K, Irkliyenko I, Woo B, Ostrowski MS, Clugston AS, Sayles LC, Xu L, Satpathy AT, Nguyen HG, Alejandro Sweet-Cordero E, Goodarzi H, Kasinathan S, Ramani V | Nature genetics | 38724748 | Nat Genet | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38724748 |
| A germline point mutation in the MYC-FBW7 phosphodegron initiates hematopoietic malignancies. | Freie B, Carroll PA, Varnum-Finney BJ, Ramsey EL, Ramani V, Bernstein I, Eisenman RN | Genes & development | 38565249 | Genes Dev | 2024 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/38565249 |
| Pervasive and programmed nucleosome distortion patterns on single mammalian chromatin fibers. | Yang MG, Richter HJ, Wang S, McNally CP, Harris N, Dhillon S, Maresca M, de Wit E, Willenbring H, Maher J, Goodarzi H, Ramani V | bioRxiv : the preprint server for biology | 39896524 | bioRxiv | 2025 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/39896524 |
| Nucleosome density shapes kilobase-scale regulation by a mammalian chromatin remodeler. | Abdulhay NJ, Hsieh LJ, McNally CP, Ostrowski MS, Moore CM, Ketavarapu M, Kasinathan S, Nanda AS, Wu K, Chio US, Zhou Z, Goodarzi H, Narlikar GJ, Ramani V | Nature structural & molecular biology | 37696956 | Nat Struct Mol Biol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37696956 |
| ATP-dependent remodeling of chromatin condensates uncovers distinct mesoscale effects of two remodelers. | Moore C, Wong E, Kaur U, Chio US, Zhou Z, Ostrowski M, Wu K, Irkliyenko I, Wang S, Ramani V, Narlikar GJ | bioRxiv : the preprint server for biology | 39314305 | bioRxiv | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/39314305 |
| The single-molecule accessibility landscape of newly replicated mammalian chromatin. | Ostrowski MS, Yang MG, McNally CP, Abdulhay NJ, Wang S, Renduchintala K, Irkliyenko I, Biran A, Chew BTL, Midha AD, Wong EV, Sandoval J, Jain IH, Groth A, Nora EP, Goodarzi H, Ramani V | Cell | 39549698 | Cell | 2025 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/39549698 |
| Alternative mRNA splicing events and regulators in epidermal differentiation. | Takashima S, Sun W, Otten ABC, Cai P, Peng SI, Tong E, Bui J, Mai M, Amarbayar O, Cheng B, Odango RJ, Li Z, Qu K, Sun BK | Cell reports | 38402585 | Cell Rep | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38402585 |
| The role of enhancers in psoriasis and atopic dermatitis. | Sui JY, Eichenfield DZ, Sun BK | The British journal of dermatology | 37658835 | Br J Dermatol | 2023 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/37658835 |
| The Long Noncoding RNA PRANCR Is Associated with Alternative Splicing of Fibronectin-1 in Keratinocytes. | Otten ABC, Amarbayar O, Cai P, Cheng B, Qu K, Sun BK | The Journal of investigative dermatology | 36906126 | J Invest Dermatol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36906126 |
| Targeted DNA integration in human cells without double-strand breaks using CRISPR-associated transposases. | Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH | Nature biotechnology | 36991112 | Nat Biotechnol | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36991112 |
| Bacterial genome engineering using CRISPR-associated transposases. | Gelsinger DR, Vo PLH, Klompe SE, Ronda C, Wang HH, Sternberg SH | Nature protocols | 38216671 | Nat Protoc | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38216671 |
| Transposon-encoded nucleases use guide RNAs to promote their selfish spread. | Meers C, Le HC, Pesari SR, Hoffmann FT, Walker MWG, Gezelle J, Tang S, Sternberg SH | Nature | 37758954 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37758954 |
| Evolutionary and mechanistic diversity of Type I-F CRISPR-associated transposons. | Klompe SE, Jaber N, Beh LY, Mohabir JT, Bernheim A, Sternberg SH | Molecular cell | 35051352 | Mol Cell | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35051352 |
| Transposon mutagenesis libraries reveal novel molecular requirements during CRISPR RNA-guided DNA integration. | Walker MWG, Klompe SE, Zhang DJ, Sternberg SH | bioRxiv : the preprint server for biology | 36711804 | bioRxiv | 2023 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/36711804 |
| Selective TnsC recruitment enhances the fidelity of RNA-guided transposition. | Hoffmann FT, Kim M, Beh LY, Wang J, Vo PLH, Gelsinger DR, George JT, Acree C, Mohabir JT, Fernández IS, Sternberg SH | Nature | 36002573 | Nature | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36002573 |
| Novel molecular requirements for CRISPR RNA-guided transposition. | Walker MWG, Klompe SE, Zhang DJ, Sternberg SH | Nucleic acids research | 37078593 | Nucleic Acids Res | 2023 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/37078593 |
| Targeted DNA integration in human cells without double-strand breaks using CRISPR RNA-guided transposases. | Lampe GD, King RT, Halpin-Healy TS, Klompe SE, Hogan MI, Vo PLH, Tang S, Chavez A, Sternberg SH | bioRxiv : the preprint server for biology | 36993517 | bioRxiv | 2023 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/36993517 |
| Genome editing with retroelements. | Tang S, Sternberg SH | Science (New York, N.Y.) | 37883564 | Science | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37883564 |
| Mechanism of target site selection by type V-K CRISPR-associated transposases. | George JT, Acree C, Park JU, Kong M, Wiegand T, Pignot YL, Kellogg EH, Greene EC, Sternberg SH | bioRxiv : the preprint server for biology | 37503092 | bioRxiv | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37503092 |
| TnpB homologues exapted from transposons are RNA-guided transcription factors. | Wiegand T, Hoffmann FT, Walker MWG, Tang S, Richard E, Le HC, Meers C, Sternberg SH | Nature | 38926585 | Nature | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38926585 |
| Evolutionary origins of archaeal and eukaryotic RNA-guided RNA modification in bacterial IS110 transposons. | Vaysset H, Meers C, Cury J, Bernheim A, Sternberg SH | Nature microbiology | 39747689 | Nat Microbiol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39747689 |
| Structure-guided engineering of type I-F CASTs for targeted gene insertion in human cells. | Lampe GD, Liang AR, Zhang DJ, Fernández IS, Sternberg SH | bioRxiv : the preprint server for biology | 39345383 | bioRxiv | 2024 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/39345383 |
| Antagonistic conflict between transposon-encoded introns and guide RNAs. | Žedaveinytė R, Meers C, Le HC, Mortman EE, Tang S, Lampe GD, Pesari SR, Gelsinger DR, Wiegand T, Sternberg SH | Science (New York, N.Y.) | 38991068 | Science | 2024 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/38991068 |
| Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing. | Vo PLH, Acree C, Smith ML, Sternberg SH | Mobile DNA | 34103093 | Mob DNA | 2021 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/34103093 |
| Mechanism of target site selection by type V-K CRISPR-associated transposases. | George JT, Acree C, Park JU, Kong M, Wiegand T, Pignot YL, Kellogg EH, Greene EC, Sternberg SH | Science (New York, N.Y.) | 37972161 | Science | 2023 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/37972161 |
| Bacterial genome engineering using CRISPR RNA-guided transposases. | Gelsinger DR, Vo PLH, Klompe SE, Ronda C, Wang H, Sternberg SH | bioRxiv : the preprint server for biology | 36993567 | bioRxiv | 2023 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/36993567 |
| Novel recombinases for large DNA insertions. | Lampe GD, Sternberg SH | Nature biotechnology | 36424492 | Nat Biotechnol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36424492 |
| De novo gene synthesis by an antiviral reverse transcriptase. | Tang S, Conte V, Zhang DJ, Žedaveinytė R, Lampe GD, Wiegand T, Tang LC, Wang M, Walker MWG, George JT, Berchowitz LE, Jovanovic M, Sternberg SH | Science (New York, N.Y.) | 39116258 | Science | 2024 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/39116258 |
| Harnessing the power of directed evolution to improve genome editing systems. | Su Q, Zhou M, Cheng C, Niu J | Current opinion in chemical biology | 33725650 | Curr Opin Chem Biol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33725650 |
| "Click handle"-modified 2'-deoxy-2'-fluoroarabino nucleic acid as a synthetic genetic polymer capable of post-polymerization functionalization. | Wu KB, Skrodzki CJA, Su Q, Lin J, Niu J | Chemical science | 35774169 | Chem Sci | 2022 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/35774169 |
| Heparan sulfate glycomimetics via iterative assembly of "clickable" disaccharides. | Yang C, Deng Y, Wang Y, Xia C, Mehta AY, Baker KJ, Samal A, Booneimsri P, Lertmaneedang C, Hwang S, Flynn JP, Cao M, Liu C, Zhu AC, Cummings RD, Lin C, Mohanty U, Niu J | Chemical science | 37006675 | Chem Sci | 2023 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/37006675 |
| A General Approach to O-Sulfation by a Sulfur(VI) Fluoride Exchange Reaction. | Liu C, Yang C, Hwang S, Ferraro SL, Flynn JP, Niu J | Angewandte Chemie (International ed. in English) | 32644280 | Angew Chem Int Ed Engl | 2020 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/32644280 |
| Genome editor-directed in vivo library diversification. | Cheng C, Zhou M, Su Q, Steigmeyer A, Niu J | Cell chemical biology | 34107297 | Cell Chem Biol | 2021 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/34107297 |
| Fluorosulfate as a Latent Sulfate in Peptides and Proteins. | Liu C, Liu X, Zhou M, Xia C, Lyu Y, Peng Q, Soni C, Zhou Z, Su Q, Wu Y, Weerapana E, Gao J, Chatterjee A, Lin C, Niu J | Journal of the American Chemical Society | 37647087 | J Am Chem Soc | 2023 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/37647087 |
| Geared Toward Applications: A Perspective on Functional Sequence-Controlled Polymers. | Yang C, Wu KB, Deng Y, Yuan J, Niu J | ACS macro letters | 34336395 | ACS Macro Lett | 2021 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/34336395 |
| Cooperative DNA looping by PRC2 complexes. | Lin X, Leicher R, Liu S, Zhang B | Nucleic acids research | 34057467 | Nucleic Acids Res | 2021 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/34057467 |
| Head-on and co-directional RNA polymerase collisions orchestrate bidirectional transcription termination. | Wang L, Watters JW, Ju X, Lu G, Liu S | Molecular cell | 36917983 | Mol Cell | 2023 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/36917983 |
| Optical tweezers in single-molecule biophysics. | Bustamante CJ, Chemla YR, Liu S, Wang MD | Nature reviews. Methods primers | 34849486 | Nat Rev Methods Primers | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34849486 |
| Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA. | Nguyen T, Li S, Chang JT, Watters JW, Ng H, Osunsade A, David Y, Liu S | Nature communications | 35810158 | Nat Commun | 2022 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/35810158 |
| The MIDAS domain of AAA mechanoenzyme Mdn1 forms catch bonds with two different substrates. | Mickolajczyk KJ, Olinares PDB, Chait BT, Liu S, Kapoor TM | eLife | 35147499 | Elife | 2022 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/35147499 |
| Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors. | Li S, Zheng EB, Zhao L, Liu S | Cell reports | 31484078 | Cell Rep | 2019 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/31484078 |
| Characterization of the kinetic cycle of an ABC transporter by single-molecule and cryo-EM analyses. | Wang L, Johnson ZL, Wasserman MR, Levring J, Chen J, Liu S | eLife | 32458799 | Elife | 2020 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/32458799 |
| Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin. | Leicher R, Ge EJ, Lin X, Reynolds MJ, Xie W, Walz T, Zhang B, Muir TW, Liu S | Proceedings of the National Academy of Sciences of the United States of America | 33208532 | Proc Natl Acad Sci U S A | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33208532 |
| Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome. | Ju X, Li S, Froom R, Wang L, Lilic M, Delbeau M, Campbell EA, Rock JM, Liu S | Nature | 38418874 | Nature | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38418874 |
| Differential dynamics specify MeCP2 function at nucleosomes and methylated DNA. | Chua GNL, Watters JW, Olinares PDB, Begum M, Vostal LE, Luo JA, Chait BT, Liu S | Nature structural & molecular biology | 39164525 | Nat Struct Mol Biol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39164525 |
| A Tour de Force on the Double Helix: Exploiting DNA Mechanics To Study DNA-Based Molecular Machines. | Wasserman MR, Liu S | Biochemistry | 31251042 | Biochemistry | 2019 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/31251042 |
| Force-dependent stimulation of RNA unwinding by SARS-CoV-2 nsp13 helicase. | Mickolajczyk KJ, Shelton PMM, Grasso M, Cao X, Warrington SE, Aher A, Liu S, Kapoor TM | Biophysical journal | 33340543 | Biophys J | 2021 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/33340543 |
| Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. | Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon MD, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ | Molecular cell | 37595555 | Mol Cell | 2023 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/37595555 |
| Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. | Abini-Agbomson S, Gretarsson K, Shih RM, Hsieh L, Lou T, De Ioannes P, Vasilyev N, Lee R, Wang M, Simon M, Armache JP, Nudler E, Narlikar G, Liu S, Lu C, Armache KJ | bioRxiv : the preprint server for biology | 36993485 | bioRxiv | 2023 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/36993485 |
| Nucleosome-directed replication origin licensing independent of a consensus DNA sequence. | Li S, Wasserman MR, Yurieva O, Bai L, O'Donnell ME, Liu S | Nature communications | 35999198 | Nat Commun | 2022 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/35999198 |
| Probing the Interaction Between Chromatin and Chromatin-Associated Complexes with Optical Tweezers. | Leicher R, Liu S | Methods in molecular biology (Clifton, N.J.) | 36063325 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36063325 |
| Origin recognition complex harbors an intrinsic nucleosome remodeling activity. | Li S, Wasserman MR, Yurieva O, Bai L, O'Donnell ME, Liu S | Proceedings of the National Academy of Sciences of the United States of America | 36215487 | Proc Natl Acad Sci U S A | 2022 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/36215487 |
| Differential dynamics specify MeCP2 function at methylated DNA and nucleosomes. | Chua GNL, Watters JW, Olinares PDB, Luo JA, Chait BT, Liu S | bioRxiv : the preprint server for biology | 37333354 | bioRxiv | 2023 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/37333354 |
| Structure and DNA bridging activity of the essential Rec114â€"Mei4 trimer interface. | Liu K, Grasso EM, Pu S, Liu S, Eliezer D, Keeney S | bioRxiv : the preprint server for biology | 36711595 | bioRxiv | 2023 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/36711595 |
| Structure and DNA-bridging activity of the essential Rec114-Mei4 trimer interface. | Liu K, Grasso EM, Pu S, Zou M, Liu S, Eliezer D, Keeney S | Genes & development | 37442580 | Genes Dev | 2023 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/37442580 |
| Full-length RNA profiling reveals pervasive bidirectional transcription terminators in bacteria. | Ju X, Li D, Liu S | Nature microbiology | 31308523 | Nat Microbiol | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31308523 |
| Molecular mechanism for direct actin force-sensing by α-catenin. | Mei L, Espinosa de Los Reyes S, Reynolds MJ, Leicher R, Liu S, Alushin GM | eLife | 32969337 | Elife | 2020 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/32969337 |
| Replication Fork Activation Is Enabled by a Single-Stranded DNA Gate in CMG Helicase. | Wasserman MR, Schauer GD, O'Donnell ME, Liu S | Cell | 31348887 | Cell | 2019 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/31348887 |
| Single-stranded nucleic acid binding and coacervation by linker histone H1. | Leicher R, Osunsade A, Chua GNL, Faulkner SC, Latham AP, Watters JW, Nguyen T, Beckwitt EC, Christodoulou-Rubalcava S, Young PG, Zhang B, David Y, Liu S | Nature structural & molecular biology | 35484234 | Nat Struct Mol Biol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35484234 |
| Identification of Required Host Factors for SARS-CoV-2 Infection in Human Cells. | Daniloski Z, Jordan TX, Wessels HH, Hoagland DA, Kasela S, Legut M, Maniatis S, Mimitou EP, Lu L, Geller E, Danziger O, Rosenberg BR, Phatnani H, Smibert P, Lappalainen T, tenOever BR, Sanjana NE | Cell | 33147445 | Cell | 2021 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/33147445 |
| High-Throughput Approaches to Pinpoint Function within the Noncoding Genome. | Montalbano A, Canver MC, Sanjana NE | Molecular cell | 28985510 | Mol Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28985510 |
| Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. | Liscovitch-Brauer N, Montalbano A, Deng J, Méndez-Mancilla A, Wessels HH, Moss NG, Kung CY, Sookdeo A, Guo X, Geller E, Jaini S, Smibert P, Sanjana NE | Nature biotechnology | 33927415 | Nat Biotechnol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33927415 |
| Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus. | Kasela S, Daniloski Z, Jordan TX, tenOever BR, Sanjana NE, Lappalainen T | medRxiv : the preprint server for health sciences | 33880488 | medRxiv | 2021 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/33880488 |
| Applying genome-wide CRISPR-Cas9 screens for therapeutic discovery in facioscapulohumeral muscular dystrophy. | Lek A, Zhang Y, Woodman KG, Huang S, DeSimone AM, Cohen J, Ho V, Conner J, Mead L, Kodani A, Pakula A, Sanjana N, King OD, Jones PL, Wagner KR, Lek M, Kunkel LM | Science translational medicine | 32213627 | Sci Transl Med | 2020 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/32213627 |
| Expanding the Scope of Bacterial CRISPR Activation with PAM-Flexible dCas9 Variants. | Kiattisewee C, Karanjia AV, Legut M, Daniloski Z, Koplik SE, Nelson J, Kleinstiver BP, Sanjana NE, Carothers JM, Zalatan JG | ACS synthetic biology | 36378874 | ACS Synth Biol | 2022 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/36378874 |
| Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase. | Ferrarone JR, Thomas J, Unni AM, Zheng Y, Nagiec MJ, Gardner EE, Mashadova O, Li K, Koundouros N, Montalbano A, Mustafa M, Cantley LC, Blenis J, Sanjana NE, Varmus H | Proceedings of the National Academy of Sciences of the United States of America | 38743625 | Proc Natl Acad Sci U S A | 2024 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/38743625 |
| Recurrent somatic mutations as predictors of immunotherapy response. | Gajic ZZ, Deshpande A, Legut M, Imieliński M, Sanjana NE | Nature communications | 35803911 | Nat Commun | 2022 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/35803911 |
| The BTB transcription factors ZBTB11 and ZFP131 maintain pluripotency by repressing pro-differentiation genes. | Garipler G, Lu C, Morrissey A, Lopez-Zepeda LS, Pei Y, Vidal SE, Zen Petisco Fiore AP, Aydin B, Stadtfeld M, Ohler U, Mahony S, Sanjana NE, Mazzoni EO | Cell reports | 35294876 | Cell Rep | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/35294876 |
| Overexpression of NEUROG2 and NEUROG1 in human embryonic stem cells produces a network of excitatory and inhibitory neurons. | Lu C, Shi X, Allen A, Baez-Nieto D, Nikish A, Sanjana NE, Pan JQ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 30698461 | FASEB J | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30698461 |
| High-Throughput Screens of PAM-Flexible Cas9 Variants for Gene Knockout and Transcriptional Modulation. | Legut M, Daniloski Z, Xue X, McKenzie D, Guo X, Wessels HH, Sanjana NE | Cell reports | 32130891 | Cell Rep | 2020 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/32130891 |
| GFAP Mutations in Astrocytes Impair Oligodendrocyte Progenitor Proliferation and Myelination in an hiPSC Model of Alexander Disease. | Li L, Tian E, Chen X, Chao J, Klein J, Qu Q, Sun G, Sun G, Huang Y, Warden CD, Ye P, Feng L, Li X, Cui Q, Sultan A, Douvaras P, Fossati V, Sanjana NE, Riggs AD, Shi Y | Cell stem cell | 30075130 | Cell Stem Cell | 2018 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/30075130 |
| A genome-wide net to catch and understand cancer. | Sanjana NE | Science translational medicine | 30089637 | Sci Transl Med | 2018 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/30089637 |
| Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens. | Morris JA, Caragine C, Daniloski Z, Domingo J, Barry T, Lu L, Davis K, Ziosi M, Glinos DA, Hao S, Mimitou EP, Smibert P, Roeder K, Katsevich E, Lappalainen T, Sanjana NE | Science (New York, N.Y.) | 37141313 | Science | 2023 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/37141313 |
| Heterozygous deletion of the autism-associated gene CHD8 impairs synaptic function through widespread changes in gene expression and chromatin compaction. | Shi X, Lu C, Corman A, Nikish A, Zhou Y, Platt RJ, Iossifov I, Zhang F, Pan JQ, Sanjana NE | American journal of human genetics | 37802044 | Am J Hum Genet | 2023 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/37802044 |
| Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition. | Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG | The Journal of experimental medicine | 36820830 | J Exp Med | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/36820830 |
| Essential transcription factors for induced neuron differentiation. | Lu C, Garipler G, Dai C, Roush T, Salome-Correa J, Martin A, Liscovitch-Brauer N, Mazzoni EO, Sanjana NE | Nature communications | 38102126 | Nat Commun | 2023 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/38102126 |
| Prediction of on-target and off-target activity of CRISPR-Cas13d guide RNAs using deep learning. | Wessels HH, Stirn A, Méndez-Mancilla A, Kim EJ, Hart SK, Knowles DA, Sanjana NE | Nature biotechnology | 37400521 | Nat Biotechnol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37400521 |
| Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. | Schertzer MD, Stirn A, Isaev K, Pereira L, Das A, Harbison C, Park SH, Wessels HH, Sanjana NE, Knowles DA | bioRxiv : the preprint server for biology | 37745416 | bioRxiv | 2023 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/37745416 |
| Next-generation forward genetic screens: uniting high-throughput perturbations with single-cell analysis. | Morris JA, Sun JS, Sanjana NE | Trends in genetics : TIG | 37989654 | Trends Genet | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37989654 |
| Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling. | Yan RE, Corman A, Katgara L, Wang X, Xue X, Gajic ZZ, Sam R, Farid M, Friedman SM, Choo J, Raimondi I, Ganesan S, Katsevich E, Greenfield JP, Dahmane N, Sanjana NE | Nature biotechnology | 39572737 | Nat Biotechnol | 2024 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/39572737 |
| The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. | Daniloski Z, Jordan TX, Ilmain JK, Guo X, Bhabha G, tenOever BR, Sanjana NE | eLife | 33570490 | Elife | 2021 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/33570490 |
| Massively parallel Cas13 screens reveal principles for guide RNA design. | Wessels HH, Méndez-Mancilla A, Guo X, Legut M, Daniloski Z, Sanjana NE | Nature biotechnology | 32518401 | Nat Biotechnol | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32518401 |
| Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells. | Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov SB, Smibert P | Nature methods | 31011186 | Nat Methods | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31011186 |
| Identification of Cancer Drivers at CTCF Insulators in 1,962 Whole Genomes. | Liu EM, Martinez-Fundichely A, Diaz BJ, Aronson B, Cuykendall T, MacKay M, Dhingra P, Wong EWP, Chi P, Apostolou E, Sanjana NE, Khurana E | Cell systems | 31078526 | Cell Syst | 2019 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/31078526 |
| A genome-scale screen for synthetic drivers of T cell proliferation. | Legut M, Gajic Z, Guarino M, Daniloski Z, Rahman JA, Xue X, Lu C, Lu L, Mimitou EP, Hao S, Davoli T, Diefenbach C, Smibert P, Sanjana NE | Nature | 35296855 | Nature | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35296855 |
| Chemically modified guide RNAs enhance CRISPR-Cas13 knockdown in human cells. | Méndez-Mancilla A, Wessels HH, Legut M, Kadina A, Mabuchi M, Walker J, Robb GB, Holden K, Sanjana NE | Cell chemical biology | 34343484 | Cell Chem Biol | 2022 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/34343484 |
| Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq. | Wessels HH, Méndez-Mancilla A, Hao Y, Papalexi E, Mauck WM 3rd, Lu L, Morris JA, Mimitou EP, Smibert P, Sanjana NE, Satija R | Nature methods | 36550277 | Nat Methods | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36550277 |
| Transcriptome-wide Cas13 guide RNA design for model organisms and viral RNA pathogens. | Guo X, Rahman JA, Wessels HH, Méndez-Mancilla A, Haro D, Chen X, Sanjana NE | Cell genomics | 35664829 | Cell Genom | 2021 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/35664829 |
| Cancer genes disfavoring T cell immunity identified via integrated systems approach. | Kishton RJ, Patel SJ, Decker AE, Vodnala SK, Cam M, Yamamoto TN, Patel Y, Sukumar M, Yu Z, Ji M, Henning AN, Gurusamy D, Palmer DC, Stefanescu RA, Girvin AT, Lo W, Pasetto A, Malekzadeh P, Deniger DC, Wood KC, Sanjana NE, Restifo NP | Cell reports | 35926468 | Cell Rep | 2022 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/35926468 |
| Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells. | Liang WW, Müller S, Hart SK, Wessels HH, Méndez-Mancilla A, Sookdeo A, Choi O, Caragine CM, Corman A, Lu L, Kolumba O, Williams B, Sanjana NE | Cell | 39532094 | Cell | 2024 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/39532094 |
| Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers. | Caragine CM, Le VT, Mustafa M, Diaz BJ, Morris JA, Müller S, Mendez-Mancilla A, Geller E, Liscovitch-Brauer N, Sanjana NE | Nature communications | 39948336 | Nat Commun | 2025 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/39948336 |
| Generation of a knock-in MAP2-tdTomato reporter human embryonic stem cell line with inducible expression of NEUROG2/1 (NYGCe001-A). | Lu C, Sanjana NE | Stem cell research | 31707212 | Stem Cell Res | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31707212 |
| The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types. | Daniloski Z, Jordan TX, Ilmain JK, Guo X, Bhabha G, tenOever BR, Sanjana NE | bioRxiv : the preprint server for biology | 32587969 | bioRxiv | 2020 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/32587969 |
| Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus. | Kasela S, Daniloski Z, Bollepalli S, Jordan TX, tenOever BR, Sanjana NE, Lappalainen T | Genome biology | 34425859 | Genome Biol | 2021 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/34425859 |
| Tracking cell lineages to improve research reproducibility. | Zaaijer S, Groen SC, Sanjana NE | Nature biotechnology | 34012093 | Nat Biotechnol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34012093 |
| Non-linear transcriptional responses to gradual modulation of transcription factor dosage. | Domingo J, Minaeva M, Morris JA, Ghatan S, Ziosi M, Sanjana NE, Lappalainen T | bioRxiv : the preprint server for biology | 38464330 | bioRxiv | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/38464330 |
| Precise RNA targeting with CRISPR-Cas13d. | Hart SK, Müller S, Wessels HH, Méndez-Mancilla A, Drabavicius G, Choi O, Sanjana NE | Nature biotechnology | 39934271 | Nat Biotechnol | 2025 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/39934271 |
| Identifying DNase I hypersensitive sites as driver distal regulatory elements in breast cancer. | D Antonio M, Weghorn D, D Antonio-Chronowska A, Coulet F, Olson KM, DeBoever C, Drees F, Arias A, Alakus H, Richardson AL, Schwab RB, Farley EK, Sunyaev SR, Frazer KA | Nature communications | 28874753 | Nat Commun | 2017 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/28874753 |
| A global transcriptional network connecting noncoding mutations to changes in tumor gene expression. | Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T | Nature genetics | 29610481 | Nat Genet | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29610481 |
| Functional genomic approaches to elucidate the role of enhancers during development. | Ryan GE, Farley EK | Wiley interdisciplinary reviews. Systems biology and medicine | 31808313 | Wiley Interdiscip Rev Syst Biol Med | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31808313 |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. | Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD | Science (New York, N.Y.) | 34045355 | Science | 2021 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/34045355 |
| Enhancer grammar in development, evolution, and disease: dependencies and interplay. | Jindal GA, Farley EK | Developmental cell | 33689769 | Dev Cell | 2021 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/33689769 |
| Diverse logics and grammar encode notochord enhancers. | Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK | Cell reports | 36729834 | Cell Rep | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/36729834 |
| Predictive analyses of regulatory sequences with EUGENe. | Klie A, Laub D, Talwar JV, Stites H, Jores T, Solvason JJ, Farley EK, Carter H | Nature computational science | 38177592 | Nat Comput Sci | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38177592 |
| Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. | DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA | Cell stem cell | 28388430 | Cell Stem Cell | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28388430 |
| Affinity-optimizing enhancer variants disrupt development. | Lim F, Solvason JJ, Ryan GE, Le SH, Jindal GA, Steffen P, Jandu SK, Farley EK | Nature | 38233525 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38233525 |
| Conserved enhancer logic controls the notochord expression of vertebrate Brachyury. | Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A | bioRxiv : the preprint server for biology | 37131681 | bioRxiv | 2023 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/37131681 |
| Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. | Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK | Developmental cell | 37848026 | Dev Cell | 2023 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/37848026 |
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| A single-cell transcriptional roadmap for cardiopharyngeal fate diversification. | Wang W, Niu X, Stuart T, Jullian E, Mauck WM 3rd, Kelly RG, Satija R, Christiaen L | Nature cell biology | 31160712 | Nat Cell Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31160712 |
| Comprehensive Integration of Single-Cell Data. | Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R | Cell | 31178118 | Cell | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31178118 |
| Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features. | Konstantinides N, Kapuralin K, Fadil C, Barboza L, Satija R, Desplan C | Cell | 29909983 | Cell | 2018 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/29909983 |
| Single cell transcriptomics in human osteoarthritis synovium and in silico deconvoluted bulk RNA sequencing. | Huang ZY, Luo ZY, Cai YR, Chou CH, Yao ML, Pei FX, Kraus VB, Zhou ZK | Osteoarthritis and cartilage | 34971754 | Osteoarthritis Cartilage | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34971754 |
| Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation. | Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R | Nature communications | 29476078 | Nat Commun | 2018 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/29476078 |
| Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. | Stoeckius M, Zheng S, Houck-Loomis B, Hao S, Yeung BZ, Mauck WM 3rd, Smibert P, Satija R | Genome biology | 30567574 | Genome Biol | 2018 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/30567574 |
| Integrating single-cell transcriptomic data across different conditions, technologies, and species. | Butler A, Hoffman P, Smibert P, Papalexi E, Satija R | Nature biotechnology | 29608179 | Nat Biotechnol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29608179 |
| Simultaneous epitope and transcriptome measurement in single cells. | Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P | Nature methods | 28759029 | Nat Methods | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28759029 |
| Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors. | Villani AC, Satija R, Reynolds G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N | Science (New York, N.Y.) | 28428369 | Science | 2017 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/28428369 |
| A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells. | Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO | Cell stem cell | 27939218 | Cell Stem Cell | 2017 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/27939218 |
| Toward a Common Coordinate Framework for the Human Body. | Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R | Cell | 31835027 | Cell | 2019 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/31835027 |
| Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens. | Papalexi E, Mimitou EP, Butler AW, Foster S, Bracken B, Mauck WM 3rd, Wessels HH, Hao Y, Yeung BZ, Smibert P, Satija R | Nature genetics | 33649593 | Nat Genet | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33649593 |
| Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | Hafemeister C, Satija R | Genome biology | 31870423 | Genome Biol | 2019 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/31870423 |
| A Reproducibility Focused Meta-Analysis Method for Single-Cell Transcriptomic Case-Control Studies Uncovers Robust Differentially Expressed Genes. | Nakatsuka N, Adler D, Jiang L, Hartman A, Cheng E, Klann E, Satija R | bioRxiv : the preprint server for biology | 39463993 | bioRxiv | 2025 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/39463993 |
| Developmental diversification of cortical inhibitory interneurons. | Mayer C, Hafemeister C, Bandler RC, Machold R, Batista Brito R, Jaglin X, Allaway K, Butler A, Fishell G, Satija R | Nature | 29513653 | Nature | 2018 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/29513653 |
| The bone marrow microenvironment at single-cell resolution. | Tikhonova AN, Dolgalev I, Hu H, Sivaraj KK, Hoxha E, Cuesta-Domínguez Á, Pinho S, Akhmetzyanova I, Gao J, Witkowski M, Guillamot M, Gutkin MC, Zhang Y, Marier C, Diefenbach C, Kousteni S, Heguy A, Zhong H, Fooksman DR, Butler JM, Economides A, Frenette PS, Adams RH, Satija R, Tsirigos A, Aifantis I | Nature | 30971824 | Nature | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30971824 |
| Comparison and evaluation of statistical error models for scRNA-seq. | Choudhary S, Satija R | Genome biology | 35042561 | Genome Biol | 2022 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/35042561 |
| Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells. | Blair JD, Hartman A, Zenk F, Dalgarno C, Treutlein B, Satija R | bioRxiv : the preprint server for biology | 37034703 | bioRxiv | 2023 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/37034703 |
| Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro. | Zhang B, Srivastava A, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R | Nature biotechnology | 35332340 | Nat Biotechnol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35332340 |
| Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells. | Blair JD, Hartman A, Zenk F, Wahle P, Brancati G, Dalgarno C, Treutlein B, Satija R | Nature communications | 39905064 | Nat Commun | 2025 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/39905064 |
| Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs. | Breton G, Zheng S, Valieris R, Tojal da Silva I, Satija R, Nussenzweig MC | The Journal of experimental medicine | 27864467 | J Exp Med | 2016 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/27864467 |
| Single-cell chromatin state analysis with Signac. | Stuart T, Srivastava A, Madad S, Lareau CA, Satija R | Nature methods | 34725479 | Nat Methods | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34725479 |
| Integrated analysis of multimodal single-cell data. | Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LM, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P, Satija R | Cell | 34062119 | Cell | 2021 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/34062119 |
| Dictionary learning for integrative, multimodal and scalable single-cell analysis. | Hao Y, Stuart T, Kowalski MH, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R | Nature biotechnology | 37231261 | Nat Biotechnol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37231261 |
| Shifting early embryology paradigms: Applications of stem cell-based embryo models in bioengineering. | Abel A, Sozen B | Current opinion in genetics & development | 37392541 | Curr Opin Genet Dev | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37392541 |
| A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression. | Cao D, Zhong L, Hemalatha A, Bergmann J, Cox AL, Greco V, Sozen B | bioRxiv : the preprint server for biology | 37333168 | bioRxiv | 2023 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/37333168 |
| Pluripotent cell states and fates in human embryo models. | Sozen B, Tam PPL, Pera MF | Development (Cambridge, England) | 40171916 | Development | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40171916 |
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| Navigating human embryogenesis through tailored model selection. | Sozen B | Nature cell biology | 39528699 | Nat Cell Biol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39528699 |
| Improving Biological Joint Moment Estimation During Real-World Tasks With EMG and Instrumented Insoles. | Scherpereel KL, Molinaro DD, Shepherd MK, Inan OT, Young AJ | IEEE transactions on bio-medical engineering | 38619965 | IEEE Trans Biomed Eng | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38619965 |
| A Data-Driven Approach to Estimate Human Center of Mass State During Perturbed Locomotion Using Simulated Wearable Sensors. | Leestma JK, Smith CR, Sawicki GS, Young AJ | Annals of biomedical engineering | 38558352 | Ann Biomed Eng | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38558352 |
| A Deep Learning Framework for End-to-End Control of Powered Prostheses. | Nuesslein CPO, Young AJ | IEEE robotics and automation letters | 40012860 | IEEE Robot Autom Lett | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/40012860 |
| A Review of Current State-of-the-Art Control Methods for Lower-Limb Powered Prostheses. | Gehlhar R, Tucker M, Young AJ, Ames AD | Annual reviews in control | 37635763 | Annu Rev Control | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37635763 |
| Dynamic Duo: Design and Validation of an Autonomous Frontal and Sagittal Actuating Hip Exoskeleton for Balance Modulation During Perturbed Locomotion. | Leestma JK, Mathur S, Anderton MD, Sawicki GS, Young AJ | IEEE robotics and automation letters | 40012859 | IEEE Robot Autom Lett | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/40012859 |
| Mode-Unified Intent Estimation of a Robotic Prosthesis using Deep-Learning. | Kim H, Lee D, Maldonado-Contreras JY, Zhou S, Herrin KR, Young AJ | IEEE robotics and automation letters | 40124848 | IEEE Robot Autom Lett | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40124848 |
| Mechanisms of Regeneration and Fibrosis in the Endometrium. | Ang CJ, Skokan TD, McKinley KL | Annual review of cell and developmental biology | 37843929 | Annu Rev Cell Dev Biol | 2023 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/37843929 |
| Emerging frontiers in regenerative medicine. | McKinley KL, Longaker MT, Naik S | Science (New York, N.Y.) | 37228215 | Science | 2023 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/37228215 |
| Reconstructing axial progenitor field dynamics in mouse stem cell-derived embryoids. | Bolondi A, Law BK, Kretzmer H, Gassaloglu SI, Buschow R, Riemenschneider C, Yang D, Walther M, Veenvliet JV, Meissner A, Smith ZD, Chan MM | Developmental cell | 38579718 | Dev Cell | 2024 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/38579718 |
| Inferring cell differentiation maps from lineage tracing data. | Sashittal P, Zhang RY, Law BK, Strzalkowski A, Schmidt H, Bolondi A, Chan MM, Raphael BJ | bioRxiv : the preprint server for biology | 39314473 | bioRxiv | 2024 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/39314473 |
| Diffusion barriers imposed by tissue topology shape Hedgehog morphogen gradients. | Schlissel G, Meziane M, Narducci D, Hansen AS, Li P | Proceedings of the National Academy of Sciences of the United States of America | 39190357 | Proc Natl Acad Sci U S A | 2024 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/39190357 |
| Lhx2 is a progenitor-intrinsic modulator of Sonic Hedgehog signaling during early retinal neurogenesis. | Li X, Gordon PJ, Gaynes JA, Fuller AW, Ringuette R, Santiago CP, Wallace V, Blackshaw S, Li P, Levine EM | eLife | 36459481 | Elife | 2022 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/36459481 |
| A cluster of RNA Polymerase II molecules is stably associated with an active gene. | Mukherjee A, Kapoor M, Shankta K, Fallacaro S, Carter RD, Ratchasanmuang P, Haloush YI, Mir M | bioRxiv : the preprint server for biology | 39990393 | bioRxiv | 2025 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/39990393 |
| A fine kinetic balance of interactions directs transcription factor hubs to genes. | Fallacaro S, Mukherjee A, Ratchasanmuang P, Zinski J, Haloush YI, Shankta K, Mir M | bioRxiv : the preprint server for biology | 38659757 | bioRxiv | 2024 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/38659757 |
| Localization of the Drosophila pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression. | Gaskill MM, Soluri IV, Branks AE, Boka AP, Stadler MR, Vietor K, Huang HS, Gibson TJ, Mukherjee A, Mir M, Blythe SA, Harrison MM | Developmental cell | 37478844 | Dev Cell | 2023 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/37478844 |
| Dynamic microenvironments shape nuclear organization and gene expression. | Hayward-Lara G, Fischer MD, Mir M | Current opinion in genetics & development | 38461773 | Curr Opin Genet Dev | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38461773 |
| DNA methylation in mammalian development and disease. | Smith ZD, Hetzel S, Meissner A | Nature reviews. Genetics | 39134824 | Nat Rev Genet | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39134824 |
| DOT1L promotes spermatid differentiation by regulating expression of genes required for histone-to-protamine replacement. | Malla AB, Rainsford SR, Smith ZD, Lesch BJ | Development (Cambridge, England) | 37082969 | Development | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/37082969 |
| Dynamic antagonism between key repressive pathways maintains the placental epigenome. | Weigert R, Hetzel S, Bailly N, Haggerty C, Ilik IA, Yung PYK, Navarro C, Bolondi A, Kumar AS, Anania C, Brändl B, Meierhofer D, Lupiáñez DG, Müller FJ, Aktas T, Elsässer SJ, Kretzmer H, Smith ZD, Meissner A | Nature cell biology | 37024684 | Nat Cell Biol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37024684 |
| DOT1L bridges transcription and heterochromatin formation at mammalian pericentromeres. | Malla AB, Yu H, Farris D, Kadimi S, Lam TT, Cox AL, Smith ZD, Lesch BJ | EMBO reports | 37317657 | EMBO Rep | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37317657 |
| Autonomous transposons tune their sequences to ensure somatic suppression. | Ilık İA, Glažar P, Tse K, Brändl B, Meierhofer D, Müller FJ, Smith ZD, Aktaş T | Nature | 38355802 | Nature | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38355802 |
| A qualitative exploration of the eight dimensions of wellness in opioid use disorder recovery during the postpartum period. | Mallahan S, Armin J, Bueno Y, Huff A, Allen A | Drug and alcohol dependence reports | 37131999 | Drug Alcohol Depend Rep | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37131999 |
| Neurophysin I is an analytically robust surrogate biomarker for oxytocin. | MacLean EL, Carranza E, Gnanadesikan GE, King KM, Allen AM, Linde-Krieger LB, Feldman R, White-Traut RC, Hammock EAD, Carter CS, Leng G, Tecot SR, Bell AF | Psychoneuroendocrinology | 38194845 | Psychoneuroendocrinology | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38194845 |
| Opportunities to expand postpartum support for those in recovery from opioid use disorder: Results from a qualitative study. | Allen A, Bueno Y, Mallahan S, MacPherson AH, Armin J | Drug and alcohol dependence reports | 37334156 | Drug Alcohol Depend Rep | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37334156 |
| Babywearing Reduces Urges to Use Substances in the Postpartum Period Among Mothers With OUDs. | Rankin L, Grisham LM, Mendoza N, Allen A | Substance use & misuse | 38404001 | Subst Use Misuse | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38404001 |
| Post-transcriptional tuning of FGF signaling mediates neural crest induction. | Copeland J, Simoes-Costa M | Proceedings of the National Academy of Sciences of the United States of America | 33376218 | Proc Natl Acad Sci U S A | 2020 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/33376218 |
| Frank Beach Award Winner: Lessons from poison frogs on ecological drivers of behavioral diversification. | O'Connell LA | Hormones and behavior | 33039350 | Horm Behav | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33039350 |
| The Parental Dilemma: How Evolution of Diverse Strategies for Infant Care Informs Social Behavior Circuits. | Autry AE, O'Connell LA | Frontiers in neural circuits | 34867211 | Front Neural Circuits | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34867211 |
| Effects of parental care on skin microbial community composition in poison frogs. | Fischer MT, Xue KS, Costello EK, Dvorak M, Raboisson G, Robaczewska A, Caty SN, Relman DA, O'Connell LA | bioRxiv : the preprint server for biology | 39314287 | bioRxiv | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/39314287 |
| Evolutionary insights into sexual behavior from whiptail lizards. | O'Connell LA, Crews D | Journal of experimental zoology. Part A, Ecological and integrative physiology | 33929097 | J Exp Zool A Ecol Integr Physiol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33929097 |
| A toxic environment selects for specialist microbiome in poison frogs. | Caty SN, Alvarez-Buylla A, Vasek C, Tapia EE, Martin NA, McLaughlin T, Weber PK, Mayali X, Coloma LA, Morris MM, O'Connell LA | bioRxiv : the preprint server for biology | 38260330 | bioRxiv | 2024 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/38260330 |
| Infanticide is driven by unfamiliarity with offspring location and associated with androgenic shifts in mimic poison frogs. | Lewis AR, Goolsby BC, Juarez BH, Lacey MP, O'Connell LA | Hormones and behavior | 39514924 | Horm Behav | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39514924 |
| Studying convergent evolution to relate genotype to behavioral phenotype. | Gallant JR, O'Connell LA | The Journal of experimental biology | 32034050 | J Exp Biol | 2020 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/32034050 |
| Social boldness correlates with brain gene expression in male green anoles. | Kabelik D, Julien AR, Ramirez D, O'Connell LA | Hormones and behavior | 34102460 | Horm Behav | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34102460 |
| Infanticide is driven by unfamiliarity with offspring location and associated with androgenic shifts in mimic poison frogs. | Lewis AR, Goolsby BC, Juarez BH, Lacey MP, O'Connell LA | bioRxiv : the preprint server for biology | 39484385 | bioRxiv | 2024 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/39484385 |
| Aggressive but not reproductive boldness in male green anole lizards correlates with baseline vasopressin activity. | Kabelik D, Julien AR, Waddell BR, Batschelett MA, O'Connell LA | Hormones and behavior | 35066329 | Horm Behav | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35066329 |
| Home security cameras as a tool for behavior observations and science affordability. | Goolsby BC, Fischer MT, Chen TG, Pareja-Mejía D, Shaykevich DA, Lewis AR, Raboisson G, Lacey MP, O'Connell LA | bioRxiv : the preprint server for biology | 37131676 | bioRxiv | 2024 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/37131676 |
| Activity of FoxP2-positive neurons is associated with tadpole begging behavior. | Ludington SC, McKinney JE, Butler JM, Goolsby BC, Callan AA, Gaines-Richardson M, O'Connell LA | bioRxiv : the preprint server for biology | 37292748 | bioRxiv | 2024 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37292748 |
| Tadpoles rely on mechanosensory stimuli for communication when visual capabilities are poor. | Butler JM, McKinney JE, Ludington SC, Mabogunje M, Baker P, Singh D, Edwards SV, O'Connell LA | Developmental biology | 38851558 | Dev Biol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38851558 |
| Physiological state matching in a pair bonded poison frog. | Nowicki JP, Rodríguez C, Lee JC, Goolsby BC, Yang C, Cleland TA, O'Connell LA | Royal Society open science | 39076367 | R Soc Open Sci | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39076367 |
| Bacterial metabolism of bile acids promotes generation of peripheral regulatory T cells. | Campbell C, McKenney PT, Konstantinovsky D, Isaeva OI, Schizas M, Verter J, Mai C, Jin WB, Guo CJ, Violante S, Ramos RJ, Cross JR, Kadaveru K, Hambor J, Rudensky AY | Nature | 32461639 | Nature | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32461639 |
| A metabolic pathway for bile acid dehydroxylation by the gut microbiome. | Funabashi M, Grove TL, Wang M, Varma Y, McFadden ME, Brown LC, Guo C, Higginbottom S, Almo SC, Fischbach MA | Nature | 32555455 | Nature | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32555455 |
| Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation. | Arifuzzaman M, Won TH, Li TT, Yano H, Digumarthi S, Heras AF, Zhang W, Parkhurst CN, Kashyap S, Jin WB, Putzel GG, Tsou AM, Chu C, Wei Q, Grier A, JRI IBD Live Cell Bank Consortium, Worgall S, Guo CJ, Schroeder FC, Artis D | Nature | 36323778 | Nature | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36323778 |
| Gut-innervating nociceptors regulate the intestinal microbiota to promote tissue protection. | Zhang W, Lyu M, Bessman NJ, Xie Z, Arifuzzaman M, Yano H, Parkhurst CN, Chu C, Zhou L, Putzel GG, Li TT, Jin WB, Zhou J, JRI Live Cell Bank, Hu H, Tsou AM, Guo CJ, Artis D | Cell | 36240781 | Cell | 2022 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/36240781 |
| Nutritional regulation of microbiota-derived metabolites: Implications for immunity and inflammation. | Arifuzzaman M, Collins N, Guo CJ, Artis D | Immunity | 38198849 | Immunity | 2024 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/38198849 |
| Host metabolism balances microbial regulation of bile acid signalling. | Won TH, Arifuzzaman M, Parkhurst CN, Miranda IC, Zhang B, Hu E, Kashyap S, Letourneau J, Jin WB, Fu Y, Guzior DV, JRI Live Cell Bank, Quinn RA, Guo CJ, David LA, Artis D, Schroeder FC | Nature | 39779854 | Nature | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39779854 |
| Adherent-invasive E. coli metabolism of propanediol in Crohn's disease regulates phagocytes to drive intestinal inflammation. | Viladomiu M, Metz ML, Lima SF, Jin WB, Chou L, JRI Live Cell Bank, Guo CJ, Diehl GE, Simpson KW, Scherl EJ, Longman RS | Cell host & microbe | 33539767 | Cell Host Microbe | 2021 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/33539767 |
| Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. | Sargsian S, Lejeune A, Ercelen D, Jin WB, Varghese A, Loke P, Lim YAL, Guo CJ, Cadwell K | bioRxiv : the preprint server for biology | 37333296 | bioRxiv | 2023 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/37333296 |
| Microbiota metabolism of intestinal amino acids impacts host nutrient homeostasis and physiology. | Li TT, Chen X, Huo D, Arifuzzaman M, Qiao S, Jin WB, Shi H, Li XV, JRI Live Cell Bank Consortium, Iliev ID, Artis D, Guo CJ | Cell host & microbe | 38657606 | Cell Host Microbe | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38657606 |
| Functional characterization of helminth-associated Clostridiales reveals covariates of Treg differentiation. | Sargsian S, Mondragón-Palomino O, Lejeune A, Ercelen D, Jin WB, Varghese A, Lim YAL, Guo CJ, Loke P, Cadwell K | Microbiome | 38730492 | Microbiome | 2024 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/38730492 |
| Gut bacteria-derived serotonin promotes immune tolerance in early life. | Sanidad KZ, Rager SL, Carrow HC, Ananthanarayanan A, Callaghan R, Hart LR, Li T, Ravisankar P, Brown JA, Amir M, Jin JC, Savage AR, Luo R, Rowdo FM, Martin ML, Silver RB, Guo CJ, Krumsiek J, Inohara N, Zeng MY | Science immunology | 38489352 | Sci Immunol | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/38489352 |
| Tumor-produced and aging-associated oncometabolite methylmalonic acid promotes cancer-associated fibroblast activation to drive metastatic progression. | Li Z, Low V, Luga V, Sun J, Earlie E, Parang B, Shobana Ganesh K, Cho S, Endress J, Schild T, Hu M, Lyden D, Jin W, Guo C, Dephoure N, Cantley LC, Laughney AM, Blenis J | Nature communications | 36266345 | Nat Commun | 2022 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/36266345 |
| Gut microbiota-derived metabolites confer protection against SARS-CoV-2 infection. | Brown JA, Sanidad KZ, Lucotti S, Lieber CM, Cox RM, Ananthanarayanan A, Basu S, Chen J, Shan M, Amir M, Schmidt F, Weisblum Y, Cioffi M, Li T, Rowdo FM, Martin ML, Guo CJ, Lyssiotis C, Layden BT, Dannenberg AJ, Bieniasz PD, Lee B, Inohara N, Matei I, Plemper RK, Zeng MY | Gut microbes | 35915556 | Gut Microbes | 2022 Jan-Dec | https://www.ncbi.nlm.nih.gov/pubmed/35915556 |
| Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome. | Jin WB, Li TT, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi HQ, Wang A, Putzel GG, Longman RS, Artis D, Guo CJ | Cell | 35051369 | Cell | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35051369 |
| Depletion of microbiome-derived molecules in the host using Clostridium genetics. | Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, Nagashima K, Fischer CR, Sonnenburg JL, Spitzer MH, Fischbach MA | Science (New York, N.Y.) | 31831639 | Science | 2019 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/31831639 |
| Dietary fiber is a critical determinant of pathologic ILC2 responses and intestinal inflammation. | Arifuzzaman M, Won TH, Yano H, Uddin J, Emanuel ER, Hu E, Zhang W, Li TT, Jin WB, Grier A, Kashyap S, JRI Live Cell Bank, Guo CJ, Schroeder FC, Artis D | The Journal of experimental medicine | 38506708 | J Exp Med | 2024 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/38506708 |
| MRI in disorders of consciousness. | Snider SB, Edlow BL | Current opinion in neurology | 33044234 | Curr Opin Neurol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33044234 |
| Tractography-Pathology Correlations in Traumatic Brain Injury: A TRACK-TBI Study. | Nolan AL, Petersen C, Iacono D, Mac Donald CL, Mukherjee P, van der Kouwe A, Jain S, Stevens A, Diamond BR, Wang R, Markowitz AJ, Fischl B, Perl DP, Manley GT, Keene CD, Diaz-Arrastia R, Edlow BL, TRACK-TBI Investigators | Journal of neurotrauma | 33412995 | J Neurotrauma | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/33412995 |
| Mapping a memory disorder using functional network analysis. | Edlow BL | Acta neurologica Scandinavica | 34231225 | Acta Neurol Scand | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34231225 |
| Early Rehabilitation for Patients with Disorders of Consciousness after Severe COVID-19. | Edlow BL | Neurocritical care | 34617252 | Neurocrit Care | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34617252 |
| Stability of extemporaneously prepared preservative-free methylphenidate 5 mg/mL intravenous solution. | Barra ME, Edlow BL, Lund JT, DeSanctis KS, Vetrano J, Reilly-Tremblay C, Zhang ER, Bodien YG, Brown EN, Solt K | American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists | 34788364 | Am J Health Syst Pharm | 2022 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/34788364 |
| Joint cortical registration of geometry and function using semi-supervised learning. | Li J, Tuckute G, Fedorenko E, Edlow BL, Fischl B, Dalca AV | ArXiv | 37744470 | ArXiv | 2023 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/37744470 |
| Ictal fMRI: Mapping Seizure Topography with Rhythmic BOLD Oscillations. | Fischer D, Rapalino O, Fecchio M, Edlow BL | Brain sciences | 36552169 | Brain Sci | 2022 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/36552169 |
| Automated detection of axonal damage along white matter tracts in acute severe traumatic brain injury. | Maffei C, Gilmore N, Snider SB, Foulkes AS, Bodien YG, Yendiki A, Edlow BL | NeuroImage. Clinical | 36529035 | Neuroimage Clin | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36529035 |
| Conventional and Investigational Approaches Leveraging Clinical EEG for Prognosis in Acute Disorders of Consciousness. | Curley WH, Comanducci A, Fecchio M | Seminars in neurology | 36100227 | Semin Neurol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36100227 |
| Pharmacologic Therapies to Promote Recovery of Consciousness. | Barra ME, Edlow BL, Brophy GM | Seminars in neurology | 36100228 | Semin Neurol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36100228 |
| Prognostication in Acute Neurological Emergencies. | Sloane KL, Miller JJ, Piquet A, Edlow BL, Rosenthal ES, Singhal AB | Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association | 35007934 | J Stroke Cerebrovasc Dis | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35007934 |
| Mapping the subcortical connectivity of the human default mode network. | Li J, Curley WH, Guerin B, Dougherty DD, Dalca AV, Fischl B, Horn A, Edlow BL | NeuroImage | 34838949 | Neuroimage | 2021 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/34838949 |
| Neuroprognostication: a conceptual framework. | Fischer D, Edlow BL, Giacino JT, Greer DM | Nature reviews. Neurology | 35352033 | Nat Rev Neurol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35352033 |
| Predicting Functional Dependency in Patients with Disorders of Consciousness: A TBI-Model Systems and TRACK-TBI Study. | Snider SB, Temkin NR, Barber J, Edlow BL, Giacino JT, Hammond FM, Izzy S, Kowalski RG, Markowitz AJ, Rovito CA, Shih SL, Zafonte RD, Manley GT, Bodien YG, TRACK-TBI investigators | Annals of neurology | 37470289 | Ann Neurol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37470289 |
| Acute biomarkers of consciousness are associated with recovery after severe traumatic brain injury. | Bodien YG, Fecchio M, Gilmore N, Freeman HJ, Sanders WR, Meydan A, Lawrence PK, Atalay AS, Kirsch J, Healy BC, Edlow BL | medRxiv : the preprint server for health sciences | 40093212 | medRxiv | 2025 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/40093212 |
| Covert consciousness. | Young MJ, Edlow BL, Bodien YG | NeuroRehabilitation | 38217619 | NeuroRehabilitation | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38217619 |
| Alpha coherence is a network signature of cognitive recovery from disorders of consciousness. | Zhou DW, Conte MM, Curley WH, Spencer-Salmon CA, Chatelle C, Rosenthal ES, Bodien YG, Victor JD, Schiff ND, Brown EN, Edlow BL | medRxiv : the preprint server for health sciences | 39417105 | medRxiv | 2024 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/39417105 |
| Model-based navigation of transcranial focused ultrasound neuromodulation in humans: Application to targeting the amygdala and thalamus. | Daneshzand M, Guerin B, Kotlarz P, Chou T, Dougherty DD, Edlow BL, Nummenmaa A | Brain stimulation | 39094682 | Brain Stimul | 2024 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/39094682 |
| Visualizing Effective Connectivity in the Human Brain. | Atalay AS, Fecchio M, Edlow BL | bioRxiv : the preprint server for biology | 40161749 | bioRxiv | 2025 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/40161749 |
| Electrophysiological correlates of thalamocortical function in acute severe traumatic brain injury. | Curley WH, Bodien YG, Zhou DW, Conte MM, Foulkes AS, Giacino JT, Victor JD, Schiff ND, Edlow BL | Cortex; a journal devoted to the study of the nervous system and behavior | 35569326 | Cortex | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35569326 |
| EEG Correlates of Language Function in Traumatic Disorders of Consciousness. | Chatelle C, Rosenthal ES, Bodien YG, Spencer-Salmon CA, Giacino JT, Edlow BL | Neurocritical care | 31900883 | Neurocrit Care | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31900883 |
| Emerging Consciousness at a Clinical Crossroads. | Young MJ, Edlow BL | AJOB neuroscience | 33960885 | AJOB Neurosci | 2021 Apr-Sep | https://www.ncbi.nlm.nih.gov/pubmed/33960885 |
| Long-Term Recovery from Disordered Consciousness Associated with COVID-19. | Fischer D, Edlow BL | Neurocritical care | 34642843 | Neurocrit Care | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34642843 |
| Risk factors for 2-year mortality in patients with prolonged disorders of consciousness: An international multicentre study. | Estraneo A, Magliacano A, Fiorenza S, Formisano R, Grippo A, Angelakis E, Cassol H, Thibaut A, Gosseries O, Lamberti G, Noé E, Bagnato S, Edlow BL, Chatelle C, Lejeune N, Veeramuthu V, Bartolo M, Mattia D, Toppi J, Zasler N, Schnakers C, Trojano L | European journal of neurology | 34657359 | Eur J Neurol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34657359 |
| Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical MRI exams with scans of different orientation, resolution and contrast. | Iglesias JE, Billot B, Balbastre Y, Tabari A, Conklin J, Gilberto González R, Alexander DC, Golland P, Edlow BL, Fischl B, Alzheimer’s Disease Neuroimaging Initiative | NeuroImage | 34048902 | Neuroimage | 2021 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/34048902 |
| Dopaminergic modulation of human consciousness via default mode network connectivity. | Edlow BL | Proceedings of the National Academy of Sciences of the United States of America | 34330840 | Proc Natl Acad Sci U S A | 2021 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/34330840 |
| Susceptibility-weighted imaging reveals cerebral microvascular injury in severe COVID-19. | Conklin J, Frosch MP, Mukerji SS, Rapalino O, Maher MD, Schaefer PW, Lev MH, Gonzalez RG, Das S, Champion SN, Magdamo C, Sen P, Harrold GK, Alabsi H, Normandin E, Shaw B, Lemieux JE, Sabeti PC, Branda JA, Brown EN, Westover MB, Huang SY, Edlow BL | Journal of the neurological sciences | 33497950 | J Neurol Sci | 2021 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/33497950 |
| Intact Brain Network Function in an Unresponsive Patient with COVID-19. | Fischer D, Threlkeld ZD, Bodien YG, Kirsch JE, Huang SY, Schaefer PW, Rapalino O, Hochberg LR, Rosen BR, Edlow BL | Annals of neurology | 32613682 | Ann Neurol | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32613682 |
| Ascending arousal network connectivity during recovery from traumatic coma. | Snider SB, Bodien YG, Frau-Pascual A, Bianciardi M, Foulkes AS, Edlow BL | NeuroImage. Clinical | 33395992 | Neuroimage Clin | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33395992 |
| Optimizing the accuracy of cortical volumetric analysis in traumatic brain injury. | Diamond BR, Donald CLM, Frau-Pascual A, Snider SB, Fischl B, Dams-O'Connor K, Edlow BL | MethodsX | 32760659 | MethodsX | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32760659 |
| Recovery from disorders of consciousness: mechanisms, prognosis and emerging therapies. | Edlow BL, Claassen J, Schiff ND, Greer DM | Nature reviews. Neurology | 33318675 | Nat Rev Neurol | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33318675 |
| SynthSR: A public AI tool to turn heterogeneous clinical brain scans into high-resolution T1-weighted images for 3D morphometry. | Iglesias JE, Billot B, Balbastre Y, Magdamo C, Arnold SE, Das S, Edlow BL, Alexander DC, Golland P, Fischl B | Science advances | 36724222 | Sci Adv | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/36724222 |
| One-Year Outcomes in Disorders of Consciousness Associated with COVID-19. | Fischer D, Edlow BL | Neurocritical care | 36324001 | Neurocrit Care | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36324001 |
| Correcting cardiorespiratory noise in resting-state functional MRI data acquired in critically ill patients. | Chan ST, Sanders WR, Fischer D, Kirsch JE, Napadow V, Bodien YG, Edlow BL | Brain communications | 36382222 | Brain Commun | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36382222 |
| Increased task-relevant fMRI responsiveness in comatose cardiac arrest patients is associated with improved neurologic outcomes. | Dhakal K, Rosenthal ES, Kulpanowski AM, Dodelson JA, Wang Z, Cudemus-Deseda G, Villien M, Edlow BL, Presciutti AM, Januzzi JL, Ning M, Taylor Kimberly W, Amorim E, Brandon Westover M, Copen WA, Schaefer PW, Giacino JT, Greer DM, Wu O | Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism | 37728641 | J Cereb Blood Flow Metab | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37728641 |
| Covert cortical processing: a diagnosis in search of a definition. | Young MJ, Fecchio M, Bodien YG, Edlow BL | Neuroscience of consciousness | 38327828 | Neurosci Conscious | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38327828 |
| Quantitative epileptiform burden and electroencephalography background features predict post-traumatic epilepsy. | Chen Y, Li S, Ge W, Jing J, Chen HY, Doherty D, Herman A, Kaleem S, Ding K, Osman G, Swisher CB, Smith C, Maciel CB, Alkhachroum A, Lee JW, Dhakar MB, Gilmore EJ, Sivaraju A, Hirsch LJ, Omay SB, Blumenfeld H, Sheth KN, Struck AF, Edlow BL, Westover MB, Kim JA | Journal of neurology, neurosurgery, and psychiatry | 36241423 | J Neurol Neurosurg Psychiatry | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36241423 |
| Characterizing coma in large vessel occlusion stroke. | Young MJ, Awad A, Andreev A, Bonkhoff AK, Schirmer MD, Dmytriw AA, Vranic JE, Rabinov JD, Doron O, Stapleton CJ, Das AS, Edlow BL, Singhal AB, Rost NS, Patel AB, Regenhardt RW | Journal of neurology | 38366071 | J Neurol | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38366071 |
| Are disorders of consciousness 'dis'connection or 'dys'connection syndromes? | Edlow BL, Massimini M | Brain communications | 38410155 | Brain Commun | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38410155 |
| A human brain network linked to restoration of consciousness after deep brain stimulation. | Warren AEL, Raguž M, Friedrich H, Schaper FLWVJ, Tasserie J, Snider SB, Li J, Chua MMJ, Butenko K, Friedrich MU, Jha R, Iglesias JE, Carney PW, Fischer D, Fox MD, Boes AD, Edlow BL, Horn A, Chudy D, Rolston JD | medRxiv : the preprint server for health sciences | 39484242 | medRxiv | 2024 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/39484242 |
| Cortical lesions and focal white matter injury are associated with attentional performance in chronic traumatic brain injury. | Snider SB, Gilmore N, Freeman HJ, Maffei C, Atalay A, Kumar RG, Li LM, Shi H, Bodien YG, Mac Donald CL, Dams-O'Connor K, Edlow BL | Brain communications | 39926612 | Brain Commun | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/39926612 |
| Early Seizures Are Predictive of Worse Health-Related Quality of Life at Follow-Up After Intracerebral Hemorrhage. | Naidech AM, Weaver B, Maas M, Bleck TP, VanHaerents S, Schuele SU | Critical care medicine | 33729725 | Crit Care Med | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/33729725 |
| A state-space model for dynamic functional connectivity. | Chakravarty S, Threlkeld ZD, Bodien YG, Edlow BL, Brown EN | Conference record. Asilomar Conference on Signals, Systems & Computers | 32801606 | Conf Rec Asilomar Conf Signals Syst Comput | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32801606 |
| 7 Tesla MRI of the ex vivo human brain at 100 micron resolution. | Edlow BL, Mareyam A, Horn A, Polimeni JR, Witzel T, Tisdall MD, Augustinack JC, Stockmann JP, Diamond BR, Stevens A, Tirrell LS, Folkerth RD, Wald LL, Fischl B, van der Kouwe A | Scientific data | 31666530 | Sci Data | 2019 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/31666530 |
| Prolonged Unconsciousness is Common in COVID-19 and Associated with Hypoxemia. | Waldrop G, Safavynia SA, Barra ME, Agarwal S, Berlin DA, Boehme AK, Brodie D, Choi JM, Doyle K, Fins JJ, Ganglberger W, Hoffman K, Mittel AM, Roh D, Mukerji SS, Der Nigoghossian C, Park S, Schenck EJ, Salazar-Schicchi J, Shen Q, Sholle E, Velazquez AG, Walline MC, Westover MB, Brown EN, Victor J, Edlow BL, Schiff ND, Claassen J | Annals of neurology | 35254675 | Ann Neurol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35254675 |
| What is a minimal clinically important difference for clinical trials in patients with disorders of consciousness? a novel probabilistic approach. | Monti MM, Spivak NM, Edlow BL, Bodien YG | PloS one | 37616196 | PLoS One | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37616196 |
| Coma Prognostication After Acute Brain Injury: A Review. | Fischer D, Edlow BL | JAMA neurology | 38436946 | JAMA Neurol | 2024 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/38436946 |
| Cross-regional coordination of activity in the human brain during autobiographical self-referential processing. | Stieger JR, Pinheiro-Chagas P, Fang Y, Li J, Lusk Z, Perry CM, Girn M, Contreras D, Chen Q, Huguenard JR, Spreng RN, Edlow BL, Wagner AD, Buch V, Parvizi J | Proceedings of the National Academy of Sciences of the United States of America | 39078679 | Proc Natl Acad Sci U S A | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39078679 |
| Measuring Consciousness in the Intensive Care Unit. | Edlow BL, Fecchio M, Bodien YG, Comanducci A, Rosanova M, Casarotto S, Young MJ, Li J, Dougherty DD, Koch C, Tononi G, Massimini M, Boly M | Neurocritical care | 37029315 | Neurocrit Care | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37029315 |
| Defining the boundary between life and death: New insights from neuropathology. | Edlow BL, Kinney HC | Journal of neuropathology and experimental neurology | 36519398 | J Neuropathol Exp Neurol | 2022 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/36519398 |
| Predicting Long-Term Recovery of Consciousness in Prolonged Disorders of Consciousness Based on Coma Recovery Scale-Revised Subscores: Validation of a Machine Learning-Based Prognostic Index. | Magliacano A, Liuzzi P, Formisano R, Grippo A, Angelakis E, Thibaut A, Gosseries O, Lamberti G, Noé E, Bagnato S, Edlow BL, Lejeune N, Veeramuthu V, Trojano L, Zasler N, Schnakers C, Bartolo M, Mannini A, Estraneo A, IBIA DoC-SIG | Brain sciences | 36672033 | Brain Sci | 2022 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/36672033 |
| Feasibility and Validity of the Coma Recovery Scale-Revised for Accelerated Standardized Testing: A Practical Assessment Tool for Detecting Consciousness in the Intensive Care Unit. | Bodien YG, Vora I, Barra A, Chiang K, Chatelle C, Goostrey K, Martens G, Malone C, Mello J, Parlman K, Ranford J, Sterling A, Waters AB, Hirschberg R, Katz DI, Mazwi N, Ni P, Velmahos G, Waak K, Edlow BL, Giacino JT | Annals of neurology | 37488068 | Ann Neurol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37488068 |
| Sustaining wakefulness: Brainstem connectivity in human consciousness. | Edlow BL, Olchanyi M, Freeman HJ, Li J, Maffei C, Snider SB, Zöllei L, Iglesias JE, Augustinack J, Bodien YG, Haynes RL, Greve DN, Diamond BR, Stevens A, Giacino JT, Destrieux C, van der Kouwe A, Brown EN, Folkerth RD, Fischl B, Kinney HC | bioRxiv : the preprint server for biology | 37502983 | bioRxiv | 2023 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37502983 |
| Histology-guided MRI segmentation of brainstem nuclei critical to consciousness. | Olchanyi MD, Augustinack J, Haynes RL, Lewis LD, Cicero N, Li J, Destrieux C, Folkerth RD, Kinney HC, Fischl B, Brown EN, Iglesias JE, Edlow BL | medRxiv : the preprint server for health sciences | 39399006 | medRxiv | 2024 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/39399006 |
| Distinct clinical phenotypes and their neuroanatomic correlates in chronic traumatic brain injury. | Kumar RG, Selmanovic E, Gilmore N, Spielman L, Li LM, Hoffman JM, Bodien YG, Snider SB, Freeman HJ, de Souza NL, Mac Donald CL, Edlow BL, Dams-O'Connor K | Brain communications | 40574978 | Brain Commun | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40574978 |
| Three-dimensional fiber orientation mapping of ex vivo human brain at micrometer resolution. | Liu CJ, Ammon W, Jones RJ, Nolan JC, Gong D, Maffei C, Blanke N, Edlow BL, Augustinack JC, Magnain C, Yendiki A, Villiger M, Fischl B, Wang H | Npj imaging.. | 40213097 | Npj Imaging | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40213097 |
| Multimodal MRI reveals brainstem connections that sustain wakefulness in human consciousness. | Edlow BL, Olchanyi M, Freeman HJ, Li J, Maffei C, Snider SB, Zöllei L, Iglesias JE, Augustinack J, Bodien YG, Haynes RL, Greve DN, Diamond BR, Stevens A, Giacino JT, Destrieux C, van der Kouwe A, Brown EN, Folkerth RD, Fischl B, Kinney HC | Science translational medicine | 38691619 | Sci Transl Med | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38691619 |
| Cortical Lesion Expansion in Chronic Traumatic Brain Injury. | Freeman HJ, Atalay AS, Li J, Sobczak E, Gilmore N, Snider SB, Healy BC, Carrington H, Selmanovic E, Pruyser A, Bura L, Sheppard D, Hunt D, Seifert AC, Bodien YG, Hoffman JM, Mac Donald CL, Dams-O'Connor K, Edlow BL | medRxiv : the preprint server for health sciences | 38978662 | medRxiv | 2025 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/38978662 |
| Distinct clinical phenotypes and their neuroanatomic correlates in chronic traumatic brain injury. | Kumar RG, Selmanovic E, Gilmore N, Spielman L, Li LM, Hoffman JM, Bodien YG, Snider SB, Freeman HJ, de Souza NL, Donald CLM, Edlow BL, Dams-O'Connor K | medRxiv : the preprint server for health sciences | 39974133 | medRxiv | 2025 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/39974133 |
| Reemergence of the language network during recovery from severe traumatic brain injury: A pilot functional MRI study. | Coffey BJ, Threlkeld ZD, Foulkes AS, Bodien YG, Edlow BL | Brain injury | 34546806 | Brain Inj | 2021 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/34546806 |
| Personalized Connectome Mapping to Guide Targeted Therapy and Promote Recovery of Consciousness in the Intensive Care Unit. | Edlow BL, Barra ME, Zhou DW, Foulkes AS, Snider SB, Threlkeld ZD, Chakravarty S, Kirsch JE, Chan ST, Meisler SL, Bleck TP, Fins JJ, Giacino JT, Hochberg LR, Solt K, Brown EN, Bodien YG | Neurocritical care | 32794142 | Neurocrit Care | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32794142 |
| Multicenter prospective study on predictors of short-term outcome in disorders of consciousness. | Estraneo A, Fiorenza S, Magliacano A, Formisano R, Mattia D, Grippo A, Romoli AM, Angelakis E, Cassol H, Thibaut A, Gosseries O, Lamberti G, Noé E, Bagnato S, Edlow BL, Chatelle C, Lejeune N, Veeramuthu V, Bartolo M, Toppi J, Zasler N, Schnakers C, Trojano L, IBIA DoC-SIG | Neurology | 32661102 | Neurology | 2020 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/32661102 |
| Unmasking Covert Language Processing in the Intensive Care Unit with Electroencephalography. | Edlow BL, Naccache L | Annals of neurology | 33491250 | Ann Neurol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33491250 |
| Common Data Elements for COVID-19 Neuroimaging: A GCS-NeuroCOVID Proposal. | Edlow BL, Boly M, Chou SH, Fischer D, Kondziella D, Li LM, Mac Donald CL, McNett M, Newcombe VFJ, Stevens RD, Menon DK, GCS-NeuroCOVID | Neurocritical care | 33575956 | Neurocrit Care | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33575956 |
| Therapies to Restore Consciousness in Patients with Severe Brain Injuries: A Gap Analysis and Future Directions. | Edlow BL, Sanz LRD, Polizzotto L, Pouratian N, Rolston JD, Snider SB, Thibaut A, Stevens RD, Gosseries O, Curing Coma Campaign and its contributing members | Neurocritical care | 34236624 | Neurocrit Care | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34236624 |
| The neuroethics of disorders of consciousness: a brief history of evolving ideas. | Young MJ, Bodien YG, Giacino JT, Fins JJ, Truog RD, Hochberg LR, Edlow BL | Brain : a journal of neurology | 34347037 | Brain | 2021 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/34347037 |
| Location of Subcortical Microbleeds and Recovery of Consciousness After Severe Traumatic Brain Injury. | Bianciardi M, Izzy S, Rosen BR, Wald LL, Edlow BL | Neurology | 34050005 | Neurology | 2021 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/34050005 |
| Update on neuroimaging in disorders of consciousness. | Sanz LRD, Thibaut A, Edlow BL, Laureys S, Gosseries O | Current opinion in neurology | 34054109 | Curr Opin Neurol | 2021 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/34054109 |
| Transcranial Pulsed-Current Stimulation versus Transcranial Direct Current Stimulation in Patients with Disorders of Consciousness: A Pilot, Sham-Controlled Cross-Over Double-Blind Study. | Barra A, Rosenfelder M, Mortaheb S, Carrière M, Martens G, Bodien YG, Morales-Quezada L, Bender A, Laureys S, Thibaut A, Fregni F | Brain sciences | 35447961 | Brain Sci | 2022 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/35447961 |
| The Quest for Covert Consciousness: Bringing Neuroethics to the Bedside. | Young MJ, Edlow BL | Neurology | 33653901 | Neurology | 2021 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33653901 |
| Recovery Potential in Patients Who Died After Withdrawal of Life-Sustaining Treatment: A TRACK-TBI Propensity Score Analysis. | Sanders WR, Barber JK, Temkin NR, Foreman B, Giacino JT, Williamson T, Edlow BL, Manley GT, Bodien YG | Journal of neurotrauma | 38739032 | J Neurotrauma | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38739032 |
| Disclosing Results of Tests for Covert Consciousness: A Framework for Ethical Translation. | Young MJ, Kazazian K, Fischer D, Lissak IA, Bodien YG, Edlow BL | Neurocritical care | 38243150 | Neurocrit Care | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38243150 |
| Common data elements for disorders of consciousness. | Edlow BL, Claassen J, Suarez JI | Neurocritical care | 38291278 | Neurocrit Care | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38291278 |
| Severe cerebral edema in substance-related cardiac arrest patients. | Kulpanowski AM, Copen WA, Hancock BL, Rosenthal ES, Schoenfeld DA, Dodelson JA, Edlow BL, Kimberly WT, Amorim E, Westover MB, Ning MM, Schaefer PW, Malhotra R, Giacino JT, Greer DM, Wu O | Resuscitation | 35149137 | Resuscitation | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35149137 |
| Toward Uniform Insurer Coverage for Functional MRI Following Severe Brain Injury. | Young MJ, Bodien YG, Freeman HJ, Fecchio M, Edlow BL | The Journal of head trauma rehabilitation | 36854104 | J Head Trauma Rehabil | 2023 Jul-Aug 01 | https://www.ncbi.nlm.nih.gov/pubmed/36854104 |
| Brain-Computer Interfaces for Communication in Patients with Disorders of Consciousness: A Gap Analysis and Scientific Roadmap. | Schiff ND, Diringer M, Diserens K, Edlow BL, Gosseries O, Hill NJ, Hochberg LR, Ismail FY, Meyer IA, Mikell CB, Mofakham S, Molteni E, Polizzotto L, Shah SA, Stevens RD, Thengone D, and the Curing Coma Campaign and its Contributing Members | Neurocritical care | 38286946 | Neurocrit Care | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38286946 |
| Cognitive Motor Dissociation in Disorders of Consciousness. | Bodien YG, Allanson J, Cardone P, Bonhomme A, Carmona J, Chatelle C, Chennu S, Conte M, Dehaene S, Finoia P, Heinonen G, Hersh JE, Kamau E, Lawrence PK, Lupson VC, Meydan A, Rohaut B, Sanders WR, Sitt JD, Soddu A, Valente M, Velazquez A, Voss HU, Vrosgou A, Claassen J, Edlow BL, Fins JJ, Gosseries O, Laureys S, Menon D, Naccache L, Owen AM, Pickard J, Stamatakis EA, Thibaut A, Victor JD, Giacino JT, Bagiella E, Schiff ND | The New England journal of medicine | 39141852 | N Engl J Med | 2024 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/39141852 |
| Three-dimensional fiber orientation mapping of the human brain at micrometer resolution. | Liu CJ, Ammon W, Jones RJ, Nolan JC, Gong D, Maffei C, Edlow BL, Augustinack JC, Magnain C, Yendiki A, Villiger M, Fischl B, Wang H | Research square | 39149445 | Res Sq | 2024 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/39149445 |
| Automated Measurement of Cerebral Hemorrhagic Contusions and Outcomes After Traumatic Brain Injury in the TRACK-TBI Study. | Snider SB, Temkin NR, Sun X, Stubbs JL, Rademaker QJ, Markowitz AJ, Rosenthal ES, Diaz-Arrastia R, Fox MD, Manley GT, Jain S, Edlow BL, TRACK-TBI Investigators | JAMA network open | 39212991 | JAMA Netw Open | 2024 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/39212991 |
| The enhanced intestinal permeability of infant mice enables oral protein and macromolecular absorption without delivery technology. | Gleeson JP, Fein KC, Chaudhary N, Doerfler R, Newby AN, Whitehead KA | International journal of pharmaceutics | 33249250 | Int J Pharm | 2021 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/33249250 |
| Lipid nanoparticle chemistry determines how nucleoside base modifications alter mRNA delivery. | Melamed JR, Hajj KA, Chaudhary N, Strelkova D, Arral ML, Pardi N, Alameh MG, Miller JB, Farbiak L, Siegwart DJ, Weissman D, Whitehead KA | Journal of controlled release : official journal of the Controlled Release Society | 34801660 | J Control Release | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34801660 |
| The mixing method used to formulate lipid nanoparticles affects mRNA delivery efficacy and organ tropism. | Strelkova Petersen DM, Chaudhary N, Arral ML, Weiss RM, Whitehead KA | European journal of pharmaceutics and biopharmaceutics : official journal of Arbeitsgemeinschaft fur Pharmazeutische Verfahrenstechnik e.V | 37838143 | Eur J Pharm Biopharm | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37838143 |
| Lipid nanoparticle structure and delivery route during pregnancy dictate mRNA potency, immunogenicity, and maternal and fetal outcomes. | Chaudhary N, Newby AN, Arral ML, Yerneni SS, LoPresti ST, Doerfler R, Petersen DMS, Montoya C, Kim JS, Fox B, Coon T, Malaney A, Sadovsky Y, Whitehead KA | Proceedings of the National Academy of Sciences of the United States of America | 38437545 | Proc Natl Acad Sci U S A | 2024 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/38437545 |
| mRNA vaccines for infectious diseases: principles, delivery and clinical translation. | Chaudhary N, Weissman D, Whitehead KA | Nature reviews. Drug discovery | 34433919 | Nat Rev Drug Discov | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34433919 |
| Anionic nanoparticles enable the oral delivery of proteins by enhancing intestinal permeability. | Lamson NG, Berger A, Fein KC, Whitehead KA | Nature biomedical engineering | 31686002 | Nat Biomed Eng | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31686002 |
| Placental drug transport and fetal exposure during pregnancy is determined by drug molecular size, chemistry, and conformation. | Fein KC, Arral ML, Kim JS, Newby AN, Whitehead KA | Journal of controlled release : official journal of the Controlled Release Society | 37473809 | J Control Release | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37473809 |
| Enhanced epigenetic modulation via mRNA-encapsulated lipid nanoparticles enables targeted anti-inflammatory control. | Mokhtari T, Taheri MN, Akhlaghi S, Aryannejad A, Xiang Y, Mahajan V, Keshavarz K, Kiani A, LoPresti S, LeGraw R, Whitehead KA, Kiani S | bioRxiv : the preprint server for biology | 40060445 | bioRxiv | 2025 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/40060445 |
| Oral delivery of peptide therapeutics in infants: Challenges and opportunities. | Gleeson JP, Fein KC, Whitehead KA | Advanced drug delivery reviews | 33774115 | Adv Drug Deliv Rev | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33774115 |
| Non-Viral RNA Delivery During Pregnancy: Opportunities and Challenges. | Chaudhary N, Newby AN, Whitehead KA | Small (Weinheim an der Bergstrasse, Germany) | 38145340 | Small | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38145340 |
| Characterization and comparison of human and mouse milk cells. | Doerfler R, Yerneni S, Newby A, Chaudhary N, Shu A, Fein K, Hofstatter Azambuja J, Whitehead KA | PloS one | 38295101 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38295101 |
| The replacement of helper lipids with charged alternatives in lipid nanoparticles facilitates targeted mRNA delivery to the spleen and lungs. | LoPresti ST, Arral ML, Chaudhary N, Whitehead KA | Journal of controlled release : official journal of the Controlled Release Society | 35346768 | J Control Release | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35346768 |
| Ionizable lipid nanoparticles deliver mRNA to pancreatic β cells via macrophage-mediated gene transfer. | Melamed JR, Yerneni SS, Arral ML, LoPresti ST, Chaudhary N, Sehrawat A, Muramatsu H, Alameh MG, Pardi N, Weissman D, Gittes GK, Whitehead KA | Science advances | 36706177 | Sci Adv | 2023 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/36706177 |
| Profiling of mature-stage human breast milk cells identifies six unique lactocyte subpopulations. | Gleeson JP, Chaudhary N, Fein KC, Doerfler R, Hredzak-Showalter P, Whitehead KA | Science advances | 35767604 | Sci Adv | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35767604 |
| The strawberry-derived permeation enhancer pelargonidin enables oral protein delivery. | Lamson NG, Fein KC, Gleeson JP, Newby AN, Xian S, Cochran K, Chaudhary N, Melamed JR, Ball RL, Suri K, Ahuja V, Zhang A, Berger A, Kolodieznyi D, Schmidt BF, Silva GL, Whitehead KA | Proceedings of the National Academy of Sciences of the United States of America | 35943988 | Proc Natl Acad Sci U S A | 2022 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/35943988 |
| The Effect of Infant Gastric Digestion on Human Maternal Milk Cells. | Doerfler R, Melamed JR, Whitehead KA | Molecular nutrition & food research | 35984112 | Mol Nutr Food Res | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35984112 |
| Branched-Tail Lipid Nanoparticles for Intravenous mRNA Delivery to Lung Immune, Endothelial, and Alveolar Cells in Mice. | Petersen DMS, Weiss RM, Hajj KA, Yerneni SS, Chaudhary N, Newby AN, Arral ML, Whitehead KA | Advanced healthcare materials | 38888972 | Adv Healthc Mater | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38888972 |
| Amine headgroups in ionizable lipids drive immune responses to lipid nanoparticles by binding to the receptors TLR4 and CD1d. | Chaudhary N, Kasiewicz LN, Newby AN, Arral ML, Yerneni SS, Melamed JR, LoPresti ST, Fein KC, Strelkova Petersen DM, Kumar S, Purwar R, Whitehead KA | Nature biomedical engineering | 39363106 | Nat Biomed Eng | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39363106 |
| Maternal milk cell components are uptaken by infant liver macrophages via extracellular vesicle mediated transport. | Doerfler R, Yerneni S, LoPresti S, Chaudhary N, Newby A, Melamed JR, Malaney A, Whitehead KA | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 39835705 | FASEB J | 2025 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/39835705 |
| The Latent Genetic Structure of Impulsivity and Its Relation to Internalizing Psychopathology. | Gustavson DE, Friedman NP, Fontanillas P, Elson SL, 23andMe Research Team, Palmer AA, Sanchez-Roige S | Psychological science | 32716714 | Psychol Sci | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32716714 |
| Medical phenome of musicians: an investigation of health records collected on 9803 musically active individuals. | Niarchou M, Lin GT, Lense MD, Gordon RL, Davis LK | Annals of the New York Academy of Sciences | 34414577 | Ann N Y Acad Sci | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34414577 |
| Interprofessional education of the next generation of musician-scientists through music cognition research training: An innovative platform for health professions and biomedical research. | Gordon RL, Lense MD | Music and medicine | 33603955 | Music Med | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33603955 |
| Is atypical rhythm a risk factor for developmental speech and language disorders? | Ladányi E, Persici V, Fiveash A, Tillmann B, Gordon RL | Wiley interdisciplinary reviews. Cognitive science | 32244259 | Wiley Interdiscip Rev Cogn Sci | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32244259 |
| Exploring individual differences in musical rhythm and grammar skills in school-aged children with typically developing language. | Nitin R, Gustavson DE, Aaron AS, Boorom OA, Bush CT, Wiens N, Vaughan C, Persici V, Blain SD, Soman U, Hambrick DZ, Camarata SM, McAuley JD, Gordon RL | Scientific reports | 36750727 | Sci Rep | 2023 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/36750727 |
| Processing rhythm in speech and music: Shared mechanisms and implications for developmental speech and language disorders. | Fiveash A, Bedoin N, Gordon RL, Tillmann B | Neuropsychology | 34435803 | Neuropsychology | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34435803 |
| Heritability of Childhood Music Engagement and Associations with Language and Executive Function: Insights from the Adolescent Brain Cognitive Development (ABCD) Study. | Gustavson DE, Nayak S, Coleman PL, Iversen JR, Lense MD, Gordon RL, Maes HH | Behavior genetics | 36757558 | Behav Genet | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36757558 |
| Musical instrument engagement in adolescence predicts verbal ability 4 years later: A twin and adoption study. | Gustavson DE, Friedman NP, Stallings MC, Reynolds CA, Coon H, Corley RP, Hewitt JK, Gordon RL | Developmental psychology | 34914455 | Dev Psychol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34914455 |
| Polygenic Associations between Motor Behaviour, Neuromotor Traits, and Active Music Engagement in Four Cohorts. | Henechowicz TL, Coleman PL, Gustavson DE, Mekki YN, Nayak S, Nitin R, Scartozzi AC, Tio ES, van Klei R, Felsky D, Thaut MH, Gordon RL | bioRxiv : the preprint server for biology | 40196524 | bioRxiv | 2025 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/40196524 |
| Rhythm and timing as vulnerabilities in neurodevelopmental disorders. | Lense MD, Ladányi E, Rabinowitch TC, Trainor L, Gordon R | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 34420385 | Philos Trans R Soc Lond B Biol Sci | 2021 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/34420385 |
| Pushing the Envelope: Developments in Neural Entrainment to Speech and the Biological Underpinnings of Prosody Perception. | Myers BR, Lense MD, Gordon RL | Brain sciences | 30909454 | Brain Sci | 2019 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/30909454 |
| Does rhythmic priming improve grammatical processing in Hungarian-speaking children with and without developmental language disorder? | Ladányi E, Lukács Á, Gervain J | Developmental science | 34060171 | Dev Sci | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34060171 |
| Mental health and music engagement: review, framework, and guidelines for future studies. | Gustavson DE, Coleman PL, Iversen JR, Maes HH, Gordon RL, Lense MD | Translational psychiatry | 34226495 | Transl Psychiatry | 2021 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/34226495 |
| The case for treatment fidelity in active music interventions: why and how. | Wiens N, Gordon RL | Annals of the New York Academy of Sciences | 29727027 | Ann N Y Acad Sci | 2018 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/29727027 |
| Individual differences in neural markers of beat processing relate to spoken grammar skills in six-year-old children. | Persici V, Blain SD, Iversen JR, Key AP, Kotz SA, Devin McAuley J, Gordon RL | Brain and language | 37994830 | Brain Lang | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37994830 |
| The shared genetic architecture and evolution of human language and musical rhythm. | Alagöz G, Eising E, Mekki Y, Bignardi G, Fontanillas P, 23andMe Research Team, Nivard MG, Luciano M, Cox NJ, Fisher SE, Gordon RL | Nature human behaviour | 39572686 | Nat Hum Behav | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39572686 |
| New evidence of a rhythmic priming effect that enhances grammaticality judgments in children. | Chern A, Tillmann B, Vaughan C, Gordon RL | Journal of experimental child psychology | 29778278 | J Exp Child Psychol | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29778278 |
| Elevated Polygenic Burden for Autism Spectrum Disorder Is Associated With the Broad Autism Phenotype in Mothers of Individuals With Autism Spectrum Disorder. | Nayar K, Sealock JM, Maltman N, Bush L, Cook EH, Davis LK, Losh M | Biological psychiatry | 33229037 | Biol Psychiatry | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/33229037 |
| Synaptic processes and immune-related pathways implicated in Tourette syndrome. | Tsetsos F, Yu D, Sul JH, Huang AY, Illmann C, Osiecki L, Darrow SM, Hirschtritt ME, Greenberg E, Muller-Vahl KR, Stuhrmann M, Dion Y, Rouleau GA, Aschauer H, Stamenkovic M, Schlögelhofer M, Sandor P, Barr CL, Grados MA, Singer HS, Nöthen MM, Hebebrand J, Hinney A, King RA, Fernandez TV, Barta C, Tarnok Z, Nagy P, Depienne C, Worbe Y, Hartmann A, Budman CL, Rizzo R, Lyon GJ, McMahon WM, Batterson JR, Cath DC, Malaty IA, Okun MS, Berlin C, Woods DW, Lee PC, Jankovic J, Robertson MM, Gilbert DL, Brown LW, Coffey BJ, Dietrich A, Hoekstra PJ, Kuperman S, Zinner SH, Wagner M, Knowles JA, Jeremy Willsey A, Tischfield JA, Heiman GA, Cox NJ, Freimer NB, Neale BM, Davis LK, Coppola G, Mathews CA, Scharf JM, Paschou P, Tourette Association of America International Consortium for Genetics, Barr CL, Batterson JR, Berlin C, Budman CL, Cath DC, Coppola G, Cox NJ, Darrow S, Davis LK, Dion Y, Freimer NB, Grados MA, Greenberg E, Hirschtritt ME, Huang AY, Illmann C, King RA, Kurlan R, Leckman JF, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Neale BM, Okun MS, Osiecki L, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Singer HS, Smit JH, Sul JH, Yu D, Gilles de la Tourette GWAS Replication Initiative, Aschauer HAH, Barta C, Budman CL, Cath DC, Depienne C, Hartmann A, Hebebrand J, Konstantinidis A, Mathews CA, Müller-Vahl K, Nagy P, Nöthen MM, Paschou P, Rizzo R, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Stamenkovic M, Stuhrmann M, Tsetsos F, Tarnok Z, Wolanczyk T, Worbe Y, Tourette International Collaborative Genetics Study, Brown L, Cheon KA, Coffey BJ, Dietrich A, Fernandez TV, Garcia-Delgar B, Gilbert D, Grice DE, Hagstrøm J, Hedderly T, Heiman GA, Heyman I, Hoekstra PJ, Huyser C, Kim YK, Kim YS, King RA, Koh YJ, Kook S, Kuperman S, Leventhal BL, Madruga-Garrido M, Mir P, Morer A, Münchau A, Plessen KJ, Roessner V, Shin EY, Song DH, Song J, Tischfield JA, Willsey AJ, Zinner S, Psychiatric Genomics Consortium Tourette Syndrome Working Group, Aschauer H, Barr CL, Barta C, Batterson JR, Berlin C, Brown L, Budman CL, Cath DC, Coffey BJ, Coppola G, Cox NJ, Darrow S, Davis LK, Depienne C, Dietrich A, Dion Y, Fernandez T, Freimer NB, Gilbert D, Grados MA, Greenberg E, Hartmann A, Hebebrand J, Heiman G, Hirschtritt ME, Hoekstra P, Huang AY, Illmann C, Jankovic J, King RA, Kuperman S, Lee PC, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Müller-Vahl K, Nagy P, Neale BM, Nöthen MM, Okun MS, Osiecki L, Paschou P, Rizzo R, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Singer HS, Stamenkovic M, Stuhrmann M, Sul JH, Tarnok Z, Tischfield J, Tsetsos F, Willsey AJ, Woods D, Worbe Y, Yu D, Zinner S | Translational psychiatry | 33462189 | Transl Psychiatry | 2021 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/33462189 |
| Neurophysiological Correlates of Dynamic Beat Tracking in Individuals With Williams Syndrome. | Kasdan A, Gordon RL, Lense MD | Biological psychiatry. Cognitive neuroscience and neuroimaging | 33419711 | Biol Psychiatry Cogn Neurosci Neuroimaging | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33419711 |
| Linking the genomic signatures of human beat synchronization and learned song in birds. | Gordon RL, Ravignani A, Hyland Bruno J, Robinson CM, Scartozzi A, Embalabala R, Niarchou M, 23andMe Research Team, Cox NJ, Creanza N | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 34420388 | Philos Trans R Soc Lond B Biol Sci | 2021 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/34420388 |
| A neurodevelopmental disorders perspective into music, social attention, and social bonding. | Kasdan A, Gordon RL, Lense MD | The Behavioral and brain sciences | 34588066 | Behav Brain Sci | 2021 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/34588066 |
| Infants' neural speech discrimination predicts individual differences in grammar ability at 6 years of age and their risk of developing speech-language disorders. | Zhao TC, Boorom O, Kuhl PK, Gordon R | Developmental cognitive neuroscience | 33823366 | Dev Cogn Neurosci | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33823366 |
| The shared genetic architecture and evolution of human language and musical rhythm. | Alagöz G, Eising E, Mekki Y, Bignardi G, Fontanillas P, 23andMe Research Team, Nivard MG, Luciano M, Cox NJ, Fisher SE, Gordon RL | bioRxiv : the preprint server for biology | 37961248 | bioRxiv | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37961248 |
| Exploring the genetics of rhythmic perception and musical engagement in the Vanderbilt Online Musicality Study. | Gustavson DE, Coleman PL, Wang Y, Nitin R, Petty LE, Bush CT, Mosing MA, Wesseldijk LW, Ullén F, 23 and Me Research Team, Below JE, Cox NJ, Gordon RL | Annals of the New York Academy of Sciences | 36718543 | Ann N Y Acad Sci | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36718543 |
| The Musical Abilities, Pleiotropy, Language, and Environment (MAPLE) Framework for Understanding Musicality-Language Links Across the Lifespan. | Nayak S, Coleman PL, Ladányi E, Nitin R, Gustavson DE, Fisher SE, Magne CL, Gordon RL | Neurobiology of language (Cambridge, Mass.) | 36742012 | Neurobiol Lang (Camb) | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36742012 |
| Regular rhythmic primes improve sentence repetition in children with developmental language disorder. | Fiveash A, Ladányi E, Camici J, Chidiac K, Bush CT, Canette LH, Bedoin N, Gordon RL, Tillmann B | NPJ science of learning | 37429839 | NPJ Sci Learn | 2023 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/37429839 |
| Genetic and Environmental Influences on Semantic Verbal Fluency Across Midlife and Later Life. | Gustavson DE, Panizzon MS, Kremen WS, Reynolds CA, Pahlen S, Nygaard M, Wod M, Catts VS, Lee T, Gatz M, Franz CE, IGEMS Consortium | Behavior genetics | 33547998 | Behav Genet | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33547998 |
| Identifying a brain network for musical rhythm: A functional neuroimaging meta-analysis and systematic review. | Kasdan AV, Burgess AN, Pizzagalli F, Scartozzi A, Chern A, Kotz SA, Wilson SM, Gordon RL | Neuroscience and biobehavioral reviews | 35259422 | Neurosci Biobehav Rev | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35259422 |
| You got rhythm, or more: The multidimensionality of rhythmic abilities. | Fiveash A, Bella SD, Bigand E, Gordon RL, Tillmann B | Attention, perception & psychophysics | 35437703 | Atten Percept Psychophys | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35437703 |
| Using a polygenic score in a family design to understand genetic influences on musicality. | Wesseldijk LW, Abdellaoui A, Gordon RL, 23andMe Research Team, Ullén F, Mosing MA | Scientific reports | 36038631 | Sci Rep | 2022 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/36038631 |
| Confronting ethical and social issues related to the genetics of musicality. | Gordon RL, Martschenko DO, Nayak S, Niarchou M, Morrison MD, Bell E, Jacoby N, Davis LK | Annals of the New York Academy of Sciences | 36851882 | Ann N Y Acad Sci | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36851882 |
| Genome-wide association study of musical beat synchronization demonstrates high polygenicity. | Niarchou M, Gustavson DE, Sathirapongsasuti JF, Anglada-Tort M, Eising E, Bell E, McArthur E, Straub P, 23andMe Research Team, McAuley JD, Capra JA, Ullén F, Creanza N, Mosing MA, Hinds DA, Davis LK, Jacoby N, Gordon RL | Nature human behaviour | 35710621 | Nat Hum Behav | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35710621 |
| The Neural Correlates of Spontaneous Beat Processing and Its Relationship with Music-Related Characteristics of the Individual. | Scartozzi AC, Wang Y, Bush CT, Kasdan AV, Fram NR, Woynaroski T, Lense MD, Gordon RL, Ladányi E | eNeuro | 39401929 | eNeuro | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39401929 |
| Discovery and Biosynthesis of Azabicyclene, a Conserved Nonribosomal Peptide in Pseudomonas aeruginosa. | Patteson JB, Lescallette AR, Li B | Organic letters | 31247735 | Org Lett | 2019 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/31247735 |
| Biosynthesis of fluopsin C, a copper-containing antibiotic from Pseudomonas aeruginosa. | Patteson JB, Putz AT, Tao L, Simke WC, Bryant LH 3rd, Britt RD, Li B | Science (New York, N.Y.) | 34793213 | Science | 2021 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/34793213 |
| Chemoproteomics Reveals Disruption of Metal Homeostasis and Metalloproteins by the Antibiotic Holomycin. | Chan AN, Chen X, Falco JA, Bak DW, Weerapana E, Li B | ACS chemical biology | 37561838 | ACS Chem Biol | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37561838 |
| Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila. | Acken KA, Li B | PloS one | 37200397 | PLoS One | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37200397 |
| Analysis of Co-localized Biosynthetic Gene Clusters Identifies a Membrane-Permeabilizing Natural Product. | Chen X, Li B | Journal of natural products | 38949271 | J Nat Prod | 2024 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/38949271 |
| Specificity of Nonribosomal Peptide Synthetases in the Biosynthesis of the Pseudomonas virulence factor. | Morgan GL, Kretsch AM, Santa Maria KC, Weeks SJ, Li B | Biochemistry | 31243997 | Biochemistry | 2019 Dec 31 | https://www.ncbi.nlm.nih.gov/pubmed/31243997 |
| Enzymatic Synthesis of Diverse Heterocycles by a Noncanonical Nonribosomal Peptide Synthetase. | Morgan GL, Li K, Crawford DM, Aubé J, Li B | ACS chemical biology | 34767712 | ACS Chem Biol | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34767712 |
| Discovery of (Dihydro)pyrazine N-Oxides via Genome Mining in Pseudomonas. | Kretsch AM, Morgan GL, Tyrrell J, Mevers E, Vallet-Gély I, Li B | Organic letters | 30073838 | Org Lett | 2018 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/30073838 |
| A Permissive Amide N-Methyltransferase for Dithiolopyrrolones. | Chen X, Johnson RM, Li B | ACS catalysis | 38106463 | ACS Catal | 2023 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/38106463 |
| Targeted Rediscovery and Biosynthesis of the Farnesyl-Transferase Inhibitor Pepticinnamin E. | Santa Maria KC, Chan AN, O'Neill EM, Li B | Chembiochem : a European journal of chemical biology | 30694017 | Chembiochem | 2019 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/30694017 |
| Inhibition of Isoleucyl-tRNA Synthetase by the Hybrid Antibiotic Thiomarinol. | Johnson RA, Chan AN, Ward RD, McGlade CA, Hatfield BM, Peters JM, Li B | Journal of the American Chemical Society | 34342433 | J Am Chem Soc | 2021 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/34342433 |
| The Hybrid Antibiotic Thiomarinol A Overcomes Intrinsic Resistance in Escherichia coli Using a Privileged Dithiolopyrrolone Moiety. | Johnson RM, Li K, Chen X, Morgan GL, Aubé J, Li B | ACS infectious diseases | 38226592 | ACS Infect Dis | 2024 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/38226592 |
| Pseudomonas Virulence Factor Pathway Synthesizes Autoinducers That Regulate the Secretome of a Pathogen. | Kretsch AM, Morgan GL, Acken KA, Barr SA, Li B | ACS chemical biology | 33595276 | ACS Chem Biol | 2021 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/33595276 |
| In Vitro Reconstitution Reveals a Central Role for the N-Oxygenase PvfB in (Dihydro)pyrazine-N-oxide and Valdiazen Biosynthesis. | Morgan GL, Li B | Angewandte Chemie (International ed. in English) | 32662921 | Angew Chem Int Ed Engl | 2020 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/32662921 |
| Purification and characterization of tomato arginine decarboxylase and its inhibition by the bacterial small molecule phevamine A. | Guo Q, Chen X, Li B | Protein expression and purification | 37348664 | Protein Expr Purif | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37348664 |
| Activation of Dithiolopyrrolone Antibiotics by Cellular Reductants. | Steiner OM, Johnson RA, Chen X, Simke WC, Li B | Biochemistry | 39665630 | Biochemistry | 2025 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/39665630 |
| Parallel High-Resolution Imaging of Leukocyte Chemotaxis Under Agarose with Rho-Family GTPase Biosensors. | Bell GRR, Natwick DE, Collins SR | Methods in molecular biology (Clifton, N.J.) | 30062406 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30062406 |
| Optimized iLID Membrane Anchors for Local Optogenetic Protein Recruitment. | Natwick DE, Collins SR | ACS synthetic biology | 33843200 | ACS Synth Biol | 2021 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/33843200 |
| Directional reorientation of migrating neutrophils is limited by suppression of receptor input signaling at the cell rear through myosin II activity. | Hadjitheodorou A, Bell GRR, Ellett F, Shastry S, Irimia D, Collins SR, Theriot JA | Nature communications | 34785640 | Nat Commun | 2021 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/34785640 |
| Signaling dynamics distinguish high- and low-priority neutrophil chemoattractant receptors. | Lundgren SM, Rocha-Gregg BL, Akdoğan E, Mysore MN, Hayes S, Collins SR | Science signaling | 37788324 | Sci Signal | 2023 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/37788324 |
| Modeling Subcellular Protein Recruitment Dynamics for Synthetic Biology. | Badu-Nkansah KA, Sernas D, Natwick DE, Collins SR | Methods in molecular biology (Clifton, N.J.) | 36227545 | Methods Mol Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36227545 |
| Identification of phagocytosis regulators using magnetic genome-wide CRISPR screens. | Haney MS, Bohlen CJ, Morgens DW, Ousey JA, Barkal AA, Tsui CK, Ego BK, Levin R, Kamber RA, Collins H, Tucker A, Li A, Vorselen D, Labitigan L, Crane E, Boyle E, Jiang L, Chan J, Rincón E, Greenleaf WJ, Li B, Snyder MP, Weissman IL, Theriot JA, Collins SR, Barres BA, Bassik MC | Nature genetics | 30397336 | Nat Genet | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30397336 |
| "Rho"ing a Cellular Boat with Rearward Membrane Flow. | Bell GRR, Collins SR | Developmental cell | 29974859 | Dev Cell | 2018 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/29974859 |
| Whole-genome screens reveal regulators of differentiation state and context-dependent migration in human neutrophils. | Belliveau NM, Footer MJ, Akdoǧan E, van Loon AP, Collins SR, Theriot JA | Nature communications | 37723145 | Nat Commun | 2023 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/37723145 |
| Flagella-driven motility is a target of human Paneth cell defensin activity. | Akahoshi DT, Natwick DE, Yuan W, Lu W, Collins SR, Bevins CL | PLoS pathogens | 36821624 | PLoS Pathog | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36821624 |
| Decoding GEFs of animated cells. | Natwick DE, Collins SR | Nature chemical biology | 32694631 | Nat Chem Biol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32694631 |
| Optogenetic control of receptors reveals distinct roles for actin- and Cdc42-dependent negative signals in chemotactic signal processing. | Bell GRR, Rincón E, Akdoğan E, Collins SR | Nature communications | 34785668 | Nat Commun | 2021 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/34785668 |
| A map of gene expression in neutrophil-like cell lines. | Rincón E, Rocha-Gregg BL, Collins SR | BMC genomics | 30068296 | BMC Genomics | 2018 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/30068296 |
| Host cells subdivide nutrient niches into discrete biogeographical microhabitats for gut microbes. | Liou MJ, Miller BM, Litvak Y, Nguyen H, Natwick DE, Savage HP, Rixon JA, Mahan SP, Hiyoshi H, Rogers AWL, Velazquez EM, Butler BP, Collins SR, McSorley SJ, Harshey RM, Byndloss MX, Simon SI, Bäumler AJ | Cell host & microbe | 35568027 | Cell Host Microbe | 2022 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/35568027 |
| Neutrophil-like cells derived from the HL-60 cell-line as a genetically-tractable model for neutrophil degranulation. | Bhakta SB, Lundgren SM, Sesti BN, Flores BA, Akdogan E, Collins SR, Mercer F | PloS one | 38324578 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38324578 |
| Vangl-dependent Wnt/planar cell polarity signaling mediates collective breast carcinoma motility and distant metastasis. | VanderVorst K, Dreyer CA, Hatakeyama J, Bell GRR, Learn JA, Berg AL, Hernandez M, Lee H, Collins SR, Carraway KL 3rd | Breast cancer research : BCR | 37147680 | Breast Cancer Res | 2023 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/37147680 |
| Leading edge competition promotes context-dependent responses to receptor inputs to resolve directional dilemmas in neutrophil migration. | Hadjitheodorou A, Bell GRR, Ellett F, Irimia D, Tibshirani R, Collins SR, Theriot JA | Cell systems | 36827986 | Cell Syst | 2023 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36827986 |
| A complex of Wnt/planar cell polarity signaling components Vangl1 and Fzd7 drives glioblastoma multiforme malignant properties. | Dreyer CA, VanderVorst K, Natwick D, Bell G, Sood P, Hernandez M, Angelastro JM, Collins SR, Carraway KL 3rd | Cancer letters | 37336284 | Cancer Lett | 2023 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/37336284 |
| Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling. | Falo-Sanjuan J, Lammers NC, Garcia HG, Bray SJ | Developmental cell | 31378591 | Dev Cell | 2019 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/31378591 |
| Genetically Encoded Fluorescent Biosensor for Rapid Detection of Protein Expression. | Eason MG, Pandelieva AT, Mayer MM, Khan ST, Garcia HG, Chica RA | ACS synthetic biology | 33044070 | ACS Synth Biol | 2020 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/33044070 |
| LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos. | Bothma JP, Norstad MR, Alamos S, Garcia HG | Cell | 29754814 | Cell | 2018 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/29754814 |
| Lighting up the central dogma for predictive developmental biology. | Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J | Current topics in developmental biology | 32143740 | Curr Top Dev Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32143740 |
| Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. | Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG | Cell systems | 36696901 | Cell Syst | 2023 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36696901 |
| Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. | González-Grandío E, Álamos S, Zhang Y, Dalton-Roesler J, Niyogi KK, García HG, Quail PH | Frontiers in plant science | 35251080 | Front Plant Sci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35251080 |
| Single cell biology-a Keystone Symposia report. | Cable J, Elowitz MB, Domingos AI, Habib N, Itzkovitz S, Hamidzada H, Balzer MS, Yanai I, Liberali P, Whited J, Streets A, Cai L, Stergachis AB, Hong CKY, Keren L, Guilliams M, Alon U, Shalek AK, Hamel R, Pfau SJ, Raj A, Quake SR, Zhang NR, Fan J, Trapnell C, Wang B, Greenwald NF, Vento-Tormo R, Santos SDM, Spencer SL, Garcia HG, Arekatla G, Gaiti F, Arbel-Goren R, Rulands S, Junker JP, Klein AM, Morris SA, Murray JI, Galloway KE, Ratz M, Romeike M | Annals of the New York Academy of Sciences | 34605044 | Ann N Y Acad Sci | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34605044 |
| DRMY1 promotes robust morphogenesis in Arabidopsis by sustaining the translation of cytokinin-signaling inhibitor proteins. | Kong S, Zhu M, Scarpin MR, Pan D, Jia L, Martinez RE, Alamos S, Vadde BVL, Garcia HG, Qian SB, Brunkard JO, Roeder AHK | Developmental cell | 39305905 | Dev Cell | 2024 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/39305905 |
| Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics. | Alamos S, Reimer A, Niyogi KK, Garcia HG | Nature plants | 34373604 | Nat Plants | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34373604 |
| Quantitative dissection of transcription in development yields evidence for transcription-factor-driven chromatin accessibility. | Eck E, Liu J, Kazemzadeh-Atoufi M, Ghoreishi S, Blythe SA, Garcia HG | eLife | 33074101 | Elife | 2020 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/33074101 |
| A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting. | Lammers NC, Kim YJ, Zhao J, Garcia HG | Current opinion in cell biology | 33242838 | Curr Opin Cell Biol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33242838 |
| The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output. | Yamada S, Whitney PH, Huang SK, Eck EC, Garcia HG, Rushlow CA | Current biology : CB | 30982648 | Curr Biol | 2019 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/30982648 |
| Multimodal transcriptional control of pattern formation in embryonic development. | Lammers NC, Galstyan V, Reimer A, Medin SA, Wiggins CH, Garcia HG | Proceedings of the National Academy of Sciences of the United States of America | 31882445 | Proc Natl Acad Sci U S A | 2020 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/31882445 |
| Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila. | Child MB 6th, Bateman JR, Jahangiri A, Reimer A, Lammers NC, Sabouni N, Villamarin D, McKenzie-Smith GC, Johnson JE, Jost D, Garcia HG | eLife | 34100718 | Elife | 2021 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/34100718 |
| Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer. | Kim YJ, Rhee K, Liu J, Jeammet S, Turner MA, Small SJ, Garcia HG | eLife | 36503705 | Elife | 2022 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/36503705 |
| Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. | Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X | Methods in molecular biology (Clifton, N.J.) | 29956254 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29956254 |
| Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. | Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG | PLoS computational biology | 34003867 | PLoS Comput Biol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/34003867 |
| Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene. | Berrocal A, Lammers NC, Garcia HG, Eisen MB | eLife | 33300492 | Elife | 2020 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/33300492 |
| Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. | Phillips R, Belliveau NM, Chure G, Garcia HG, Razo-Mejia M, Scholes C | Annual review of biophysics | 31084583 | Annu Rev Biophys | 2019 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/31084583 |
| Competing constraints shape the nonequilibrium limits of cellular decision-making. | Lammers NC, Flamholz AI, Garcia HG | Proceedings of the National Academy of Sciences of the United States of America | 36862689 | Proc Natl Acad Sci U S A | 2023 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/36862689 |
| TCF21(+) mesenchymal cells contribute to testis somatic cell development, homeostasis, and regeneration in mice. | Shen YC, Shami AN, Moritz L, Larose H, Manske GL, Ma Q, Zheng X, Sukhwani M, Czerwinski M, Sultan C, Chen H, Gurczynski SJ, Spence JR, Orwig KE, Tallquist M, Li JZ, Hammoud SS | Nature communications | 34162856 | Nat Commun | 2021 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/34162856 |
| Single-Cell RNA Sequencing of Human, Macaque, and Mouse Testes Uncovers Conserved and Divergent Features of Mammalian Spermatogenesis. | Shami AN, Zheng X, Munyoki SK, Ma Q, Manske GL, Green CD, Sukhwani M, Orwig KE, Li JZ, Hammoud SS | Developmental cell | 32504559 | Dev Cell | 2020 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/32504559 |
| Cellular heterogeneity of human fallopian tubes in normal and hydrosalpinx disease states identified using scRNA-seq. | Ulrich ND, Shen YC, Ma Q, Yang K, Hannum DF, Jones A, Machlin J, Randolph JF Jr, Smith YR, Schon SB, Shikanov A, Marsh EE, Lieberman R, Gurczynski SJ, Moore BB, Li JZ, Hammoud S | Developmental cell | 35320732 | Dev Cell | 2022 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/35320732 |
| Cellular heterogeneity and dynamics of the human uterus in healthy premenopausal women. | Ulrich ND, Vargo A, Ma Q, Shen YC, Bazzano D, Hannum DF, Gurczynski SJ, Moore BB, Schon S, Lieberman R, Shikanov A, Marsh EE, Fazleabas A, Li JZ, Hammoud SS | Proceedings of the National Academy of Sciences of the United States of America | 39471215 | Proc Natl Acad Sci U S A | 2024 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/39471215 |
| Decoding the Spermatogenesis Program: New Insights from Transcriptomic Analyses. | Rabbani M, Zheng X, Manske GL, Vargo A, Shami AN, Li JZ, Hammoud SS | Annual review of genetics | 36070560 | Annu Rev Genet | 2022 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/36070560 |
| Proteomic analysis of human sperm reveals changes in protamine 1 phosphorylation in men with infertility. | Schon SB, Moritz L, Rabbani M, Meguid J, Juliano BR, Ruotolo BT, Aston K, Hammoud SS | F&S science | 38065301 | F S Sci | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38065301 |
| Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells. | Ma B, Yang G, Yao J, Wu C, Vega JP, Manske G, Hammoud SS, Sinha S, Singh A, Zhao H, Chen X | bioRxiv : the preprint server for biology | 40093102 | bioRxiv | 2025 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/40093102 |
| Regulation of meiotic progression by Sertoli-cell androgen signaling. | Larose H, Kent T, Ma Q, Shami AN, Harerimana N, Li JZ, Hammoud SS, Handel MA | Molecular biology of the cell | 33026960 | Mol Biol Cell | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33026960 |
| Differential impact of a dyskeratosis congenita mutation in TPP1 on mouse hematopoiesis and germline. | Graniel JV, Bisht K, Friedman A, White J, Perkey E, Vanderbeck A, Moroz A, Carrington LJ, Brandstadter JD, Allen F, Shami AN, Thomas P, Crayton A, Manzor M, Mychalowych A, Chase J, Hammoud SS, Keegan CE, Maillard I, Nandakumar J | Life science alliance | 34645668 | Life Sci Alliance | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34645668 |
| Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1. | Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS | Nature structural & molecular biology | 37460896 | Nat Struct Mol Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37460896 |
| A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq. | Green CD, Ma Q, Manske GL, Shami AN, Zheng X, Marini S, Moritz L, Sultan C, Gurczynski SJ, Moore BB, Tallquist MD, Li JZ, Hammoud SS | Developmental cell | 30146481 | Dev Cell | 2018 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/30146481 |
| Two Separation-of-Function Isoforms of Human TPP1 Dictate Telomerase Regulation in Somatic and Germ Cells. | Grill S, Bisht K, Tesmer VM, Shami AN, Hammoud SS, Nandakumar J | Cell reports | 31216472 | Cell Rep | 2019 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/31216472 |
| The Art of Packaging the Sperm Genome: Molecular and Structural Basis of the Histone-To-Protamine Exchange. | Moritz L, Hammoud SS | Frontiers in endocrinology | 35813619 | Front Endocrinol (Lausanne) | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35813619 |
| Genetic determinants of cellular addiction to DNA polymerase theta. | Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP | Nature communications | 31537809 | Nat Commun | 2019 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/31537809 |
| The structure of the human cell cycle. | Stallaert W, Kedziora KM, Taylor CD, Zikry TM, Ranek JS, Sobon HK, Taylor SR, Young CL, Cook JG, Purvis JE | Cell systems | 34800361 | Cell Syst | 2022 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/34800361 |
| Integrating temporal single-cell gene expression modalities for trajectory inference and disease prediction. | Ranek JS, Stanley N, Purvis JE | Genome biology | 36064614 | Genome Biol | 2022 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/36064614 |
| Autophagy regulates the localization and degradation of p16(INK4a). | Coryell PR, Goraya SK, Griffin KA, Redick MA, Sisk SR, Purvis JE | Aging cell | 32662244 | Aging Cell | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32662244 |
| Cyclin F drives proliferation through SCF-dependent degradation of the retinoblastoma-like tumor suppressor p130/RBL2. | Enrico TP, Stallaert W, Wick ET, Ngoi P, Wang X, Rubin SM, Brown NG, Purvis JE, Emanuele MJ | eLife | 34851822 | Elife | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/34851822 |
| The structure of the human cell cycle. | Stallaert W, Kedziora KM, Taylor CD, Zikry TM, Ranek JS, Sobon HK, Taylor SR, Young CL, Cook JG, Purvis JE | Cell systems | 35051372 | Cell Syst | 2022 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/35051372 |
| The Cell Cycle Browser: An Interactive Tool for Visualizing, Simulating, and Perturbing Cell-Cycle Progression. | Borland D, Yi H, Grant GD, Kedziora KM, Chao HX, Haggerty RA, Kumar J, Wolff SC, Cook JG, Purvis JE | Cell systems | 30077635 | Cell Syst | 2018 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/30077635 |
| Orchestration of DNA Damage Checkpoint Dynamics across the Human Cell Cycle. | Chao HX, Poovey CE, Privette AA, Grant GD, Chao HY, Cook JG, Purvis JE | Cell systems | 29102360 | Cell Syst | 2017 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/29102360 |
| Natural language processing: put your model where your mouth is. | Haggerty RA, Purvis JE | Molecular systems biology | 29254950 | Mol Syst Biol | 2017 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/29254950 |
| Inferring the structures of signaling motifs from paired dynamic traces of single cells. | Haggerty RA, Purvis JE | PLoS computational biology | 33539338 | PLoS Comput Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33539338 |
| Bistable switches as integrators and actuators during cell cycle progression. | Stallaert W, Kedziora KM, Chao HX, Purvis JE | FEBS letters | 31566708 | FEBS Lett | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31566708 |
| The consequences of differential origin licensing dynamics in distinct chromatin environments. | Mei L, Kedziora KM, Song EA, Purvis JE, Cook JG | Nucleic acids research | 35079814 | Nucleic Acids Res | 2022 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/35079814 |
| Inheritance of OCT4 predetermines fate choice in human embryonic stem cells. | Wolff SC, Kedziora KM, Dumitru R, Dungee CD, Zikry TM, Beltran AS, Haggerty RA, Cheng J, Redick MA, Purvis JE | Molecular systems biology | 30177503 | Mol Syst Biol | 2018 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/30177503 |
| Dual inhibition of DNA-PK and DNA polymerase theta overcomes radiation resistance induced by p53 deficiency. | Kumar RJ, Chao HX, Simpson DA, Feng W, Cho MG, Roberts VR, Sullivan AR, Shah SJ, Wozny AS, Fagan-Solis K, Kumar S, Luthman A, Ramsden DA, Purvis JE, Gupta GP | NAR cancer | 33385162 | NAR Cancer | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33385162 |
| Chemical screen for epigenetic barriers to single allele activation of Oct4. | Headley KM, Kedziora KM, Alejo A, Lai EZ, Purvis JE, Hathaway NA | Stem cell research | 31170660 | Stem Cell Res | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31170660 |
| Evidence that the human cell cycle is a series of uncoupled, memoryless phases. | Chao HX, Fakhreddin RI, Shimerov HK, Kedziora KM, Kumar RJ, Perez J, Limas JC, Grant GD, Cook JG, Gupta GP, Purvis JE | Molecular systems biology | 30886052 | Mol Syst Biol | 2019 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/30886052 |
| Accurate delineation of cell cycle phase transitions in living cells with PIP-FUCCI. | Grant GD, Kedziora KM, Limas JC, Cook JG, Purvis JE | Cell cycle (Georgetown, Tex.) | 30421640 | Cell Cycle | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30421640 |
| Rapid DNA replication origin licensing protects stem cell pluripotency. | Matson JP, Dumitru R, Coryell P, Baxley RM, Chen W, Twaroski K, Webber BR, Tolar J, Bielinsky AK, Purvis JE, Cook JG | eLife | 29148972 | Elife | 2017 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/29148972 |
| A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. | Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST | Cellular and molecular gastroenterology and hepatology | 35176508 | Cell Mol Gastroenterol Hepatol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35176508 |
| Exposure, hazard, and survival analysis of diffusion on social networks. | Wu J, Crawford FW, Kim DA, Stafford D, Christakis NA | Statistics in medicine | 29707798 | Stat Med | 2018 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/29707798 |
| Dynamics of the HIV outbreak and response in Scott County, IN, USA, 2011-15: a modelling study. | Gonsalves GS, Crawford FW | The lancet. HIV | 30220531 | Lancet HIV | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30220531 |
| Hidden population size estimation from respondent-driven sampling: a network approach. | Crawford FW, Wu J, Heimer R | Journal of the American Statistical Association | 30828120 | J Am Stat Assoc | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30828120 |
| Estimating dose-specific cell division and apoptosis rates from chemo-sensitivity experiments. | Liu Y, Crawford FW | Scientific reports | 29426887 | Sci Rep | 2018 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/29426887 |
| Predictors of Mortality within Prison and after Release among Persons Living with HIV in Indonesia. | Culbert GJ, Crawford FW, Murni A, Waluyo A, Bazazi AR, Sahar J, Altice FL | Research and reports in tropical medicine | 29238241 | Res Rep Trop Med | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29238241 |
| The Burden of Stigma on Health and Well-Being: A Taxonomy of Concealment, Course, Disruptiveness, Aesthetics, Origin, and Peril Across 93 Stigmas. | Pachankis JE, Hatzenbuehler ML, Wang K, Burton CL, Crawford FW, Phelan JC, Link BG | Personality & social psychology bulletin | 29290150 | Pers Soc Psychol Bull | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29290150 |
| Violence and Discrimination Against Men Who Have Sex With Men in Lebanon: The Role of International Displacement and Migration. | Orr L, Shebl FM, Heimer R, Khoshnood K, Barbour R, Khouri D, Aaraj E, Mokhbat JE, Crawford FW | Journal of interpersonal violence | 31658847 | J Interpers Violence | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31658847 |
| Transmission Modeling with Regression Adjustment for Analyzing Household-based Studies of Infectious Disease: Application to Tuberculosis. | Crawford FW, Marx FM, Zelner J, Cohen T | Epidemiology (Cambridge, Mass.) | 31764276 | Epidemiology | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31764276 |
| SARS-CoV-2 attack rate and population immunity in southern New England, March 2020 - May 2021. | Tran TN, Wikle NB, Yang F, Inam H, Leighow S, Gentilesco B, Chan P, Albert E, Strong ER, Pritchard JR, Hanage WP, Hanks EM, Crawford FW, Boni MF | medRxiv : the preprint server for health sciences | 34909789 | medRxiv | 2021 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/34909789 |
| Randomization for the susceptibility effect of an infectious disease intervention. | Eck DJ, Morozova O, Crawford FW | Journal of mathematical biology | 36127558 | J Math Biol | 2022 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/36127558 |
| Impact of close interpersonal contact on COVID-19 incidence: Evidence from 1 year of mobile device data. | Crawford FW, Jones SA, Cartter M, Dean SG, Warren JL, Li ZR, Barbieri J, Campbell J, Kenney P, Valleau T, Morozova O | Science advances | 34995121 | Sci Adv | 2022 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/34995121 |
| Evaluating the Mediating Role of Recall of Intervention Knowledge in the Relationship Between a Peer-Driven Intervention and HIV Risk Behaviors Among People Who Inject Drugs. | Aroke H, Buchanan A, Katenka N, Crawford FW, Lee T, Halloran ME, Latkin C | AIDS and behavior | 35932359 | AIDS Behav | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35932359 |
| Vaccination with BNT162b2 reduces transmission of SARS-CoV-2 to household contacts in Israel. | Prunas O, Warren JL, Crawford FW, Gazit S, Patalon T, Weinberger DM, Pitzer VE | Science (New York, N.Y.) | 35084937 | Science | 2022 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/35084937 |
| An Adaptive Approach to Locating Mobile HIV Testing Services. | Gonsalves GS, Crawford FW, Cleary PD, Kaplan EH, Paltiel AD | Medical decision making : an international journal of the Society for Medical Decision Making | 28699382 | Med Decis Making | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28699382 |
| Suspected heroin-related overdoses incidents in Cincinnati, Ohio: A spatiotemporal analysis. | Li ZR, Xie E, Crawford FW, Warren JL, McConnell K, Copple JT, Johnson T, Gonsalves GS | PLoS medicine | 31714940 | PLoS Med | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31714940 |
| Divergent estimates of HIV incidence among people who inject drugs in Ukraine. | Morozova O, Booth RE, Dvoriak S, Dumchev K, Sazonova Y, Saliuk T, Crawford FW | The International journal on drug policy | 31405731 | Int J Drug Policy | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31405731 |
| One year of modeling and forecasting COVID-19 transmission to support policymakers in Connecticut. | Morozova O, Li ZR, Crawford FW | Scientific reports | 34642405 | Sci Rep | 2021 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/34642405 |
| Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood. | Li S, Crawford FW, Gerstein MB | Nature communications | 32681003 | Nat Commun | 2020 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/32681003 |
| One year of modeling and forecasting COVID-19 transmission to support policymakers in Connecticut. | Morozova O, Li ZR, Crawford FW | medRxiv : the preprint server for health sciences | 32587978 | medRxiv | 2021 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/32587978 |
| Computational methods for birth-death processes. | Crawford FW, Ho LST, Suchard MA | Wiley interdisciplinary reviews. Computational statistics | 29942419 | Wiley Interdiscip Rev Comput Stat | 2018 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/29942419 |
| Estimates of people who injected drugs within the last 12 months in Belgium based on a capture-recapture and multiplier method. | Plettinckx E, Crawford FW, Antoine J, Gremeaux L, Van Baelen L | Drug and alcohol dependence | 33310486 | Drug Alcohol Depend | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33310486 |
| Randomized controlled trials of biomarker targets. | Erlendsdottir M, Crawford FW | Clinical trials (London, England) | 36373783 | Clin Trials | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36373783 |
| Geographic and temporal trends in fentanyl-detected deaths in Connecticut, 2009-2019. | Lu H, Crawford FW, Gonsalves GS, Grau LE | Annals of epidemiology | 36669599 | Ann Epidemiol | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36669599 |
| Interpretation of the Individual Effect Under Treatment Spillover. | Crawford FW, Morozova O, Buchanan AL, Spiegelman D | American journal of epidemiology | 31094425 | Am J Epidemiol | 2019 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/31094425 |
| COVID-19 projections for reopening Connecticut. | Crawford FW, Li ZR, Morozova O | medRxiv : the preprint server for health sciences | 32588003 | medRxiv | 2020 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/32588003 |
| Identification of causal intervention effects under contagion. | Cai X, Loh WW, Crawford FW | Journal of causal inference | 34676152 | J Causal Inference | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34676152 |
| Cost-effectiveness of expanding the capacity of opioid agonist treatment in Ukraine: dynamic modeling analysis. | Morozova O, Crawford FW, Cohen T, Paltiel AD, Altice FL | Addiction (Abingdon, England) | 31478285 | Addiction | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31478285 |
| Creating a Framework for Conducting Randomized Clinical Trials during Disease Outbreaks. | Dean NE, Gsell PS, Brookmeyer R, Crawford FW, Donnelly CA, Ellenberg SS, Fleming TR, Halloran ME, Horby P, Jaki T, Krause PR, Longini IM, Mulangu S, Muyembe-Tamfum JJ, Nason MC, Smith PG, Wang R, Henao-Restrepo AM, De Gruttola V | The New England journal of medicine | 32242365 | N Engl J Med | 2020 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/32242365 |
| HIV Risk, Prevalence, and Access to Care Among Men Who Have Sex with Men in Lebanon. | Heimer R, Barbour R, Khouri D, Crawford FW, Shebl F, Aaraj E, Khoshnood K | AIDS research and human retroviruses | 28540733 | AIDS Res Hum Retroviruses | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28540733 |
| Estimating the early death toll of COVID-19 in the United States. | Weinberger DM, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C | medRxiv : the preprint server for health sciences | 32511293 | medRxiv | 2020 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/32511293 |
| Vaccination with BNT162b2 reduces transmission of SARS-CoV-2 to household contacts in Israel. | Prunas O, Warren JL, Crawford FW, Gazit S, Patalon T, Weinberger DM, Pitzer VE | medRxiv : the preprint server for health sciences | 34981074 | medRxiv | 2021 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/34981074 |
| Opioid Agonist Treatment and Improved Outcomes at Each Stage of the HIV Treatment Cascade in People Who Inject Drugs in Ukraine. | Mazhnaya A, Marcus R, Bojko MJ, Zelenev A, Makarenko I, Pykalo I, Filippovych S, Dvoriak S, Altice FL | Journal of acquired immune deficiency syndromes (1999) | 30312275 | J Acquir Immune Defic Syndr | 2018 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/30312275 |
| Estimating the Size of a Large Network and its Communities from a Random Sample. | Chen L, Karbasi A, Crawford FW | Advances in neural information processing systems | 28867924 | Adv Neural Inf Process Syst | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28867924 |
| HIV Testing and awareness of HIV status among people who inject drugs in greater Kuala Lumpur, Malaysia. | Bazazi AR, Vijay A, Crawford FW, Heimer R, Kamarulzaman A, Altice FL | AIDS care | 28803503 | AIDS Care | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28803503 |
| Empirical evidence of recruitment bias in a network study of people who inject drugs. | Zeng L, Li J, Crawford FW | The American journal of drug and alcohol abuse | 30896982 | Am J Drug Alcohol Abuse | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30896982 |
| Risk ratios for contagious outcomes. | Morozova O, Cohen T, Crawford FW | Journal of the Royal Society, Interface | 29343627 | J R Soc Interface | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29343627 |
| Impact of close interpersonal contact on COVID-19 incidence: evidence from one year of mobile device data. | Crawford FW, Jones SA, Cartter M, Dean SG, Warren JL, Li ZR, Barbieri J, Campbell J, Kenney P, Valleau T, Morozova O | medRxiv : the preprint server for health sciences | 33758869 | medRxiv | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33758869 |
| Dependence-Robust Confidence Intervals for Capture-Recapture Surveys. | Sun J, Van Baelen L, Plettinckx E, Crawford FW | Journal of survey statistics and methodology | 37975066 | J Surv Stat Methodol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37975066 |
| A semi-synthetic regulon enables rapid growth of yeast on xylose. | Endalur Gopinarayanan V, Nair NU | Nature communications | 29581426 | Nat Commun | 2018 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/29581426 |
| Directed evolution of Anabaena variabilis phenylalanine ammonia-lyase (PAL) identifies mutants with enhanced activities. | Mays ZJ , Mohan K , Trivedi VD , Chappell TC , Nair NU | Chemical communications (Cambridge, England) | 32270162 | Chem Commun (Camb) | 2020 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/32270162 |
| Pentose Metabolism in Saccharomyces cerevisiae: The Need to Engineer Global Regulatory Systems. | Endalur Gopinarayanan V, Nair NU | Biotechnology journal | 30171750 | Biotechnol J | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30171750 |
| A quantitative model for metabolic intervention using gut microbes. | Mays ZJS, Nair NU | Biotechnology progress | 33426814 | Biotechnol Prog | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33426814 |
| Engineered lactobacilli display anti-biofilm and growth suppressing activities against Pseudomonas aeruginosa. | Chappell TC, Nair NU | NPJ biofilms and microbiomes | 33127888 | NPJ Biofilms Microbiomes | 2020 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/33127888 |
| Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates. | Trivedi VD, Sullivan SF, Choudhury D, Endalur Gopinarayanan V, Hart T, Nair NU | Cell chemical biology | 37421944 | Cell Chem Biol | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37421944 |
| Specific codons control cellular resources and fitness. | Love AM, Nair NU | Science advances | 38381824 | Sci Adv | 2024 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/38381824 |
| Synthetic biology in probiotic lactic acid bacteria: At the frontier of living therapeutics. | Mays ZJ, Nair NU | Current opinion in biotechnology | 29550614 | Curr Opin Biotechnol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29550614 |
| Toward a genetic tool development pipeline for host-associated bacteria. | Waller MC, Bober JR, Nair NU, Beisel CL | Current opinion in microbiology | 28624690 | Curr Opin Microbiol | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28624690 |
| Quantifying and Engineering Mucus Adhesion of Probiotics. | Mays ZJS, Chappell TC, Nair NU | ACS synthetic biology | 31909976 | ACS Synth Biol | 2020 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/31909976 |
| Galactose to tagatose isomerization at moderate temperatures with high conversion and productivity. | Bober JR, Nair NU | Nature communications | 31591402 | Nat Commun | 2019 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/31591402 |
| Cheating the Cheater: Suppressing False-Positive Enrichment during Biosensor-Guided Biocatalyst Engineering. | Trivedi VD, Mohan K, Chappell TC, Mays ZJS, Nair NU | ACS synthetic biology | 34914365 | ACS Synth Biol | 2022 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/34914365 |
| A Silk-Based Platform to Stabilize Phenylalanine Ammonia-lyase for Orally Administered Enzyme Replacement Therapy. | d'Amone L, Trivedi VD, Nair NU, Omenetto FG | Molecular pharmaceutics | 35862031 | Mol Pharm | 2022 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/35862031 |
| Towards universal synthetic heterotrophy using a metabolic coordinator. | Sullivan SF, Shetty A, Bharadwaj T, Krishna N, Trivedi VD, Endalur Gopinarayanan V, Chappell TC, Sellers DM, Pravin Kumar R, Nair NU | Metabolic engineering | 37406763 | Metab Eng | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37406763 |
| Establishing synthesis pathway-host compatibility via enzyme solubility. | Amin SA, Endalur Gopinarayanan V, Nair NU, Hassoun S | Biotechnology and bioengineering | 30802311 | Biotechnol Bioeng | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30802311 |
| Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. | Amin SA, Chavez E, Porokhin V, Nair NU, Hassoun S | Microbial cell factories | 31196115 | Microb Cell Fact | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31196115 |
| Characterization of a membrane enzymatic complex for heterologous production of poly-γ-glutamate in E. coli. | Motta Nascimento B, Nair NU | Metabolic engineering communications | 32963960 | Metab Eng Commun | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32963960 |
| Synthetic Biology Approaches to Engineer Probiotics and Members of the Human Microbiota for Biomedical Applications. | Bober JR, Beisel CL, Nair NU | Annual review of biomedical engineering | 29528686 | Annu Rev Biomed Eng | 2018 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/29528686 |
| In-depth Sequence-Function Characterization Reveals Multiple Pathways to Enhance Enzymatic Activity. | Trivedi VD, Chappell TC, Krishna NB, Shetty A, Sigamani GG, Mohan K, Ramesh A, Pravin KR, Nair NU | ACS catalysis | 37325394 | ACS Catal | 2022 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/37325394 |
| Enhanced intratumoural activity of CAR T cells engineered to produce immunomodulators under photothermal control. | Miller IC, Zamat A, Sun LK, Phuengkham H, Harris AM, Gamboa L, Yang J, Murad JP, Priceman SJ, Kwong GA | Nature biomedical engineering | 34385695 | Nat Biomed Eng | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34385695 |
| DNA-Barcoded pMHC Tetramers for Detection of Single Antigen-Specific T Cells by Digital PCR. | Dahotre SN, Chang YM, Romanov AM, Kwong GA | Analytical chemistry | 30656939 | Anal Chem | 2019 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/30656939 |
| Dimensionless parameter predicts bacterial prodrug success. | Holt BA, Tuttle M, Xu Y, Su M, Røise JJ, Wang X, Murthy N, Kwong GA | Molecular systems biology | 35005851 | Mol Syst Biol | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35005851 |
| Remote Control of Mammalian Cells with Heat-Triggered Gene Switches and Photothermal Pulse Trains. | Miller IC, Gamboa Castro M, Maenza J, Weis JP, Kwong GA | ACS synthetic biology | 29579381 | ACS Synth Biol | 2018 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/29579381 |
| Deconvolving multiplexed protease signatures with substrate reduction and activity clustering. | Zhuang Q, Holt BA, Kwong GA, Qiu P | PLoS computational biology | 31479443 | PLoS Comput Biol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31479443 |
| Interfacing Biomaterials with Synthetic T Cell Immunity. | Su FY, Mac QD, Sivakumar A, Kwong GA | Advanced healthcare materials | 33887123 | Adv Healthc Mater | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33887123 |
| Macrophage Sensors for Early Cancer Detection. | Kwong GA | Clinical chemistry | 32040571 | Clin Chem | 2020 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/32040571 |
| Nanosensors to Detect Protease Activity In Vivo for Noninvasive Diagnostics. | Holt BA, Mac QD, Kwong GA | Journal of visualized experiments : JoVE | 30059042 | J Vis Exp | 2018 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/30059042 |
| Non-invasive early detection of acute transplant rejection via nanosensors of granzyme B activity. | Mac QD, Mathews DV, Kahla JA, Stoffers CM, Delmas OM, Holt BA, Adams AB, Kwong GA | Nature biomedical engineering | 30952979 | Nat Biomed Eng | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30952979 |
| Synthetic immunity by remote control. | Gamboa L, Zamat AH, Kwong GA | Theranostics | 32206114 | Theranostics | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32206114 |
| Individually addressable and dynamic DNA gates for multiplexed cell sorting. | Dahotre SN, Chang YM, Wieland A, Stammen SR, Kwong GA | Proceedings of the National Academy of Sciences of the United States of America | 29632190 | Proc Natl Acad Sci U S A | 2018 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/29632190 |
| Heat-Triggered Remote Control of CRISPR-dCas9 for Tunable Transcriptional Modulation. | Gamboa L, Phung EV, Li H, Meyers JP, Hart AC, Miller IC, Kwong GA | ACS chemical biology | 31904924 | ACS Chem Biol | 2020 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/31904924 |
| In vivo mRNA delivery to virus-specific T cells by light-induced ligand exchange of MHC class I antigen-presenting nanoparticles. | Su FY, Zhao QH, Dahotre SN, Gamboa L, Bawage SS, Silva Trenkle AD, Zamat A, Phuengkham H, Ahmed R, Santangelo PJ, Kwong GA | Science advances | 35196075 | Sci Adv | 2022 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/35196075 |
| Embracing enzyme promiscuity with activity-based compressed biosensing. | Holt BA, Lim HS, Sivakumar A, Phuengkham H, Su M, Tuttle M, Xu Y, Liakakos H, Qiu P, Kwong GA | Cell reports methods | 36814844 | Cell Rep Methods | 2023 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/36814844 |
| AND-gated protease-activated nanosensors for programmable detection of anti-tumour immunity. | Sivakumar A, Phuengkham H, Rajesh H, Mac QD, Rogers LC, Silva Trenkle AD, Bawage SS, Hincapie R, Li Z, Vainikos S, Lee I, Xue M, Qiu P, Finn MG, Kwong GA | Nature nanotechnology | 39753733 | Nat Nanotechnol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39753733 |
| Synthetic biomarkers: a twenty-first century path to early cancer detection. | Kwong GA, Ghosh S, Gamboa L, Patriotis C, Srivastava S, Bhatia SN | Nature reviews. Cancer | 34489588 | Nat Rev Cancer | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34489588 |
| Synthetic Antigen-Presenting Cells for Adoptive T Cell Therapy. | Dahotre SN, Romanov AM, Su FY, Kwong GA | Advanced therapeutics | 34541300 | Adv Ther (Weinh) | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34541300 |
| Protease circuits for processing biological information. | Holt BA, Kwong GA | Nature communications | 33024117 | Nat Commun | 2020 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/33024117 |
| Urinary detection of early responses to checkpoint blockade and of resistance to it via protease-cleaved antibody-conjugated sensors. | Mac QD, Sivakumar A, Phuengkham H, Xu C, Bowen JR, Su FY, Stentz SZ, Sim H, Harris AM, Li TT, Qiu P, Kwong GA | Nature biomedical engineering | 35241815 | Nat Biomed Eng | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35241815 |
| Single-cell transcriptomics reveals receptor transformations during olfactory neurogenesis. | Hanchate NK, Kondoh K, Lu Z, Kuang D, Ye X, Qiu X, Pachter L, Trapnell C, Buck LB | Science (New York, N.Y.) | 26541607 | Science | 2015 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/26541607 |
| A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. | Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI | Science (New York, N.Y.) | 31488706 | Science | 2019 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/31488706 |
| iPSC-Derived Macrophages Effectively Treat Pulmonary Alveolar Proteinosis in Csf2rb-Deficient Mice. | Mucci A, Lopez-Rodriguez E, Hetzel M, Liu S, Suzuki T, Happle C, Ackermann M, Kempf H, Hillje R, Kunkiel J, Janosz E, Brennig S, Glage S, Bankstahl JP, Dettmer S, Rodt T, Gohring G, Trapnell B, Hansen G, Trapnell C, Knudsen L, Lachmann N, Moritz T | Stem cell reports | 30100408 | Stem Cell Reports | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30100408 |
| Aligning Single-Cell Developmental and Reprogramming Trajectories Identifies Molecular Determinants of Myogenic Reprogramming Outcome. | Cacchiarelli D, Qiu X, Srivatsan S, Manfredi A, Ziller M, Overbey E, Grimaldi A, Grimsby J, Pokharel P, Livak KJ, Li S, Meissner A, Mikkelsen TS, Rinn JL, Trapnell C | Cell systems | 30195438 | Cell Syst | 2018 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/30195438 |
| Defining cell types and states with single-cell genomics. | Trapnell C | Genome research | 26430159 | Genome Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26430159 |
| Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. | McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C | Cell genomics | 38278156 | Cell Genom | 2024 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/38278156 |
| A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets. | Sharon N, Chawla R, Mueller J, Vanderhooft J, Whitehorn LJ, Rosenthal B, Gürtler M, Estanboulieh RR, Shvartsman D, Gifford DK, Trapnell C, Melton D | Cell | 30661759 | Cell | 2019 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/30661759 |
| A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens. | Gasperini M, Hill AJ, McFaline-Figueroa JL, Martin B, Kim S, Zhang MD, Jackson D, Leith A, Schreiber J, Noble WS, Trapnell C, Ahituv N, Shendure J | Cell | 30612741 | Cell | 2019 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/30612741 |
| Dimensionality reduction by UMAP to visualize physical and genetic interactions. | Dorrity MW, Saunders LM, Queitsch C, Fields S, Trapnell C | Nature communications | 32210240 | Nat Commun | 2020 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/32210240 |
| MaveDB 2024: a curated community database with over seven million variant effects from multiplexed functional assays. | Rubin AF, Stone J, Bianchi AH, Capodanno BJ, Da EY, Dias M, Esposito D, Frazer J, Fu Y, Grindstaff SB, Harrington MR, Li I, McEwen AE, Min JK, Moore N, Moscatelli OG, Ong J, Polunina PV, Rollins JE, Rollins NJ, Snyder AE, Tam A, Wakefield MJ, Ye SS, Starita LM, Bryant VL, Marks DS, Fowler DM | Genome biology | 39838450 | Genome Biol | 2025 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/39838450 |
| Single-Cell Multi-omics: An Engine for New Quantitative Models of Gene Regulation. | Packer J, Trapnell C | Trends in genetics : TIG | 30007833 | Trends Genet | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30007833 |
| Joint profiling of chromatin accessibility and gene expression in thousands of single cells. | Cao J, Cusanovich DA, Ramani V, Aghamirzaie D, Pliner HA, Hill AJ, Daza RM, McFaline-Figueroa JL, Packer JS, Christiansen L, Steemers FJ, Adey AC, Trapnell C, Shendure J | Science (New York, N.Y.) | 30166440 | Science | 2018 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/30166440 |
| Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. | Pliner HA, Packer JS, McFaline-Figueroa JL, Cusanovich DA, Daza RM, Aghamirzaie D, Srivatsan S, Qiu X, Jackson D, Minkina A, Adey AC, Steemers FJ, Shendure J, Trapnell C | Molecular cell | 30078726 | Mol Cell | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/30078726 |
| Comprehensive single-cell transcriptional profiling of a multicellular organism. | Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J | Science (New York, N.Y.) | 28818938 | Science | 2017 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/28818938 |
| On the design of CRISPR-based single-cell molecular screens. | Hill AJ, McFaline-Figueroa JL, Starita LM, Gasperini MJ, Matreyek KA, Packer J, Jackson D, Shendure J, Trapnell C | Nature methods | 29457792 | Nat Methods | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29457792 |
| Thyroid hormone regulates distinct paths to maturation in pigment cell lineages. | Saunders LM, Mishra AK, Aman AJ, Lewis VM, Toomey MB, Packer JS, Qiu X, McFaline-Figueroa JL, Corbo JC, Trapnell C, Parichy DM | eLife | 31140974 | Elife | 2019 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/31140974 |
| A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility. | Cusanovich DA, Hill AJ, Aghamirzaie D, Daza RM, Pliner HA, Berletch JB, Filippova GN, Huang X, Christiansen L, DeWitt WS, Lee C, Regalado SG, Read DF, Steemers FJ, Disteche CM, Trapnell C, Shendure J | Cell | 30078704 | Cell | 2018 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/30078704 |
| Massively multiplex chemical transcriptomics at single-cell resolution. | Srivatsan SR, McFaline-Figueroa JL, Ramani V, Saunders L, Cao J, Packer J, Pliner HA, Jackson DL, Daza RM, Christiansen L, Zhang F, Steemers F, Shendure J, Trapnell C | Science (New York, N.Y.) | 31806696 | Science | 2020 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/31806696 |
| Sci-fate characterizes the dynamics of gene expression in single cells. | Cao J, Zhou W, Steemers F, Trapnell C, Shendure J | Nature biotechnology | 32284584 | Nat Biotechnol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32284584 |
| High-throughput, microscope-based sorting to dissect cellular heterogeneity. | Hasle N, Cooke A, Srivatsan S, Huang H, Stephany JJ, Krieger Z, Jackson D, Tang W, Pendyala S, Monnat RJ Jr, Trapnell C, Hatch EM, Fowler DM | Molecular systems biology | 32500953 | Mol Syst Biol | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32500953 |
| Connect-seq to superimpose molecular on anatomical neural circuit maps. | Hanchate NK, Lee EJ, Ellis A, Kondoh K, Kuang D, Basom R, Trapnell C, Buck LB | Proceedings of the National Academy of Sciences of the United States of America | 32034095 | Proc Natl Acad Sci U S A | 2020 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/32034095 |
| A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. | McFaline-Figueroa JL, Hill AJ, Qiu X, Jackson D, Shendure J, Trapnell C | Nature genetics | 31477929 | Nat Genet | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31477929 |
| A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface. | Gabrovsek L, Collins KB, Aggarwal S, Saunders LM, Lau HT, Suh D, Sancak Y, Trapnell C, Ong SE, Smith FD, Scott JD | The Journal of biological chemistry | 32482893 | J Biol Chem | 2020 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/32482893 |
| Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy. | McFaline-Figueroa JL, Srivatsan S, Hill AJ, Gasperini M, Jackson DL, Saunders L, Domcke S, Regalado SG, Lazarchuck P, Alvarez S, Monnat RJ Jr, Shendure J, Trapnell C | bioRxiv : the preprint server for biology | 37398090 | bioRxiv | 2023 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37398090 |
| Single-cell mRNA quantification and differential analysis with Census. | Qiu X, Hill A, Packer J, Lin D, Ma YA, Trapnell C | Nature methods | 28114287 | Nat Methods | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28114287 |
| Single-cell transcriptome sequencing: recent advances and remaining challenges. | Liu S, Trapnell C | F1000Research | 26949524 | F1000Res | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26949524 |
| Activated CARD11 accelerates germinal center kinetics, promoting mTORC1 and terminal differentiation. | Wray-Dutra MN, Chawla R, Thomas KR, Seymour BJ, Arkatkar T, Sommer KM, Khim S, Trapnell C, James RG, Rawlings DJ | The Journal of experimental medicine | 30127060 | J Exp Med | 2018 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/30127060 |
| Reversed graph embedding resolves complex single-cell trajectories. | Qiu X, Mao Q, Tang Y, Wang L, Chawla R, Pliner HA, Trapnell C | Nature methods | 28825705 | Nat Methods | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28825705 |
| Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe. | Qiu X, Rahimzamani A, Wang L, Ren B, Mao Q, Durham T, McFaline-Figueroa JL, Saunders L, Trapnell C, Kannan S | Cell systems | 32135093 | Cell Syst | 2020 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/32135093 |
| The single-cell transcriptional landscape of mammalian organogenesis. | Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L, Steemers FJ, Trapnell C, Shendure J | Nature | 30787437 | Nature | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30787437 |
| Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development. | Sharon N, Vanderhooft J, Straubhaar J, Mueller J, Chawla R, Zhou Q, Engquist EN, Trapnell C, Gifford DK, Melton DA | Cell reports | 31116975 | Cell Rep | 2019 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/31116975 |
| Supervised classification enables rapid annotation of cell atlases. | Pliner HA, Shendure J, Trapnell C | Nature methods | 31501545 | Nat Methods | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31501545 |
| IL-2 enhances ex vivo-expanded regulatory T-cell persistence after adoptive transfer. | Furlan SN, Singh K, Lopez C, Tkachev V, Hunt DJ, Hibbard J, Betz KM, Blazar BR, Trapnell C, Kean LS | Blood advances | 32311015 | Blood Adv | 2020 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/32311015 |
| Dynamics of Gene Expression in Single Root Cells of Arabidopsis thaliana. | Jean-Baptiste K, McFaline-Figueroa JL, Alexandre CM, Dorrity MW, Saunders L, Bubb KL, Trapnell C, Fields S, Queitsch C, Cuperus JT | The Plant cell | 30923229 | Plant Cell | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30923229 |
| The accessible chromatin landscape of the murine hippocampus at single-cell resolution. | Sinnamon JR, Torkenczy KA, Linhoff MW, Vitak SA, Mulqueen RM, Pliner HA, Trapnell C, Steemers FJ, Mandel G, Adey AC | Genome research | 30936163 | Genome Res | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30936163 |
| Plug-and-play control of a brain-computer interface through neural map stabilization. | Silversmith DB, Abiri R, Hardy NF, Natraj N, Tu-Chan A, Chang EF, Ganguly K | Nature biotechnology | 32895549 | Nat Biotechnol | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32895549 |
| Sampling representational plasticity of simple imagined movements across days enables long-term neuroprosthetic control. | Natraj N, Seko S, Abiri R, Miao R, Yan H, Graham Y, Tu-Chan A, Chang EF, Ganguly K | Cell | 40054446 | Cell | 2025 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/40054446 |
| Muscle synergies after stroke are correlated with perilesional high gamma. | Godlove J, Gulati T, Dichter B, Chang E, Ganguly K | Annals of clinical and translational neurology | 28097208 | Ann Clin Transl Neurol | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28097208 |
| Flexible regulation of representations on a drifting manifold enables long-term stable complex neuroprosthetic control. | Natraj N, Seko S, Abiri R, Yan H, Graham Y, Tu-Chan A, Chang EF, Ganguly K | bioRxiv : the preprint server for biology | 37645922 | bioRxiv | 2023 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/37645922 |
| Compartmentalized dynamics within a common multi-area mesoscale manifold represent a repertoire of human hand movements. | Natraj N, Silversmith DB, Chang EF, Ganguly K | Neuron | 34678147 | Neuron | 2022 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/34678147 |
| Cortical neuroprosthetics from a clinical perspective. | Tsu AP, Burish MJ, GodLove J, Ganguly K | Neurobiology of disease | 26253606 | Neurobiol Dis | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26253606 |
| Embryonic Stem Cell Engineering with a Glycomimetic FGF2/BMP4 Co-Receptor Drives Mesodermal Differentiation in a Three-Dimensional Culture. | Naticchia MR, Laubach LK, Tota EM, Lucas TM, Huang ML, Godula K | ACS chemical biology | 30157624 | ACS Chem Biol | 2018 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/30157624 |
| Influencing Early Stages of Neuromuscular Junction Formation through Glycocalyx Engineering. | Huang ML, Tota EM, Lucas TM, Godula K | ACS chemical neuroscience | 30095249 | ACS Chem Neurosci | 2018 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/30095249 |
| Small Molecule Antagonist of Cell Surface Glycosaminoglycans Restricts Mouse Embryonic Stem Cells in a Pluripotent State. | Huang ML, Michalak AL, Fisher CJ, Christy M, Smith RAA, Godula K | Stem cells (Dayton, Ohio) | 28984039 | Stem Cells | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28984039 |
| Genome-wide screens uncover KDM2B as a modifier of protein binding to heparan sulfate. | Weiss RJ, Spahn PN, Chiang AWT, Liu Q, Li J, Hamill KM, Rother S, Clausen TM, Hoeksema MA, Timm BM, Godula K, Glass CK, Tor Y, Gordts PLSM, Lewis NE, Esko JD | Nature chemical biology | 33846619 | Nat Chem Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33846619 |
| Body mass index, calcium supplementation and risk of colorectal adenomas. | Barry EL, Lund JL, Westreich D, Mott LA, Ahnen DJ, Beck GJ, Bostick RM, Bresalier RS, Burke CA, Church TR, Rees JR, Robertson DJ, Baron JA | International journal of cancer | 30117164 | Int J Cancer | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30117164 |
| Generalizability of randomized trial results to target populations: Design and analysis possibilities. | Stuart EA, Ackerman B, Westreich D | Research on social work practice | 30034203 | Res Soc Work Pract | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30034203 |
| Invited Commentary: Beware the Test-Negative Design. | Westreich D, Hudgens MG | American journal of epidemiology | 27587722 | Am J Epidemiol | 2016 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/27587722 |
| The Authors Respond. | Breskin A, Cole SR, Hudgens MG | Epidemiology (Cambridge, Mass.) | 30052540 | Epidemiology | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30052540 |
| Comparison of Methods to Generalize Randomized Clinical Trial Results Without Individual-Level Data for the Target Population. | Hong JL, Webster-Clark M, Jonsson Funk M, Stürmer T, Dempster SE, Cole SR, Herr I, LoCasale R | American journal of epidemiology | 30312378 | Am J Epidemiol | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30312378 |
| The Effects of Hepatitis C Infection and Treatment on All-cause Mortality Among People Living With Human Immunodeficiency Virus. | Breskin A, Westreich D, Cole SR, Hudgens MG, Hurt CB, Seaberg EC, Thio CL, Tien PC, Adimora AA | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 30321289 | Clin Infect Dis | 2019 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/30321289 |
| Generalizing Randomized Clinical Trial Results: Implementation and Challenges Related to Missing Data in the Target Population. | Hong JL, Jonsson Funk M, LoCasale R, Dempster SE, Cole SR, Webster-Clark M, Edwards JK, Stürmer T | American journal of epidemiology | 29020193 | Am J Epidemiol | 2018 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/29020193 |
| Transporting Subgroup Analyses of Randomized Controlled Trials for Planning Implementation of New Interventions. | Mehrotra ML, Westreich D, Glymour MM, Geng E, Glidden DV | American journal of epidemiology | 33615327 | Am J Epidemiol | 2021 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/33615327 |
| The effect of early life antibiotic exposures on diarrheal rates among young children in Vellore, India. | Rogawski ET, Westreich D, Becker-Dreps S, Adair LS, Sandler RS, Sarkar R, Kattula D, Ward HD, Meshnick SR, Kang G | The Pediatric infectious disease journal | 25742244 | Pediatr Infect Dis J | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25742244 |
| Invited commentary: every good randomization deserves observation. | Westreich D, Edwards JK | American journal of epidemiology | 26487342 | Am J Epidemiol | 2015 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/26487342 |
| Causal Impact: Epidemiological Approaches for a Public Health of Consequence. | Westreich D, Edwards JK, Rogawski ET, Hudgens MG, Stuart EA, Cole SR | American journal of public health | 27153017 | Am J Public Health | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27153017 |
| From Patients to Policy: Population Intervention Effects in Epidemiology. | Westreich D | Epidemiology (Cambridge, Mass.) | 28282339 | Epidemiology | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28282339 |
| Marginal Structural Models for Risk or Prevalence Ratios for a Point Exposure Using a Disease Risk Score. | Richardson DB, Keil AP, Kinlaw AC, Cole SR | American journal of epidemiology | 30726868 | Am J Epidemiol | 2019 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/30726868 |
| Toward a Clearer Definition of Selection Bias When Estimating Causal Effects. | Lu H, Cole SR, Howe CJ, Westreich D | Epidemiology (Cambridge, Mass.) | 35700187 | Epidemiology | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/35700187 |
| Quantifying Cancer Risk from Radiation. | Keil AP, Richardson DB | Risk analysis : an official publication of the Society for Risk Analysis | 29211917 | Risk Anal | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29211917 |
| Generalizing the per-protocol treatment effect: The case of ACTG A5095. | Lu H, Cole SR, Hall HI, Schisterman EF, Breger TL, K Edwards J, Westreich D | Clinical trials (London, England) | 30326736 | Clin Trials | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30326736 |
| A review of time scale fundamentals in the g-formula and insidious selection bias. | Keil AP, Edwards JK | Current epidemiology reports | 30555772 | Curr Epidemiol Rep | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30555772 |
| Using Bounds to Compare the Strength of Exchangeability Assumptions for Internal and External Validity. | Breskin A, Westreich D, Cole SR, Edwards JK | American journal of epidemiology | 30834430 | Am J Epidemiol | 2019 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/30834430 |
| UK Biobank, big data, and the consequences of non-representativeness. | Keyes KM, Westreich D | Lancet (London, England) | 30938313 | Lancet | 2019 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/30938313 |
| Improving Depression Among HIV-Infected Adults: Transporting the Effect of a Depression Treatment Intervention to Routine Care. | Bengtson AM, Pence BW, Gaynes BN, Quinlivan EB, Heine AD, OʼDonnell JK, Crane HM, Mathews WC, Moore RD, Westreich D, OʼCleirigh C, Christopoulos K, Mimiaga MJ, Mugavero MJ | Journal of acquired immune deficiency syndromes (1999) | 27668804 | J Acquir Immune Defic Syndr | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27668804 |
| Generalizing Study Results: A Potential Outcomes Perspective. | Lesko CR, Buchanan AL, Westreich D, Edwards JK, Hudgens MG, Cole SR | Epidemiology (Cambridge, Mass.) | 28346267 | Epidemiology | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28346267 |
| Use of electronic health record data and machine learning to identify candidates for HIV pre-exposure prophylaxis: a modelling study. | Marcus JL, Hurley LB, Krakower DS, Alexeeff S, Silverberg MJ, Volk JE | The lancet. HIV | 31285183 | Lancet HIV | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31285183 |
| Use of Intrauterine Devices and Risk of Human Immunodeficiency Virus Acquisition Among Insured Women in the United States. | Marcus JL, Snowden JM, Murray Horwitz ME, Toh S, Horgan C, Tilney RC, Rajbhandari R, Back S, Westreich DJ | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 31412356 | Clin Infect Dis | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/31412356 |
| Brief Report: Estimating Differences and Ratios in Median Times to Event. | Rogawski ET, Westreich DJ, Kang G, Ward HD, Cole SR | Epidemiology (Cambridge, Mass.) | 27465526 | Epidemiology | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27465526 |
| Smoking, HIV, and risk of pregnancy loss. | Westreich D, Cates J, Cohen M, Weber KM, Seidman D, Cropsey K, Wright R, Milam J, Young MA, Mehta CC, Gustafson DR, Golub ET, Fischl MA, Adimora AA | AIDS (London, England) | 27902507 | AIDS | 2017 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/27902507 |
| When Is a Complete-Case Approach to Missing Data Valid? The Importance of Effect-Measure Modification. | Ross RK, Breskin A, Westreich D | American journal of epidemiology | 32601706 | Am J Epidemiol | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/32601706 |
| Estimating the Impact of Changes to Occupational Standards for Silica Exposure on Lung Cancer Mortality. | Keil AP, Richardson DB, Westreich D, Steenland K | Epidemiology (Cambridge, Mass.) | 29870429 | Epidemiology | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29870429 |
| Target Validity and the Hierarchy of Study Designs. | Westreich D, Edwards JK, Lesko CR, Cole SR, Stuart EA | American journal of epidemiology | 30299451 | Am J Epidemiol | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30299451 |
| The Effects of Hepatitis C Treatment Eligibility Criteria on All-cause Mortality Among People With Human Immunodeficiency Virus. | Breskin A, Westreich D, Hurt CB, Cole SR, Hudgens MG, Seaberg EC, Thio CL, Tien PC, Adimora AA | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 30615096 | Clin Infect Dis | 2019 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/30615096 |
| An Illustration of Inverse Probability Weighting to Estimate Policy-Relevant Causal Effects. | Edwards JK, Cole SR, Lesko CR, Mathews WC, Moore RD, Mugavero MJ, Westreich D | American journal of epidemiology | 27469514 | Am J Epidemiol | 2016 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/27469514 |
| An updated systematic review of epidemiological evidence on hormonal contraceptive methods and HIV acquisition in women. | Polis CB, Curtis KM, Hannaford PC, Phillips SJ, Chipato T, Kiarie JN, Westreich DJ, Steyn PS | AIDS (London, England) | 27500670 | AIDS | 2016 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/27500670 |
| Commentary: Epidemiology in the era of big data. | Mooney SJ, Westreich DJ, El-Sayed AM | Epidemiology (Cambridge, Mass.) | 25756221 | Epidemiology | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25756221 |
| Risk. | Cole SR, Hudgens MG, Brookhart MA, Westreich D | American journal of epidemiology | 25660080 | Am J Epidemiol | 2015 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/25660080 |
| The Authors Respond. | Lesko CR, Buchanan AL, Westreich D, Edwards JK, Hudgens MG, Cole SR | Epidemiology (Cambridge, Mass.) | 29023242 | Epidemiology | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29023242 |
| Invited Commentary: Causal Inference Across Space and Time-Quixotic Quest, Worthy Goal, or Both? | Edwards JK, Lesko CR, Keil AP | American journal of epidemiology | 28679174 | Am J Epidemiol | 2017 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/28679174 |
| Primary non-adherence and the new-user design. | Li X, Cole SR, Westreich D, Brookhart MA | Pharmacoepidemiology and drug safety | 29460385 | Pharmacoepidemiol Drug Saf | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29460385 |
| G-computation for policy-relevant effects of interventions on time-to-event outcomes. | Breskin A, Edmonds A, Cole SR, Westreich D, Cocohoba J, Cohen MH, Kassaye SG, Metsch LR, Sharma A, Williams MS, Adimora AA | International journal of epidemiology | 33141177 | Int J Epidemiol | 2021 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/33141177 |
| Exploring the Subtleties of Inverse Probability Weighting and Marginal Structural Models. | Breskin A, Cole SR, Westreich D | Epidemiology (Cambridge, Mass.) | 29384789 | Epidemiology | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29384789 |
| RESOLVING AN APPARENT PARADOX IN DOUBLY ROBUST ESTIMATORS. | Keil AP, Mooney SJ, Jonsson Funk M, Cole SR, Edwards JK, Westreich D | American journal of epidemiology | 29394330 | Am J Epidemiol | 2018 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/29394330 |
| Two-stage g-computation: Evaluating Treatment and Intervention Impacts in Observational Cohorts When Exposure Information Is Partly Missing. | Breger TL, Edwards JK, Cole SR, Westreich D, Pence BW, Adimora AA | Epidemiology (Cambridge, Mass.) | 32657953 | Epidemiology | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32657953 |
| Incident obstructive lung disease and mortality among people with HIV and a history of injecting drugs. | Kalmin MM, Westreich D, Drummond BM, Sun J, Mehta SH, Kirk GD | AIDS (London, England) | 33831913 | AIDS | 2021 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/33831913 |
| A longitudinal, HIV care continuum: 10-year restricted mean time in each care continuum stage after enrollment in care, by history of IDU. | Lesko CR, Edwards JK, Moore RD, Lau B | AIDS (London, England) | 27314178 | AIDS | 2016 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/27314178 |
| Effect of Postnatal HIV Treatment on Clinical Mastitis and Breast Inflammation in HIV-Infected Breast-feeding Women. | Zadrozny S, Westreich D, Hudgens MG, Chasela C, Jamieson DJ, Martinson F, Zimba C, Tegha G, Hoffman I, Miller WC, Pence BW, King CC, Kourtis AP, Msungama W, van der Horst C, BAN Study Team | Paediatric and perinatal epidemiology | 28205255 | Paediatr Perinat Epidemiol | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28205255 |
| Early Life Antibiotic Exposure Is Not Associated with Growth in Young Children of Vellore, India. | Rogawski ET, Westreich DJ, Adair LS, Becker-Dreps S, Sandler RS, Sarkar R, Kattula D, Ward HD, Meshnick S, Kang G | The Journal of pediatrics | 26372535 | J Pediatr | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26372535 |
| Transportability of Trial Results Using Inverse Odds of Sampling Weights. | Westreich D, Edwards JK, Lesko CR, Stuart E, Cole SR | American journal of epidemiology | 28535275 | Am J Epidemiol | 2017 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/28535275 |
| Thirteen Questions About Using Machine Learning in Causal Research (You Won't Believe the Answer to Number 10!). | Mooney SJ, Keil AP, Westreich DJ | American journal of epidemiology | 33751024 | Am J Epidemiol | 2021 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/33751024 |
| Inverse Probability Weights for the Analysis of Polytomous Outcomes. | Richardson DB, Kinlaw AC, Keil AP, Naimi AI, Kaufman JS, Cole SR | American journal of epidemiology | 29390115 | Am J Epidemiol | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29390115 |
| You are smarter than you think: (super) machine learning in context. | Keil AP, Edwards JK | European journal of epidemiology | 29744711 | Eur J Epidemiol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29744711 |
| Age at Entry Into Care, Timing of Antiretroviral Therapy Initiation, and 10-Year Mortality Among HIV-Seropositive Adults in the United States. | Edwards JK, Cole SR, Westreich D, Mugavero MJ, Eron JJ, Moore RD, Mathews WC, Hunt P, Williams C, Centers for AIDS Research Network of Integrated Clinical Systems investigators | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 26082505 | Clin Infect Dis | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26082505 |
| The Impact of Implementation Fidelity on Mortality Under a CD4-Stratified Timing Strategy for Antiretroviral Therapy in Patients With Tuberculosis. | Patel MR, Westreich D, Yotebieng M, Nana M, Eron JJ, Behets F, Van Rie A | American journal of epidemiology | 25787266 | Am J Epidemiol | 2015 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/25787266 |
| Misclassification in defining and diagnosing microcephaly. | Kalmin MM, Gower EW, Stringer EM, Bowman NM, Rogawski McQuade ET, Westreich D | Paediatric and perinatal epidemiology | 31347726 | Paediatr Perinat Epidemiol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31347726 |
| The Intersections of COVID-19, HIV, and Race/Ethnicity: Machine Learning Methods to Identify and Model Risk Factors for Severe COVID-19 in a Large U.S. National Dataset. | Kunz M, Rott KW, Hurwitz E, Kunisaki K, Sun J, Wilkins KJ, Islam JY, Patel R, Safo SE, National Covid Cohort Collaborative (N3C) Consortium | AIDS and behavior | 38326668 | AIDS Behav | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38326668 |
| Next-generation libraries for robust RNA interference-based genome-wide screens. | Kampmann M, Horlbeck MA, Chen Y, Tsai JC, Bassik MC, Gilbert LA, Villalta JE, Kwon SC, Chang H, Kim VN, Weissman JS | Proceedings of the National Academy of Sciences of the United States of America | 26080438 | Proc Natl Acad Sci U S A | 2015 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/26080438 |
| Systematic Identification of Host Cell Regulators of Legionella pneumophila Pathogenesis Using a Genome-wide CRISPR Screen. | Jeng EE, Bhadkamkar V, Ibe NU, Gause H, Jiang L, Chan J, Jian R, Jimenez-Morales D, Stevenson E, Krogan NJ, Swaney DL, Snyder MP, Mukherjee S, Bassik MC | Cell host & microbe | 31540829 | Cell Host Microbe | 2019 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/31540829 |
| LRRC8A:C/E Heteromeric Channels Are Ubiquitous Transporters of cGAMP. | Lahey LJ, Mardjuki RE, Wen X, Hess GT, Ritchie C, Carozza JA, Böhnert V, Maduke M, Bassik MC, Li L | Molecular cell | 33171122 | Mol Cell | 2020 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/33171122 |
| Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs. | Gu S, Zhang Y, Jin L, Huang Y, Zhang F, Bassik MC, Kampmann M, Kay MA | Nucleic acids research | 25270879 | Nucleic Acids Res | 2014 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/25270879 |
| KIF15 nanomechanics and kinesin inhibitors, with implications for cancer chemotherapeutics. | Milic B, Chakraborty A, Han K, Bassik MC, Block SM | Proceedings of the National Academy of Sciences of the United States of America | 29703754 | Proc Natl Acad Sci U S A | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29703754 |
| Genome-wide interrogation of extracellular vesicle biology using barcoded miRNAs. | Lu A, Wawro P, Morgens DW, Portela F, Bassik MC, Pfeffer SR | eLife | 30556811 | Elife | 2018 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/30556811 |
| Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. | Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC | Nature communications | 28474669 | Nat Commun | 2017 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/28474669 |
| An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens. | Coukos R, Yao D, Sanchez MI, Strand ET, Olive ME, Udeshi ND, Weissman JS, Carr SA, Bassik MC, Ting AY | eLife | 34414886 | Elife | 2021 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/34414886 |
| Retro-2 protects cells from ricin toxicity by inhibiting ASNA1-mediated ER targeting and insertion of tail-anchored proteins. | Morgens DW, Chan C, Kane AJ, Weir NR, Li A, Dubreuil MM, Tsui CK, Hess GT, Lavertu A, Han K, Polyakov N, Zhou J, Handy EL, Alabi P, Dombroski A, Yao D, Altman RB, Sello JK, Denic V, Bassik MC | eLife | 31674906 | Elife | 2019 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/31674906 |
| Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells. | Hess GT, Frésard L, Han K, Lee CH, Li A, Cimprich KA, Montgomery SB, Bassik MC | Nature methods | 27798611 | Nat Methods | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27798611 |
| Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators. | Liu N, Lee CH, Swigut T, Grow E, Gu B, Bassik MC, Wysocka J | Nature | 29211708 | Nature | 2018 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/29211708 |
| A genome-wide analysis of targets of macrolide antibiotics in mammalian cells. | Gupta A, Ökesli-Armlovich A, Morgens D, Bassik MC, Khosla C | The Journal of biological chemistry | 31915244 | J Biol Chem | 2020 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/31915244 |
| Systematic comparison of CRISPR/Cas9 and RNAi screens for essential genes. | Morgens DW, Deans RM, Li A, Bassik MC | Nature biotechnology | 27159373 | Nat Biotechnol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27159373 |
| METTL13 Methylation of eEF1A Increases Translational Output to Promote Tumorigenesis. | Liu S, Hausmann S, Carlson SM, Fuentes ME, Francis JW, Pillai R, Lofgren SM, Hulea L, Tandoc K, Lu J, Li A, Nguyen ND, Caporicci M, Kim MP, Maitra A, Wang H, Wistuba II, Porco JA Jr, Bassik MC, Elias JE, Song J, Topisirovic I, Van Rechem C, Mazur PK, Gozani O | Cell | 30612740 | Cell | 2019 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/30612740 |
| Genome-scale CRISPR screening reveals that C3aR signaling is critical for rapid capture of fungi by macrophages. | Cohen A, Jeng EE, Voorhies M, Symington J, Ali N, Rodriguez RA, Bassik MC, Sil A | PLoS pathogens | 36174103 | PLoS Pathog | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36174103 |
| E2A-PBX1 Remodels Oncogenic Signaling Networks in B-cell Precursor Acute Lymphoid Leukemia. | Duque-Afonso J, Lin CH, Han K, Wei MC, Feng J, Kurzer JH, Schneidawind C, Wong SH, Bassik MC, Cleary ML | Cancer research | 27758892 | Cancer Res | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27758892 |
| Parallel shRNA and CRISPR-Cas9 screens enable antiviral drug target identification. | Deans RM, Morgens DW, Ökesli A, Pillay S, Horlbeck MA, Kampmann M, Gilbert LA, Li A, Mateo R, Smith M, Glenn JS, Carette JE, Khosla C, Bassik MC | Nature chemical biology | 27018887 | Nat Chem Biol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27018887 |
| Human pyrimidine nucleotide biosynthesis as a target for antiviral chemotherapy. | Okesli A, Khosla C, Bassik MC | Current opinion in biotechnology | 28458037 | Curr Opin Biotechnol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28458037 |
| Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. | Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y, Whitehead EH, Guimaraes C, Panning B, Ploegh HL, Bassik MC, Qi LS, Kampmann M, Weissman JS | Cell | 25307932 | Cell | 2014 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/25307932 |
| SLC19A1 Is an Importer of the Immunotransmitter cGAMP. | Ritchie C, Cordova AF, Hess GT, Bassik MC, Li L | Molecular cell | 31126740 | Mol Cell | 2019 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/31126740 |
| Systematic Identification of Regulators of Oxidative Stress Reveals Non-canonical Roles for Peroxisomal Import and the Pentose Phosphate Pathway. | Dubreuil MM, Morgens DW, Okumoto K, Honsho M, Contrepois K, Lee-McMullen B, Traber GM, Sood RS, Dixon SJ, Snyder MP, Fujiki Y, Bassik MC | Cell reports | 32023459 | Cell Rep | 2020 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/32023459 |
| CRISPR-Cas9 screens identify regulators of antibody-drug conjugate toxicity. | Tsui CK, Barfield RM, Fischer CR, Morgens DW, Li A, Smith BAH, Gray MA, Bertozzi CR, Rabuka D, Bassik MC | Nature chemical biology | 31451760 | Nat Chem Biol | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31451760 |
| A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. | Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A | Nature genetics | 33859415 | Nat Genet | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33859415 |
| Translation readthrough mitigation. | Arribere JA, Cenik ES, Jain N, Hess GT, Lee CH, Bassik MC, Fire AZ | Nature | 27281202 | Nature | 2016 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/27281202 |
| Unraveling the mechanism of cell death induced by chemical fibrils. | Julien O, Kampmann M, Bassik MC, Zorn JA, Venditto VJ, Shimbo K, Agard NJ, Shimada K, Rheingold AL, Stockwell BR, Weissman JS, Wells JA | Nature chemical biology | 25262416 | Nat Chem Biol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25262416 |
| Bithionol blocks pathogenicity of bacterial toxins, ricin, and Zika virus. | Leonardi W, Zilbermintz L, Cheng LW, Zozaya J, Tran SH, Elliott JH, Polukhina K, Manasherob R, Li A, Chi X, Gharaibeh D, Kenny T, Zamani R, Soloveva V, Haddow AD, Nasar F, Bavari S, Bassik MC, Cohen SN, Levitin A, Martchenko M | Scientific reports | 27686742 | Sci Rep | 2016 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/27686742 |
| Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions. | Han K, Jeng EE, Hess GT, Morgens DW, Li A, Bassik MC | Nature biotechnology | 28319085 | Nat Biotechnol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28319085 |
| Inter-cellular CRISPR screens reveal regulators of cancer cell phagocytosis. | Kamber RA, Nishiga Y, Morton B, Banuelos AM, Barkal AA, Vences-Catalán F, Gu M, Fernandez D, Seoane JA, Yao D, Liu K, Lin S, Spees K, Curtis C, Jerby-Arnon L, Weissman IL, Sage J, Bassik MC | Nature | 34497417 | Nature | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34497417 |
| SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy. | Wang Z, Hausmann S, Lyu R, Li TM, Lofgren SM, Flores NM, Fuentes ME, Caporicci M, Yang Z, Meiners MJ, Cheek MA, Howard SA, Zhang L, Elias JE, Kim MP, Maitra A, Wang H, Bassik MC, Keogh MC, Sage J, Gozani O, Mazur PK | Cancer cell | 32442403 | Cancer Cell | 2020 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/32442403 |
| Methods and Applications of CRISPR-Mediated Base Editing in Eukaryotic Genomes. | Hess GT, Tycko J, Yao D, Bassik MC | Molecular cell | 28985508 | Mol Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28985508 |
| CRISPR screens in cancer spheroids identify 3D growth-specific vulnerabilities. | Han K, Pierce SE, Li A, Spees K, Anderson GR, Seoane JA, Lo YH, Dubreuil M, Olivas M, Kamber RA, Wainberg M, Kostyrko K, Kelly MR, Yousefi M, Simpkins SW, Yao D, Lee K, Kuo CJ, Jackson PK, Sweet-Cordero A, Kundaje A, Gentles AJ, Curtis C, Winslow MM, Bassik MC | Nature | 32238925 | Nature | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32238925 |
| Lipid-droplet-accumulating microglia represent a dysfunctional and proinflammatory state in the aging brain. | Marschallinger J, Iram T, Zardeneta M, Lee SE, Lehallier B, Haney MS, Pluvinage JV, Mathur V, Hahn O, Morgens DW, Kim J, Tevini J, Felder TK, Wolinski H, Bertozzi CR, Bassik MC, Aigner L, Wyss-Coray T | Nature neuroscience | 31959936 | Nat Neurosci | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31959936 |
| CRISPR-Cas9 screens in human cells and primary neurons identify modifiers of C9ORF72 dipeptide-repeat-protein toxicity. | Kramer NJ, Haney MS, Morgens DW, Jovičić A, Couthouis J, Li A, Ousey J, Ma R, Bieri G, Tsui CK, Shi Y, Hertz NT, Tessier-Lavigne M, Ichida JK, Bassik MC, Gitler AD | Nature genetics | 29507424 | Nat Genet | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29507424 |
| A semi-supervised approach to extract pharmacogenomics-specific drug-gene pairs from biomedical literature for personalized medicine. | Xu R, Wang Q | Journal of biomedical informatics | 23570835 | J Biomed Inform | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23570835 |
| Disease Comorbidity Network Guides the Detection of Molecular Evidence for the Link Between Colorectal Cancer and Obesity. | Chen Y, Li L, Xu R | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 26306270 | AMIA Jt Summits Transl Sci Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26306270 |
| Phenome-driven disease genetics prediction toward drug discovery. | Chen Y, Li L, Zhang GQ, Xu R | Bioinformatics (Oxford, England) | 26072493 | Bioinformatics | 2015 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/26072493 |
| Analysis of disease organ as a novel phenotype towards disease genetics understanding. | Luo L, Zheng C, Wang J, Tan M, Li Y, Xu R | Journal of biomedical informatics | 31207382 | J Biomed Inform | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31207382 |
| Combining mechanism-based prediction with patient-based profiling for psoriasis metabolomics biomarker discovery. | Wang Q, McCormick TS, Ward NL, Cooper KD, Conic R, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854244 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854244 |
| Using a novel computational drug-repositioning approach (DrugPredict) to rapidly identify potent drug candidates for cancer treatment. | Nagaraj AB, Wang QQ, Joseph P, Zheng C, Chen Y, Kovalenko O, Singh S, Armstrong A, Resnick K, Zanotti K, Waggoner S, Xu R, DiFeo A | Oncogene | 28967908 | Oncogene | 2018 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/28967908 |
| Comparative analysis of a novel disease phenotype network based on clinical manifestations. | Chen Y, Zhang X, Zhang GQ, Xu R | Journal of biomedical informatics | 25277758 | J Biomed Inform | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25277758 |
| Molecular subtyping of Alzheimer's disease with consensus non-negative matrix factorization. | Zheng C, Xu R | PloS one | 34014928 | PLoS One | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34014928 |
| COVID-19 risk, disparities and outcomes in patients with chronic liver disease in the United States. | Wang Q, Davis PB, Xu R | EClinicalMedicine | 33521611 | EClinicalMedicine | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33521611 |
| DenseCNN: A Densely Connected CNN Model for Alzheimer's Disease Classification Based on Hippocampus MRI Data. | Wang Q, Li Y, Zheng C, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 33936504 | AMIA Annu Symp Proc | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33936504 |
| Drug repurposing for opioid use disorders: integration of computational prediction, clinical corroboration, and mechanism of action analyses. | Zhou M, Wang Q, Zheng C, John Rush A, Volkow ND, Xu R | Molecular psychiatry | 33432189 | Mol Psychiatry | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33432189 |
| Predict Alzheimer's disease using hippocampus MRI data: a lightweight 3D deep convolutional network model with visual and global shape representations. | Katabathula S, Wang Q, Xu R | Alzheimer's research & therapy | 34030743 | Alzheimers Res Ther | 2021 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/34030743 |
| Association of Epigenetic Clock with Consensus Molecular Subtypes and Overall Survival of Colorectal Cancer. | Zheng C, Li L, Xu R | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 31375479 | Cancer Epidemiol Biomarkers Prev | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31375479 |
| Towards precision medicine-based therapies for glioblastoma: interrogating human disease genomics and mouse phenotypes. | Chen Y, Gao Z, Wang B, Xu R | BMC genomics | 27557118 | BMC Genomics | 2016 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/27557118 |
| Explore Small Molecule-induced Genome-wide Transcriptional Profiles for Novel Inflammatory Bowel Disease Drug. | Cai X, Chen Y, Gao Z, Xu R | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 27570643 | AMIA Jt Summits Transl Sci Proc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27570643 |
| Data-driven multiple-level analysis of gut-microbiome-immune-joint interactions in rheumatoid arthritis. | Wang Q, Xu R | BMC genomics | 30744546 | BMC Genomics | 2019 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/30744546 |
| Aspirin Use and Risk of Alzheimer's Disease: A 2-Sample Mendelian Randomization Study. | Ding P, Gorenflo MP, Zhu X, Xu R | Journal of Alzheimer's disease : JAD | 36846997 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36846997 |
| A knowledge graph-based disease-gene prediction system using multi-relational graph convolution networks. | Gao Z, Pan Y, Ding P, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 37128437 | AMIA Annu Symp Proc | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37128437 |
| Association of COVID-19 with Risk and Progression of Alzheimer's Disease: Non-Overlapping Two-Sample Mendelian Randomization Analysis of 2.6 Million Subjects. | Ding P, Gurney M, Perry G, Xu R | Journal of Alzheimer's disease : JAD | 38007657 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38007657 |
| Association of semaglutide with risk of suicidal ideation in a real-world cohort. | Wang W, Volkow ND, Berger NA, Davis PB, Kaelber DC, Xu R | Nature medicine | 38182782 | Nat Med | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38182782 |
| ATAD3A oligomerization promotes neuropathology and cognitive deficits in Alzheimer's disease models. | Zhao Y, Hu D, Wang R, Sun X, Ropelewski P, Hubler Z, Lundberg K, Wang Q, Adams DJ, Xu R, Qi X | Nature communications | 35236834 | Nat Commun | 2022 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/35236834 |
| A Drug-Side Effect Context-Sensitive Network approach for drug target prediction. | Zhou M, Chen Y, Xu R | Bioinformatics (Oxford, England) | 30428013 | Bioinformatics | 2019 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/30428013 |
| Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. | Chen Y, Cai X, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 26958284 | AMIA Annu Symp Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26958284 |
| MetabolitePredict: A de novo human metabolomics prediction system and its applications in rheumatoid arthritis. | Wang Q, Xu R | Journal of biomedical informatics | 28600026 | J Biomed Inform | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28600026 |
| Drug repurposing for glioblastoma based on molecular subtypes. | Chen Y, Xu R | Journal of biomedical informatics | 27697594 | J Biomed Inform | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27697594 |
| Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS). | Xu R, Wang Q | Journal of biomedical informatics | 24177320 | J Biomed Inform | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24177320 |
| Large-scale automatic extraction of side effects associated with targeted anticancer drugs from full-text oncological articles. | Xu R, Wang Q | Journal of biomedical informatics | 25817969 | J Biomed Inform | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25817969 |
| A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat. | Xu R, Wang Q, Li L | BMC genomics | 26100814 | BMC Genomics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26100814 |
| PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery. | Xu R, Wang Q | Journal of biomedical informatics | 26151312 | J Biomed Inform | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26151312 |
| Combining automatic table classification and relationship extraction in extracting anticancer drug-side effect pairs from full-text articles. | Xu R, Wang Q | Journal of biomedical informatics | 25445920 | J Biomed Inform | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25445920 |
| Drug repositioning for prostate cancer: using a data-driven approach to gain new insights. | Wang Q, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 29854243 | AMIA Annu Symp Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29854243 |
| A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer. | Wang Q, Li L, Xu R | Scientific reports | 29670137 | Sci Rep | 2018 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/29670137 |
| Automatic extraction, prioritization and analysis of gut microbial metabolites from biomedical literature. | Wang Q, Xu R | Scientific reports | 32561832 | Sci Rep | 2020 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/32561832 |
| Correction: COVID-19 risk and outcomes in patients with substance use disorders: analyses from electronic health records in the United States. | Wang QQ, Kaelber DC, Xu R, Volkow ND | Molecular psychiatry | 32999436 | Mol Psychiatry | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32999436 |
| COVID-19 risk and outcomes in patients with substance use disorders: analyses from electronic health records in the United States. | Wang QQ, Kaelber DC, Xu R, Volkow ND | Molecular psychiatry | 32929211 | Mol Psychiatry | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32929211 |
| Tumor Necrosis Factor (TNF) blocking agents are associated with lower risk for Alzheimer's disease in patients with rheumatoid arthritis and psoriasis. | Zhou M, Xu R, Kaelber DC, Gurney ME | PloS one | 32203525 | PLoS One | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32203525 |
| A CHCHD6-APP axis connects amyloid and mitochondrial pathology in Alzheimer's disease. | Shang Y, Sun X, Chen X, Wang Q, Wang EJ, Miller E, Xu R, Pieper AA, Qi X | Acta neuropathologica | 36104602 | Acta Neuropathol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36104602 |
| Integrin β3-Mediated Cell Senescence Associates with Gut Inflammation and Intestinal Degeneration in Models of Alzheimer's Disease. | Tun X, Wang EJ, Gao Z, Lundberg K, Xu R, Hu D | International journal of molecular sciences | 36982771 | Int J Mol Sci | 2023 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/36982771 |
| GLP-1 Receptor Agonists and Colorectal Cancer Risk in Drug-Naive Patients With Type 2 Diabetes, With and Without Overweight/Obesity. | Wang L, Wang W, Kaelber DC, Xu R, Berger NA | JAMA oncology | 38060218 | JAMA Oncol | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/38060218 |
| An iterative searching and ranking algorithm for prioritising pharmacogenomics genes. | Xu R, Wang Q | International journal of computational biology and drug design | 23428471 | Int J Comput Biol Drug Des | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23428471 |
| Evaluating class III antiarrhythmic agents as novel MYC targeting drugs in ovarian cancer. | Belur Nagaraj A, Joseph P, Kovalenko O, Wang Q, Xu R, DiFeo A | Gynecologic oncology | 30301560 | Gynecol Oncol | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30301560 |
| Towards understanding brain-gut-microbiome connections in Alzheimer's disease. | Xu R, Wang Q | BMC systems biology | 27585440 | BMC Syst Biol | 2016 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/27585440 |
| Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature. | Xu R, Wang Q | Journal of biomedical informatics | 24928448 | J Biomed Inform | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24928448 |
| DenguePredict: An Integrated Drug Repositioning Approach towards Drug Discovery for Dengue. | Wang Q, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 26958268 | AMIA Annu Symp Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26958268 |
| Oligodendroglial glycolytic stress triggers inflammasome activation and neuropathology in Alzheimer's disease. | Zhang X, Wang R, Hu D, Sun X, Fujioka H, Lundberg K, Chan ER, Wang Q, Xu R, Flanagan ME, Pieper AA, Qi X | Science advances | 33277246 | Sci Adv | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33277246 |
| COVID-19 and dementia: Analyses of risk, disparity, and outcomes from electronic health records in the US. | Wang Q, Davis PB, Gurney ME, Xu R | Alzheimer's & dementia : the journal of the Alzheimer's Association | 33559975 | Alzheimers Dement | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33559975 |
| When hematologic malignancies meet COVID-19 in the United States: Infections, death and disparities. | Wang Q, Berger NA, Xu R | Blood reviews | 33187811 | Blood Rev | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33187811 |
| Disease comorbidity-guided drug repositioning: a case study in schizophrenia. | Wang Q, Xu R | AMIA ... Annual Symposium proceedings. AMIA Symposium | 30815174 | AMIA Annu Symp Proc | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30815174 |
| Gut-microbiota-microglia-brain interactions in Alzheimer's disease: knowledge-based, multi-dimensional characterization. | Wang Q, Davis PB, Qi X, Chen SG, Gurney ME, Perry G, Doraiswamy PM, Xu R | Alzheimer's research & therapy | 34670619 | Alzheimers Res Ther | 2021 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/34670619 |
| Glucagon-Like Peptide 1 Receptor Agonists and 13 Obesity-Associated Cancers in Patients With Type 2 Diabetes. | Wang L, Xu R, Kaelber DC, Berger NA | JAMA network open | 38967919 | JAMA Netw Open | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38967919 |
| Sex-Specific Heterogeneity of Mild Cognitive Impairment Identified Based on Multi-Modal Data Analysis. | Katabathula S, Davis PB, Xu R, Alzheimer’s Disease Neuroimaging Initiative | Journal of Alzheimer's disease : JAD | 36404544 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36404544 |
| A genomics-based systems approach towards drug repositioning for rheumatoid arthritis. | Xu R, Wang Q | BMC genomics | 27557330 | BMC Genomics | 2016 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/27557330 |
| Phenome-based gene discovery provides information about Parkinson's disease drug targets. | Chen Y, Xu R | BMC genomics | 27586503 | BMC Genomics | 2016 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/27586503 |
| Predict drug permeability to blood-brain-barrier from clinical phenotypes: drug side effects and drug indications. | Gao Z, Chen Y, Cai X, Xu R | Bioinformatics (Oxford, England) | 27993785 | Bioinformatics | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/27993785 |
| Context-sensitive network-based disease genetics prediction and its implications in drug discovery. | Chen Y, Xu R | Bioinformatics (Oxford, England) | 28062449 | Bioinformatics | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28062449 |
| Interrogating Patient-level Genomics and Mouse Phenomics towards Understanding Cytokines in Colorectal Cancer Metastasis. | Cai X, Chen Y, Zheng C, Xu R | AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science | 28815134 | AMIA Jt Summits Transl Sci Proc | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28815134 |
| Network-based gene prediction for Plasmodium falciparum malaria towards genetics-based drug discovery. | Chen Y, Xu R | BMC genomics | 26099491 | BMC Genomics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26099491 |
| Potential long-term effect of tumor necrosis factor inhibitors on dementia risk: A propensity score matched retrospective cohort study in US veterans. | Zheng C, Fillmore NR, Ramos-Cejudo J, Brophy M, Osorio R, Gurney ME, Qiu WQ, Au R, Perry G, Dubreuil M, Chen SG, Qi X, Davis PB, Do N, Xu R | Alzheimer's & dementia : the journal of the Alzheimer's Association | 34569707 | Alzheimers Dement | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34569707 |
| CoMNRank: An integrated approach to extract and prioritize human microbial metabolites from MEDLINE records. | Wang Q, Xu R | Journal of biomedical informatics | 32791237 | J Biomed Inform | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32791237 |
| Epigenetic age acceleration and clinical outcomes in gliomas. | Zheng C, Berger NA, Li L, Xu R | PloS one | 32692766 | PLoS One | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32692766 |
| Predicting cancer origins with a DNA methylation-based deep neural network model. | Zheng C, Xu R | PloS one | 32384093 | PLoS One | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32384093 |
| tcTKB: an integrated cardiovascular toxicity knowledge base for targeted cancer drugs. | Xu R, Wang Q | AMIA ... Annual Symposium proceedings. AMIA Symposium | 26958275 | AMIA Annu Symp Proc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26958275 |
| Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data. | Zheng C, Xu R | BMC bioinformatics | 30591027 | BMC Bioinformatics | 2018 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/30591027 |
| An iterative approach to detect pleiotropy and perform Mendelian Randomization analysis using GWAS summary statistics. | Zhu X, Li X, Xu R, Wang T | Bioinformatics (Oxford, England) | 33226062 | Bioinformatics | 2021 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/33226062 |
| Immunotherapy-related adverse events (irAEs): extraction from FDA drug labels and comparative analysis. | Wang Q, Xu R | JAMIA open | 30976759 | JAMIA Open | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30976759 |
| Combining phenome-driven drug-target interaction prediction with patients' electronic health records-based clinical corroboration toward drug discovery. | Zhou M, Zheng C, Xu R | Bioinformatics (Oxford, England) | 32657406 | Bioinformatics | 2020 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/32657406 |
| Psoriasis and Psoriatic Arthritis Cardiovascular Disease Endotypes Identified by Red Blood Cell Distribution Width and Mean Platelet Volume. | Conic RR, Damiani G, Schrom KP, Ramser AE, Zheng C, Xu R, McCormick TS, Cooper KD | Journal of clinical medicine | 31936662 | J Clin Med | 2020 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/31936662 |
| Context-sensitive network analysis identifies food metabolites associated with Alzheimer's disease: an exploratory study. | Chen Y, Xu R | BMC medical genomics | 30704467 | BMC Med Genomics | 2019 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/30704467 |
| The Alzheimer's comorbidity phenome: mining from a large patient database and phenome-driven genetics prediction. | Zheng C, Xu R | JAMIA open | 30944912 | JAMIA Open | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30944912 |
| Glucagon-like peptide-1 receptor agonists and pancreatic cancer risk: target trial emulation using real-world data. | Wang L, Wang Q, Li L, Kaelber DC, Xu R | Journal of the National Cancer Institute | 39418202 | J Natl Cancer Inst | 2025 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/39418202 |
| Causal association of COVID-19 with brain structure changes: Findings from a non-overlapping 2-sample Mendelian randomization study. | Ding P, Xu R | Journal of the neurological sciences | 37925898 | J Neurol Sci | 2023 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/37925898 |
| Association of Aspirin Use with Reduced Risk of Developing Alzheimer's Disease in Elderly Ischemic Stroke Patients: A Retrospective Cohort Study. | Gorenflo MP, Davis PB, Kendall EK, Olaker VR, Kaelber DC, Xu R | Journal of Alzheimer's disease : JAD | 36502331 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36502331 |
| Comorbidity-driven multi-modal subtype analysis in mild cognitive impairment of Alzheimer's disease. | Katabathula S, Davis PB, Xu R | Alzheimer's & dementia : the journal of the Alzheimer's Association | 36166485 | Alzheimers Dement | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36166485 |
| Hyaluronic Acid Biomaterials for Central Nervous System Regenerative Medicine. | Jensen G, Holloway JL, Stabenfeldt SE | Cells | 32957463 | Cells | 2020 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/32957463 |
| Sex-Dependent Macromolecule and Nanoparticle Delivery in Experimental Brain Injury. | Bharadwaj VN, Copeland C, Mathew E, Newbern J, Anderson TR, Lifshitz J, Kodibagkar VD, Stabenfeldt SE | Tissue engineering. Part A | 32697674 | Tissue Eng Part A | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32697674 |
| Temporal assessment of nanoparticle accumulation after experimental brain injury: Effect of particle size. | Bharadwaj VN, Lifshitz J, Adelson PD, Kodibagkar VD, Stabenfeldt SE | Scientific reports | 27444615 | Sci Rep | 2016 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/27444615 |
| Tunable Controlled Release of Bioactive SDF-1α via Protein Specific Interactions within Fibrin/Nanoparticle Composites. | Dutta D, Fauer C, Mulleneux HL, Stabenfeldt SE | Journal of materials chemistry. B | 26660666 | J Mater Chem B | 2015 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/26660666 |
| Blood-brainbarrier disruption dictates nanoparticle accumulation following experimental brain injury. | Bharadwaj VN, Rowe RK, Harrison J, Wu C, Anderson TR, Lifshitz J, Adelson PD, Kodibagkar VD, Stabenfeldt SE | Nanomedicine : nanotechnology, biology, and medicine | 29933022 | Nanomedicine | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29933022 |
| pH driven precipitation of quisinostat onto PLA-PEG nanoparticles enables treatment of intracranial glioblastoma. | Householder KT, DiPerna DM, Chung EP, Luning AR, Nguyen DT, Stabenfeldt SE, Mehta S, Sirianni RW | Colloids and surfaces. B, Biointerfaces | 29533842 | Colloids Surf B Biointerfaces | 2018 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/29533842 |
| Stromal Cell-Derived Factor-1a Autocrine/Paracrine Signaling Contributes to Spatiotemporal Gradients in the Brain. | Hickey KN, Grassi SM, Caplan MR, Stabenfeldt SE | Cellular and molecular bioengineering | 33643467 | Cell Mol Bioeng | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33643467 |
| Hyaluronic acid-laminin hydrogels increase neural stem cell transplant retention and migratory response to SDF-1α. | Addington CP, Dharmawaj S, Heffernan JM, Sirianni RW, Stabenfeldt SE | Matrix biology : journal of the International Society for Matrix Biology | 27645115 | Matrix Biol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27645115 |
| Endogenous repair signaling after brain injury and complementary bioengineering approaches to enhance neural regeneration. | Addington CP, Roussas A, Dutta D, Stabenfeldt SE | Biomarker insights | 25983552 | Biomark Insights | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25983552 |
| In Vivo Phage Display as a Biomarker Discovery Tool for the Complex Neural Injury Microenvironment. | Martinez BI, Stabenfeldt SE | Current protocols | 33625787 | Curr Protoc | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33625787 |
| Siloxane Nanoprobes for Labeling and Dual Modality Functional Imaging of Neural Stem Cells. | Addington CP, Cusick A, Shankar RV, Agarwal S, Stabenfeldt SE, Kodibagkar VD | Annals of biomedical engineering | 26597417 | Ann Biomed Eng | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26597417 |
| Nanoparticle-Based Therapeutics for Brain Injury. | Bharadwaj VN, Nguyen DT, Kodibagkar VD, Stabenfeldt SE | Advanced healthcare materials | 29034608 | Adv Healthc Mater | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29034608 |
| Exploiting Phage Display for Development of Novel Cellular Targeting Strategies. | Marsh W, Witten A, Stabenfeldt SE | Methods in molecular biology (Clifton, N.J.) | 30051426 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30051426 |
| Enhancing neural stem cell response to SDF-1α gradients through hyaluronic acid-laminin hydrogels. | Addington CP, Heffernan JM, Millar-Haskell CS, Tucker EW, Sirianni RW, Stabenfeldt SE | Biomaterials | 26340314 | Biomaterials | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26340314 |
| Tunable delayed controlled release profile from layered polymeric microparticles. | Dutta D, Fauer C, Hickey K, Salifu M, Stabenfeldt SE | Journal of materials chemistry. B | 28652916 | J Mater Chem B | 2017 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/28652916 |
| Spatiotemporal presentation of exogenous SDF-1 with PLGA nanoparticles modulates SDF-1/CXCR4 signaling axis in the rodent cortex. | Dutta D, Hickey K, Salifu M, Fauer C, Willingham C, Stabenfeldt SE | Biomaterials science | 28703822 | Biomater Sci | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28703822 |
| Biomimetic Strategies To Treat Traumatic Brain Injury by Leveraging Fibrinogen. | Brown AC, Lavik E, Stabenfeldt SE | Bioconjugate chemistry | 31246419 | Bioconjug Chem | 2019 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/31246419 |
| Leveraging the Dynamic Blood-Brain Barrier for Central Nervous System Nanoparticle-based Drug Delivery Applications. | Copeland C, Stabenfeldt SE | Current opinion in biomedical engineering | 32432210 | Curr Opin Biomed Eng | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32432210 |
| Platelet-like particles reduce coagulopathy-related and neuroinflammatory pathologies post-experimental traumatic brain injury. | Todd J, Bharadwaj VN, Nellenbach K, Nandi S, Mihalko E, Copeland C, Brown AC, Stabenfeldt SE | Journal of biomedical materials research. Part B, Applied biomaterials | 34117693 | J Biomed Mater Res B Appl Biomater | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34117693 |
| GdDO3NI Enhanced Magnetic Resonance Imaging Allows Imaging of Hypoxia After Brain Injury. | Moghadas B, Bharadwaj VN, Tobey JP, Tian Y, Stabenfeldt SE, Kodibagkar VD | Journal of magnetic resonance imaging : JMRI | 34499791 | J Magn Reson Imaging | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34499791 |
| Tailoring sub-micron PLGA particle release profiles via centrifugal fractioning. | Dutta D, Salifu M, Sirianni RW, Stabenfeldt SE | Journal of biomedical materials research. Part A | 26517011 | J Biomed Mater Res A | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26517011 |
| Using biomaterials to modulate chemotactic signaling for central nervous system repair. | Hickey K, Stabenfeldt SE | Biomedical materials (Bristol, England) | 29411713 | Biomed Mater | 2018 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/29411713 |
| Current trends in biomarker discovery and analysis tools for traumatic brain injury. | Martinez BI, Stabenfeldt SE | Journal of biological engineering | 30828380 | J Biol Eng | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30828380 |
| Uncovering temporospatial sensitive TBI targeting strategies via in vivo phage display. | Martinez BI, Mousa GA, Fleck K, MacCulloch T, Diehnelt CW, Stephanopoulos N, Stabenfeldt SE | Science advances | 35867794 | Sci Adv | 2022 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/35867794 |
| Solid phase chemistry to covalently and reversibly capture thiolated RNA. | Duffy EE, Canzio D, Maniatis T, Simon MD | Nucleic acids research | 29986098 | Nucleic Acids Res | 2018 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/29986098 |
| m(6)A mRNA methylation controls T cell homeostasis by targeting the IL-7/STAT5/SOCS pathways. | Li HB, Tong J, Zhu S, Batista PJ, Duffy EE, Zhao J, Bailis W, Cao G, Kroehling L, Chen Y, Wang G, Broughton JP, Chen YG, Kluger Y, Simon MD, Chang HY, Yin Z, Flavell RA | Nature | 28792938 | Nature | 2017 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/28792938 |
| Catching RNAs on chromatin using hybridization capture methods. | Machyna M, Simon MD | Briefings in functional genomics | 29126220 | Brief Funct Genomics | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29126220 |
| Expanding the Nucleoside Recoding Toolkit: Revealing RNA Population Dynamics with 6-Thioguanosine. | Kiefer L, Schofield JA, Simon MD | Journal of the American Chemical Society | 30353734 | J Am Chem Soc | 2018 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/30353734 |
| Enriching s(4) U-RNA Using Methane Thiosulfonate (MTS) Chemistry. | Duffy EE, Simon MD | Current protocols in chemical biology | 27925666 | Curr Protoc Chem Biol | 2016 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/27925666 |
| The NBDY Microprotein Regulates Cellular RNA Decapping. | Na Z, Luo Y, Schofield JA, Smelyansky S, Khitun A, Muthukumar S, Valkov E, Simon MD, Slavoff SA | Biochemistry | 33059440 | Biochemistry | 2020 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/33059440 |
| Discovery of cellular substrates of human RNA-decapping enzyme DCP2 using a stapled bicyclic peptide inhibitor. | Luo Y, Schofield JA, Na Z, Hann T, Simon MD, Slavoff SA | Cell chemical biology | 33357462 | Cell Chem Biol | 2021 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33357462 |
| The Properties of Long Noncoding RNAs That Regulate Chromatin. | Rutenberg-Schoenberg M, Sexton AN, Simon MD | Annual review of genomics and human genetics | 27147088 | Annu Rev Genomics Hum Genet | 2016 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/27147088 |
| Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry. | Duffy EE, Rutenberg-Schoenberg M, Stark CD, Kitchen RR, Gerstein MB, Simon MD | Molecular cell | 26340425 | Mol Cell | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26340425 |
| TimeLapse-seq: adding a temporal dimension to RNA sequencing through nucleoside recoding. | Schofield JA, Duffy EE, Kiefer L, Sullivan MC, Simon MD | Nature methods | 29355846 | Nat Methods | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29355846 |
| STL-seq reveals pause-release and termination kinetics for promoter-proximal paused RNA polymerase II transcripts. | Zimmer JT, Rosa-Mercado NA, Canzio D, Steitz JA, Simon MD | Molecular cell | 34520723 | Mol Cell | 2021 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/34520723 |
| Enhanced nucleotide chemistry and toehold nanotechnology reveals lncRNA spreading on chromatin. | Machyna M, Kiefer L, Simon MD | Nature structural & molecular biology | 32157249 | Nat Struct Mol Biol | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32157249 |
| Acetyl-methyllysine marks chromatin at active transcription start sites. | Lu-Culligan WJ, Connor LJ, Xie Y, Ekundayo BE, Rose BT, Machyna M, Pintado-Urbanc AP, Zimmer JT, Vock IW, Bhanu NV, King MC, Garcia BA, Bleichert F, Simon MD | Nature | 37731000 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37731000 |
| Insight into lncRNA biology using hybridization capture analyses. | Simon MD | Biochimica et biophysica acta | 26381323 | Biochim Biophys Acta | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26381323 |
| Probing Xist RNA Structure in Cells Using Targeted Structure-Seq. | Fang R, Moss WN, Rutenberg-Schoenberg M, Simon MD | PLoS genetics | 26646615 | PLoS Genet | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26646615 |
| Interpreting Reverse Transcriptase Termination and Mutation Events for Greater Insight into the Chemical Probing of RNA. | Sexton AN, Wang PY, Rutenberg-Schoenberg M, Simon MD | Biochemistry | 28820243 | Biochemistry | 2017 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/28820243 |
| Global Profiling of Cellular Substrates of Human Dcp2. | Luo Y, Schofield JA, Simon MD, Slavoff SA | Biochemistry | 32365300 | Biochemistry | 2020 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/32365300 |
| Stella's Role in Oocyte DNA Methylation Suggests Additional Activities of DNMT1. | Kiefer L, Simon MD | Biochemistry | 30920202 | Biochemistry | 2019 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/30920202 |
| Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice. | Canzio D, Nwakeze CL, Horta A, Rajkumar SM, Coffey EL, Duffy EE, Duffié R, Monahan K, O'Keeffe S, Simon MD, Lomvardas S, Maniatis T | Cell | 30955885 | Cell | 2019 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/30955885 |
| Carbodiimide reagents for the chemical probing of RNA structure in cells. | Wang PY, Sexton AN, Culligan WJ, Simon MD | RNA (New York, N.Y.) | 30389828 | RNA | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30389828 |
| Gaining insight into transcriptome-wide RNA population dynamics through the chemistry of 4-thiouridine. | Duffy EE, Schofield JA, Simon MD | Wiley interdisciplinary reviews. RNA | 30370679 | Wiley Interdiscip Rev RNA | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30370679 |
| Internally controlled RNA sequencing comparisons using nucleoside recoding chemistry. | Courvan MCS, Niederer RO, Vock IW, Kiefer L, Gilbert WV, Simon MD | Nucleic acids research | 36018791 | Nucleic Acids Res | 2022 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/36018791 |
| Epithelial Cell Chirality Revealed by Three-Dimensional Spontaneous Rotation. | Chin AS, Worley KE, Ray P, Kaur G, Fan J, Wan LQ | Proceedings of the National Academy of Sciences of the United States of America | 30429314 | Proc Natl Acad Sci U S A | 2018 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/30429314 |
| Cell Chirality as a Novel Measure for Cytotoxicity. | Zhang H, Wan LQ | Advanced biology | 34796704 | Adv Biol (Weinh) | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34796704 |
| Cell jamming regulates epithelial chiral morphogenesis. | Rahman T, Peters F, Wan LQ | Journal of biomechanics | 36641827 | J Biomech | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36641827 |
| A Micropatterning Assay for Measuring Cell Chirality. | Zhang H, Ronaldson-Bouchard K, Vunjak-Novakovic G, Wan LQ | Journal of visualized experiments : JoVE | 35343954 | J Vis Exp | 2022 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/35343954 |
| Multiaxial Polarity Determines Individual Cellular and Nuclear Chirality. | Raymond MJ Jr, Ray P, Kaur G, Fredericks M, Singh AV, Wan LQ | Cellular and molecular bioengineering | 28360944 | Cell Mol Bioeng | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28360944 |
| Teratogen screening with human pluripotent stem cells. | Worley KE, Rico-Varela J, Ho D, Wan LQ | Integrative biology : quantitative biosciences from nano to macro | 30095839 | Integr Biol (Camb) | 2018 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/30095839 |
| Cellular and Nuclear Alignment Analysis for Determining Epithelial Cell Chirality. | Raymond MJ Jr, Ray P, Kaur G, Singh AV, Wan LQ | Annals of biomedical engineering | 26294010 | Ann Biomed Eng | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26294010 |
| Cell chirality in cardiovascular development and disease. | Rahman T, Zhang H, Fan J, Wan LQ | APL bioengineering | 32903894 | APL Bioeng | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32903894 |
| Lineage-Specific Chiral Biases of Human Embryonic Stem Cells during Differentiation. | Worley KE, Chin AS, Wan LQ | Stem cells international | 30627170 | Stem Cells Int | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30627170 |
| Intrinsic cellular chirality regulates left-right symmetry breaking during cardiac looping. | Ray P, Chin AS, Worley KE, Fan J, Kaur G, Wu M, Wan LQ | Proceedings of the National Academy of Sciences of the United States of America | 30459275 | Proc Natl Acad Sci U S A | 2018 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/30459275 |
| Cell chirality regulates intercellular junctions and endothelial permeability. | Fan J, Ray P, Lu YW, Kaur G, Schwarz JJ, Wan LQ | Science advances | 30397640 | Sci Adv | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30397640 |
| Cell chirality: emergence of asymmetry from cell culture. | Wan LQ, Chin AS, Worley KE, Ray P | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 27821525 | Philos Trans R Soc Lond B Biol Sci | 2016 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/27821525 |
| In Vitro Microscale Models for Embryogenesis. | Rico-Varela J, Ho D, Wan LQ | Advanced biosystems | 30533517 | Adv Biosyst | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30533517 |
| Cell organelle-based analysis of cell chirality. | Fan J, Zhang H, Rahman T, Stanton DN, Wan LQ | Communicative & integrative biology | 31143366 | Commun Integr Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31143366 |
| The Actin Crosslinker Fascin Regulates Cell Chirality. | Zhang H, Fan J, Maclin JMA, Wan LQ | Advanced biology | 36658789 | Adv Biol (Weinh) | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36658789 |
| Helical vasculogenesis driven by cell chirality. | Zhang H, Rahman T, Lu S, Adam AP, Wan LQ | Science advances | 38381835 | Sci Adv | 2024 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/38381835 |
| Enhanced fitness of adult spermatogonial stem cells bearing a paternal age-associated FGFR2 mutation. | Martin LA, Assif N, Gilbert M, Wijewarnasuriya D, Seandel M | Stem cell reports | 25254335 | Stem Cell Reports | 2014 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/25254335 |
| Faithful Artificial Chromosome Propagation Using Spermatogonial Stem Cells. | Yamada M, Seandel M | Trends in genetics : TIG | 29107344 | Trends Genet | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29107344 |
| Loss of tyrosine kinase receptor Ephb2 impairs proliferation and stem cell activity of spermatogonia in culture†. | N'Tumba-Byn T, Yamada M, Seandel M | Biology of reproduction | 31836902 | Biol Reprod | 2020 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/31836902 |
| Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. | Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M | Nature communications | 27117588 | Nat Commun | 2016 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/27117588 |
| Evaluation of candidate spermatogonial markers ID4 and GPR125 in testes of adult human cadaveric organ donors. | Sachs C, Robinson BD, Andres Martin L, Webster T, Gilbert M, Lo HY, Rafii S, Ng CK, Seandel M | Andrology | 24902969 | Andrology | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24902969 |
| Spermatogonial Stem Cells: Implications for Genetic Disorders and Prevention. | Yamada M, De Chiara L, Seandel M | Stem cells and development | 27596369 | Stem Cells Dev | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27596369 |
| Male germ cells support long-term propagation of Zika virus. | Robinson CL, Chong ACN, Ashbrook AW, Jeng G, Jin J, Chen H, Tang EI, Martin LA, Kim RS, Kenyon RM, Do E, Luna JM, Saeed M, Zeltser L, Ralph H, Dudley VL, Goldstein M, Rice CM, Cheng CY, Seandel M, Chen S | Nature communications | 29844387 | Nat Commun | 2018 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/29844387 |
| Functional robustness of adult spermatogonial stem cells after induction of hyperactive Hras. | Yamada M, Cai W, Martin LA, N'Tumba-Byn T, Seandel M | PLoS genetics | 31050682 | PLoS Genet | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31050682 |
| Simple, Affordable, and Modular Patterning of Cells using DNA. | Cabral KA, Patterson DM, Scheideler OJ, Cole R, Abate AR, Schaffer DV, Sohn LL, Gartner ZJ | Journal of visualized experiments : JoVE | 33720126 | J Vis Exp | 2021 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/33720126 |
| Production and targeting of monovalent quantum dots. | Seo D, Farlow J, Southard K, Jun YW, Gartner ZJ | Journal of visualized experiments : JoVE | 25407345 | J Vis Exp | 2014 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/25407345 |
| Effects of cell type and configuration on anabolic and catabolic activity in 3D co-culture of mesenchymal stem cells and nucleus pulposus cells. | Ouyang A, Cerchiari AE, Tang X, Liebenberg E, Alliston T, Gartner ZJ, Lotz JC | Journal of orthopaedic research : official publication of the Orthopaedic Research Society | 27699833 | J Orthop Res | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27699833 |
| Mapping hormone-regulated cell-cell interaction networks in the human breast at single-cell resolution. | Murrow LM, Weber RJ, Caruso JA, McGinnis CS, Phong K, Gascard P, Rabadam G, Borowsky AD, Desai TA, Thomson M, Tlsty T, Gartner ZJ | Cell systems | 35863345 | Cell Syst | 2022 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/35863345 |
| Programming the Self-Organization of Endothelial Cells into Perfusable Microvasculature. | Cabral KA, Srivastava V, Graham AJ, Coyle MC, Stashko C, Weaver V, Gartner ZJ | Tissue engineering. Part A | 36181350 | Tissue Eng Part A | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36181350 |
| Mysteries in a Minimal Genome. | Coyle M, Hu J, Gartner Z | ACS central science | 27280161 | ACS Cent Sci | 2016 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/27280161 |
| Compact and modular multicolour fluorescence detector for droplet microfluidics. | Cole RH, de Lange N, Gartner ZJ, Abate AR | Lab on a chip | 26032595 | Lab Chip | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26032595 |
| A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity. | Cerchiari AE, Garbe JC, Jee NY, Todhunter ME, Broaders KE, Peehl DM, Desai TA, LaBarge MA, Thomson M, Gartner ZJ | Proceedings of the National Academy of Sciences of the United States of America | 25633040 | Proc Natl Acad Sci U S A | 2015 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/25633040 |
| Coupling between apical tension and basal adhesion allow epithelia to collectively sense and respond to substrate topography over long distances. | Broaders KE, Cerchiari AE, Gartner ZJ | Integrative biology : quantitative biosciences from nano to macro | 26507156 | Integr Biol (Camb) | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26507156 |
| Probing the luminal microenvironment of reconstituted epithelial microtissues. | Cerchiari AE, Samy KE, Todhunter ME, Schlesinger E, Henise J, Rieken C, Gartner ZJ, Desai TA | Scientific reports | 27619235 | Sci Rep | 2016 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/27619235 |
| Dissecting the stem cell niche with organoid models: an engineering-based approach. | Murrow LM, Weber RJ, Gartner ZJ | Development (Cambridge, England) | 28292846 | Development | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28292846 |
| Characterizing cellular mechanical phenotypes with mechano-node-pore sensing. | Kim J, Han S, Lei A, Miyano M, Bloom J, Srivastava V, Stampfer MM, Gartner ZJ, LaBarge MA, Sohn LL | Microsystems & nanoengineering | 29780657 | Microsyst Nanoeng | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29780657 |
| Getting the measure of living biomaterials. | Gartner Z, Hughes A | Nature | 31358937 | Nature | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31358937 |
| Formation of spatially and geometrically controlled three-dimensional tissues in soft gels by sacrificial micromolding. | Cerchiari A, Garbe JC, Todhunter ME, Jee NY, Pinney JR, LaBarge MA, Desai TA, Gartner ZJ | Tissue engineering. Part C, Methods | 25351430 | Tissue Eng Part C Methods | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25351430 |
| Efficient targeting of fatty-acid modified oligonucleotides to live cell membranes through stepwise assembly. | Weber RJ, Liang SI, Selden NS, Desai TA, Gartner ZJ | Biomacromolecules | 25325667 | Biomacromolecules | 2014 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/25325667 |
| Expanding the boundaries of synthetic development. | Martyn I, Gartner ZJ | Developmental biology | 33587913 | Dev Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33587913 |
| A Mechanogenetic Toolkit for Interrogating Cell Signaling in Space and Time. | Seo D, Southard KM, Kim JW, Lee HJ, Farlow J, Lee JU, Litt DB, Haas T, Alivisatos AP, Cheon J, Gartner ZJ, Jun YW | Cell | 28622515 | Cell | 2017 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/28622515 |
| Printed droplet microfluidics for on demand dispensing of picoliter droplets and cells. | Cole RH, Tang SY, Siltanen CA, Shahi P, Zhang JQ, Poust S, Gartner ZJ, Abate AR | Proceedings of the National Academy of Sciences of the United States of America | 28760972 | Proc Natl Acad Sci U S A | 2017 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/28760972 |
| Unraveling cell-to-cell signaling networks with chemical biology. | Gartner ZJ, Prescher JA, Lavis LD | Nature chemical biology | 28514428 | Nat Chem Biol | 2017 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/28514428 |
| MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. | McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ | Nature methods | 31209384 | Nat Methods | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31209384 |
| Interrogating cellular fate decisions with high-throughput arrays of multiplexed cellular communities. | Chen S, Bremer AW, Scheideler OJ, Na YS, Todhunter ME, Hsiao S, Bomdica PR, Maharbiz MM, Gartner ZJ, Schaffer DV | Nature communications | 26754526 | Nat Commun | 2016 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/26754526 |
| Quanti.us: a tool for rapid, flexible, crowd-based annotation of images. | Hughes AJ, Mornin JD, Biswas SK, Beck LE, Bauer DP, Raj A, Bianco S, Gartner ZJ | Nature methods | 30065368 | Nat Methods | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30065368 |
| Chitosan enhances nanoparticle delivery from the reproductive tract to target draining lymphoid organs. | Park J, Ramanathan R, Pham L, Woodrow KA | Nanomedicine : nanotechnology, biology, and medicine | 28435136 | Nanomedicine | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28435136 |
| Sustained Intracellular Raltegravir Depots Generated with Prodrugs Designed for Nanoparticle Delivery. | Creighton RL, Suydam IT, Ebner ME, Afunugo WE, Bever AM, Cao S, Jiang Y, Woodrow KA | ACS biomaterials science & engineering | 33117884 | ACS Biomater Sci Eng | 2019 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/33117884 |
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| Flt3-L enhances trans-epithelial migration and antigen presentation of dendritic cells adoptively transferred to genital mucosa. | Park J, Frizzell H, Zhang H, Cao S, Hughes SM, Hladik F, Koelle DM, Woodrow KA | Journal of controlled release : official journal of the Controlled Release Society | 33035616 | J Control Release | 2021 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/33035616 |
| Vaginal delivery of vaccines. | VanBenschoten HM, Woodrow KA | Advanced drug delivery reviews | 34481031 | Adv Drug Deliv Rev | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34481031 |
| Cross-Platform Comparison of Therapeutic Delivery from Multilamellar Lipid-Coated Polymer Nanoparticles. | Golan-Paz S, Frizzell H, Woodrow KA | Macromolecular bioscience | 30589222 | Macromol Biosci | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30589222 |
| Microneedle-Mediated Vaccine Delivery to the Oral Mucosa. | Creighton RL, Woodrow KA | Advanced healthcare materials | 30537400 | Adv Healthc Mater | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30537400 |
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| Fc Characteristics Mediate Selective Placental Transfer of IgG in HIV-Infected Women. | Martinez DR, Fong Y, Li SH, Yang F, Jennewein MF, Weiner JA, Harrell EA, Mangold JF, Goswami R, Seage GR 3rd, Alter G, Ackerman ME, Peng X, Fouda GG, Permar SR | Cell | 31204101 | Cell | 2019 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/31204101 |
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| Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model. | Otero CE, Barfield R, Scheef E, Nelson CS, Rodgers N, Wang HY, Moström MJ, Manuel TD, Sass J, Schmidt K, Taher H, Papen C, Sprehe L, Kendall S, Davalos A, Barry PA, Früh K, Pollara J, Malouli D, Chan C, Kaur A, Permar SR | PLoS pathogens | 37871009 | PLoS Pathog | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37871009 |
| Relationship of maternal cytomegalovirus-specific antibody responses and viral load to vertical transmission risk following primary maternal infection in a rhesus macaque model. | Otero CE, Barfield R, Scheef E, Nelson CS, Rodgers N, Wang HY, Moström MJ, Manuel TD, Sass J, Schmidt K, Taher H, Papen C, Sprehe L, Kendall S, Davalos A, Barry PA, Früh K, Pollara J, Malouli D, Chan C, Kaur A, Permar SR | bioRxiv : the preprint server for biology | 37131785 | bioRxiv | 2023 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/37131785 |
| Rhesus Cytomegalovirus-encoded Fcγ-binding glycoproteins facilitate viral evasion from IgG-mediated humoral immunity. | Otero CE, Petkova S, Ebermann M, Taher H, John N, Hoffmann K, Davalos A, Moström MJ, Gilbride RM, Papen CR, Barber-Axthelm A, Scheef EA, Barfield R, Sprehe LM, Kendall S, Manuel TD, Beechwood T, Nguyen LK, Vande Burgt NH, Chan C, Denton M, Streblow ZJ, Streblow DN, Tarantal AF, Hansen SG, Kaur A, Permar S, Früh K, Hengel H, Malouli D, Kolb P | Nature communications | 39885150 | Nat Commun | 2025 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/39885150 |
| The Excess Burden of Cytomegalovirus in African American Communities: A Geospatial Analysis. | Lantos PM, Permar SR, Hoffman K, Swamy GK | Open forum infectious diseases | 26716106 | Open Forum Infect Dis | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26716106 |
| Plasmablast Response to Primary Rhesus Cytomegalovirus (CMV) Infection in a Monkey Model of Congenital CMV Transmission. | Fan Q, Nelson CS, Bialas KM, Chiuppesi F, Amos J, Gurley TC, Marshall DJ, Eudailey J, Heimsath H, Himes J, Deshpande A, Walter MR, Wussow F, Diamond DJ, Barry PA, Moody MA, Kaur A, Permar SR | Clinical and vaccine immunology : CVI | 28298291 | Clin Vaccine Immunol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28298291 |
| Maternal Broadly Neutralizing Antibodies Can Select for Neutralization-Resistant, Infant-Transmitted/Founder HIV Variants. | Martinez DR, Tu JJ, Kumar A, Mangold JF, Mangan RJ, Goswami R, Giorgi EE, Chen J, Mengual M, Douglas AO, Heimsath H, Saunders KO, Nicely NI, Eudailey J, Hernandez G, Morgan-Asiedu PK, Wiehe K, Haynes BF, Moody MA, LaBranche C, Montefiori DC, Gao F, Permar SR | mBio | 32156815 | mBio | 2020 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/32156815 |
| Humoral Immune Correlates for Prevention of Postnatal Cytomegalovirus Acquisition. | Saccoccio FM, Jenks JA, Itell HL, Li SH, Berry M, Pollara J, Casper C, Gantt S, Permar SR | The Journal of infectious diseases | 31107951 | J Infect Dis | 2019 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/31107951 |
| Breast Milk and Saliva Lactoferrin Levels and Postnatal Cytomegalovirus Infection. | Weimer KED, Roark H, Fisher K, Cotten CM, Kaufman DA, Bidegain M, Permar SR | American journal of perinatology | 32069486 | Am J Perinatol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32069486 |
| Intrahost Dynamics of Human Cytomegalovirus Variants Acquired by Seronegative Glycoprotein B Vaccinees. | Nelson CS, Vera Cruz D, Su M, Xie G, Vandergrift N, Pass RF, Forman M, Diener-West M, Koelle K, Arav-Boger R, Permar SR | Journal of virology | 30518646 | J Virol | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/30518646 |
| In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome. | Taher H, Mahyari E, Kreklywich C, Uebelhoer LS, McArdle MR, Moström MJ, Bhusari A, Nekorchuk M, E X, Whitmer T, Scheef EA, Sprehe LM, Roberts DL, Hughes CM, Jackson KA, Selseth AN, Ventura AB, Cleveland-Rubeor HC, Yue Y, Schmidt KA, Shao J, Edlefsen PT, Smedley J, Kowalik TF, Stanton RJ, Axthelm MK, Estes JD, Hansen SG, Kaur A, Barry PA, Bimber BN, Picker LJ, Streblow DN, Früh K, Malouli D | PLoS pathogens | 33232376 | PLoS Pathog | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33232376 |
| Neighborhood Disadvantage is Associated with High Cytomegalovirus Seroprevalence in Pregnancy. | Lantos PM, Hoffman K, Permar SR, Jackson P, Hughes BL, Kind A, Swamy G | Journal of racial and ethnic health disparities | 28840519 | J Racial Ethn Health Disparities | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28840519 |
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| Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys. | Nelson CS, Cruz DV, Tran D, Bialas KM, Stamper L, Wu H, Gilbert M, Blair R, Alvarez X, Itell H, Chen M, Deshpande A, Chiuppesi F, Wussow F, Diamond DJ, Vandergrift N, Walter MR, Barry PA, Cohen-Wolkowiez M, Koelle K, Kaur A, Permar SR | JCI insight | 28679960 | JCI Insight | 2017 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/28679960 |
| Geographic and Racial Disparities in Infant Hearing Loss. | Lantos PM, Maradiaga-Panayotti G, Barber X, Raynor E, Tucci D, Hoffman K, Permar SR, Jackson P, Hughes BL, Kind A, Swamy GK | Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery | 30296906 | Otolaryngol Head Neck Surg | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30296906 |
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| A rhesus macaque model of Asian-lineage Zika virus infection. | Dudley DM, Aliota MT, Mohr EL, Weiler AM, Lehrer-Brey G, Weisgrau KL, Mohns MS, Breitbach ME, Rasheed MN, Newman CM, Gellerup DD, Moncla LH, Post J, Schultz-Darken N, Schotzko ML, Hayes JM, Eudailey JA, Moody MA, Permar SR, O'Connor SL, Rakasz EG, Simmons HA, Capuano S, Golos TG, Osorio JE, Friedrich TC, O'Connor DH | Nature communications | 27352279 | Nat Commun | 2016 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/27352279 |
| Maternal Antibody Responses and Nonprimary Congenital Cytomegalovirus Infection of HIV-1-Exposed Infants. | Bialas KM, Westreich D, Cisneros de la Rosa E, Nelson CS, Kauvar LM, Fu TM, Permar SR | The Journal of infectious diseases | 27923951 | J Infect Dis | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27923951 |
| Maternal CD4+ T cells protect against severe congenital cytomegalovirus disease in a novel nonhuman primate model of placental cytomegalovirus transmission. | Bialas KM, Tanaka T, Tran D, Varner V, Cisneros De La Rosa E, Chiuppesi F, Wussow F, Kattenhorn L, Macri S, Kunz EL, Estroff JA, Kirchherr J, Yue Y, Fan Q, Lauck M, O'Connor DH, Hall AH, Xavier A, Diamond DJ, Barry PA, Kaur A, Permar SR | Proceedings of the National Academy of Sciences of the United States of America | 26483473 | Proc Natl Acad Sci U S A | 2015 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/26483473 |
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| Perinatal cytomegalovirus and varicella zoster virus infections: epidemiology, prevention, and treatment. | Bialas KM, Swamy GK, Permar SR | Clinics in perinatology | 25677997 | Clin Perinatol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25677997 |
| Preventing postnatal cytomegalovirus infection in the preterm infant: should it be done, can it be done, and at what cost? | Wright CJ, Permar SR | The Journal of pediatrics | 25662832 | J Pediatr | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25662832 |
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| The March towards a Vaccine for Congenital CMV: Rationale and Models. | Bialas KM, Permar SR | PLoS pathogens | 26866914 | PLoS Pathog | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26866914 |
| Noncanonical placental Fc receptors: What is their role in modulating transplacental transfer of maternal IgG? | Martinez DR, Fouda GG, Peng X, Ackerman ME, Permar SR | PLoS pathogens | 30161231 | PLoS Pathog | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30161231 |
| Natural history of postnatal rhesus cytomegalovirus shedding by dams and acquisition by infant rhesus monkeys. | Kaur A, Itell HL, Ehlinger EP, Varner V, Gantt S, Permar SR | PloS one | 30356332 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30356332 |
| Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. | Moström M, Yu S, Tran D, Saccoccio F, Versoza CJ, Malouli D, Mirza A, Valencia S, Gilbert M, Blair R, Hansen S, Barry P, Früh K, Jensen JD, Pfeifer SP, Kowalik TF, Permar SR, Kaur A | bioRxiv : the preprint server for biology | 37090643 | bioRxiv | 2023 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/37090643 |
| Protective effect of pre-existing natural immunity in a nonhuman primate reinfection model of congenital cytomegalovirus infection. | Moström MJ, Yu S, Tran D, Saccoccio FM, Versoza CJ, Malouli D, Mirza A, Valencia S, Gilbert M, Blair RV, Hansen S, Barry P, Früh K, Jensen JD, Pfeifer SP, Kowalik TF, Permar SR, Kaur A | PLoS pathogens | 37796819 | PLoS Pathog | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37796819 |
| Prior dengue virus serotype 3 infection modulates subsequent plasmablast responses to Zika virus infection in rhesus macaques. | Singh T, Miller IG, Venkatayogi S, Webster H, Heimsath HJ, Eudailey JA, Dudley DM, Kumar A, Mangan RJ, Thein A, Aliota MT, Newman CM, Mohns MS, Breitbach ME, Berry M, Friedrich TC, Wiehe K, O'Connor DH, Permar SR | mBio | 38349142 | mBio | 2024 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/38349142 |
| DNA-Carbon Nanotube Complexation Affinity and Photoluminescence Modulation Are Independent. | Jena PV, Safaee MM, Heller DA, Roxbury D | ACS applied materials & interfaces | 28573867 | ACS Appl Mater Interfaces | 2017 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/28573867 |
| Quantitative self-assembly prediction yields targeted nanomedicines. | Shamay Y, Shah J, Işık M, Mizrachi A, Leibold J, Tschaharganeh DF, Roxbury D, Budhathoki-Uprety J, Nawaly K, Sugarman JL, Baut E, Neiman MR, Dacek M, Ganesh KS, Johnson DC, Sridharan R, Chu EL, Rajasekhar VK, Lowe SW, Chodera JD, Heller DA | Nature materials | 29403054 | Nat Mater | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29403054 |
| A Carbon Nanotube Optical Reporter Maps Endolysosomal Lipid Flux. | Jena PV, Roxbury D, Galassi TV, Akkari L, Horoszko CP, Iaea DB, Budhathoki-Uprety J, Pipalia N, Haka AS, Harvey JD, Mittal J, Maxfield FR, Joyce JA, Heller DA | ACS nano | 28898055 | ACS Nano | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/28898055 |
| Long-term in vivo biocompatibility of single-walled carbon nanotubes. | Galassi TV, Antman-Passig M, Yaari Z, Jessurun J, Schwartz RE, Heller DA | PloS one | 32374764 | PLoS One | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32374764 |
| Helical polycarbodiimide cloaking of carbon nanotubes enables inter-nanotube exciton energy transfer modulation. | Budhathoki-Uprety J, Jena PV, Roxbury D, Heller DA | Journal of the American Chemical Society | 25343218 | J Am Chem Soc | 2014 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/25343218 |
| A Fluorescent Carbon Nanotube Sensor Detects the Metastatic Prostate Cancer Biomarker uPA. | Williams RM, Lee C, Heller DA | ACS sensors | 30169018 | ACS Sens | 2018 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/30169018 |
| Optical Voltammetry of Polymer-Encapsulated Single-Walled Carbon Nanotubes. | Horoszko CP, Jena PV, Roxbury D, Rotkin SV, Heller DA | The journal of physical chemistry. C, Nanomaterials and interfaces | 32690989 | J Phys Chem C Nanomater Interfaces | 2019 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/32690989 |
| Glutathione-S-transferase Fusion Protein Nanosensor. | Williams RM, Harvey JD, Budhathoki-Uprety J, Heller DA | Nano letters | 32955895 | Nano Lett | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32955895 |
| Photoluminescent carbon nanotubes interrogate the permeability of multicellular tumor spheroids. | Jena PV, Shamay Y, Shah J, Roxbury D, Paknejad N, Heller DA | Carbon | 26456974 | Carbon N Y | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26456974 |
| Mesoscale nanoparticles selectively target the renal proximal tubule epithelium. | Williams RM, Shah J, Ng BD, Minton DR, Gudas LJ, Park CY, Heller DA | Nano letters | 25811353 | Nano Lett | 2015 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/25811353 |
| Cell Membrane Proteins Modulate the Carbon Nanotube Optical Bandgap via Surface Charge Accumulation. | Roxbury D, Jena PV, Shamay Y, Horoszko CP, Heller DA | ACS nano | 26654246 | ACS Nano | 2016 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/26654246 |
| Synthesis, pharmacokinetics, and biological use of lysine-modified single-walled carbon nanotubes. | Mulvey JJ, Feinberg EN, Alidori S, McDevitt MR, Heller DA, Scheinberg DA | International journal of nanomedicine | 25228803 | Int J Nanomedicine | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25228803 |
| Single Nanotube Spectral Imaging To Determine Molar Concentrations of Isolated Carbon Nanotube Species. | Galassi TV, Jena PV, Roxbury D, Heller DA | Analytical chemistry | 28194986 | Anal Chem | 2017 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/28194986 |
| Nanoreporter of an Enzymatic Suicide Inactivation Pathway. | Yaari Z, Cheung JM, Baker HA, Frederiksen RS, Jena PV, Horoszko CP, Jiao F, Scheuring S, Luo M, Heller DA | Nano letters | 33119310 | Nano Lett | 2020 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/33119310 |
| Tumour-specific PI3K inhibition via nanoparticle-targeted delivery in head and neck squamous cell carcinoma. | Mizrachi A, Shamay Y, Shah J, Brook S, Soong J, Rajasekhar VK, Humm JL, Healey JH, Powell SN, Baselga J, Heller DA, Haimovitz-Friedman A, Scaltriti M | Nature communications | 28194032 | Nat Commun | 2017 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/28194032 |
| Noninvasive ovarian cancer biomarker detection via an optical nanosensor implant. | Williams RM, Lee C, Galassi TV, Harvey JD, Leicher R, Sirenko M, Dorso MA, Shah J, Olvera N, Dao F, Levine DA, Heller DA | Science advances | 29675469 | Sci Adv | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29675469 |
| Nanomedicines for kidney diseases. | Williams RM, Jaimes EA, Heller DA | Kidney international | 27292222 | Kidney Int | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27292222 |
| Selective Nanoparticle Targeting of the Renal Tubules. | Williams RM, Shah J, Tian HS, Chen X, Geissmann F, Jaimes EA, Heller DA | Hypertension (Dallas, Tex. : 1979) | 29133360 | Hypertension | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29133360 |
| A Carbon Nanotube Reporter of miRNA Hybridization Events In Vivo. | Harvey JD, Jena PV, Baker HA, Zerze GH, Williams RM, Galassi TV, Roxbury D, Mittal J, Heller DA | Nature biomedical engineering | 28845337 | Nat Biomed Eng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28845337 |
| An in Vivo Nanosensor Measures Compartmental Doxorubicin Exposure. | Harvey JD, Williams RM, Tully KM, Baker HA, Shamay Y, Heller DA | Nano letters | 31244242 | Nano Lett | 2019 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/31244242 |
| Nanosensor-based monitoring of autophagy-associated lysosomal acidification in vivo. | Kim M, Chen C, Yaari Z, Frederiksen R, Randall E, Wollowitz J, Cupo C, Wu X, Shah J, Worroll D, Lagenbacher RE, Goerzen D, Li YM, An H, Wang Y, Heller DA | Nature chemical biology | 37322156 | Nat Chem Biol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37322156 |
| Hyperspectral Counting of Multiplexed Nanoparticle Emitters in Single Cells and Organelles. | Jena PV, Gravely M, Cupo C, Safaee MM, Roxbury D, Heller DA | ACS nano | 35049273 | ACS Nano | 2022 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/35049273 |
| Harnessing nanotechnology to expand the toolbox of chemical biology. | Williams RM, Chen S, Langenbacher RE, Galassi TV, Harvey JD, Jena PV, Budhathoki-Uprety J, Luo M, Heller DA | Nature chemical biology | 33414556 | Nat Chem Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33414556 |
| Advances in the clinical translation of nanotechnology. | Scheinberg DA, Grimm J, Heller DA, Stater EP, Bradbury M, McDevitt MR | Current opinion in biotechnology | 28187340 | Curr Opin Biotechnol | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28187340 |
| Hyperspectral Microscopy of Near-Infrared Fluorescence Enables 17-Chirality Carbon Nanotube Imaging. | Roxbury D, Jena PV, Williams RM, Enyedi B, Niethammer P, Marcet S, Verhaegen M, Blais-Ouellette S, Heller DA | Scientific reports | 26387482 | Sci Rep | 2015 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/26387482 |
| P-selectin is a nanotherapeutic delivery target in the tumor microenvironment. | Shamay Y, Elkabets M, Li H, Shah J, Brook S, Wang F, Adler K, Baut E, Scaltriti M, Jena PV, Gardner EE, Poirier JT, Rudin CM, Baselga J, Haimovitz-Friedman A, Heller DA | Science translational medicine | 27358497 | Sci Transl Med | 2016 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/27358497 |
| Redox-active nanomaterials for nanomedicine applications. | Sims CM, Hanna SK, Heller DA, Horoszko CP, Johnson ME, Montoro Bustos AR, Reipa V, Riley KR, Nelson BC | Nanoscale | 28991962 | Nanoscale | 2017 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/28991962 |
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| HIV Detection via a Carbon Nanotube RNA Sensor. | Harvey JD, Baker HA, Ortiz MV, Kentsis A, Heller DA | ACS sensors | 31056899 | ACS Sens | 2019 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/31056899 |
| Electroporation-induced changes in tumor vasculature and microenvironment can promote the delivery and increase the efficacy of sorafenib nanoparticles. | Kodama H, Shamay Y, Kimura Y, Shah J, Solomon SB, Heller D, Srimathveeravalli G | Bioelectrochemistry (Amsterdam, Netherlands) | 31306879 | Bioelectrochemistry | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31306879 |
| Targeted drug delivery strategies for precision medicines. | Manzari MT, Shamay Y, Kiguchi H, Rosen N, Scaltriti M, Heller DA | Nature reviews. Materials | 34950512 | Nat Rev Mater | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34950512 |
| Non-Covalent Coatings on Carbon Nanotubes Mediate Photosensitizer Interactions. | Horoszko CP, Schnatz PJ, Budhathoki-Uprety J, Rao-Pothuraju RV, Koder RL, Heller DA | ACS applied materials & interfaces | 34672190 | ACS Appl Mater Interfaces | 2021 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/34672190 |
| An optical nanoreporter of endolysosomal lipid accumulation reveals enduring effects of diet on hepatic macrophages in vivo. | Galassi TV, Jena PV, Shah J, Ao G, Molitor E, Bram Y, Frankel A, Park J, Jessurun J, Ory DS, Haimovitz-Friedman A, Roxbury D, Mittal J, Zheng M, Schwartz RE, Heller DA | Science translational medicine | 30282694 | Sci Transl Med | 2018 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/30282694 |
| A Carbon Nanotube Optical Sensor Reports Nuclear Entry via a Noncanonical Pathway. | Budhathoki-Uprety J, Langenbacher RE, Jena PV, Roxbury D, Heller DA | ACS nano | 28398031 | ACS Nano | 2017 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/28398031 |
| Single-Chirality Near-Infrared Carbon Nanotube Sub-Cellular Imaging and FRET Probes. | Langenbacher R, Budhathoki-Uprety J, Jena PV, Roxbury D, Streit J, Zheng M, Heller DA | Nano letters | 34296885 | Nano Lett | 2021 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/34296885 |
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| Role of Sporopollenin Shell Interfacial Properties in Protein Adsorption. | Uddin MJ, Liyanage S, Warzywoda J, Abidi N, Gill HS | Langmuir : the ACS journal of surfaces and colloids | 35212551 | Langmuir | 2022 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/35212551 |
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| A chemical treatment method for obtaining clean and intact pollen shells of different species. | Gonzalez-Cruz P, Uddin MJ, Atwe SU, Abidi N, Gill HS | ACS biomaterials science & engineering | 31106262 | ACS Biomater Sci Eng | 2018 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/31106262 |
| Demystifying particle-based oral vaccines. | Gonzalez-Cruz P, Gill HS | Expert opinion on drug delivery | 34148474 | Expert Opin Drug Deliv | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34148474 |
| Physical and Biochemical Characterization of Chemically Treated Pollen Shells for Potential Use in Oral Delivery of Therapeutics. | Uddin MJ, Liyanage S, Abidi N, Gill HS | Journal of pharmaceutical sciences | 30096353 | J Pharm Sci | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30096353 |
| Ragweed pollen as an oral vaccine delivery system: Mechanistic insights. | Uddin MJ, Gill HS | Journal of controlled release : official journal of the Controlled Release Society | 29054371 | J Control Release | 2017 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/29054371 |
| Multidimensional third-generation sequencing of modified DNA bases allows interrogation of complex biological systems. | David SS, Pacheco BA, Kishimoto K, Vantine S, Hu K, Liu H, Davis DL, Tran H, Sallis BF, Ali L, Haynes CM, McCormick BA, Zhu LJ, Flavahan WA | Nature communications | 40593667 | Nat Commun | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40593667 |
| Regulatable assembly of synthetic microtubule architectures using engineered MAP-IDR condensates. | Chang CC, Coyle SM | bioRxiv : the preprint server for biology | 38105997 | bioRxiv | 2023 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/38105997 |
| Genetically encoded protein oscillators for FM streaming of single-cell data. | Rajasekaran R, Galateo TM, Xu Z, Bolshakov DT, Weix EWZ, Coyle SM | bioRxiv : the preprint server for biology | 40060462 | bioRxiv | 2025 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/40060462 |
| Comparative profiling of cellular gait on adhesive micropatterns defines statistical patterns of activity that underlie native and cancerous cell dynamics. | Ahn JC, Coyle SM | bioRxiv : the preprint server for biology | 37961146 | bioRxiv | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37961146 |
| Noise-guided tuning of synthetic protein waves in living cells. | Bolshakov DT, Weix EWZ, Galateo TM, Rajasekaran R, Coyle SM | bioRxiv : the preprint server for biology | 40166177 | bioRxiv | 2025 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/40166177 |
| Synthetic Forms Most Beautiful: Engineering Insights into Self-Organization. | Xu Z, Chang CC, Coyle SM | Physiology (Bethesda, Md.) | 39938118 | Physiology (Bethesda) | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/39938118 |
| A programmable reaction-diffusion system for spatiotemporal cell signaling circuit design. | Rajasekaran R, Chang CC, Weix EWZ, Galateo TM, Coyle SM | Cell | 38181787 | Cell | 2024 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/38181787 |
| A mitochondrial redox switch licenses the onset of morphogenesis in animals. | Kahlon U, Ricca FD, Pillai SJ, Olivetta M, Tharp KM, Jao LE, Dudin O, McDonald K, Aydogan MG | bioRxiv : the preprint server for biology | 39553983 | bioRxiv | 2024 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/39553983 |
| Cytoplasmic division cycles without the nucleus and mitotic CDK/cyclin complexes. | Bakshi A, Iturra FE, Alamban A, Rosas-Salvans M, Dumont S, Aydogan MG | Cell | 37832525 | Cell | 2023 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/37832525 |
| Dissecting host-microbe interactions with modern functional genomics. | Russell BJ, Verma M, Maier NK, Jost M | Current opinion in microbiology | 39368241 | Curr Opin Microbiol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39368241 |
| Comprehensive interrogation of synthetic lethality in the DNA damage response. | Fielden J, Siegner SM, Gallagher DN, Schröder MS, Dello Stritto MR, Lam S, Kobel L, Schlapansky MF, Jackson SP, Cejka P, Jost M, Corn JE | Nature | 40205037 | Nature | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40205037 |
| Engineering Tripartite Gene Editing Machinery for Highly Efficient Non-Viral Targeted Genome Integration. | Nam H, Xie K, Majumdar I, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H | Research square | 37961210 | Res Sq | 2023 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/37961210 |
| A New Bacterial Chassis for Enhanced Surface Display of Recombinant Proteins. | Zhang R, Ye N, Wang Z, Yang S, Li J | Cellular and molecular bioengineering | 39513006 | Cell Mol Bioeng | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39513006 |
| Non-pathogenic E. coli displaying decoy-resistant IL18 mutein boosts anti-tumor and CAR NK cell responses. | Yang S, Sheffer M, Kaplan IE, Wang Z, Tarannum M, Dinh K, Abdulhamid Y, Bobilev E, Shapiro R, Porter R, Soiffer R, Ritz J, Koreth J, Wei Y, Chen P, Zhang K, Márquez-Pellegrin V, Bonanno S, Joshi N, Guan M, Yang M, Li D, Bellini C, Liu F, Chen J, Wu CJ, Barbie D, Li J, Romee R | Nature biotechnology | 39367093 | Nat Biotechnol | 2024 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/39367093 |
| Nonpathogenic E. coli engineered to surface display cytokines as a new platform for immunotherapy. | Yang S, Sheffer M, Kaplan IE, Wang Z, Tarannum M, Dinh K, Abdulhamid Y, Shapiro R, Porter R, Soiffer R, Ritz J, Koreth J, Wei Y, Chen P, Zhang K, Márquez-Pellegrin V, Bonanno S, Joshi N, Guan M, Yang M, Li D, Bellini C, Chen J, Wu CJ, Barbie D, Li J, Romee R | Research square | 38562821 | Res Sq | 2024 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/38562821 |
| Engineered Bacillus subtilis as Oral Probiotics To Enhance Clearance of Blood Lactate. | Yang M, Hutchinson N, Ye N, Timek H, Jennings M, Yin J, Guan M, Wang Z, Chen P, Yang S, Crane JD, Zhang K, He X, Li J | ACS synthetic biology | 39739838 | ACS Synth Biol | 2025 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/39739838 |
| Engineering tripartite gene editing machinery for highly efficient non-viral targeted genome integration. | Nam H, Xie K, Majumdar I, Wang J, Yang S, Starzyk J, Lee D, Shan R, Li J, Wu H | Nature communications | 40379664 | Nat Commun | 2025 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/40379664 |
| Squeezable Hydrogel Microparticles for Single Extracellular Vesicle Protein Profiling. | Roh YH, Morales RT, Huynh E, Chintapula U, Reynolds DE, Agosto-Nieves RJ, Oh D, Seiner AJ, Lim J, Rodell CB, Ko J | Small (Weinheim an der Bergstrasse, Germany) | 39468876 | Small | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39468876 |
| Enhancing Chimeric Antigen Receptor T-Cell Generation via Microfluidic Mechanoporation and Lipid Nanoparticles. | Lim J, Oh D, Cheng M, Chintapula U, Liu S, Reynolds D, Zhang X, Zhou Y, Xu X, Ko J | Small (Weinheim an der Bergstrasse, Germany) | 40103509 | Small | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40103509 |
| Vertically Aligned Nanowires for Longitudinal Intracellular Sampling. | Reynolds DE, Roh YH, Chintapula U, Huynh E, Vallapureddy P, Tran HH, Lee D, Allen MG, Xu X, Ko J | ACS nano | 40146010 | ACS Nano | 2025 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/40146010 |
| Targeted protein relocalization via protein transport coupling. | Ng CSC, Liu A, Cui B, Banik SM | Nature | 39294374 | Nature | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39294374 |
| Self-Assembled Nanocoatings Protect Microbial Fertilizers for Climate-Resilient Agriculture. | Burke B, Fan G, Wasuwanich P, Moore EB, Furst AL | JACS Au | 38034965 | JACS Au | 2023 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/38034965 |
| Transferrin receptor targeting chimeras for membrane protein degradation. | Zhang D, Duque-Jimenez J, Facchinetti F, Brixi G, Rhee K, Feng WW, Jänne PA, Zhou X | Nature | 39322661 | Nature | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39322661 |
| A Genetically Encoded Fluorescent Biosensor for Intracellular Measurement of Malonyl-CoA. | Ranzau BL, Robinson TD, Scully JM, Kapelczack ED, Dean TS, TeSlaa T, Schmitt DL | bioRxiv : the preprint server for biology | 39386450 | bioRxiv | 2024 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/39386450 |
| A Genetically Encoded Fluorescent Biosensor for Intracellular Measurement of Malonyl-CoA. | Ranzau BL, Robinson TD, Scully JM, Kapelczak ED, Dean TS, TeSlaa T, Schmitt DL | ACS bio & med chem Au | 39990938 | ACS Bio Med Chem Au | 2025 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/39990938 |
| Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability. | Bai D, Cao Z, Attada N, Song J, Zhu C | Nature methods | 40128288 | Nat Methods | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40128288 |
| A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction. | Li X, Gamuyao R, Wu ML, Cho WJ, King SV, Petersen RA, Stabley DR, Lindow C, Climer LK, Shirinifard A, Ferrara F, Throm RE, Robinson CG, Zhou Y, Carisey AF, Tebo AG, Chang CL | The Journal of cell biology | 38949658 | J Cell Biol | 2024 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/38949658 |
| A fluorogenic complementation tool kit for interrogating lipid droplet-organelle interaction. | Li X, Gamuyao R, Wu ML, Cho WJ, Kurtz NB, King SV, Petersen RA, Stabley DR, Lindow C, Climer L, Shirinifard A, Ferrara F, Throm RE, Robinson CG, Carisey A, Tebo AG, Chang CL | bioRxiv : the preprint server for biology | 38076863 | bioRxiv | 2023 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/38076863 |
| Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing. | Abe KM, Li G, He Q, Grant T, Lim CJ | Nature communications | 39231985 | Nat Commun | 2024 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/39231985 |
| Models for human telomere C-strand fill-in by CST-Polα-primase. | He Q, Lim CJ | Trends in biochemical sciences | 37586999 | Trends Biochem Sci | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37586999 |
| Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing. | Abe KM, Lim CJ | bioRxiv : the preprint server for biology | 38370693 | bioRxiv | 2024 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/38370693 |
| LiveLattice: Real-time visualisation of tilted light-sheet microscopy data using a memory-efficient transformation algorithm. | Wang Z, Hakozaki H, McMahon G, Medina-Carbonero M, Schöneberg J | Journal of microscopy | 39360400 | J Microsc | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39360400 |
| MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data. | Wang Z, Natekar P, Tea C, Tamir S, Hakozaki H, Schöneberg J | PLoS computational biology | 37083820 | PLoS Comput Biol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37083820 |
| LiveLattice: Real-time visualization of tilted light-sheet microscopy data using a memory-efficient transformation algorithm. | Wang Z, Hakozaki H, McMahon G, Medina-Carbonero M, Schöneberg J | bioRxiv : the preprint server for biology | 38854017 | bioRxiv | 2024 May 30 | https://www.ncbi.nlm.nih.gov/pubmed/38854017 |
| A nucleosome switch primes Hepatitis B Virus infection. | Prescott NA, Mansisidor A, Bram Y, Biaco T, Rendleman J, Faulkner SC, Lemmon AA, Lim C, Hamard PJ, Koche RP, Risca VI, Schwartz RE, David Y | bioRxiv : the preprint server for biology | 38915612 | bioRxiv | 2024 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/38915612 |
| Chromatin accessibility: methods, mechanisms, and biological insights. | Mansisidor AR, Risca VI | Nucleus (Austin, Tex.) | 36404679 | Nucleus | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36404679 |
| Determining mesoscale chromatin structure parameters from spatially correlated cleavage data using a coarse-grained oligonucleosome model. | Clerkin AB, Pagane N, West DW, Spakowitz AJ, Risca VI | bioRxiv : the preprint server for biology | 39131347 | bioRxiv | 2024 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/39131347 |
| Technological advances in probing 4D genome organization. | Soroczynski J, Risca VI | Current opinion in cell biology | 37556867 | Curr Opin Cell Biol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37556867 |
| OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization. | Soroczynski J, Anderson LJ, Yeung JL, Rendleman JM, Oren DA, Konishi HA, Risca VI | bioRxiv : the preprint server for biology | 39026714 | bioRxiv | 2024 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/39026714 |
| Rapid structural analysis of bacterial ribosomes in situ. | Powell BM, Brant TS, Davis JH, Mosalaganti S | bioRxiv : the preprint server for biology | 38585831 | bioRxiv | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38585831 |
| BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III. | Chen B, Stark DC, Jadhav PV, Lynn-Nguyen TM, Halligan BS, Rossiter NJ, Sindoni N, Shin M, Paulo JA, Chang M, Koo I, Koshkin S, Eyunni S, Ronchi P, Paulsen MT, Morlacchi P, Hanna DA, Lin J, Guerra RM, Pagliarini DJ, Banerjee R, Parolia A, Ljungman ME, Patterson AD, Mancias JD, Mosalaganti S, Sexton JZ, Calì T, Lyssiotis CA, Shah YM | bioRxiv : the preprint server for biology | 38352460 | bioRxiv | 2024 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/38352460 |
| Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. | Navratna V, Kumar A, Rana JK, Mosalaganti S | Life science alliance | 38925866 | Life Sci Alliance | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38925866 |
| Structure of the human heparan-α-glucosaminide N-acetyltransferase (HGSNAT). | Navratna V, Kumar A, Rana JK, Mosalaganti S | eLife | 39196614 | Elife | 2024 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/39196614 |
| Neutrophils secrete exosome-associated DNA to resolve sterile acute inflammation. | Arya SB, Collie SP, Xu Y, Fernandez M, Sexton JZ, Mosalaganti S, Coulombe PA, Parent CA | Nature cell biology | 40404894 | Nat Cell Biol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40404894 |
| Structure of the human heparan-α-glucosaminide N-acetyltransferase (HGSNAT). | Navratna V, Kumar A, Rana JK, Mosalaganti S | bioRxiv : the preprint server for biology | 37961489 | bioRxiv | 2024 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/37961489 |
| Rapid structural analysis of bacterial ribosomes in situ. | Powell BM, Brant TS, Davis JH, Mosalaganti S | Communications biology | 39875527 | Commun Biol | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39875527 |
| Molecular Visualization of Neuronal TDP43 Pathology In Situ. | Erwin AL, Chang ML, Fernandez MG, Attili D, Russ JE, Sutanto R, Pinarbasi ES, Bekier M, Brant TS, Hahn T, Dykstra M, Thomas D, Li X, Baldridge RD, Tank EMH, Barmada SJ, Mosalaganti S | bioRxiv : the preprint server for biology | 39229019 | bioRxiv | 2024 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/39229019 |
| Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. | Navratna V, Kumar A, Rana JK, Mosalaganti S | bioRxiv : the preprint server for biology | 38187772 | bioRxiv | 2024 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/38187772 |
| Towards sustainable and humane dairy farming: A low-cost electrochemical sensor for on-site diagnosis of milk fever. | Soleimani A, Amirghasemi F, Al-Shami A, Khazaee Nejad S, Tsung A, Wang Y, Lara Galindo S, Parvin D, Olson A, Avishai A, Mousavi MPS | Biosensors & bioelectronics | 38749287 | Biosens Bioelectron | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/38749287 |
| Toward Personalized Treatment of Depression: An Affordable Citalopram Test based on a Solid-Contact Potentiometric Electrode for at-Home Monitoring of the Antidepressant Dosage. | Chen R, Amirghasemi F, Ma H, Ong V, Tran A, Mousavi MPS | ACS sensors | 37734027 | ACS Sens | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37734027 |
| SPOOC (Sensor for Periodic Observation of Choline): An Integrated Lab-on-a-Spoon Platform for At-Home Quantification of Choline in Infant Formula. | Al-Shami A, Amirghasemi F, Soleimani A, Khazaee Nejad S, Ong V, Berkmen A, Ainla A, Mousavi MPS | Small (Weinheim an der Bergstrasse, Germany) | 38587168 | Small | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38587168 |
| Flexible Acetylcholine Neural Probe with a Hydrophobic Laser-Induced Graphene Electrode and a Fluorous-Phase Sensing Membrane. | Amirghasemi F, Al-Shami A, Ushijima K, Mousavi MPS | ACS materials letters | 39309214 | ACS Mater Lett | 2024 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/39309214 |
| Sustainable Agriculture with LEAFS: a Low-cost Electrochemical Analyzer of Foliage Stress. | Nejad SK, Ma H, Al-Shami A, Soleimani A, Mohamed MA, Dankwah P, Lee HJ, Mousavi MPS | Sensors & diagnostics | 40352404 | Sens Diagn | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/40352404 |
| Lab-on-a-lollipop (LoL) platform for preventing food-induced toxicity: all-in-one system for saliva sampling and electrochemical detection of vanillin. | Ma H, Khazaee Nejad S, Vargas Ramos D, Al-Shami A, Soleimani A, Amirghasemi F, Mohamed MA, Mousavi MPS | Lab on a chip | 39207360 | Lab Chip | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/39207360 |
| LiFT (a Lithium Fiber-Based Test): An At-Home Companion Diagnostics for a Safer Lithium Therapy in Bipolar Disorder. | Amirghasemi F, Nejad SK, Chen R, Soleimani A, Ong V, Shroff N, Eftekhari T, Ushijima K, Ainla A, Siegel S, Mousavi MPS | Advanced healthcare materials | 38563494 | Adv Healthc Mater | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38563494 |
| Coaching ribosome biogenesis from the nuclear periphery. | Zhuang Y, Guo X, Razorenova OV, Miles CE, Zhao W, Shi X | bioRxiv : the preprint server for biology | 38948754 | bioRxiv | 2024 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/38948754 |
| RBBP6 anchors pre-mRNA 3' end processing to nuclear speckles for efficient gene expression. | Yoon Y, Bournique E, Soles LV, Yin H, Chu HF, Yin C, Zhuang Y, Liu X, Liu L, Jeong J, Yu C, Valdez M, Tian L, Huang L, Shi X, Seelig G, Ding F, Tong L, Buisson R, Shi Y | Molecular cell | 39798570 | Mol Cell | 2025 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39798570 |
| Expansion microscopy: A chemical approach for super-resolution microscopy. | Zhuang Y, Shi X | Current opinion in structural biology | 37253290 | Curr Opin Struct Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37253290 |
| Label-Retention Expansion Microscopy (LR-ExM) for Enhanced Fluorescent Signals using Trifunctional Probes. | Zhuang Y, Shi X | Current protocols | 38265180 | Curr Protoc | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38265180 |
| Proximity labeling expansion microscopy (PL-ExM) evaluates interactome labeling techniques. | Park S, Wang X, Mo Y, Zhang S, Li X, Fong KC, Yu C, Tran AA, Scipioni L, Dai Z, Huang X, Huang L, Shi X | Journal of materials chemistry. B | 39105364 | J Mater Chem B | 2024 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/39105364 |
| Proximity Labeling Expansion Microscopy (PL-ExM) resolves structure of the interactome. | Park S, Wang X, Li X, Huang X, Fong KC, Yu C, Tran AA, Scipioni L, Dai Z, Huang L, Shi X | bioRxiv : the preprint server for biology | 38014020 | bioRxiv | 2023 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/38014020 |
| Cationic peptides erase memories by removing synaptic AMPA receptors through endophilin-mediated endocytosis. | Stokes E, Zhuang Y, Toledano M, Vasquez J, Azouz G, Hui M, Tyler I, Shi X, Aoto J, Beier KT | Research square | 38045269 | Res Sq | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/38045269 |
| Enhanced dynamic coupling in a nuclear receptor underlies ligand activity. | Yu T, Villalona P, Khan SH, Mikeasky N, Meinert E, Magafas J, Pulahinge T, Bader A, Okafor CD | The Journal of biological chemistry | 39675705 | J Biol Chem | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39675705 |
| Phase Separation in Biology and Disease; Current Perspectives and Open Questions. | Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R | Journal of molecular biology | 36690068 | J Mol Biol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36690068 |
| Hierarchal single-cell lineage tracing reveals differential fate commitment of CD8 T-cell clones in response to acute infection. | Abdullah L, Emiliani FE, Vaidya CM, Stuart H, Kolling FW, Ackerman ME, Song L, McKenna A, Huang YH | bioRxiv : the preprint server for biology | 38585810 | bioRxiv | 2024 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/38585810 |
| The endogenous antigen-specific CD8(+) T cell repertoire is composed of unbiased and biased clonotypes with differential fate commitments. | Abdullah L, Emiliani FE, Vaidya CM, Stuart H, Musial SC, Kolling FW, Obar JJ, Rosato PC, Ackerman ME, Song L, McKenna A, Huang YH | Immunity | 40020673 | Immunity | 2025 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/40020673 |
| Genetically-Encoded Phase Separation Sensors Enable High-Fidelity Live-Cell Probing of Biomolecular Condensates. | Avecilla ARC, Thomas J, Quiroz FG | ACS sensors | 39987501 | ACS Sens | 2025 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/39987501 |
| Genetically-encoded phase separation sensors for intracellular probing of biomolecular condensates. | Regina Chua Avecilla A, Thomas J, Quiroz FG | bioRxiv : the preprint server for biology | 39257779 | bioRxiv | 2024 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/39257779 |
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| Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning. | Laubscher E, Wang X, Razin N, Dougherty T, Xu RJ, Ombelets L, Pao E, Graf W, Moffitt JR, Yue Y, Van Valen D | Cell systems | 38754367 | Cell Syst | 2024 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/38754367 |
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| Stimulating Transcription in Antibiotic-Tolerant Escherichia coli Sensitizes It to Fluoroquinolone and Nonfluoroquinolone Topoisomerase Inhibitors. | LaGree TJ, Byrd BA, Quelle RM, Schofield SL, Mok WWK | Antimicrobial agents and chemotherapy | 36951560 | Antimicrob Agents Chemother | 2023 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/36951560 |
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| Chemical and topological design of multicapped mRNA and capped circular RNA to augment translation. | Chen H, Liu D, Aditham A, Guo J, Huang J, Kostas F, Maher K, Friedrich MJ, Xavier RJ, Zhang F, Wang X | Nature biotechnology | 39313647 | Nat Biotechnol | 2024 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/39313647 |
| Scalable spatial single-cell transcriptomics and translatomics in 3D thick tissue blocks. | Sui X, Lo JA, Luo S, He Y, Tang Z, Lin Z, Zhou Y, Wang WX, Liu J, Wang X | bioRxiv : the preprint server for biology | 39149316 | bioRxiv | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39149316 |
| Tracking the transition from an ATG9A vesicle to an autophagosome. | Broadbent D, Barnaba C, Schmidt JC | Autophagy | 37405380 | Autophagy | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37405380 |
| Systematic analysis of the molecular and biophysical properties of key DNA damage response factors. | Heyza JR, Mikhova M, Bahl A, Broadbent DG, Schmidt JC | eLife | 37341699 | Elife | 2023 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/37341699 |
| The formation of ubiquitin rich condensates triggers recruitment of the ATG9A lipid transfer complex to initiate basal autophagy. | Broadbent DG, McEwan CM, Tsang TM, Poole DM, Naylor BC, Price JC, Schmidt JC, Andersen JL | bioRxiv : the preprint server for biology | 38077022 | bioRxiv | 2023 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/38077022 |
| The PST repeat region of MDC1 is a tunable multivalent chromatin tethering domain. | Heyza JR, Mikhova M, Perez GI, Broadbent DG, Schmidt JC | bioRxiv : the preprint server for biology | 39868091 | bioRxiv | 2025 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/39868091 |
| Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells. | Mikhova M, Goff NJ, Janovič T, Heyza JR, Meek K, Schmidt JC | Nature communications | 39578493 | Nat Commun | 2024 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/39578493 |
| Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells. | Mikhova M, Goff NJ, Janovič T, Heyza JR, Meek K, Schmidt JC | bioRxiv : the preprint server for biology | 38826211 | bioRxiv | 2024 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/38826211 |
| AMPK regulates phagophore-to-autophagosome maturation. | Barnaba C, Broadbent DG, Kaminsky EG, Perez GI, Schmidt JC | The Journal of cell biology | 38775785 | J Cell Biol | 2024 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/38775785 |
| AMPK Regulates Phagophore-to-Autophagosome Maturation. | Barnaba C, Broadbent DG, Perez GI, Schmidt JC | bioRxiv : the preprint server for biology | 37808644 | bioRxiv | 2023 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/37808644 |
| RHINO restricts MMEJ activity to mitosis. | Brambati A, Sacco O, Porcella S, Heyza J, Kareh M, Schmidt JC, Sfeir A | bioRxiv : the preprint server for biology | 36993461 | bioRxiv | 2023 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/36993461 |
| Quantitative analysis of autophagy reveals the role of ATG9 and ATG2 in autophagosome formation. | Broadbent DG, Barnaba C, Perez GI, Schmidt JC | The Journal of cell biology | 37115157 | J Cell Biol | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/37115157 |
| TRF1 and TRF2 form distinct shelterin subcomplexes at telomeres. | Janovič T, Perez GI, Schmidt JC | bioRxiv : the preprint server for biology | 39763972 | bioRxiv | 2024 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/39763972 |
| Live cell single-molecule imaging to study DNA repair in human cells. | Heyza JR, Mikhova M, Schmidt JC | DNA repair | 37467632 | DNA Repair (Amst) | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37467632 |
| RHINO directs MMEJ to repair DNA breaks in mitosis. | Brambati A, Sacco O, Porcella S, Heyza J, Kareh M, Schmidt JC, Sfeir A | Science (New York, N.Y.) | 37440612 | Science | 2023 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/37440612 |
| PNKP safeguards stalled replication forks from nuclease-dependent degradation during replication stress. | Mashayekhi F, Ganje C, Caron MC, Heyza JR, Gao Y, Zeinali E, Fanta M, Li L, Ali J, Mersaoui SY, Schmidt JC, Godbout R, Masson JY, Weinfeld M, Ismail IH | Cell reports | 39671289 | Cell Rep | 2024 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/39671289 |
| Ubiquitin-mediated recruitment of the ATG9A-ATG2 lipid transfer complex drives clearance of phosphorylated p62 aggregates. | Broadbent DG, McEwan CM, Jayatunge D, Kaminsky EG, Tsang TM, Poole DM, Naylor BC, Price JC, Schmidt JC, Andersen JL | Molecular biology of the cell | 39718773 | Mol Biol Cell | 2025 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/39718773 |
| Native SAD phasing at room temperature. | Greisman JB, Dalton KM, Sheehan CJ, Klureza MA, Kurinov I, Hekstra DR | Acta crystallographica. Section D, Structural biology | 35916223 | Acta Crystallogr D Struct Biol | 2022 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/35916223 |
| MatchMaps: Non-isomorphous difference maps for X-ray crystallography. | Brookner DE, Hekstra DR | bioRxiv : the preprint server for biology | 37732267 | bioRxiv | 2024 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/37732267 |
| Correcting systematic errors in diffraction data with modern scaling algorithms. | Aldama LA, Dalton KM, Hekstra DR | Acta crystallographica. Section D, Structural biology | 37584427 | Acta Crystallogr D Struct Biol | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37584427 |
| Resolving conformational changes that mediate a two-step catalytic mechanism in a model enzyme. | Greisman JB, Dalton KM, Brookner DE, Klureza MA, Sheehan CJ, Kim IS, Henning RW, Russi S, Hekstra DR | bioRxiv : the preprint server for biology | 37398233 | bioRxiv | 2023 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/37398233 |
| Mapping Protein Conformational Landscapes from Crystallographic Drug Fragment Screens. | Saeed AA, Klureza MA, Hekstra DR | Journal of chemical information and modeling | 39530154 | J Chem Inf Model | 2024 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/39530154 |
| Laue-DIALS: Open-source software for polychromatic x-ray diffraction data. | Hewitt RA, Dalton KM, Mendez DA, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR | Structural dynamics (Melville, N.Y.) | 39386198 | Struct Dyn | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39386198 |
| AlphaFold as a Prior: Experimental Structure Determination Conditioned on a Pretrained Neural Network. | Fadini A, Li M, McCoy AJ, Terwilliger TC, Read RJ, Hekstra D, AlQuraishi M | bioRxiv : the preprint server for biology | 40027838 | bioRxiv | 2025 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/40027838 |
| Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. | Hekstra DR | Annual review of biophysics | 37159292 | Annu Rev Biophys | 2023 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/37159292 |
| SFCalculator: connecting deep generative models and crystallography. | Li M, Dalton K, Hekstra D | bioRxiv : the preprint server for biology | 39868231 | bioRxiv | 2025 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/39868231 |
| Scaling and merging time-resolved pink-beam diffraction with variational inference. | Zielinski KA, Dolamore C, Wang HK, Henning RW, Wilson MA, Pollack L, Srajer V, Hekstra DR, Dalton KM | Structural dynamics (Melville, N.Y.) | 39629168 | Struct Dyn | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39629168 |
| Laue-DIALS: open-source software for polychromatic X-ray diffraction data. | Hewitt RA, Dalton KM, Mendez D, Wang HK, Klureza MA, Brookner DE, Greisman JB, McDonagh D, Šrajer V, Sauter NK, Brewster AS, Hekstra DR | bioRxiv : the preprint server for biology | 39091818 | bioRxiv | 2024 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/39091818 |
| MatchMaps: non-isomorphous difference maps for X-ray crystallography. | Brookner DE, Hekstra DR | Journal of applied crystallography | 38846758 | J Appl Crystallogr | 2024 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/38846758 |
| Mapping protein conformational landscapes from crystallographic drug fragment screens. | Saeed AA, Klureza MA, Hekstra DR | bioRxiv : the preprint server for biology | 39131376 | bioRxiv | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39131376 |
| Sensitive Detection of Structural Differences using a Statistical Framework for Comparative Crystallography. | Hekstra DR, Wang HK, Klureza MA, Greisman JB, Dalton KM | bioRxiv : the preprint server for biology | 39091831 | bioRxiv | 2024 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/39091831 |
| Insights into VDAC Gating: Room-Temperature X-ray Crystal Structure of mVDAC-1. | Gonzalez-DeWhitt KR, Ermolova N, Wang HK, Hekstra DR, Althoff T, Abramson J | Biomolecules | 39456136 | Biomolecules | 2024 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/39456136 |
| Direct visualization of electric-field-stimulated ion conduction in a potassium channel. | Lee B, White KI, Socolich M, Klureza MA, Henning R, Srajer V, Ranganathan R, Hekstra DR | Cell | 39793560 | Cell | 2025 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/39793560 |
| Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism. | Greisman JB, Dalton KM, Brookner DE, Klureza MA, Sheehan CJ, Kim IS, Henning RW, Russi S, Hekstra DR | Proceedings of the National Academy of Sciences of the United States of America | 38386706 | Proc Natl Acad Sci U S A | 2024 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/38386706 |
| A unifying Bayesian framework for merging X-ray diffraction data. | Dalton KM, Greisman JB, Hekstra DR | Nature communications | 36522310 | Nat Commun | 2022 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36522310 |
| Resolving DJ-1 Glyoxalase Catalysis Using Mix-and-Inject Serial Crystallography at a Synchrotron. | Zielinski KA, Dolamore C, Dalton KM, Smith N, Termini J, Henning R, Srajer V, Hekstra DR, Pollack L, Wilson MA | bioRxiv : the preprint server for biology | 39071394 | bioRxiv | 2024 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/39071394 |
| Scaling and Merging Time-Resolved Laue Data with Variational Inference. | Zielinski KA, Dolamore C, Wang HK, Henning RW, Wilson MA, Pollack L, Srajer V, Hekstra DR, Dalton KM | bioRxiv : the preprint server for biology | 39131362 | bioRxiv | 2024 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/39131362 |
| Programmable RNA targeting with CRISPR-Cas13. | Shi P, Wu X | RNA biology | 38764173 | RNA Biol | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38764173 |
| Collateral activity of the CRISPR/RfxCas13d system in human cells. | Shi P, Murphy MR, Aparicio AO, Kesner JS, Fang Z, Chen Z, Trehan A, Guo Y, Wu X | Communications biology | 36977923 | Commun Biol | 2023 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/36977923 |
| Noncoding translation mitigation. | Kesner JS, Chen Z, Shi P, Aparicio AO, Murphy MR, Guo Y, Trehan A, Lipponen JE, Recinos Y, Myeku N, Wu X | Nature | 37046090 | Nature | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37046090 |
| Finding functional microproteins. | Azam S, Yang F, Wu X | Trends in genetics : TIG | 39753408 | Trends Genet | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39753408 |
| Mechanisms suppressing noncoding translation. | Kesner JS, Wu X | Trends in cell biology | 39443270 | Trends Cell Biol | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39443270 |
| Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. | Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S | Molecular cell | 37419111 | Mol Cell | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37419111 |
| An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. | Waterbury AL, Kwok HS, Lee C, Narducci DN, Freedy AM, Su C, Raval S, Reiter AH, Hawkins W, Lee K, Li J, Hoenig SM, Vinyard ME, Cole PA, Hansen AS, Carr SA, Papanastasiou M, Liau BB | Molecular cell | 38870936 | Mol Cell | 2024 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/38870936 |
| Genome-wide absolute quantification of chromatin looping. | Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny LA, Hansen AS | bioRxiv : the preprint server for biology | 39935886 | bioRxiv | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39935886 |
| A Protocol for Studying Transcription Factor Dynamics Using Fast Single-Particle Tracking and Spot-On Model-Based Analysis. | Jha A, Hansen AS | Methods in molecular biology (Clifton, N.J.) | 35103967 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35103967 |
| Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging. | Brandão HB, Gabriele M, Hansen AS | Current opinion in cell biology | 33310227 | Curr Opin Cell Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33310227 |
| Promoters adopt distinct dynamic manifestations depending on transcription factor context. | Hansen AS, Zechner C | Molecular systems biology | 33595925 | Mol Syst Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33595925 |
| Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments. | Goel VY, Huseyin MK, Hansen AS | Nature genetics | 37157000 | Nat Genet | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37157000 |
| Integrative PTEN Enhancer Discovery Reveals a New Model of Enhancer Organization. | Cerda-Smith CG, Hutchinson HM, Liu A, Goel VY, Sept C, Kim H, Casaní-Galdón S, Burkman KG, Bassil CF, Hansen AS, Aryee MJ, Johnstone SE, Eyler CE, Wood KC | bioRxiv : the preprint server for biology | 37786671 | bioRxiv | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37786671 |
| Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. | Yang JH, Hansen AS | Nature reviews. Molecular cell biology | 38413840 | Nat Rev Mol Cell Biol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38413840 |
| Dynamics of microcompartment formation at the mitosis-to-G1 transition. | Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS | bioRxiv : the preprint server for biology | 39345388 | bioRxiv | 2024 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/39345388 |
| Molecular models of bidirectional promoter regulation. | Nemsick S, Hansen AS | Current opinion in structural biology | 38905929 | Curr Opin Struct Biol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38905929 |
| Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging. | Gabriele M, Brandão HB, Grosse-Holz S, Jha A, Dailey GM, Cattoglio C, Hsieh TS, Mirny L, Zechner C, Hansen AS | Science (New York, N.Y.) | 35420890 | Science | 2022 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/35420890 |
| Reeling it in: how DNA topology drives loop extrusion by condensin. | Narducci DN, Hansen AS | Nature structural & molecular biology | 35835869 | Nat Struct Mol Biol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35835869 |
| Enhancer-promoter interactions and transcription are largely maintained upon acute loss of CTCF, cohesin, WAPL or YY1. | Hsieh TS, Cattoglio C, Slobodyanyuk E, Hansen AS, Darzacq X, Tjian R | Nature genetics | 36471071 | Nat Genet | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36471071 |
| DNA double-strand break end synapsis by DNA loop extrusion. | Yang JH, Brandão HB, Hansen AS | Nature communications | 37024496 | Nat Commun | 2023 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/37024496 |
| Dynamics of endogenous PARP1 and PARP2 during DNA damage revealed by live-cell single-molecule imaging. | Mahadevan J, Jha A, Rudolph J, Bowerman S, Narducci D, Hansen AS, Luger K | iScience | 36594010 | iScience | 2023 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/36594010 |
| Right on target: Chromatin jets arise from targeted cohesin loading in wild-type cells. | Drayton JA, Hansen AS | Molecular cell | 36270244 | Mol Cell | 2022 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/36270244 |
| Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation. | Kim KL, Rahme GJ, Goel VY, El Farran CA, Hansen AS, Bernstein BE | Molecular cell | 38452764 | Mol Cell | 2024 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/38452764 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | bioRxiv : the preprint server for biology | 39229045 | bioRxiv | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39229045 |
| Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude. | Mazzocca M, Narducci DN, Grosse-Holz S, Matthias J, Hansen AS | bioRxiv : the preprint server for biology | 40463058 | bioRxiv | 2025 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/40463058 |
| Genome manipulation by guide-directed Argonaute cleavage. | Huang S, Wang K, Mayo SL | Nucleic acids research | 36928676 | Nucleic Acids Res | 2023 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/36928676 |
| Removal of Antibiotic Resistant Bacteria and Genes by UV-Assisted Electrochemical Oxidation on Degenerative TiO(2) Nanotube Arrays. | Wang S, Yang S, Quispe E, Yang H, Sanfiorenzo C, Rogers SW, Wang K, Yang Y, Hoffmann MR | ACS ES&T engineering | 39605952 | ACS ES T Eng | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/39605952 |
| Creating custom synthetic genomes in Escherichia coli with REXER and GENESIS. | Robertson WE, Funke LFH, de la Torre D, Fredens J, Wang K, Chin JW | Nature protocols | 33903757 | Nat Protoc | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33903757 |
| Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation. | Kim TE, Tsuboyama K, Houliston S, Martell CM, Phoumyvong CM, Lemak A, Haddox HK, Arrowsmith CH, Rocklin GJ | Proceedings of the National Academy of Sciences of the United States of America | 36191185 | Proc Natl Acad Sci U S A | 2022 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/36191185 |
| Structural and energetic analysis of stabilizing indel mutations. | Gutierrez YM, Rocklin GJ | bioRxiv : the preprint server for biology | 39763793 | bioRxiv | 2024 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/39763793 |
| Large-scale discovery, analysis, and design of protein energy landscapes. | Ferrari ÁJR, Dixit SM, Thibeault J, Garcia M, Houliston S, Ludwig RW, Notin P, Phoumyvong CM, Martell CM, Jung MD, Tsuboyama K, Carter L, Arrowsmith CH, Guttman M, Rocklin GJ | bioRxiv : the preprint server for biology | 40196533 | bioRxiv | 2025 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/40196533 |
| A proteome-wide map of chaperone-assisted protein refolding in a cytosol-like milieu. | To P, Xia Y, Lee SO, Devlin T, Fleming KG, Fried SD | Proceedings of the National Academy of Sciences of the United States of America | 36417429 | Proc Natl Acad Sci U S A | 2022 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/36417429 |
| Nucleosome recognition and DNA distortion by the Chd1 remodeler in a nucleotide-free state. | Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP | Nature structural & molecular biology | 35173352 | Nat Struct Mol Biol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35173352 |
| Universal protein misfolding intermediates can bypass the proteostasis network and remain soluble and less functional. | Nissley DA, Jiang Y, Trovato F, Sitarik I, Narayan KB, To P, Xia Y, Fried SD, O'Brien EP | Nature communications | 35654797 | Nat Commun | 2022 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/35654797 |
| Secretion-Catalyzed Assembly of Protein Biomaterials on a Bacterial Membrane Surface. | Xie Q, On Lee S, Vissamsetti N, Guo S, Johnson ME, Fried SD | Angewandte Chemie (International ed. in English) | 37469298 | Angew Chem Int Ed Engl | 2023 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/37469298 |
| Progress toward Proteome-Wide Photo-Cross-Linking to Enable Residue-Level Visualization of Protein Structures and Networks In Vivo. | Faustino AM, Sharma P, Manriquez-Sandoval E, Yadav D, Fried SD | Analytical chemistry | 37341467 | Anal Chem | 2023 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/37341467 |
| Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements. | Lan PD, Nissley DA, Sitarik I, Vu QV, Jiang Y, To P, Xia Y, Fried SD, Li MS, O'Brien EP | Journal of molecular biology | 38341172 | J Mol Biol | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/38341172 |
| Early Selection of the Amino Acid Alphabet Was Adaptively Shaped by Biophysical Constraints of Foldability. | Makarov M, Sanchez Rocha AC, Krystufek R, Cherepashuk I, Dzmitruk V, Charnavets T, Faustino AM, Lebl M, Fujishima K, Fried SD, Hlouchova K | Journal of the American Chemical Society | 36826345 | J Am Chem Soc | 2023 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/36826345 |
| Cognition-Associated Protein Structural Changes in a Rat Model of Aging are Related to Reduced Refolding Capacity. | Tarbox HE, Branch A, Fried SD | bioRxiv : the preprint server for biology | 39386726 | bioRxiv | 2024 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/39386726 |
| Cryo-EM structures of the Plant Augmin reveal its intertwined coiled-coil assembly, antiparallel dimerization and NEDD1 binding mechanisms. | Ashaduzzaman M, Taheri A, Lee YJ, Tang Y, Guo F, Fried SD, Liu B, Al-Bassam J | bioRxiv : the preprint server for biology | 40034650 | bioRxiv | 2025 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/40034650 |
| Proteome-Wide Assessment of Protein Structural Perturbations Under High Pressure. | Moran HM, Manriquez-Sandoval E, Sharma P, Fried SD, Gillilan RE | PRX life | 40491869 | PRX Life | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40491869 |
| Nonrefoldability is Pervasive Across the E. coli Proteome. | To P, Whitehead B, Tarbox HE, Fried SD | Journal of the American Chemical Society | 34308638 | J Am Chem Soc | 2021 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/34308638 |
| FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Data Sets Built on FragPipe. | Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD | Journal of proteome research | 38787630 | J Proteome Res | 2024 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/38787630 |
| Intracellular Formation of a DNA Damage-Induced, Histone Post-Translational Modification Following Bleomycin Treatment. | Jacinto MP, Fried SD, Greenberg MM | Journal of the American Chemical Society | 35467863 | J Am Chem Soc | 2022 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/35467863 |
| How synonymous mutations alter enzyme structure and function over long timescales. | Jiang Y, Neti SS, Sitarik I, Pradhan P, To P, Xia Y, Fried SD, Booker SJ, O'Brien EP | Nature chemistry | 36471044 | Nat Chem | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36471044 |
| FLiPPR: A Processor for Limited Proteolysis (LiP) Mass Spectrometry Datasets Built on FragPipe. | Manriquez-Sandoval E, Brewer J, Lule G, Lopez S, Fried SD | bioRxiv : the preprint server for biology | 38106106 | bioRxiv | 2023 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/38106106 |
| Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome. | Metzner E, Southard KM, Norman TM | Cell systems | 39689711 | Cell Syst | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39689711 |
| Multiome Perturb-seq unlocks scalable discovery of integrated perturbation effects on the transcriptome and epigenome. | Metzner E, Southard KM, Norman TM | bioRxiv : the preprint server for biology | 39091800 | bioRxiv | 2024 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/39091800 |
| Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq. | Replogle JM, Saunders RA, Pogson AN, Hussmann JA, Lenail A, Guna A, Mascibroda L, Wagner EJ, Adelman K, Lithwick-Yanai G, Iremadze N, Oberstrass F, Lipson D, Bonnar JL, Jost M, Norman TM, Weissman JS | Cell | 35688146 | Cell | 2022 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/35688146 |
| Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states. | Southard KM, Ardy RC, Tang A, O'Sullivan DD, Metzner E, Guruvayurappan K, Norman TM | bioRxiv : the preprint server for biology | 39131349 | bioRxiv | 2024 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/39131349 |
| Revealing the hidden reality of the mammalian 12-h ultradian rhythms. | Ballance H, Zhu B | Cellular and molecular life sciences : CMLS | 33449146 | Cell Mol Life Sci | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33449146 |
| Logic of the Temporal Compartmentalization of the Hepatic Metabolic Cycle. | Zhu B | Physiology (Bethesda, Md.) | 35658626 | Physiology (Bethesda) | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/35658626 |
| Four-dimensional nuclear speckle phase separation dynamics regulate proteostasis. | Dion W, Ballance H, Lee J, Pan Y, Irfan S, Edwards C, Sun M, Zhang J, Zhang X, Liu S, Zhu B | Science advances | 34985945 | Sci Adv | 2022 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/34985945 |
| SON-dependent nuclear speckle rehabilitation alleviates proteinopathies. | Dion W, Tao Y, Chambers M, Zhao S, Arbuckle RK, Sun M, Kubra S, Schaich MA, Nie Y, Ye M, Jamal I, Larsen MB, Camarco D, Ickes E, Wang HH, DuPont C, Wang B, Liu S, Pi S, Van Houten B, Chen BB, Chen Y, Chen X, Zhu B | bioRxiv : the preprint server for biology | 38659924 | bioRxiv | 2025 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/38659924 |
| Preservation of ∼12-hour ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. | Zhu B, Liu S | bioRxiv : the preprint server for biology | 37205336 | bioRxiv | 2023 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/37205336 |
| XBP1 links the 12-hour clock to NAFLD and regulation of membrane fluidity and lipid homeostasis. | Meng H, Gonzales NM, Lonard DM, Putluri N, Zhu B, Dacso CC, York B, O'Malley BW | Nature communications | 33277471 | Nat Commun | 2020 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/33277471 |
| Temporal gene expression patterns in the coral Euphyllia paradivisa reveal the complexity of biological clocks in the cnidarian-algal symbiosis. | Rinsky M, Weizman E, Ben-Asher HW, Eyal G, Zhu B, Levy O | Science advances | 36112690 | Sci Adv | 2022 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/36112690 |
| Beyond circadian rhythms: emerging roles of ultradian rhythms in control of liver functions. | Asher G, Zhu B | Hepatology (Baltimore, Md.) | 35591797 | Hepatology | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/35591797 |
| LEF1 isoforms regulate cellular senescence and aging. | Jia M, Sayed K, Kapetanaki MG, Dion W, Rosas L, Irfan S, Valenzi E, Mora AL, Lafyatis RA, Rojas M, Zhu B, Benos PV | bioRxiv : the preprint server for biology | 37502913 | bioRxiv | 2023 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/37502913 |
| The SET1/COMPASS subunit RBBP5 orchestrates epigenetic control of global proteostasis and the 12h oscillator to safeguard metabolic and cellular homeostasis. | Kubra S, Sun M, Dion W, Catak A, Luong H, Wang H, Pan Y, Liu JJ, Ponna A, Liu L, Sipula I, Luo JH, Jurczak MJ, Liu S, Zhu B | bioRxiv : the preprint server for biology | 39314427 | bioRxiv | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/39314427 |
| Evidence for ~12-h ultradian gene programs in humans. | Zhu B, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Kumar GVN, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PK, Steinhauser ML | Npj biological timing and sleep | 39148626 | NPJ Biol Timing Sleep | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39148626 |
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| Defining the mammalian coactivation of hepatic 12-h clock and lipid metabolism. | Meng H, Gonzales NM, Jung SY, Lu Y, Putluri N, Zhu B, Dacso CC, Lonard DM, O'Malley BW | Cell reports | 35263593 | Cell Rep | 2022 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/35263593 |
| LEF1 isoforms regulate cellular senescence and aging. | Jia M, Sayed K, Kapetanaki MG, Dion W, Rosas L, Irfan S, Valenzi E, Mora AL, Lafyatis RA, Rojas M, Zhu B, Benos PV | Aging cell | 37961030 | Aging Cell | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37961030 |
| Twelve-hour rhythms in transcript expression within the human dorsolateral prefrontal cortex are altered in schizophrenia. | Scott MR, Zong W, Ketchesin KD, Seney ML, Tseng GC, Zhu B, McClung CA | PLoS biology | 36693045 | PLoS Biol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36693045 |
| Evidence for conservation of primordial ~12-hour ultradian gene programs in humans under free-living conditions. | Zhu B, Liu S, David NL, Dion W, Doshi NK, Siegel LB, Amorim T, Andrews RE, Naveen Kumar GV, Li H, Irfan S, Pesaresi T, Sharma AX, Sun M, Fazeli PK, Steinhauser ML | bioRxiv : the preprint server for biology | 37205600 | bioRxiv | 2023 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/37205600 |
| Preservation of ∼12-h ultradian rhythms of gene expression of mRNA and protein metabolism in the absence of canonical circadian clock. | Zhu B, Liu S | Frontiers in physiology | 37324401 | Front Physiol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37324401 |
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| AxoDen: An Algorithm for the Automated Quantification of Axonal Density in Defined Brain Regions. | Sandoval Ortega RA, Li E, Joseph O, Dufour PA, Corder G | eNeuro | 40379480 | eNeuro | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40379480 |
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| Mixing microbiomes in vitro reveals rules of community assembly. | Mitchell AH, Lieberman TD | Proceedings of the National Academy of Sciences of the United States of America | 40193618 | Proc Natl Acad Sci U S A | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/40193618 |
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| The microbiome of the human facial skin is unique compared to that of other hominids. | Degregori S, Manus MB, Qu EB, Mendall CP, Baker JS, Hopper LM, Amato KR, Lieberman TD | mSystems | 40434114 | mSystems | 2025 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/40434114 |
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| A High-Throughput Colocalization Pipeline for Quantification of Mitochondrial Targeting across Different Protein Types. | Lear SK, Nunez JA, Shipman SL | ACS synthetic biology | 37506292 | ACS Synth Biol | 2023 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/37506292 |
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| Profiling the Landscape of Drug Resistance Mutations in Neosubstrates to Molecular Glue Degraders. | Gosavi PM, Ngan KC, Yeo MJR, Su C, Li J, Lue NZ, Hoenig SM, Liau BB | ACS central science | 35505873 | ACS Cent Sci | 2022 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/35505873 |
| Chromatin complex dependencies reveal targeting opportunities in leukemia. | Najm FJ, DeWeirdt P, Moore MM, Bevill SM, El Farran CA, Macias KA, Hegde M, Waterbury AL, Liau BB, van Galen P, Doench JG, Bernstein BE | Nature communications | 36707513 | Nat Commun | 2023 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/36707513 |
| Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. | Zhang J, Simpson CM, Berner J, Chong HB, Fang J, Ordulu Z, Weiss-Sadan T, Possemato AP, Harry S, Takahashi M, Yang TY, Richter M, Patel H, Smith AE, Carlin AD, Hubertus de Groot AF, Wolf K, Shi L, Wei TY, Dürr BR, Chen NJ, Vornbäumen T, Wichmann NO, Mahamdeh MS, Pooladanda V, Matoba Y, Kumar S, Kim E, Bouberhan S, Oliva E, Rueda BR, Soberman RJ, Bardeesy N, Liau BB, Lawrence M, Stokes MP, Beausoleil SA, Bar-Peled L | Cell | 37192619 | Cell | 2023 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/37192619 |
| Base editor scanning charts the DNMT3A activity landscape. | Lue NZ, Garcia EM, Ngan KC, Lee C, Doench JG, Liau BB | Nature chemical biology | 36266353 | Nat Chem Biol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36266353 |
| Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma. | Kwok HS, Freedy AM, Siegenfeld AP, Morriss JW, Waterbury AL, Kissler SM, Liau BB | Nature chemical biology | 36973442 | Nat Chem Biol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36973442 |
| DrugMap: A quantitative pan-cancer analysis of cysteine ligandability. | Takahashi M, Chong HB, Zhang S, Yang TY, Lazarov MJ, Harry S, Maynard M, Hilbert B, White RD, Murrey HE, Tsou CC, Vordermark K, Assaad J, Gohar M, Dürr BR, Richter M, Patel H, Kryukov G, Brooijmans N, Alghali ASO, Rubio K, Villanueva A, Zhang J, Ge M, Makram F, Griesshaber H, Harrison D, Koglin AS, Ojeda S, Karakyriakou B, Healy A, Popoola G, Rachmin I, Khandelwal N, Neil JR, Tien PC, Chen N, Hosp T, van den Ouweland S, Hara T, Bussema L, Dong R, Shi L, Rasmussen MQ, Domingues AC, Lawless A, Fang J, Yoda S, Nguyen LP, Reeves SM, Wakefield FN, Acker A, Clark SE, Dubash T, Kastanos J, Oh E, Fisher DE, Maheswaran S, Haber DA, Boland GM, Sade-Feldman M, Jenkins RW, Hata AN, Bardeesy NM, Suvà ML, Martin BR, Liau BB, Ott CJ, Rivera MN, Lawrence MS, Bar-Peled L | Cell | 38653237 | Cell | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38653237 |
| KBTBD4 Cancer Hotspot Mutations Drive Neomorphic Degradation of HDAC1/2 Corepressor Complexes. | Xie X, Zhang O, Yeo MJR, Lee C, Harry SA, Paul L, Li Y, Payne NC, Nam E, Kwok HS, Jiang H, Mao H, Hadley JL, Lin H, Batts M, Gosavi PM, D'Angiolella V, Cole PA, Mazitschek R, Northcott PA, Zheng N, Liau BB | bioRxiv : the preprint server for biology | 38798357 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798357 |
| Asymmetric Engagement of Dimeric CRL3 (KBTBD4) by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes. | Yeo MJ, Zhang O, Xie X, Nam E, Payne NC, Gosavi PM, Kwok HS, Iram I, Lee C, Li J, Chen NJ, Jiang H, Wang ZA, Lee K, Mao H, Harry SA, Barakat IA, Takahashi M, Waterbury AL, Barone M, Mattevi A, Bar-Peled L, Cole PA, Mazitschek R, Liau BB, Zheng N | bioRxiv : the preprint server for biology | 38798619 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798619 |
| Uncoupling histone modification crosstalk by engineering lysine demethylase LSD1. | Lee K, Barone M, Waterbury AL, Jiang H, Nam E, DuBois-Coyne SE, Whedon SD, Wang ZA, Caroli J, Neal K, Ibeabuchi B, Dhoondia Z, Kuroda MI, Liau BB, Beck S, Mattevi A, Cole PA | Nature chemical biology | 38965385 | Nat Chem Biol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38965385 |
| Covalent adduct Grob fragmentation underlies LSD1 demethylase-specific inhibitor mechanism of action and resistance. | Waterbury AL, Caroli J, Zhang O, Tuttle PR, Liu C, Li J, Park JS, Hoenig SM, Barone M, Furui A, Mattevi A, Liau BB | Nature communications | 40175327 | Nat Commun | 2025 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/40175327 |
| UM171 glues asymmetric CRL3-HDAC1/2 assembly to degrade CoREST corepressors. | Yeo MJR, Zhang O, Xie X, Nam E, Payne NC, Gosavi PM, Kwok HS, Iram I, Lee C, Li J, Chen NJ, Nguyen K, Jiang H, Wang ZA, Lee K, Mao H, Harry SA, Barakat IA, Takahashi M, Waterbury AL, Barone M, Mattevi A, Carr SA, Udeshi ND, Bar-Peled L, Cole PA, Mazitschek R, Liau BB, Zheng N | Nature | 39939761 | Nature | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39939761 |
| Base Editor Scanning Reveals Activating Mutations of DNMT3A. | Garcia EM, Lue NZ, Liang JK, Lieberman WK, Hwang DD, Woods JC, Liau BB | ACS chemical biology | 37603861 | ACS Chem Biol | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37603861 |
| Base editor screens for in situ mutational scanning at scale. | Lue NZ, Liau BB | Molecular cell | 37390819 | Mol Cell | 2023 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/37390819 |
| Discovering new biology with drug-resistance alleles. | Freedy AM, Liau BB | Nature chemical biology | 34799733 | Nat Chem Biol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34799733 |
| CRISPR-Suppressor Scanning for Systematic Discovery of Drug-Resistance Mutations. | Ngan KC, Lue NZ, Lee C, Liau BB | Current protocols | 36541895 | Curr Protoc | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36541895 |
| CRISPR tiling screen reveals cancer epigenetic 'Goldilocks' state. | Barka A, Kohli RM, Shi J | Trends in pharmacological sciences | 37328396 | Trends Pharmacol Sci | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37328396 |
| Converging mechanism of UM171 and KBTBD4 neomorphic cancer mutations. | Xie X, Zhang O, Yeo MJR, Lee C, Tao R, Harry SA, Payne NC, Nam E, Paul L, Li Y, Kwok HS, Jiang H, Mao H, Hadley JL, Lin H, Batts M, Gosavi PM, D'Angiolella V, Cole PA, Mazitschek R, Northcott PA, Zheng N, Liau BB | Nature | 39939763 | Nature | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39939763 |
| Metabolic engineering of Escherichia coli for optimized biosynthesis of nicotinamide mononucleotide, a noncanonical redox cofactor. | Black WB, Aspacio D, Bever D, King E, Zhang L, Li H | Microbial cell factories | 32718347 | Microb Cell Fact | 2020 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/32718347 |
| Engineering natural and noncanonical nicotinamide cofactor-dependent enzymes: design principles and technology development. | King E, Maxel S, Li H | Current opinion in biotechnology | 32956903 | Curr Opin Biotechnol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32956903 |
| Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. | King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H | Nature communications | 36435948 | Nat Commun | 2022 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/36435948 |
| Aldehyde Production in Crude Lysate- and Whole Cell-Based Biotransformation Using a Noncanonical Redox Cofactor System. | Richardson KN, Black WB, Li H | ACS catalysis | 34306803 | ACS Catal | 2020 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/34306803 |
| Growth-Based, High-Throughput Selection for NADH Preference in an Oxygen-Dependent Biocatalyst. | Maxel S, Saleh S, King E, Aspacio D, Zhang L, Luo R, Li H | ACS synthetic biology | 34469126 | ACS Synth Biol | 2021 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/34469126 |
| Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. | Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H | Nature chemical biology | 31768035 | Nat Chem Biol | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31768035 |
| Leveraging Oxidative Stress to Regulate Redox Balance-Based, In Vivo Growth Selections for Oxygenase Engineering. | Maxel S, King E, Zhang Y, Luo R, Li H | ACS synthetic biology | 32966747 | ACS Synth Biol | 2020 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/32966747 |
| Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. | King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H | ACS catalysis | 37622090 | ACS Catal | 2022 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37622090 |
| Design, construction, and application of noncanonical redox cofactor infrastructures. | Black WB, Perea S, Li H | Current opinion in biotechnology | 37939631 | Curr Opin Biotechnol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37939631 |
| Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. | Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H | Nature communications | 36028482 | Nat Commun | 2022 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/36028482 |
| A Growth-Based, High-Throughput Selection Platform Enables Remodeling of 4-Hydroxybenzoate Hydroxylase Active Site. | Maxel S, Aspacio D, King E, Zhang L, Acosta AP, Li H | ACS catalysis | 34295569 | ACS Catal | 2020 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/34295569 |
| In Vivo, High-Throughput Selection of Thermostable Cyclohexanone Monooxygenase (CHMO). | Maxel S, Zhang L, King E, Acosta AP, Luo R, Li H | Catalysts (Basel, Switzerland) | 37637965 | Catalysts | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37637965 |
| Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. | Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H | bioRxiv : the preprint server for biology | 37693387 | bioRxiv | 2023 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/37693387 |
| Developmental transcriptomes predict adult social behaviors in the socially flexible sweat bee, Lasioglossum baleicum. | Omufwoko KS, Cronin AL, Nguyen TTH, Webb AE, Traniello IM, Kocher SD | bioRxiv : the preprint server for biology | 37645955 | bioRxiv | 2023 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/37645955 |
| Repeated Shifts in Sociality Are Associated With Fine-tuning of Highly Conserved and Lineage-Specific Enhancers in a Socially Flexible Bee. | Jones BM, Webb AE, Geib SM, Sim S, Schweizer RM, Branstetter MG, Evans JD, Kocher SD | Molecular biology and evolution | 39487572 | Mol Biol Evol | 2024 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/39487572 |
| Developmental transcriptomes predict adult social behaviours in the socially flexible sweat bee, Lasioglossum baleicum. | Omufwoko KS, Cronin AL, Nguyen TTH, Webb AE, Traniello IM, Kocher SD | Molecular ecology | 38108560 | Mol Ecol | 2023 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/38108560 |
| Integrating computer vision and molecular neurobiology to bridge the gap between behavior and the brain. | Traniello IM, Kocher SD | Current opinion in insect science | 39244088 | Curr Opin Insect Sci | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39244088 |
| NAPS: Integrating pose estimation and tag-based tracking. | Wolf SW, Ruttenberg DM, Knapp DY, Webb AE, Traniello IM, McKenzie-Smith GC, Leheny SA, Shaevitz JW, Kocher SD | Methods in ecology and evolution | 38681746 | Methods Ecol Evol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38681746 |
| Variation in season length and development time is sufficient to drive the emergence and coexistence of social and solitary behavioral strategies. | Ruttenberg DM, Levin SA, Wingreen NS, Kocher SD | bioRxiv : the preprint server for biology | 38948882 | bioRxiv | 2024 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/38948882 |
| Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. | Ju L, Glastad KM, Sheng L, Gospocic J, Kingwell CJ, Davidson SM, Kocher SD, Bonasio R, Berger SL | Cell | 37683635 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37683635 |
| Isolation disrupts social interactions and destabilizes brain development in bumblebees. | Wang ZY, McKenzie-Smith GC, Liu W, Cho HJ, Pereira T, Dhanerawala Z, Shaevitz JW, Kocher SD | Current biology : CB | 35584698 | Curr Biol | 2022 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/35584698 |
| The Molecular Substrates of Insect Eusociality. | Kocher S, Kingwell C | Annual review of genetics | 39146360 | Annu Rev Genet | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39146360 |
| Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. | Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD | Nature ecology & evolution | 36941345 | Nat Ecol Evol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36941345 |
| Progenitor cell diversity in the developing mouse neocortex. | Ruan X, Kang B, Qi C, Lin W, Wang J, Zhang X | Proceedings of the National Academy of Sciences of the United States of America | 33649223 | Proc Natl Acad Sci U S A | 2021 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/33649223 |
| Upregulation of SYNGAP1 expression in mice and human neurons by redirecting alternative splicing. | Yang R, Feng X, Arias-Cavieres A, Mitchell RM, Polo A, Hu K, Zhong R, Qi C, Zhang RS, Westneat N, Portillo CA, Nobrega MA, Hansel C, Garcia Iii AJ, Zhang X | Neuron | 36917980 | Neuron | 2023 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/36917980 |
| PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing. | Ruan X, Hu K, Zhang X | Nature communications | 37280234 | Nat Commun | 2023 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/37280234 |
| Single-cell long-read sequencing in human cerebral organoids uncovers cell-type-specific and autism-associated exons. | Yang Y, Yang R, Kang B, Qian S, He X, Zhang X | Cell reports | 37889749 | Cell Rep | 2023 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/37889749 |
| Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain. | Kang B, Yang Y, Hu K, Ruan X, Liu YL, Lee P, Lee J, Wang J, Zhang X | Genome research | 37907328 | Genome Res | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37907328 |
| Cell-type-specific splicing of transcription regulators and Ptbp1 by Rbfox1/2/3 in the developing neocortex. | Ruan X, Hu K, Yang Y, Yang R, Tseng E, Kang B, Kauffman A, Zhong R, Zhang X | bioRxiv : the preprint server for biology | 39314274 | bioRxiv | 2024 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/39314274 |
| Variants in ADD1 cause intellectual disability, corpus callosum dysgenesis, and ventriculomegaly in humans. | Qi C, Feng I, Costa AR, Pinto-Costa R, Neil JE, Caluseriu O, Li D, Ganetzky RD, Brasch-Andersen C, Fagerberg C, Hansen LK, Bupp C, Muraresku CC, Ruan X, Kang B, Hu K, Zhong R, Brites P, Bhoj EJ, Hill RS, Falk MJ, Hakonarson H, Kahle KT, Sousa MM, Walsh CA, Zhang X | Genetics in medicine : official journal of the American College of Medical Genetics | 34906466 | Genet Med | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34906466 |
| Splice-switching antisense oligonucleotides for pediatric neurological disorders. | Zhang X | Frontiers in molecular neuroscience | 39119251 | Front Mol Neurosci | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39119251 |
| LI Detector: a framework for sensitive colony-based screens regardless of the distribution of fitness effects. | Parikh SB, Castilho Coelho N, Carvunis AR | G3 (Bethesda, Md.) | 33693606 | G3 (Bethesda) | 2021 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/33693606 |
| Biological factors and statistical limitations prevent detection of most noncanonical proteins by mass spectrometry. | Wacholder A, Carvunis AR | PLoS biology | 38048358 | PLoS Biol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38048358 |
| Standardized annotation of translated open reading frames. | Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S | Nature biotechnology | 35831657 | Nat Biotechnol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35831657 |
| A vast evolutionarily transient translatome contributes to phenotype and fitness. | Wacholder A, Parikh SB, Coelho NC, Acar O, Houghton C, Chou L, Carvunis AR | Cell systems | 37164009 | Cell Syst | 2023 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/37164009 |
| Ancestral Sequence Reconstruction as a Tool to Detect and Study De Novo Gene Emergence. | Vakirlis N, Acar O, Cherupally V, Carvunis AR | Genome biology and evolution | 39004885 | Genome Biol Evol | 2024 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/39004885 |
| Integrative detection of genome-wide translation using iRibo. | Turcan A, Lee J, Wacholder A, Carvunis AR | STAR protocols | 38217852 | STAR Protoc | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/38217852 |
| De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences. | Vakirlis N, Acar O, Hsu B, Castilho Coelho N, Van Oss SB, Wacholder A, Medetgul-Ernar K, Bowman RW 2nd, Hines CP, Iannotta J, Parikh SB, McLysaght A, Camacho CJ, O'Donnell AF, Ideker T, Carvunis AR | Nature communications | 32034123 | Nat Commun | 2020 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/32034123 |
| De novo proteins integrate cellular systems using ancient protein targeting and degradation pathways. | Houghton CJ, Coelho NC, Chiang A, Hedayati S, Parikh SB, Ozbaki-Yagan N, Wacholder A, Iannotta J, Berger A, Wohlever ML, Carvunis AR, O'Donnell AF | bioRxiv : the preprint server for biology | 39257767 | bioRxiv | 2025 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/39257767 |
| Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases. | Black MH, Osinski A, Gradowski M, Servage KA, Pawłowski K, Tomchick DR, Tagliabracci VS | Science (New York, N.Y.) | 31123136 | Science | 2019 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/31123136 |
| Bacterial ubiquitin ligase engineered for small molecule and protein target identification. | Ye JS, Majumdar A, Park BC, Black MH, Hsieh TS, Osinski A, Servage KA, Kulkarni K, Naidoo J, Alto NM, Stratton MM, Alfandari D, Ready JM, Pawłowski K, Tomchick DR, Tagliabracci VS | bioRxiv : the preprint server for biology | 40166235 | bioRxiv | 2025 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/40166235 |
| Structural and mechanistic basis for protein glutamylation by the kinase fold. | Osinski A, Black MH, Pawłowski K, Chen Z, Li Y, Tagliabracci VS | Molecular cell | 34407442 | Mol Cell | 2021 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/34407442 |
| Methods for discovering catalytic activities for pseudokinases. | Black MH, Gradowski M, Pawłowski K, Tagliabracci VS | Methods in enzymology | 35525554 | Methods Enzymol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35525554 |
| The mechanism of RNA capping by SARS-CoV-2. | Park GJ, Osinski A, Hernandez G, Eitson JL, Majumdar A, Tonelli M, Henzler-Wildman K, Pawłowski K, Chen Z, Li Y, Schoggins JW, Tagliabracci VS | Research square | 35194601 | Res Sq | 2022 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/35194601 |
| A Legionella effector ADP-ribosyltransferase inactivates glutamate dehydrogenase. | Black MH, Osinski A, Park GJ, Gradowski M, Servage KA, Pawłowski K, Tagliabracci VS | The Journal of biological chemistry | 33476647 | J Biol Chem | 2021 Jan-Jun | https://www.ncbi.nlm.nih.gov/pubmed/33476647 |
| A Legionella effector kinase is activated by host inositol hexakisphosphate. | Sreelatha A, Nolan C, Park BC, Pawłowski K, Tomchick DR, Tagliabracci VS | The Journal of biological chemistry | 32229585 | J Biol Chem | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32229585 |
| Dynamic remodeling of host membranes by self-organizing bacterial effectors. | Hsieh TS, Lopez VA, Black MH, Osinski A, Pawłowski K, Tomchick DR, Liou J, Tagliabracci VS | Science (New York, N.Y.) | 33927055 | Science | 2021 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/33927055 |
| Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. | Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS | bioRxiv : the preprint server for biology | 38712170 | bioRxiv | 2024 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/38712170 |
| Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation. | Hu Y, Lopez VA, Xu H, Pfister JP, Song B, Servage KA, Sakurai M, Jones BT, Mendell JT, Wang T, Wu J, Lambowitz AM, Tomchick DR, Pawłowski K, Tagliabracci VS | Proceedings of the National Academy of Sciences of the United States of America | 39388274 | Proc Natl Acad Sci U S A | 2024 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/39388274 |
| Probing the signaling requirements for naive human pluripotency by high-throughput chemical screening. | Khan SA, Park KM, Fischer LA, Dong C, Lungjangwa T, Jimenez M, Casalena D, Chew B, Dietmann S, Auld DS, Jaenisch R, Theunissen TW | Cell reports | 34133938 | Cell Rep | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/34133938 |
| Derivation of trophoblast stem cells from naïve human pluripotent stem cells. | Dong C, Beltcheva M, Gontarz P, Zhang B, Popli P, Fischer LA, Khan SA, Park KM, Yoon EJ, Xing X, Kommagani R, Wang T, Solnica-Krezel L, Theunissen TW | eLife | 32048992 | Elife | 2020 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/32048992 |
| Modeling X-chromosome inactivation and reactivation during human development. | Khan SA, Theunissen TW | Current opinion in genetics & development | 37597506 | Curr Opin Genet Dev | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37597506 |
| Induction of Human Naïve Pluripotency Using 5i/L/A Medium. | Fischer LA, Khan SA, Theunissen TW | Methods in molecular biology (Clifton, N.J.) | 34870827 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34870827 |
| Tracking and mitigating imprint erasure during induction of naive human pluripotency at single-cell resolution. | Fischer LA, Meyer B, Reyes M, Zemke JE, Harrison JK, Park KM, Wang T, Jüppner H, Dietmann S, Theunissen TW | Stem cell reports | 39952244 | Stem Cell Reports | 2025 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/39952244 |
| Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens. | Karvas RM, Khan SA, Verma S, Yin Y, Kulkarni D, Dong C, Park KM, Chew B, Sane E, Fischer LA, Kumar D, Ma L, Boon ACM, Dietmann S, Mysorekar IU, Theunissen TW | Cell stem cell | 35523141 | Cell Stem Cell | 2022 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/35523141 |
| Generating Trophoblast Stem Cells from Human Naïve Pluripotent Stem Cells. | Dong C, Theunissen TW | Methods in molecular biology (Clifton, N.J.) | 34870832 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34870832 |
| OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human. | Huang X, Park KM, Gontarz P, Zhang B, Pan J, McKenzie Z, Fischer LA, Dong C, Dietmann S, Xing X, Shliaha PV, Yang J, Li D, Ding J, Lungjangwa T, Mitalipova M, Khan SA, Imsoonthornruksa S, Jensen N, Wang T, Kadoch C, Jaenisch R, Wang J, Theunissen TW | Nature communications | 34446700 | Nat Commun | 2021 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/34446700 |
| iPSC-based modeling of preeclampsia identifies epigenetic defects in extravillous trophoblast differentiation. | Morey R, Bui T, Cheung VC, Dong C, Zemke JE, Requena D, Arora H, Jackson MG, Pizzo D, Theunissen TW, Horii M | iScience | 38623329 | iScience | 2024 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/38623329 |
| SARS-CoV-2 ORF3a Protein Impairs Syncytiotrophoblast Maturation, Alters ZO-1 Localization, and Shifts Autophagic Pathways in Trophoblast Cells and 3D Organoids. | Kumar D, Karvas RM, Jones BR, McColl ER, Diveley E, Sukanta J, Surendra S, Kelly JC, Theunissen TW, Mysorekar IU | bioRxiv : the preprint server for biology | 39386577 | bioRxiv | 2024 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/39386577 |
| A genome-wide CRISPR-Cas9 knockout screen identifies essential and growth-restricting genes in human trophoblast stem cells. | Dong C, Fu S, Karvas RM, Chew B, Fischer LA, Xing X, Harrison JK, Popli P, Kommagani R, Wang T, Zhang B, Theunissen TW | Nature communications | 35538076 | Nat Commun | 2022 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/35538076 |
| Accessing the human trophoblast stem cell state from pluripotent and somatic cells. | Karvas RM, David L, Theunissen TW | Cellular and molecular life sciences : CMLS | 36434136 | Cell Mol Life Sci | 2022 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/36434136 |
| Generation of 3D Trophoblast Organoids from Human Naïve Pluripotent Stem Cells. | Karvas RM, Theunissen TW | Methods in molecular biology (Clifton, N.J.) | 37402094 | Methods Mol Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/37402094 |
| Recent insights into the naïve state of human pluripotency and its applications. | Dong C, Fischer LA, Theunissen TW | Experimental cell research | 31585117 | Exp Cell Res | 2019 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31585117 |
| Biomaterials to enhance stem cell transplantation. | Kharbikar BN, Mohindra P, Desai TA | Cell stem cell | 35483364 | Cell Stem Cell | 2022 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/35483364 |
| Modular control of l-tryptophan isotopic substitution via an efficient biosynthetic cascade. | Thompson CM, McDonald AD, Yang H, Cavagnero S, Buller AR | Organic & biomolecular chemistry | 32452506 | Org Biomol Chem | 2020 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/32452506 |
| Engineered Biocatalytic Synthesis of β-N-Substituted-α-Amino Acids. | Villalona J, Higgins PM, Buller AR | Angewandte Chemie (International ed. in English) | 37625129 | Angew Chem Int Ed Engl | 2023 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/37625129 |
| Biocatalytic asymmetric aldol addition into unactivated ketones. | Bruffy SK, Meza A, Soler J, Doyon TJ, Young SH, Lim J, Huseth KG, Willoughby PH, Garcia-Borràs M, Buller AR | Nature chemistry | 39333392 | Nat Chem | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39333392 |
| Occupational modulation in the (3+1)-dimensional incommensurate structure of (2S,3S)-2-amino-3-hydroxy-3-methyl-4-phenoxybutanoic acid dihydrate. | Sanders KM, Bruffy SK, Buller AR, Petříček V, Guzei IA | Acta crystallographica. Section C, Structural chemistry | 39115533 | Acta Crystallogr C Struct Chem | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/39115533 |
| Promiscuity Guided Evolution of Decarboxylative Aldolases for Synthesis of Tertiary γ-Hydroxy Amino Acids. | Campbell ME, Ohler AR, McGill MJ, Buller AR | Angewandte Chemie (International ed. in English) | 39874202 | Angew Chem Int Ed Engl | 2025 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/39874202 |
| Investigation of β-Substitution Activity of O-Acetylserine Sulfhydrolase from Citrullus vulgaris. | Smith JL, Harrison IM, Bingman CA, Buller AR | Chembiochem : a European journal of chemical biology | 35476889 | Chembiochem | 2022 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/35476889 |
| Efficient chemoenzymatic synthesis of α-aryl aldehydes as intermediates in C-C bond forming biocatalytic cascades. | Meza A, Campbell ME, Zmich A, Thein SA, Grieger AM, McGill MJ, Willoughby PH, Buller AR | ACS catalysis | 36420479 | ACS Catal | 2022 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/36420479 |
| Asymmetric Alkylation of Ketones Catalyzed by Engineered TrpB. | Watkins-Dulaney EJ, Dunham NP, Straathof S, Turi S, Arnold FH, Buller AR | Angewandte Chemie (International ed. in English) | 34269506 | Angew Chem Int Ed Engl | 2021 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/34269506 |
| Site-Selective Deuteration of Amino Acids through Dual-Protein Catalysis. | Doyon TJ, Buller AR | Journal of the American Chemical Society | 35416652 | J Am Chem Soc | 2022 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/35416652 |
| Substrate multiplexed protein engineering facilitates promiscuous biocatalytic synthesis. | McDonald AD, Higgins PM, Buller AR | Nature communications | 36068220 | Nat Commun | 2022 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/36068220 |
| Engineering Enzyme Substrate Scope Complementarity for Promiscuous Cascade Synthesis of 1,2-Amino Alcohols. | McDonald AD, Bruffy SK, Kasat AT, Buller AR | Angewandte Chemie (International ed. in English) | 36136093 | Angew Chem Int Ed Engl | 2022 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/36136093 |
| Biocatalytic synthesis of non-standard amino acids by a decarboxylative aldol reaction. | Ellis JM, Campbell ME, Kumar P, Geunes EP, Bingman CA, Buller AR | Nature catalysis | 35935533 | Nat Catal | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35935533 |
| Substrate-Multiplexed Assessment of Aromatic Prenyltransferase Activity. | Higgins PM, Wehrli NG, Buller AR | Chembiochem : a European journal of chemical biology | 39317170 | Chembiochem | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39317170 |
| Elucidation of the stereochemical mechanism of cystathionine γ-lyase reveals how substrate specificity constrains catalysis. | Zmich A, Perkins LJ, Bingman C, Buller AR | ACS catalysis | 39391268 | ACS Catal | 2024 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/39391268 |
| Scalable and Selective β-Hydroxy-α-Amino Acid Synthesis Catalyzed by Promiscuous l-Threonine Transaldolase ObiH. | Doyon TJ, Kumar P, Thein S, Kim M, Stitgen A, Grieger AM, Madigan C, Willoughby PH, Buller AR | Chembiochem : a European journal of chemical biology | 34699683 | Chembiochem | 2022 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/34699683 |
| l-Threonine Transaldolase Activity Is Enabled by a Persistent Catalytic Intermediate. | Kumar P, Meza A, Ellis JM, Carlson GA, Bingman CA, Buller AR | ACS chemical biology | 33337128 | ACS Chem Biol | 2021 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/33337128 |
| Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. | Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR | ACS catalysis | 37720819 | ACS Catal | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37720819 |
| CRISPR screen for rAAV production implicates genes associated with infection. | O'Driscoll EE, Arora S, Lang JF, Davidson BL, Shalem O | bioRxiv : the preprint server for biology | 39345423 | bioRxiv | 2024 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/39345423 |
| Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses. | Sansbury SE, Serebrenik YV, Lapidot T, Burslem GM, Shalem O | bioRxiv : the preprint server for biology | 37503003 | bioRxiv | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37503003 |
| CRISPR associated enzymes are mislocalized to the cytoplasm in iPSC-derived neurons resulting in KRAB-specific degradation. | Cajka G, Liu M, Shalem O | bioRxiv : the preprint server for biology | 39464063 | bioRxiv | 2024 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/39464063 |
| Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses. | Sansbury SE, Serebrenik YV, Lapidot T, Smith DG, Burslem GM, Shalem O | Molecular cell | 40273915 | Mol Cell | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40273915 |
| Efficient and flexible tagging of endogenous genes by homology-independent intron targeting. | Serebrenik YV, Sansbury SE, Kumar SS, Henao-Mejia J, Shalem O | Genome research | 31239279 | Genome Res | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31239279 |
| Pooled endogenous protein tagging and recruitment for scalable discovery of effectors for induced proximity therapeutics. | Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O | Research square | 37790450 | Res Sq | 2023 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/37790450 |
| Large-scale genetic screens identify BET-1 as a cytoskeleton regulator promoting actin function and life span. | Garcia G, Bar-Ziv R, Averbukh M, Dasgupta N, Dutta N, Zhang H, Fan W, Moaddeli D, Tsui CK, Castro Torres T, Alcala A, Moehle EA, Hoang S, Shalem O, Adams PD, Thorwald MA, Higuchi-Sanabria R | Aging cell | 36404134 | Aging Cell | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36404134 |
| High-throughput optimized prime editing mediated endogenous protein tagging for pooled imaging of protein localization. | Sanchez HM, Lapidot T, Shalem O | bioRxiv : the preprint server for biology | 39345511 | bioRxiv | 2024 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/39345511 |
| Intracellular Protein Editing to Enable Incorporation of Non-Canonical Residues into Endogenous Proteins. | Beyer JN, Serebrenik YV, Toy K, Najar MA, Raniszewski NR, Shalem O, Burslem GM | bioRxiv : the preprint server for biology | 39026884 | bioRxiv | 2024 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/39026884 |
| Pooled endogenous protein tagging and recruitment for systematic profiling of protein function. | Serebrenik YV, Mani D, Maujean T, Burslem GM, Shalem O | Cell genomics | 39255790 | Cell Genom | 2024 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/39255790 |
| Impaired ribosome-associated quality control of C9orf72 arginine-rich dipeptide-repeat proteins. | Viera Ortiz AP, Cajka G, Olatunji OA, Mikytuck B, Shalem O, Lee EB | Brain : a journal of neurology | 36516294 | Brain | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/36516294 |
| CRISPR screen for protein inclusion formation uncovers a role for SRRD in the regulation of intermediate filament dynamics and aggresome assembly. | Sweeney KM, Chantarawong S, Barbieri EM, Cajka G, Liu M, Spruce L, Fazelinia H, Portz B, Copley K, Lapidot T, Duhamel L, Greenwald P, Saida N, Shalgi R, Shorter J, Shalem O | PLoS genetics | 38315730 | PLoS Genet | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38315730 |
| Structural insights into metazoan pretargeting GET complexes. | Keszei AFA, Yip MCJ, Hsieh TC, Shao S | Nature structural & molecular biology | 34887561 | Nat Struct Mol Biol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34887561 |
| Mechanism of client selection by the protein quality-control factor UBE2O. | Yip MCJ, Sedor SF, Shao S | Nature structural & molecular biology | 35915257 | Nat Struct Mol Biol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35915257 |
| Detecting and Rescuing Stalled Ribosomes. | Yip MCJ, Shao S | Trends in biochemical sciences | 33966939 | Trends Biochem Sci | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33966939 |
| The endoplasmic reticulum P5A-ATPase is a transmembrane helix dislocase. | McKenna MJ, Sim SI, Ordureau A, Wei L, Harper JW, Shao S, Park E | Science (New York, N.Y.) | 32973005 | Science | 2020 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/32973005 |
| ELAC1 Repairs tRNAs Cleaved during Ribosome-Associated Quality Control. | Yip MCJ, Savickas S, Gygi SP, Shao S | Cell reports | 32075755 | Cell Rep | 2020 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/32075755 |
| ATP13A1 prevents ERAD of folding-competent mislocalized and misoriented proteins. | McKenna MJ, Adams BM, Chu V, Paulo JA, Shao S | Molecular cell | 36283413 | Mol Cell | 2022 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/36283413 |
| Selective destabilization of polypeptides synthesized from NMD-targeted transcripts. | Chu V, Feng Q, Lim Y, Shao S | Molecular biology of the cell | 34586879 | Mol Biol Cell | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/34586879 |
| Mechanism of ASF1 Inhibition by CDAN1. | Sedor SF, Shao S | bioRxiv : the preprint server for biology | 39149339 | bioRxiv | 2024 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/39149339 |
| Discovery of C13-Aminobenzoyl Cycloheximide Derivatives that Potently Inhibit Translation Elongation. | Koga Y, Hoang EM, Park Y, Keszei AFA, Murray J, Shao S, Liau BB | Journal of the American Chemical Society | 34403584 | J Am Chem Soc | 2021 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/34403584 |
| The Endoplasmic Reticulum and the Fidelity of Nascent Protein Localization. | McKenna MJ, Shao S | Cold Spring Harbor perspectives in biology | 36041782 | Cold Spring Harb Perspect Biol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36041782 |
| The eRF1 degrader SRI-41315 acts as a molecular glue at the ribosomal decoding center. | Coelho JPL, Yip MCJ, Oltion K, Taunton J, Shao S | Nature chemical biology | 38172604 | Nat Chem Biol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38172604 |
| Mechanism of ASF1 engagement by CDAN1. | Sedor SF, Shao S | Nature communications | 40091041 | Nat Commun | 2025 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/40091041 |
| Multiplexed imaging of nucleome architectures in single cells of mammalian tissue. | Liu M, Lu Y, Yang B, Chen Y, Radda JSD, Hu M, Katz SG, Wang S | Nature communications | 32518300 | Nat Commun | 2020 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/32518300 |
| Regulation of gene editing using T-DNA concatenation. | Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y | Nature plants | 37653336 | Nat Plants | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37653336 |
| An integrated platform for high-throughput nanoscopy. | Barentine AES, Lin Y, Courvan EM, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace MR, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer KM, Bewersdorf J, Baddeley D | Nature biotechnology | 36914886 | Nat Biotechnol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36914886 |
| Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery. | Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Townsend JP, Muzumdar MD, Wang S | bioRxiv : the preprint server for biology | 37546882 | bioRxiv | 2024 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/37546882 |
| Cotranslational molecular condensation of cochaperones and assembly factors facilitates axonemal dynein biogenesis. | Li Y, Xu W, Cheng Y, Djenoune L, Zhuang C, Cox AL, Britto CJ, Yuan S, Wang S, Sun Z | Proceedings of the National Academy of Sciences of the United States of America | 39541357 | Proc Natl Acad Sci U S A | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39541357 |
| New mechanism of chromatin compartmentalization by BRD2. | Cheng Y, Wang S | Trends in genetics : TIG | 35811175 | Trends Genet | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35811175 |
| TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations. | Cheng Y, Liu M, Hu M, Wang S | Genome biology | 34749781 | Genome Biol | 2021 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/34749781 |
| Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue. | Liu M, Yang B, Hu M, Radda JSD, Chen Y, Jin S, Cheng Y, Wang S | Nature protocols | 33903756 | Nat Protoc | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33903756 |
| Induction of T-DNA amplification by retrotransposon-derived sequences. | Dickinson L, Yuan W, LeBlanc C, Thomson G, Wang S, Jacob Y | bioRxiv : the preprint server for biology | 36945545 | bioRxiv | 2023 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/36945545 |
| Female naïve human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations. | Patterson B, Yang B, Tanaka Y, Kim KY, Cakir B, Xiang Y, Kim J, Wang S, Park IH | Science advances | 37540754 | Sci Adv | 2023 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/37540754 |
| Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome. | Wang SE, Cheng Y, Lim J, Jang MA, Forrest EN, Kim Y, Donahue M, Qiao SN, Xiong Y, Jin J, Wang S, Jiang YH | Research square | 39011107 | Res Sq | 2024 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/39011107 |
| Chromatin Tracing: Imaging 3D Genome and Nucleome. | Hu M, Wang S | Trends in cell biology | 33191055 | Trends Cell Biol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33191055 |
| Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos. | Sawh AN, Shafer MER, Su JH, Zhuang X, Wang S, Mango SE | Molecular cell | 32105612 | Mol Cell | 2020 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/32105612 |
| Sequencing-free whole genome spatial transcriptomics at molecular resolution in intact tissue. | Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S | bioRxiv : the preprint server for biology | 40161724 | bioRxiv | 2025 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/40161724 |
| Perturb-tracing enables high-content screening of multi-scale 3D genome regulators. | Cheng Y, Hu M, Yang B, Jensen TB, Zhang Y, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S | Nature methods | 40211002 | Nat Methods | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40211002 |
| Perturb-tracing enables high-content screening of multiscale 3D genome regulators. | Cheng Y, Hu M, Yang B, Jensen TB, Yang T, Yu R, Ma Z, Radda JSD, Jin S, Zang C, Wang S | bioRxiv : the preprint server for biology | 36778402 | bioRxiv | 2023 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/36778402 |
| G3BP1 ribonucleoprotein complexes regulate focal adhesion protein mobility and cell migration. | Boraas LC, Hu M, Martino P, Thornton L, Vejnar CE, Zhen G, Zeng L, Parker DM, Cox AL, Giraldez AJ, Su X, Mayr C, Wang S, Nicoli S | Cell reports | 39883578 | Cell Rep | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39883578 |
| Chemical Gradients of Plant Substrates in an Atta texana Fungus Garden. | Caraballo-Rodríguez AM, Puckett SP, Kyle KE, Petras D, da Silva R, Nothias LF, Ernst M, van der Hooft JJJ, Tripathi A, Wang M, Balunas MJ, Klassen JL, Dorrestein PC | mSystems | 34342533 | mSystems | 2021 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/34342533 |
| Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. | Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H | Nature communications | 34050176 | Nat Commun | 2021 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/34050176 |
| A Metabolome- and Metagenome-Wide Association Network Reveals Microbial Natural Products and Microbial Biotransformation Products from the Human Microbiota. | Cao L, Shcherbin E, Mohimani H | mSystems | 31455639 | mSystems | 2019 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/31455639 |
| De Novo Peptide Sequencing Reveals Many Cyclopeptides in the Human Gut and Other Environments. | Behsaz B, Mohimani H, Gurevich A, Prjibelski A, Fisher M, Vargas F, Smarr L, Dorrestein PC, Mylne JS, Pevzner PA | Cell systems | 31864964 | Cell Syst | 2020 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/31864964 |
| MS2Planner: improved fragmentation spectra coverage in untargeted mass spectrometry by iterative optimized data acquisition. | Zuo Z, Cao L, Nothia LF, Mohimani H | Bioinformatics (Oxford, England) | 34252948 | Bioinformatics | 2021 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/34252948 |
| MolDiscovery: learning mass spectrometry fragmentation of small molecules. | Cao L, Guler M, Tagirdzhanov A, Lee YY, Gurevich A, Mohimani H | Nature communications | 34140479 | Nat Commun | 2021 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/34140479 |
| Feature-based molecular networking in the GNPS analysis environment. | Nothias LF, Petras D, Schmid R, Dührkop K, Rainer J, Sarvepalli A, Protsyuk I, Ernst M, Tsugawa H, Fleischauer M, Aicheler F, Aksenov AA, Alka O, Allard PM, Barsch A, Cachet X, Caraballo-Rodriguez AM, Da Silva RR, Dang T, Garg N, Gauglitz JM, Gurevich A, Isaac G, Jarmusch AK, Kameník Z, Kang KB, Kessler N, Koester I, Korf A, Le Gouellec A, Ludwig M, Martin H C, McCall LI, McSayles J, Meyer SW, Mohimani H, Morsy M, Moyne O, Neumann S, Neuweger H, Nguyen NH, Nothias-Esposito M, Paolini J, Phelan VV, Pluskal T, Quinn RA, Rogers S, Shrestha B, Tripathi A, van der Hooft JJJ, Vargas F, Weldon KC, Witting M, Yang H, Zhang Z, Zubeil F, Kohlbacher O, Böcker S, Alexandrov T, Bandeira N, Wang M, Dorrestein PC | Nature methods | 32839597 | Nat Methods | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32839597 |
| An interpretable machine learning approach to identify mechanism of action of antibiotics. | Mongia M, Guler M, Mohimani H | Scientific reports | 35725893 | Sci Rep | 2022 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/35725893 |
| A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. | Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC | Research square | 37577622 | Res Sq | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37577622 |
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| Bacillus subtilis biofilm matrix components target seed oil bodies to promote growth and anti-fungal resistance in melon. | Berlanga-Clavero MV, Molina-Santiago C, Caraballo-Rodríguez AM, Petras D, Díaz-Martínez L, Pérez-García A, de Vicente A, Carrión VJ, Dorrestein PC, Romero D | Nature microbiology | 35668112 | Nat Microbiol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35668112 |
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| A TAle of Two Pathways: Tail-Anchored Protein Insertion at the Endoplasmic Reticulum. | Guna A, Hazu M, Pinton Tomaleri G, Voorhees RM | Cold Spring Harbor perspectives in biology | 36041783 | Cold Spring Harb Perspect Biol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36041783 |
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| A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. | Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM | bioRxiv : the preprint server for biology | 36711738 | bioRxiv | 2023 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/36711738 |
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| A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. | Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM | BMC genomics | 37904134 | BMC Genomics | 2023 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/37904134 |
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| Differential Modes of Orphan Subunit Recognition for the WRB/CAML Complex. | Inglis AJ, Page KR, Guna A, Voorhees RM | Cell reports | 32187542 | Cell Rep | 2020 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/32187542 |
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| Deep learning enables fast and dense single-molecule localization with high accuracy. | Speiser A, Müller LR, Hoess P, Matti U, Obara CJ, Legant WR, Kreshuk A, Macke JH, Ries J, Turaga SC | Nature methods | 34480155 | Nat Methods | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34480155 |
| u-track3D: Measuring, navigating, and validating dense particle trajectories in three dimensions. | Roudot P, Legant WR, Zou Q, Dean KM, Isogai T, Welf ES, David AF, Gerlich DW, Fiolka R, Betzig E, Danuser G | Cell reports methods | 38042149 | Cell Rep Methods | 2023 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/38042149 |
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| A multi-functional microfluidic device compatible with widefield and light sheet microscopy. | Moore RP, O'Shaughnessy EC, Shi Y, Nogueira AT, Heath KM, Hahn KM, Legant WR | Lab on a chip | 34859808 | Lab Chip | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34859808 |
| Posterior approach to correct for focal plane offsets in lattice light-sheet structured illumination microscopy. | Shi Y, Daugird TA, Legant WR | Journal of biomedical optics | 39086928 | J Biomed Opt | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39086928 |
| Smart lattice light-sheet microscopy for imaging rare and complex cellular events. | Shi Y, Tabet JS, Milkie DE, Daugird TA, Yang CQ, Ritter AT, Giovannucci A, Legant WR | Nature methods | 38167656 | Nat Methods | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38167656 |
| Shared and redundant proteins coordinate signal cross-talk between MAPK pathways in yeast. | Zhang S, Wang H, Sipko EL, Li S, Daugird TA, Legant WR, Dohlman HG | Molecular biology of the cell | 39083355 | Mol Biol Cell | 2024 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/39083355 |
| A quantitative analysis of various patterns applied in lattice light sheet microscopy. | Shi Y, Daugird TA, Legant WR | Nature communications | 35941165 | Nat Commun | 2022 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/35941165 |
| Correlative single molecule lattice light sheet imaging reveals the dynamic relationship between nucleosomes and the local chromatin environment. | Daugird TA, Shi Y, Holland KL, Rostamian H, Liu Z, Lavis LD, Rodriguez J, Strahl BD, Legant WR | Nature communications | 38755200 | Nat Commun | 2024 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/38755200 |
| Phase separation drives aberrant chromatin looping and cancer development. | Ahn JH, Davis ES, Daugird TA, Zhao S, Quiroga IY, Uryu H, Li J, Storey AJ, Tsai YH, Keeley DP, Mackintosh SG, Edmondson RD, Byrum SD, Cai L, Tackett AJ, Zheng D, Legant WR, Phanstiel DH, Wang GG | Nature | 34163069 | Nature | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34163069 |
| Superresolution microscopy reveals actomyosin dynamics in medioapical arrays. | Moore RP, Fogerson SM, Tulu US, Yu JW, Cox AH, Sican MA, Li D, Legant WR, Weigel AV, Crawford JM, Betzig E, Kiehart DP | Molecular biology of the cell | 35544300 | Mol Biol Cell | 2022 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/35544300 |
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| Bacterial amylases enable glycogen degradation by the vaginal microbiome. | Jenkins DJ, Woolston BM, Hood-Pishchany MI, Pelayo P, Konopaski AN, Quinn Peters M, France MT, Ravel J, Mitchell CM, Rakoff-Nahoum S, Whidbey C, Balskus EP | Nature microbiology | 37563289 | Nat Microbiol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37563289 |
| RELMβ sets the threshold for microbiome-dependent oral tolerance. | Stephen-Victor E, Kuziel GA, Martinez-Blanco M, Jugder BE, Benamar M, Wang Z, Chen Q, Lozano GL, Abdel-Gadir A, Cui Y, Fong J, Saint-Denis E, Chang I, Nadeau KC, Phipatanakul W, Zhang A, Farraj FA, Holder-Niles F, Zeve D, Breault DT, Schmitz-Abe K, Rachid R, Crestani E, Rakoff-Nahoum S, Chatila TA | Nature | 39843735 | Nature | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39843735 |
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| Saturation transposon mutagenesis enables genome-wide identification of genes required for growth and fluconazole resistance in the human fungal pathogen Cryptococcus neoformans. | Billmyre RB, Craig CJ, Lyon J, Reichardt C, Eickbush MT, Zanders SE | bioRxiv : the preprint server for biology | 39131341 | bioRxiv | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39131341 |
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| Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression. | Campbell AE, Dyle MC, Albanese R, Matheny T, Sudheendran K, Cortázar MA, Forman T, Fu R, Gillen AE, Caruthers MH, Floor SN, Calviello L, Jagannathan S | Cell reports | 37314931 | Cell Rep | 2023 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/37314931 |
| A Legionella toxin exhibits tRNA mimicry and glycosyl transferase activity to target the translation machinery and trigger a ribotoxic stress response. | Subramanian A, Wang L, Moss T, Voorhies M, Sangwan S, Stevenson E, Pulido EH, Kwok S, Chalkley RJ, Li KH, Krogan NJ, Swaney DL, Burlingame AL, Floor SN, Sil A, Walter P, Mukherjee S | Nature cell biology | 37857833 | Nat Cell Biol | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37857833 |
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| DDX3 depletion represses translation of mRNAs with complex 5' UTRs. | Calviello L, Venkataramanan S, Rogowski KJ, Wyler E, Wilkins K, Tejura M, Thai B, Krol J, Filipowicz W, Landthaler M, Floor SN | Nucleic acids research | 33905506 | Nucleic Acids Res | 2021 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/33905506 |
| Control of ribosomal protein synthesis by the Microprocessor complex. | Jiang X, Prabhakar A, Van der Voorn SM, Ghatpande P, Celona B, Venkataramanan S, Calviello L, Lin C, Wang W, Black BL, Floor SN, Lagna G, Hata A | Science signaling | 33622983 | Sci Signal | 2021 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/33622983 |
| Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model. | Hoye ML, Calviello L, Poff AJ, Ejimogu NE, Newman CR, Montgomery MD, Ou J, Floor SN, Silver DL | eLife | 35762573 | Elife | 2022 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/35762573 |
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| Functionalizing DNA nanostructures for therapeutic applications. | Henry SJW, Stephanopoulos N | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 34008347 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34008347 |
| Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures. | Narayanan RP, Procyk J, Nandi P, Prasad A, Xu Y, Poppleton E, Williams D, Zhang F, Yan H, Chiu PL, Stephanopoulos N, Šulc P | ACS nano | 35980981 | ACS Nano | 2022 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/35980981 |
| Calcium-triggered DNA-mediated membrane fusion in synthetic cells. | Hsu YY, Chen SJ, Bernal-Chanchavac J, Sharma B, Moghimianavval H, Stephanopoulos N, Liu AP | Chemical communications (Cambridge, England) | 37365952 | Chem Commun (Camb) | 2023 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/37365952 |
| Construction of Reconfigurable and Polymorphic DNA Origami Assemblies with Coiled-Coil Patches and Patterns. | Teng T, Bernal-Chanchavac J, Stephanopoulos N, Castro CE | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 38459678 | Adv Sci (Weinh) | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38459678 |
| The interactions between DNA nanostructures and cells: A critical overview from a cell biology perspective. | Frtús A, Smolková B, Uzhytchak M, Lunova M, Jirsa M, Henry SJW, Dejneka A, Stephanopoulos N, Lunov O | Acta biomaterialia | 35523414 | Acta Biomater | 2022 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/35523414 |
| Calcium-triggered DNA-mediated membrane fusion in synthetic cells. | Hsu YY, Chen SJ, Bernal-Chanchavac J, Sharma B, Moghimianavval H, Stephanopoulos N, Liu AP | bioRxiv : the preprint server for biology | 37205334 | bioRxiv | 2023 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/37205334 |
| Bioactive Fibronectin-III(10)-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. | Buchberger A, Riker K, Bernal-Chanchavac J, Narayanan RP, Simmons CR, Fahmi NE, Freeman R, Stephanopoulos N | ACS applied bio materials | 36108278 | ACS Appl Bio Mater | 2022 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/36108278 |
| Nanoscale Structures and Materials from the Self-assembly of Polypeptides and DNA. | Bernal-Chanchavac J, Al-Amin M, Stephanopoulos N | Current topics in medicinal chemistry | 34911426 | Curr Top Med Chem | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34911426 |
| Site-Specific Arrangement and Structure Determination of Minor Groove Binding Molecules in Self-Assembled Three-Dimensional DNA Crystals. | Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H | Journal of the American Chemical Society | 37987645 | J Am Chem Soc | 2023 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/37987645 |
| Site-specific arrangement and structure determination of minor groove binding molecules in self-assembled three-dimensional DNA crystals. | Simmons CR, Buchberger A, Henry SJW, Novacek A, Fahmi NE, MacCulloch T, Stephanopoulos N, Yan H | bioRxiv : the preprint server for biology | 37873139 | bioRxiv | 2023 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/37873139 |
| Construction and reconfiguration of dynamic DNA origami assemblies with coiled-coil patches and patterns. | Teng T, Bernal-Chanchavac J, Stephanopoulos N, Castro CE | bioRxiv : the preprint server for biology | 37790447 | bioRxiv | 2023 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/37790447 |
| DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes. | Lu Q, Xu Y, Poppleton E, Zhou K, Sulc P, Stephanopoulos N, Ke Y | Nano letters | 38278134 | Nano Lett | 2024 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/38278134 |
| Geometrically constrained cytoskeletal reorganisation modulates DNA nanostructures uptake. | Elblová P, Andělová H, Lunova M, Anthi J, Henry SJW, Tu X, Dejneka A, Jirsa M, Stephanopoulos N, Lunov O | Journal of materials chemistry. B | 39835937 | J Mater Chem B | 2025 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/39835937 |
| Structure-based discovery of hydrocarbon-stapled paxillin peptides that block FAK scaffolding in cancer. | Reyes L, Naser L, Weiner WS, Thifault D, Stahl E, McCreary L, Nott R, Quick C, Buchberger A, Alvarado C, Rivera A, Miller JA, Khatiwala R, Cherry BR, Nelson R, Martin-Garcia JM, Stephanopoulos N, Fromme R, Fromme P, Cance W, Marlowe T | Nature communications | 40021642 | Nat Commun | 2025 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/40021642 |
| Peptide-coated DNA nanostructures as a platform for control of lysosomal function in cells. | Elblová P, Lunova M, Henry SJW, Tu X, Calé A, Dejneka A, Havelková J, Petrenko Y, Jirsa M, Stephanopoulos N, Lunov O | Chemical engineering journal (Lausanne, Switzerland : 1996) | 39372137 | Chem Eng J | 2024 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/39372137 |
| Protein Corona Inhibits Endosomal Escape of Functionalized DNA Nanostructures in Living Cells. | Smolková B, MacCulloch T, Rockwood TF, Liu M, Henry SJW, Frtús A, Uzhytchak M, Lunova M, Hof M, Jurkiewicz P, Dejneka A, Stephanopoulos N, Lunov O | ACS applied materials & interfaces | 34569777 | ACS Appl Mater Interfaces | 2021 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/34569777 |
| Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules. | MacCulloch T, Novacek A, Stephanopoulos N | Chemical communications (Cambridge, England) | 35260875 | Chem Commun (Camb) | 2022 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/35260875 |
| Self-Assembly of Hybrid Peptide-DNA Nanostructures using Homotrimeric Coiled-Coil/Nucleic Acid Building Blocks. | Buchberger A, Al-Amin M, Simmons CR, Stephanopoulos N | Chembiochem : a European journal of chemical biology | 37099451 | Chembiochem | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37099451 |
| High-Affinity Host-Guest Recognition for Efficient Assembly and Enzymatic Responsiveness of DNA Nanostructures. | Narayanan RP, Prasad A, Buchberger A, Zou L, Bernal-Chanchavac J, MacCulloch T, Fahmi NE, Yan H, Zhang F, Webber MJ, Stephanopoulos N | Small (Weinheim an der Bergstrasse, Germany) | 37849034 | Small | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/37849034 |
| Using dynamic biomaterials to study the temporal role of bioactive peptides during osteogenesis. | Fumasi FM, MacCulloch T, Bernal-Chanchavac J, Stephanopoulos N, Holloway JL | Biomaterials advances | 38096646 | Biomater Adv | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38096646 |
| CytoDirect: A Nucleic Acid Nanodevice for Specific and Efficient Delivery of Functional Payloads to the Cytoplasm. | Yu L, Xu Y, Al-Amin M, Jiang S, Sample M, Prasad A, Stephanopoulos N, Šulc P, Yan H | Journal of the American Chemical Society | 38055928 | J Am Chem Soc | 2023 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/38055928 |
| Systematic generation and imaging of tandem repeats reveal base-pairing properties that promote RNA aggregation. | Isiktas AU, Eshov A, Yang S, Guo JU | Cell reports methods | 36452875 | Cell Rep Methods | 2022 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/36452875 |
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| Restriction of SARS-CoV-2 Replication by Targeting Programmed -1 Ribosomal Frameshifting In Vitro. | Sun Y, Abriola L, Surovtseva YV, Lindenbach BD, Guo JU | bioRxiv : the preprint server for biology | 33106809 | bioRxiv | 2020 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/33106809 |
| Restriction of SARS-CoV-2 replication by targeting programmed -1 ribosomal frameshifting. | Sun Y, Abriola L, Niederer RO, Pedersen SF, Alfajaro MM, Silva Monteiro V, Wilen CB, Ho YC, Gilbert WV, Surovtseva YV, Lindenbach BD, Guo JU | Proceedings of the National Academy of Sciences of the United States of America | 34185680 | Proc Natl Acad Sci U S A | 2021 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/34185680 |
| Stress promotes RNA G-quadruplex folding in human cells. | Kharel P, Fay M, Manasova EV, Anderson PJ, Kurkin AV, Guo JU, Ivanov P | Nature communications | 36639366 | Nat Commun | 2023 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/36639366 |
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| Aberrant splicing exonizes C9ORF72 repeat expansion in ALS/FTD. | Yang S, Wijegunawardana D, Sheth U, Veire AM, Salgado JMS, Agrawal M, Zhou J, Pereira JD, Gendron TF, Guo JU | bioRxiv : the preprint server for biology | 38014069 | bioRxiv | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/38014069 |
| A Neuropeptide Signaling Network That Regulates Developmental Timing and Systemic Growth in Drosophila. | Ohhara Y, Blick M, Park D, Yoon SE, Kim YJ, Pankratz MJ, O'Connor MB, Yamanaka N | The Journal of comparative neurology | 39415613 | J Comp Neurol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39415613 |
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| Internal sensory neurons regulate stage-specific growth in Drosophila. | Ohhara Y, Yamanaka N | Development (Cambridge, England) | 36227580 | Development | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36227580 |
| Essential functions of mosquito ecdysone importers in development and reproduction. | Hun LV, Okamoto N, Imura E, Maxson R, Bittar R, Yamanaka N | Proceedings of the National Academy of Sciences of the United States of America | 35696563 | Proc Natl Acad Sci U S A | 2022 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/35696563 |
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| Large-scale discovery of chromatin dysregulation induced by oncofusions and other protein-coding variants. | Frenkel M, Corban JE, Hujoel MLA, Morris Z, Raman S | Nature biotechnology | 39048711 | Nat Biotechnol | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/39048711 |
| A parametrized two-domain thermodynamic model explains diverse mutational effects on protein allostery. | Liu Z, Gillis T, Raman S, Cui Q | bioRxiv : the preprint server for biology | 37662419 | bioRxiv | 2024 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/37662419 |
| Discovering chromatin dysregulation induced by protein-coding perturbations at scale. | Frenkel M, Hujoel MLA, Morris Z, Raman S | bioRxiv : the preprint server for biology | 37781603 | bioRxiv | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37781603 |
| Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors. | Meger AT, Spence MA, Sandhu M, Matthews D, Chen J, Jackson CJ, Raman S | Cell systems | 38537640 | Cell Syst | 2024 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/38537640 |
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| De novo design of programmable inducible promoters. | Liu X, Gupta STP, Bhimsaria D, Reed JL, Rodríguez-Martínez JA, Ansari AZ, Raman S | Nucleic acids research | 31552424 | Nucleic Acids Res | 2019 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/31552424 |
| Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins. | Leander M, Liu Z, Cui Q, Raman S | eLife | 36226916 | Elife | 2022 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/36226916 |
| Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis. | Tian R, Abarientos A, Hong J, Hashemi SH, Yan R, Dräger N, Leng K, Nalls MA, Singleton AB, Xu K, Faghri F, Kampmann M | Nature neuroscience | 34031600 | Nat Neurosci | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34031600 |
| Single-Molecule Displacement Mapping Indicates Unhindered Intracellular Diffusion of Small (≲1 kDa) Solutes. | Choi AA, Xiang L, Li W, Xu K | Journal of the American Chemical Society | 37027457 | J Am Chem Soc | 2023 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/37027457 |
| Single-Molecule Displacement Mapping Unveils Sign-Asymmetric Protein Charge Effects on Intraorganellar Diffusion. | Xiang L, Yan R, Chen K, Li W, Xu K | Nano letters | 36802676 | Nano Lett | 2023 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/36802676 |
| The endoplasmic reticulum adopts two distinct tubule forms. | Wang B, Zhao Z, Xiong M, Yan R, Xu K | Proceedings of the National Academy of Sciences of the United States of America | 35471903 | Proc Natl Acad Sci U S A | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35471903 |
| Displacement Statistics of Unhindered Single Molecules Show no Enhanced Diffusion in Enzymatic Reactions. | Choi AA, Park HH, Chen K, Yan R, Li W, Xu K | Journal of the American Chemical Society | 35258969 | J Am Chem Soc | 2022 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/35258969 |
| SURF4-induced tubular ERGIC selectively expedites ER-to-Golgi transport. | Yan R, Chen K, Wang B, Xu K | Developmental cell | 35051356 | Dev Cell | 2022 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/35051356 |
| Multidimensional super-resolution microscopy unveils nanoscale surface aggregates in the aging of FUS condensates. | He C, Wu CY, Li W, Xu K | bioRxiv : the preprint server for biology | 37503034 | bioRxiv | 2023 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/37503034 |
| Graphene-Enabled, Spatially Controlled Electroporation of Adherent Cells for Live-Cell Super-resolution Microscopy. | Moon S, Li W, Hauser M, Xu K | ACS nano | 32282180 | ACS Nano | 2020 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/32282180 |
| Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. | Xiang L, Chen K, Xu K | ACS nano | 34304562 | ACS Nano | 2021 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/34304562 |
| Vertebrate cells differentially interpret ciliary and extraciliary cAMP. | Truong ME, Bilekova S, Choksi SP, Li W, Bugaj LJ, Xu K, Reiter JF | Cell | 33932338 | Cell | 2021 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/33932338 |
| Branched actin networks are organized for asymmetric force production during clathrin-mediated endocytosis in mammalian cells. | Jin M, Shirazinejad C, Wang B, Yan A, Schöneberg J, Upadhyayula S, Xu K, Drubin DG | Nature communications | 35732852 | Nat Commun | 2022 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/35732852 |
| Single-molecule displacement mapping unveils nanoscale heterogeneities in intracellular diffusivity. | Xiang L, Chen K, Yan R, Li W, Xu K | Nature methods | 32203387 | Nat Methods | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32203387 |
| Probing Nanoscale Diffusional Heterogeneities in Cellular Membranes through Multidimensional Single-Molecule and Super-Resolution Microscopy. | Yan R, Chen K, Xu K | Journal of the American Chemical Society | 33084318 | J Am Chem Soc | 2020 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/33084318 |
| Excitation spectral microscopy for highly multiplexed fluorescence imaging and quantitative biosensing. | Chen K, Yan R, Xiang L, Xu K | Light, science & applications | 33963178 | Light Sci Appl | 2021 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/33963178 |
| Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. | He C, Wu CY, Li W, Xu K | Journal of the American Chemical Society | 37782826 | J Am Chem Soc | 2023 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/37782826 |
| Super-multiplexing excitation spectral microscopy with multiple fluorescence bands. | Chen K, Li W, Xu K | Biomedical optics express | 36733753 | Biomed Opt Express | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36733753 |
| Single-Molecule Spectroscopy and Super-Resolution Mapping of Physicochemical Parameters in Living Cells. | Steves MA, He C, Xu K | Annual review of physical chemistry | 38360526 | Annu Rev Phys Chem | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38360526 |
| Carborane Guests for Cucurbit[7]uril Facilitate Strong Binding and On-Demand Removal. | Kataki-Anastasakou A, Axtell JC, Hernandez S, Dziedzic RM, Balaich GJ, Rheingold AL, Spokoyny AM, Sletten EM | Journal of the American Chemical Society | 33253553 | J Am Chem Soc | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33253553 |
| Expanding the Scope of Palladium-Catalyzed B - N Cross-Coupling Chemistry in Carboranes. | Mu X, Hopp M, Dziedzic RM, Waddington MA, Rheingold AL, Sletten EM, Axtell JC, Spokoyny AM | Organometallics | 34012188 | Organometallics | 2020 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/34012188 |
| Cell-surface Labeling via Bioorthogonal Host-Guest Chemistry. | Kataki-Anastasakou A, Hernandez S, Sletten EM | ACS chemical biology | 34669367 | ACS Chem Biol | 2021 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/34669367 |
| Arene-Perfluoroarene Interactions in Solution. | Lee GY, Hu E, Rheingold AL, Houk KN, Sletten EM | The Journal of organic chemistry | 34077211 | J Org Chem | 2021 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/34077211 |
| Bioorthogonal chemistry: Bridging chemistry, biology, and medicine. | Hartung KM, Sletten EM | Chem | 39006002 | Chem | 2023 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/39006002 |
| A Fluorescent Unnatural Mannosamine Derivative with Enhanced Emission Upon Complexation with Cucurbit[7]uril. | Kataki-Anastasakou A, Jia S, Axtell JC, Sletten EM | Israel journal of chemistry | 37636996 | Isr J Chem | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37636996 |
| Digital Assembly of Colloidal Particles for Nanoscale Manufacturing. | Kotnala A, Zheng Y | Particle & particle systems characterization : measurement and description of particle properties and behavior in powders and other disperse systems | 33041521 | Part Part Syst Charact | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33041521 |
| Optothermally Assembled Nanostructures. | Li J, Zheng Y | Accounts of materials research | 34396151 | Acc Mater Res | 2021 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/34396151 |
| Liquid Optothermoelectrics: Fundamentals and Applications. | Chen Z, Kollipara PS, Ding H, Pughazhendi A, Zheng Y | Langmuir : the ACS journal of surfaces and colloids | 33410698 | Langmuir | 2021 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/33410698 |
| Directional Modulation of Exciton Emission Using Single Dielectric Nanospheres. | Fang J, Wang M, Yao K, Zhang T, Krasnok A, Jiang T, Choi J, Kahn E, Korgel BA, Terrones M, Li X, Alù A, Zheng Y | Advanced materials (Deerfield Beach, Fla.) | 33837615 | Adv Mater | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33837615 |
| Tunable Chiral Optics in All-Solid-Phase Reconfigurable Dielectric Nanostructures. | Li J, Wang M, Wu Z, Li H, Hu G, Jiang T, Guo J, Liu Y, Yao K, Chen Z, Fang J, Fan D, Korgel BA, Alù A, Zheng Y | Nano letters | 33372805 | Nano Lett | 2021 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/33372805 |
| All-optical reconfigurable chiral meta-molecules. | Lin L, Lepeshov S, Krasnok A, Jiang T, Peng X, Korgel BA, Alù A, Zheng Y | Materials today (Kidlington, England) | 31777449 | Mater Today (Kidlington) | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31777449 |
| Optothermophoretic Manipulation of Colloidal Particles in Nonionic Liquids. | Peng X, Lin L, Hill EH, Kunal P, Humphrey SM, Zheng Y | The journal of physical chemistry. C, Nanomaterials and interfaces | 30766650 | J Phys Chem C Nanomater Interfaces | 2018 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/30766650 |
| Enhancing Surface Capture and Sensing of Proteins with Low-Power Optothermal Bubbles in a Biphasic Liquid. | Kim Y, Ding H, Zheng Y | Nano letters | 32667815 | Nano Lett | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32667815 |
| Controlling the polarization of chiral dipolar emission with a spherical dielectric nanoantenna. | Yao K, Zheng Y | The Journal of chemical physics | 34911301 | J Chem Phys | 2021 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/34911301 |
| Room-Temperature Observation of Near-Intrinsic Exciton Linewidth in Monolayer WS(2). | Fang J, Yao K, Zhang T, Wang M, Jiang T, Huang S, Korgel BA, Terrones M, Alù A, Zheng Y | Advanced materials (Deerfield Beach, Fla.) | 35170105 | Adv Mater | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35170105 |
| Opto-thermoelectric speckle tweezers. | Kotnala A, Kollipara PS, Zheng Y | Nanophotonics (Berlin, Germany) | 34290954 | Nanophotonics | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34290954 |
| Atomistic modeling and rational design of optothermal tweezers for targeted applications. | Ding H, Kollipara PS, Lin L, Zheng Y | Nano research | 35475031 | Nano Res | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35475031 |
| Tunable Strong Coupling in Transition Metal Dichalcogenide Nanowires. | Li J, Yao K, Huang Y, Fang J, Kollipara PS, Fan DE, Zheng Y | Advanced materials (Deerfield Beach, Fla.) | 35793202 | Adv Mater | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35793202 |
| Enhancing Single-Molecule Fluorescence Spectroscopy with Simple and Robust Hybrid Nanoapertures. | Kotnala A, Ding H, Zheng Y | ACS photonics | 35445142 | ACS Photonics | 2021 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/35445142 |
| Broadband Forward Light Scattering by Architectural Design of Core-Shell Silicon Particles. | De Marco ML, Jiang T, Fang J, Lacomme S, Zheng Y, Baron A, Korgel BA, Barois P, Drisko GL, Aymonier C | Advanced functional materials | 38031546 | Adv Funct Mater | 2021 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/38031546 |
| Opto-thermophoretic fiber tweezers. | Kotnala A, Zheng Y | Nanophotonics (Berlin, Germany) | 34290953 | Nanophotonics | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34290953 |
| Heat-Mediated Optical Manipulation. | Chen Z, Li J, Zheng Y | Chemical reviews | 34797041 | Chem Rev | 2022 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/34797041 |
| Overcoming Diffusion-Limited Trapping in Nanoaperture Tweezers Using Opto-Thermal-Induced Flow. | Kotnala A, Kollipara PS, Li J, Zheng Y | Nano letters | 31834809 | Nano Lett | 2020 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/31834809 |
| Opto-thermoelectric nanotweezers. | Lin L, Wang M, Peng X, Lissek EN, Mao Z, Scarabelli L, Adkins E, Coskun S, Unalan HE, Korgel BA, Liz-Marzán LM, Florin EL, Zheng Y | Nature photonics | 29785202 | Nat Photonics | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29785202 |
| Sensitivity-Enhancing Strategies in Optical Biosensing. | Kim Y, Gonzales J, Zheng Y | Small (Weinheim an der Bergstrasse, Germany) | 33369864 | Small | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33369864 |
| Directional light emission by electric and magnetic dipoles near a nanosphere: an analytical approach based on the generalized Mie theory. | Yao K, Zheng Y | Optics letters | 33449012 | Opt Lett | 2021 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/33449012 |
| Opto-refrigerative tweezers. | Li J, Chen Z, Liu Y, Kollipara PS, Feng Y, Zhang Z, Zheng Y | Science advances | 34172454 | Sci Adv | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34172454 |
| Bubble-pen lithography: Fundamentals and applications: Nanoscience: Special Issue Dedicated to Professor Paul S. Weiss. | Kollipara PS, Mahendra R, Li J, Zheng Y | Aggregate (Hoboken, N.J.) | 37441005 | Aggregate (Hoboken) | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37441005 |
| Deep Convolutional Mixture Density Network for Inverse Design of Layered Photonic Structures. | Unni R, Yao K, Zheng Y | ACS photonics | 38031541 | ACS Photonics | 2020 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/38031541 |
| Light-driven C-H activation mediated by 2D transition metal dichalcogenides. | Li J, Zhang D, Guo Z, Chen Z, Jiang X, Larson JM, Zhu H, Zhang T, Gu Y, Blankenship BW, Chen M, Wu Z, Huang S, Kostecki R, Minor AM, Grigoropoulos CP, Akinwande D, Terrones M, Redwing JM, Li H, Zheng Y | Nature communications | 38956055 | Nat Commun | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38956055 |
| Opto-Thermophoretic Attraction, Trapping, and Dynamic Manipulation of Lipid Vesicles. | Hill EH, Li J, Lin L, Liu Y, Zheng Y | Langmuir : the ACS journal of surfaces and colloids | 30350700 | Langmuir | 2018 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/30350700 |
| Opto-thermoelectric microswimmers. | Peng X, Chen Z, Kollipara PS, Liu Y, Fang J, Lin L, Zheng Y | Light, science & applications | 32864116 | Light Sci Appl | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32864116 |
| Suppressing material loss in the visible and near-infrared range for functional nanophotonics using bandgap engineering. | Wang M, Krasnok A, Lepeshov S, Hu G, Jiang T, Fang J, Korgel BA, Alù A, Zheng Y | Nature communications | 33028825 | Nat Commun | 2020 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/33028825 |
| Thermo-Electro-Mechanics at Individual Particles in Complex Colloidal Systems. | Kollipara PS, Lin L, Zheng Y | The journal of physical chemistry. C, Nanomaterials and interfaces | 32913480 | J Phys Chem C Nanomater Interfaces | 2019 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/32913480 |
| Optical manipulation and assembly of micro/nanoscale objects on solid substrates. | Li J, Alfares A, Zheng Y | iScience | 35313687 | iScience | 2022 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/35313687 |
| Optical nanomanipulation on solid substrates via optothermally-gated photon nudging. | Li J, Liu Y, Lin L, Wang M, Jiang T, Guo J, Ding H, Kollipara PS, Inoue Y, Fan D, Korgel BA, Zheng Y | Nature communications | 31831746 | Nat Commun | 2019 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/31831746 |
| Intelligent nanophotonics: merging photonics and artificial intelligence at the nanoscale. | Yao K, Unni R, Zheng Y | Nanophotonics (Berlin, Germany) | 34290952 | Nanophotonics | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34290952 |
| Plasmonic Nanotweezers and Nanosensors for Point-of-Care Applications. | Peng X, Kotnala A, Rajeeva BB, Wang M, Yao K, Bhatt N, Penley D, Zheng Y | Advanced optical materials | 34434691 | Adv Opt Mater | 2021 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/34434691 |
| Label-Free Ultrasensitive Detection of Abnormal Chiral Metabolites in Diabetes. | Liu Y, Wu Z, Kollipara PS, Montellano R, Sharma K, Zheng Y | ACS nano | 33760602 | ACS Nano | 2021 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/33760602 |
| Opto-Thermoelectric Tweezers: Principles and Applications. | Pughazhendi A, Chen Z, Wu Z, Li J, Zheng Y | Frontiers in physics | 38031585 | Front Phys | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/38031585 |
| Opto-Thermophoretic Tweezers and Assembly. | Li J, Lin L, Inoue Y, Zheng Y | Journal of micro- and nano-manufacturing | 35832388 | J Micro Nanomanuf | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35832388 |
| Light-driven single-cell rotational adhesion frequency assay. | Liu Y, Ding H, Li J, Lou X, Yang M, Zheng Y | eLight | 35965781 | eLight | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35965781 |
| Universal optothermal micro/nanoscale rotors. | Ding H, Kollipara PS, Kim Y, Kotnala A, Li J, Chen Z, Zheng Y | Science advances | 35704582 | Sci Adv | 2022 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/35704582 |
| Decoding Optical Data with Machine Learning. | Fang J, Swain A, Unni R, Zheng Y | Laser & photonics reviews | 34539925 | Laser Photon Rev | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34539925 |
| Digital manufacturing of advanced materials: challenges and perspective. | Lin L, Kollipara PS, Zheng Y | Materials today (Kidlington, England) | 32831619 | Mater Today (Kidlington) | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32831619 |
| Optothermal Manipulations of Colloidal Particles and Living Cells. | Lin L, Hill EH, Peng X, Zheng Y | Accounts of chemical research | 29799720 | Acc Chem Res | 2018 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/29799720 |
| Nanoradiator-Mediated Deterministic Opto-Thermoelectric Manipulation. | Liu Y, Lin L, Bangalore Rajeeva B, Jarrett JW, Li X, Peng X, Kollipara P, Yao K, Akinwande D, Dunn AK, Zheng Y | ACS nano | 30226980 | ACS Nano | 2018 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/30226980 |
| Optical Nanoprinting of Colloidal Particles and Functional Structures. | Li J, Hill EH, Lin L, Zheng Y | ACS nano | 30875190 | ACS Nano | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/30875190 |
| Evolutionary Engineering a Larger Porin Using a Loop-to-Hairpin Mechanism. | Dhar R, Bowman AM, Hatungimana B, Sg Slusky J | Journal of molecular biology | 37769963 | J Mol Biol | 2023 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/37769963 |
| MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. | Feehan R, Copeland M, Franklin MW, Slusky JSG | bioRxiv : the preprint server for biology | 36945603 | bioRxiv | 2023 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/36945603 |
| Colicin E1 opens its hinge to plug TolC. | Budiardjo SJ, Stevens JJ, Calkins AL, Ikujuni AP, Wimalasena VK, Firlar E, Case DA, Biteen JS, Kaelber JT, Slusky JSG | eLife | 35199644 | Elife | 2022 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/35199644 |
| Machine learning for enzyme engineering, selection and design. | Feehan R, Montezano D, Slusky JSG | Protein engineering, design & selection : PEDS | 34296736 | Protein Eng Des Sel | 2021 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/34296736 |
| Tight Turns of Outer Membrane Proteins: An Analysis of Sequence, Structure, and Hydrogen Bonding. | Franklin MW, Slusky JSG | Journal of molecular biology | 29944853 | J Mol Biol | 2018 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/29944853 |
| Efflux Pumps Represent Possible Evolutionary Convergence onto the β-Barrel Fold. | Franklin MW, Nepomnyachiy S, Feehan R, Ben-Tal N, Kolodny R, Slusky JSG | Structure (London, England : 1993) | 30057025 | Structure | 2018 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/30057025 |
| General features of transmembrane beta barrels from a large database. | Montezano D, Bernstein R, Copeland MM, Slusky JSG | Proceedings of the National Academy of Sciences of the United States of America | 37432995 | Proc Natl Acad Sci U S A | 2023 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/37432995 |
| Machine learning differentiates enzymatic and non-enzymatic metals in proteins. | Feehan R, Franklin MW, Slusky JSG | Nature communications | 34140507 | Nat Commun | 2021 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/34140507 |
| MAHOMES II: A webserver for predicting if a metal binding site is enzymatic. | Feehan R, Copeland M, Franklin MW, Slusky JSG | Protein science : a publication of the Protein Society | 36916762 | Protein Sci | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36916762 |
| Membrane Barrels Are Taller, Fatter, Inside-Out Soluble Barrels. | Dhar R, Feehan R, Slusky JSG | The journal of physical chemistry. B | 33797916 | J Phys Chem B | 2021 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33797916 |
| High-Yield Preparation of Outer Membrane Protein Efflux Pumps by in Vitro Refolding is Concentration Dependent. | Budiardjo SJ, Ikujuni AP, Firlar E, Cordova A, Kaelber JT, Slusky JSG | The Journal of membrane biology | 33462665 | J Membr Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33462665 |
| Outer membrane protein evolution. | Dhar R, Slusky JS | Current opinion in structural biology | 33493965 | Curr Opin Struct Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33493965 |
| Discovery and Characterization of Two Folded Intermediates for Outer Membrane Protein TolC Biogenesis. | Ikujuni AP, Dhar R, Cordova A, Bowman AM, Noga S, Slusky JSG | Journal of molecular biology | 38871177 | J Mol Biol | 2024 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/38871177 |
| Tuning Optical Absorption and Emission Using Strongly Coupled Dimers in Programmable DNA Scaffolds. | Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS | The journal of physical chemistry letters | 35175058 | J Phys Chem Lett | 2022 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/35175058 |
| Observation of robust energy transfer in the photosynthetic protein allophycocyanin using single-molecule pump-probe spectroscopy. | Moya R, Norris AC, Kondo T, Schlau-Cohen GS | Nature chemistry | 34992285 | Nat Chem | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34992285 |
| Concerted Differential Changes of Helical Dynamics and Packing upon Ligand Occupancy in a Bacterial Chemoreceptor. | Gordon JB, Hoffman MC, Troiano JM, Li M, Hazelbauer GL, Schlau-Cohen GS | ACS chemical biology | 34647725 | ACS Chem Biol | 2021 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/34647725 |
| Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. | Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M | Nature communications | 35999227 | Nat Commun | 2022 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/35999227 |
| Observation of conformational dynamics in single light-harvesting proteins from cryptophyte algae. | Moya R, Norris AC, Spangler LC, Scholes GD, Schlau-Cohen GS | The Journal of chemical physics | 35868944 | J Chem Phys | 2022 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/35868944 |
| Phosphorylation-Dependent Conformations of the Disordered Carboxyl-Terminus Domain in the Epidermal Growth Factor Receptor. | Regmi R, Srinivasan S, Latham AP, Kukshal V, Cui W, Zhang B, Bose R, Schlau-Cohen GS | The journal of physical chemistry letters | 33179922 | J Phys Chem Lett | 2020 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/33179922 |
| Spectrally-tunable femtosecond single-molecule pump-probe spectroscopy. | Moya R, Kondo T, Norris AC, Schlau-Cohen GS | Optics express | 34614960 | Opt Express | 2021 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/34614960 |
| Ligand-induced transmembrane conformational coupling in monomeric EGFR. | Srinivasan S, Regmi R, Lin X, Dreyer CA, Chen X, Quinn SD, He W, Coleman MA, Carraway KL 3rd, Zhang B, Schlau-Cohen GS | Nature communications | 35794108 | Nat Commun | 2022 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/35794108 |
| Versatile Peptide Macrocyclization with Diels-Alder Cycloadditions. | Montgomery JE, Donnelly JA, Fanning SW, Speltz TE, Shangguan X, Coukos JS, Greene GL, Moellering RE | Journal of the American Chemical Society | 31523967 | J Am Chem Soc | 2019 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/31523967 |
| Diels-Alder Cycloadditions for Peptide Macrocycle Formation. | Montgomery JE, Moellering RE | Methods in molecular biology (Clifton, N.J.) | 34596848 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34596848 |
| Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains. | Speltz TE, Qiao Z, Swenson CS, Shangguan X, Coukos JS, Lee CW, Thomas DM, Santana J, Fanning SW, Greene GL, Moellering RE | Nature biotechnology | 36302987 | Nat Biotechnol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36302987 |
| High throughput discovery of functional protein modifications by Hotspot Thermal Profiling. | Huang JX, Lee G, Cavanaugh KE, Chang JW, Gardel ML, Moellering RE | Nature methods | 31384043 | Nat Methods | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31384043 |
| Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors. | Qiao Z, Nguyen LC, Yang D, Dann C, Thomas DM, Henn M, Valdespino A, Swenson CS, Oakes SA, Rosner MR, Moellering RE | Nature chemical biology | 39215099 | Nat Chem Biol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39215099 |
| An activity-dependent proximity ligation platform for spatially resolved quantification of active enzymes in single cells. | Li G, Montgomery JE, Eckert MA, Chang JW, Tienda SM, Lengyel E, Moellering RE | Nature communications | 29176560 | Nat Commun | 2017 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/29176560 |
| Ultrasensitive, multiplexed chemoproteomic profiling with soluble activity-dependent proximity ligation. | Li G, Eckert MA, Chang JW, Montgomery JE, Chryplewicz A, Lengyel E, Moellering RE | Proceedings of the National Academy of Sciences of the United States of America | 31591248 | Proc Natl Acad Sci U S A | 2019 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/31591248 |
| Photoproximity Profiling of Protein-Protein Interactions in Cells. | McCutcheon DC, Lee G, Carlos A, Montgomery JE, Moellering RE | Journal of the American Chemical Society | 31820968 | J Am Chem Soc | 2020 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/31820968 |
| A Concise, Modular Antibody-Oligonucleotide Conjugation Strategy Based on Disuccinimidyl Ester Activation Chemistry. | Li G, Moellering RE | Chembiochem : a European journal of chemical biology | 30767357 | Chembiochem | 2019 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/30767357 |
| Evolving artificial metalloenzymes via random mutagenesis. | Yang H, Swartz AM, Park HJ, Srivastava P, Ellis-Guardiola K, Upp DM, Lee G, Belsare K, Gu Y, Zhang C, Moellering RE, Lewis JC | Nature chemistry | 29461523 | Nat Chem | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29461523 |
| Family-Wide Photoproximity Profiling of Integrin Protein Social Networks in Cancer. | Carlos AJ, Yang D, Thomas DM, Huang S, Harter KI, Moellering RE | bioRxiv : the preprint server for biology | 39345550 | bioRxiv | 2024 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/39345550 |
| Proteomics reveals NNMT as a master metabolic regulator of cancer-associated fibroblasts. | Eckert MA, Coscia F, Chryplewicz A, Chang JW, Hernandez KM, Pan S, Tienda SM, Nahotko DA, Li G, Blaženović I, Lastra RR, Curtis M, Yamada SD, Perets R, McGregor SM, Andrade J, Fiehn O, Moellering RE, Mann M, Lengyel E | Nature | 31043742 | Nature | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31043742 |
| Chemoproteomic Profiling of Phosphoaspartate Modifications in Prokaryotes. | Chang JW, Montgomery JE, Lee G, Moellering RE | Angewandte Chemie (International ed. in English) | 30231186 | Angew Chem Int Ed Engl | 2018 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/30231186 |
| Chemical probes for spatially resolved measurement of active enzymes in single cells. | Li G, Moellering RE | Methods in enzymology | 31668232 | Methods Enzymol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31668232 |
| A metabolite-derived protein modification integrates glycolysis with KEAP1-NRF2 signalling. | Bollong MJ, Lee G, Coukos JS, Yun H, Zambaldo C, Chang JW, Chin EN, Ahmad I, Chatterjee AK, Lairson LL, Schultz PG, Moellering RE | Nature | 30323285 | Nature | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30323285 |
| Spectroscopy-Assisted Label-free Molecular Analysis of Live Cell Surface with Vertically Aligned Plasmonic Nanopillars. | Zhang C, Siddhanta S, Paria D, Li Y, Zheng C, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 33942486 | Small | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33942486 |
| Integration of diffraction phase microscopy and Raman imaging for label-free morpho-molecular assessment of live cells. | Pandey R, Zhou R, Bordett R, Hunter C, Glunde K, Barman I, Valdez T, Finck C | Journal of biophotonics | 30421505 | J Biophotonics | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30421505 |
| Plexcitonic Quasi-Bound States in the Continuum. | Zheng P, Raj P, Mizutani T, Szabo M, Hanson WA, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 34411423 | Small | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34411423 |
| Self-Folding Hybrid Graphene Skin for 3D Biosensing. | Xu W, Paidi SK, Qin Z, Huang Q, Yu CH, Pagaduan JV, Buehler MJ, Barman I, Gracias DH | Nano letters | 30433789 | Nano Lett | 2019 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/30433789 |
| Raman spectroscopy reveals phenotype switches in breast cancer metastasis. | Paidi SK, Troncoso JR, Harper MG, Liu Z, Nguyen KG, Ravindranathan S, Rebello L, Lee DE, Ivers JD, Zaharoff DA, Rajaram N, Barman I | Theranostics | 35910801 | Theranostics | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35910801 |
| Silver-Coated Disordered Silicon Nanowires Provide Highly Sensitive Label-Free Glycated Albumin Detection through Molecular Trapping and Plasmonic Hotspot Formation. | Paria D, Convertino A, Mussi V, Maiolo L, Barman I | Advanced healthcare materials | 33236490 | Adv Healthc Mater | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33236490 |
| Surface-enhanced Raman scattering: An emerging tool for sensing cellular function. | Tanwar S, Kim JH, Bulte JWM, Barman I | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 35510405 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35510405 |
| Label-Free Vibrational and Quantitative Phase Microscopy Reveals Remarkable Pathogen-Induced Morphomolecular Divergence in Tumor-Derived Cells. | Liu Z, Parida S, Wu S, Sears CL, Sharma D, Barman I | ACS sensors | 35583030 | ACS Sens | 2022 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/35583030 |
| Towards rational design and optimization of near-field enhancement and spectral tunability of hybrid core-shell plasmonic nanoprobes. | Paria D, Zhang C, Barman I | Scientific reports | 31690763 | Sci Rep | 2019 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/31690763 |
| A Smart Intracellular Self-Assembling Bioorthogonal Raman Active Nanoprobe for Targeted Tumor Imaging. | Tanwar S, Ghaemi B, Raj P, Singh A, Wu L, Yuan Y, Arifin DR, McMahon MT, Bulte JWM, Barman I | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 37715297 | Adv Sci (Weinh) | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37715297 |
| Targeted Enzyme Activity Imaging with Quantitative Phase Microscopy. | Tanwar S, Wu L, Zahn N, Raj P, Ghaemi B, Chatterjee A, Bulte JWM, Barman I | Nano letters | 37154678 | Nano Lett | 2023 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/37154678 |
| Label-free spectrochemical probe for determination of hemoglobin glycation in clinical blood samples. | Pandey R, Singh SP, Zhang C, Horowitz GL, Lue N, Galindo L, Dasari RR, Barman I | Journal of biophotonics | 29726123 | J Biophotonics | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29726123 |
| Rapid, Label-free Optical Spectroscopy Platform for Diagnosis of Heparin-Induced Thrombocytopenia. | Huang Z, Siddhanta S, Zheng G, Kickler T, Barman I | Angewandte Chemie (International ed. in English) | 31972060 | Angew Chem Int Ed Engl | 2020 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/31972060 |
| Label-Free Spectroscopic SARS-CoV-2 Detection on Versatile Nanoimprinted Substrates. | Paria D, Kwok KS, Raj P, Zheng P, Gracias DH, Barman I | Nano letters | 35348344 | Nano Lett | 2022 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/35348344 |
| A Dual-Modal Single-Antibody Plasmonic Spectro-Immunoassay for Detection of Small Molecules. | Zheng P, Wu L, Raj P, Mizutani T, Szabo M, Hanson WA, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 35373504 | Small | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35373504 |
| Nanowire Assisted Mechanotyping of Cellular Metastatic Potential. | Paria D, Convertino A, Raj P, Glunde K, Chen Y, Barman I | Advanced functional materials | 34512229 | Adv Funct Mater | 2021 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/34512229 |
| Coarse Raman and optical diffraction tomographic imaging enable label-free phenotyping of isogenic breast cancer cells of varying metastatic potential. | Paidi SK, Shah V, Raj P, Glunde K, Pandey R, Barman I | Biosensors & bioelectronics | 33272866 | Biosens Bioelectron | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/33272866 |
| Optical properties of symmetry-breaking tetrahedral nanoparticles. | Zheng P , Paria D , Wang H , Li M , Barman I | Nanoscale | 31830188 | Nanoscale | 2020 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/31830188 |
| Identification and Staging of B-Cell Acute Lymphoblastic Leukemia Using Quantitative Phase Imaging and Machine Learning. | Ayyappan V, Chang A, Zhang C, Paidi SK, Bordett R, Liang T, Barman I, Pandey R | ACS sensors | 33092347 | ACS Sens | 2020 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/33092347 |
| Rapid, quantitative determination of aggregation and particle formation for antibody drug conjugate therapeutics with label-free Raman spectroscopy. | Zhang C, Springall JS, Wang X, Barman I | Analytica chimica acta | 31446951 | Anal Chim Acta | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31446951 |
| Composite-Scattering Plasmonic Nanoprobes for Label-Free, Quantitative Biomolecular Sensing. | Zhang C, Paria D, Semancik S, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 31394029 | Small | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31394029 |
| Mapping the genetic basis of breast microcalcifications and their role in metastasis. | Rizwan A, Paidi SK, Zheng C, Cheng M, Barman I, Glunde K | Scientific reports | 30038419 | Sci Rep | 2018 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/30038419 |
| Shedding Light on the Trehalose-Enabled Mucopermeation of Nanoparticles with Label-Free Raman Spectroscopy. | Siddhanta S, Bhattacharjee S, Harrison SM, Scholz D, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 31267720 | Small | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31267720 |
| Reagent-Free and Rapid Assessment of T Cell Activation State Using Diffraction Phase Microscopy and Deep Learning. | Karandikar SH, Zhang C, Meiyappan A, Barman I, Finck C, Srivastava PK, Pandey R | Analytical chemistry | 30741527 | Anal Chem | 2019 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/30741527 |
| A Programmable DNA-Silicification-Based Nanocavity for Single-Molecule Plasmonic Sensing. | Liang L, Zheng P, Zhang C, Barman I | Advanced materials (Deerfield Beach, Fla.) | 33458901 | Adv Mater | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33458901 |
| Vibrational spectroscopy for decoding cancer microbiota interactions: Current evidence and future perspective. | Liu Z, Parida S, Prasad R, Pandey R, Sharma D, Barman I | Seminars in cancer biology | 34273519 | Semin Cancer Biol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34273519 |
| Raman and quantitative phase imaging allow morpho-molecular recognition of malignancy and stages of B-cell acute lymphoblastic leukemia. | Paidi SK, Raj P, Bordett R, Zhang C, Karandikar SH, Pandey R, Barman I | Biosensors & bioelectronics | 34130086 | Biosens Bioelectron | 2021 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/34130086 |
| Leveraging Nanomechanical Perturbations in Raman Spectro-Immunoassays to Design a Versatile Serum Biomarker Detection Platform. | Zheng P, Raj P, Wu L, Szabo M, Hanson WA, Mizutani T, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 36117050 | Small | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36117050 |
| Label-Free Morpho-Molecular Imaging for Studying the Differential Interaction of Black Phosphorus with Tumor Cells. | Mussi V, Fasolino I, Paria D, De Simone S, Caporali M, Serrano-Ruiz M, Ambrosio L, Barman I, Raucci MG, Convertino A | Nanomaterials (Basel, Switzerland) | 35745333 | Nanomaterials (Basel) | 2022 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/35745333 |
| Hyperspectral Raman Imaging for Automated Recognition of Human Renal Amyloid. | Kim JH, Zhang C, Sperati CJ, Barman I, Bagnasco SM | The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society | 37833851 | J Histochem Cytochem | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37833851 |
| RaMALDI: Enabling simultaneous Raman and MALDI imaging of the same tissue section. | Yang E, Kim JH, Tressler CM, Shen XE, Brown DR, Johnson CC, Hahm TH, Barman I, Glunde K | Biosensors & bioelectronics | 37597501 | Biosens Bioelectron | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/37597501 |
| Noninvasive morpho-molecular imaging reveals early therapy-induced senescence in human cancer cells. | Bresci A, Kim JH, Ghislanzoni S, Manetti F, Wu L, Vernuccio F, Ceconello C, Sorrentino S, Barman I, Bongarzone I, Cerullo G, Vanna R, Polli D | Science advances | 37703362 | Sci Adv | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37703362 |
| Optical diffraction tomography and Raman spectroscopy reveal distinct cellular phenotypes during white and brown adipocyte differentiation. | Anantha P, Liu Z, Raj P, Barman I | Biosensors & bioelectronics | 37207582 | Biosens Bioelectron | 2023 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/37207582 |
| Label-Free Raman Spectroscopy Reveals Signatures of Radiation Resistance in the Tumor Microenvironment. | Paidi SK, Diaz PM, Dadgar S, Jenkins SV, Quick CM, Griffin RJ, Dings RPM, Rajaram N, Barman I | Cancer research | 30819665 | Cancer Res | 2019 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/30819665 |
| A Fluorescence and Surface-Enhanced Raman Spectroscopic Dual-Modal Aptasensor for Sensitive Detection of Cyanotoxins. | Li M, Lin H, Paidi SK, Mesyngier N, Preheim S, Barman I | ACS sensors | 32314582 | ACS Sens | 2020 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/32314582 |
| Raman Spectroscopy and Machine Learning Reveals Early Tumor Microenvironmental Changes Induced by Immunotherapy. | Paidi SK, Rodriguez Troncoso J, Raj P, Monterroso Diaz P, Ivers JD, Lee DE, Avaritt NL, Gies AJ, Quick CM, Byrum SD, Tackett AJ, Rajaram N, Barman I | Cancer research | 34645610 | Cancer Res | 2021 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/34645610 |
| Decoding Live Cell Interactions with Multi-Nanoparticle Systems: Differential Implications for Uptake, Trafficking, and Gene Regulation. | Liang L, Liu Z, Barman I | ACS applied materials & interfaces | 31436085 | ACS Appl Mater Interfaces | 2019 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/31436085 |
| Ultrasensitive Detection of Hepatotoxic Microcystin Production from Cyanobacteria Using Surface-Enhanced Raman Scattering Immunosensor. | Li M, Paidi SK, Sakowski E, Preheim S, Barman I | ACS sensors | 30990314 | ACS Sens | 2019 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/30990314 |
| Molecular Radiative Energy Shifts under Strong Oscillating Fields. | Zheng P, Kang J, Paria D, Kang JU, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 33354911 | Small | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33354911 |
| Furin-Mediated Self-Assembly of Olsalazine Nanoparticles for Targeted Raman Imaging of Tumors. | Yuan Y, Raj P, Zhang J, Siddhanta S, Barman I, Bulte JWM | Angewandte Chemie (International ed. in English) | 33325142 | Angew Chem Int Ed Engl | 2021 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/33325142 |
| Cancer cells display increased migration and deformability in pace with metastatic progression. | Liu Z, Lee SJ, Park S, Konstantopoulos K, Glunde K, Chen Y, Barman I | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 32463148 | FASEB J | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32463148 |
| Non-Perturbative Identification and Subtyping of Amyloidosis in Human Kidney Tissue with Raman Spectroscopy and Machine Learning. | Kim JH, Zhang C, Sperati CJ, Bagnasco SM, Barman I | Biosensors | 37185541 | Biosensors (Basel) | 2023 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/37185541 |
| Engineering vascularized skin-mimetic phantom for non-invasive Raman spectroscopy. | Raj P, Wu L, Arora S, Bhatt R, Zuo Y, Fang Z, Verdoold R, Koch T, Gu L, Barman I | Sensors and actuators. B, Chemical | 38524639 | Sens Actuators B Chem | 2024 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/38524639 |
| Pyramidal hyperbolic metasurfaces enhance spontaneous emission of nitrogen-vacancy centers in nanodiamond. | Zheng P, Liang L, Arora S, Ray K, Semancik S, Barman I | Advanced optical materials | 37920689 | Adv Opt Mater | 2023 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/37920689 |
| Quantitative Detection of Thyroid-Stimulating Hormone in Patient Samples with a Nanomechanical Single-Antibody Spectro-Immunoassay. | Zheng P, Raj P, Wu L, Mizutani T, Szabo M, Hanson WA, Barman I | Small (Weinheim an der Bergstrasse, Germany) | 37752776 | Small | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37752776 |
| Mechanical expansion microscopy. | Fan Y, Lim Y, Wyss LS, Park S, Xu C, Fu H, Fei J, Hong Y, Wang B | Methods in cell biology | 33478686 | Methods Cell Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33478686 |
| RNA Localization in Bacteria. | Fei J, Sharma CM | Microbiology spectrum | 30191804 | Microbiol Spectr | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30191804 |
| Continuous active development of super-resolution fluorescence microscopy. | Wang Y, Fei J | Physical biology | 32066124 | Phys Biol | 2020 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/32066124 |
| Kinetic modeling reveals additional regulation at co-transcriptional level by post-transcriptional sRNA regulators. | Reyer MA, Chennakesavalu S, Heideman EM, Ma X, Bujnowska M, Hong L, Dinner AR, Vanderpool CK, Fei J | Cell reports | 34592145 | Cell Rep | 2021 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/34592145 |
| Dynamic interactions between the RNA chaperone Hfq, small regulatory RNAs, and mRNAs in live bacterial cells. | Park S, Prévost K, Heideman EM, Carrier MC, Azam MS, Reyer MA, Liu W, Massé E, Fei J | eLife | 33616037 | Elife | 2021 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/33616037 |
| Translational T-box riboswitches bind tRNA by modulating conformational flexibility. | Campos-Chavez E, Paul S, Zhou Z, Alonso D, Verma AR, Fei J, Mondragón A | Nature communications | 39097611 | Nat Commun | 2024 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/39097611 |
| Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency. | Wu J, Xiao Y, Liu Y, Wen L, Jin C, Liu S, Paul S, He C, Regev O, Fei J | Science advances | 39413186 | Sci Adv | 2024 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/39413186 |
| FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. | Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Chung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, Ha T, Hanke CA, Haran G, Hatzakis NS, Hohng S, Hong SC, Hugel T, Ingargiola A, Joo C, Kapanidis AN, Kim HD, Laurence T, Lee NK, Lee TH, Lemke EA, Margeat E, Michaelis J, Michalet X, Myong S, Nettels D, Peulen TO, Ploetz E, Razvag Y, Robb NC, Schuler B, Soleimaninejad H, Tang C, Vafabakhsh R, Lamb DC, Seidel CA, Weiss S | eLife | 33779550 | Elife | 2021 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/33779550 |
| An Improved Method for Bacterial Immunofluorescence Staining To Eliminate Antibody Exclusion from the Fixed Nucleoid. | Park S, Reyer MA, McLean EL, Liu W, Fei J | Biochemistry | 31657208 | Biochemistry | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31657208 |
| Deoxyribozyme-based method for absolute quantification of N(6)-methyladenosine fractions at specific sites of RNA. | Bujnowska M, Zhang J, Dai Q, Heideman EM, Fei J | The Journal of biological chemistry | 32269077 | J Biol Chem | 2020 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/32269077 |
| RNA molecules display distinctive organization at nuclear speckles. | Paul S, Arias MA, Wen L, Liao SE, Zhang J, Wang X, Regev O, Fei J | iScience | 38638569 | iScience | 2024 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/38638569 |
| Evidence that polyphenols do not inhibit the phospholipid scramblase TMEM16F. | Le T, Le SC, Zhang Y, Liang P, Yang H | The Journal of biological chemistry | 32709749 | J Biol Chem | 2020 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/32709749 |
| Safety Profile of Rapamycin Perfluorocarbon Nanoparticles for Preventing Cisplatin-Induced Kidney Injury. | Zhou Q, Doherty J, Akk A, Springer LE, Fan P, Spasojevic I, Halade GV, Yang H, Pham CTN, Wickline SA, Pan H | Nanomaterials (Basel, Switzerland) | 35159680 | Nanomaterials (Basel) | 2022 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/35159680 |
| PIEZO1 Drives Trophoblast Fusion and Placental Development. | Zhang Y, Shan KZ, Liang P, Lowry AJ, Feng L, Yang H | bioRxiv : the preprint server for biology | 40196526 | bioRxiv | 2025 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/40196526 |
| Deciphering and disrupting PIEZO1-TMEM16F interplay in hereditary xerocytosis. | Liang P, Zhang Y, Wan YCS, Ma S, Dong P, Lowry AJ, Francis SJ, Khandelwal S, Delahunty M, Telen MJ, Strouse JJ, Arepally GM, Yang H | Blood | 38033286 | Blood | 2024 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/38033286 |
| An inner activation gate controls TMEM16F phospholipid scrambling. | Le T, Jia Z, Le SC, Zhang Y, Chen J, Yang H | Nature communications | 31015464 | Nat Commun | 2019 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/31015464 |
| Gating and Regulatory Mechanisms of TMEM16 Ion Channels and Scramblases. | Le SC, Liang P, Lowry AJ, Yang H | Frontiers in physiology | 34867487 | Front Physiol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34867487 |
| Threading the biophysics of mammalian Slo1 channels onto structures of an invertebrate Slo1 channel. | Zhou Y, Yang H, Cui J, Lingle CJ | The Journal of general physiology | 29025867 | J Gen Physiol | 2017 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/29025867 |
| TMEM16F phospholipid scramblase mediates trophoblast fusion and placental development. | Zhang Y, Le T, Grabau R, Mohseni Z, Kim H, Natale DR, Feng L, Pan H, Yang H | Science advances | 32494719 | Sci Adv | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32494719 |
| A simple and robust fluorescent labeling method to quantify trophoblast fusion. | Zhang Y, Yang H | Placenta | 30827351 | Placenta | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30827351 |
| An Additional Ca(2+) Binding Site Allosterically Controls TMEM16A Activation. | Le SC, Yang H | Cell reports | 33378669 | Cell Rep | 2020 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/33378669 |
| Molecular basis of PIP(2)-dependent regulation of the Ca(2+)-activated chloride channel TMEM16A. | Le SC, Jia Z, Chen J, Yang H | Nature communications | 31434906 | Nat Commun | 2019 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/31434906 |
| Molecular underpinning of intracellular pH regulation on TMEM16F. | Liang P, Yang H | The Journal of general physiology | 33346788 | J Gen Physiol | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33346788 |
| Niclosamide potentiates TMEM16A and induces vasoconstriction. | Liang P, Wan YCS, Yu K, Hartzell HC, Yang H | The Journal of general physiology | 38814250 | J Gen Physiol | 2024 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38814250 |
| Drosophila Subdued is a moonlighting transmembrane protein 16 (TMEM16) that transports ions and phospholipids. | Le T, Le SC, Yang H | The Journal of biological chemistry | 30700552 | J Biol Chem | 2019 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/30700552 |
| Structure-Function of TMEM16 Ion Channels and Lipid Scramblases. | Le SC, Yang H | Advances in experimental medicine and biology | 35138612 | Adv Exp Med Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35138612 |
| Functional coupling between TRPV4 channel and TMEM16F modulates human trophoblast fusion. | Zhang Y, Liang P, Yang L, Shan KZ, Feng L, Chen Y, Liedtke W, Coyne CB, Yang H | eLife | 35670667 | Elife | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35670667 |
| Trophoblast organoids with physiological polarity model placental structure and function. | Yang L, Liang P, Yang H, Coyne CB | Journal of cell science | 37676312 | J Cell Sci | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/37676312 |
| TMEM16 and OSCA/TMEM63 proteins share a conserved potential to permeate ions and phospholipids. | Lowry AJ, Liang P, Song M, Serena Wan YC, Pei ZM, Yang H, Zhang Y | bioRxiv : the preprint server for biology | 38370744 | bioRxiv | 2024 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/38370744 |
| Niclosamide potentiates TMEM16A and induces vasoconstriction. | Liang P, Wan YCS, Yu K, Hartzell HC, Yang H | bioRxiv : the preprint server for biology | 37577682 | bioRxiv | 2023 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/37577682 |
| Trophoblast organoids with physiological polarity model placental structure and function. | Yang L, Liang P, Yang H, Coyne CB | bioRxiv : the preprint server for biology | 36711688 | bioRxiv | 2023 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/36711688 |
| TMEM16F scramblase regulates angiogenesis via endothelial intracellular signaling. | Shan KZ, Le T, Liang P, Dong P, Lowry AJ, Kremmyda P, Claesson-Welsh L, Yang H | Journal of cell science | 38940198 | J Cell Sci | 2024 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/38940198 |
| TMEM16 and OSCA/TMEM63 proteins share a conserved potential to permeate ions and phospholipids. | Lowry AJ, Liang P, Song M, Wan Y, Pei ZM, Yang H, Zhang Y | eLife | 39495104 | Elife | 2024 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/39495104 |
| Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel. | Yin Y, Le SC, Hsu AL, Borgnia MJ, Yang H, Lee SY | Science (New York, N.Y.) | 30733385 | Science | 2019 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/30733385 |
| Conformational plasticity in the selectivity filter of the TRPV2 ion channel. | Zubcevic L, Le S, Yang H, Lee SY | Nature structural & molecular biology | 29728656 | Nat Struct Mol Biol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29728656 |
| Corrigendum to "A simple and robust fluorescent labeling method to quantify trophoblast fusion" [Placenta 77 (2019) 16-18]. | Zhang Y, Yang H | Placenta | 31130263 | Placenta | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31130263 |
| Endothelial TMEM16F lipid scramblase regulates angiogenesis. | Shan KZ, Le T, Liang P, Dong P, Yang H | bioRxiv : the preprint server for biology | 37645870 | bioRxiv | 2023 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/37645870 |
| Improved Yield for the Enzymatic Synthesis of Radiolabeled Nicotinamide Adenine Dinucleotide. | Eller J, Goyal S, Cambronne XA | ACS bio & med chem Au | 36820310 | ACS Bio Med Chem Au | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36820310 |
| SLC25A51 decouples the mitochondrial NAD(+)/NADH ratio to control proliferation of AML cells. | Lu MJ, Busquets J, Impedovo V, Wilson CN, Chan HR, Chang YT, Matsui W, Tiziani S, Cambronne XA | Cell metabolism | 38354740 | Cell Metab | 2024 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/38354740 |
| Dynamics of SLC25A51 reveal preference for oxidized NAD(+) and substrate led transport. | Goyal S, Paspureddi A, Lu MJ, Chan HR, Lyons SN, Wilson CN, Niere M, Ziegler M, Cambronne XA | EMBO reports | 37575034 | EMBO Rep | 2023 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/37575034 |
| Methods for Using a Genetically Encoded Fluorescent Biosensor to Monitor Nuclear NAD<sup/>. | Cohen MS, Stewart ML, Goodman RH, Cambronne XA | Methods in molecular biology (Clifton, N.J.) | 30097882 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30097882 |
| Location, Location, Location: Compartmentalization of NAD(+) Synthesis and Functions in Mammalian Cells. | Cambronne XA, Kraus WL | Trends in biochemical sciences | 32595066 | Trends Biochem Sci | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32595066 |
| SLC25A51 is a mammalian mitochondrial NAD(+) transporter. | Luongo TS, Eller JM, Lu MJ, Niere M, Raith F, Perry C, Bornstein MR, Oliphint P, Wang L, McReynolds MR, Migaud ME, Rabinowitz JD, Johnson FB, Johnsson K, Ziegler M, Cambronne XA, Baur JA | Nature | 32906142 | Nature | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32906142 |
| The mitochondrial NAD(+) transporter SLC25A51 is a fasting-induced gene affecting SIRT3 functions. | Fu Z, Kim H, Morse PT, Lu MJ, Hüttemann M, Cambronne XA, Zhang K, Zhang R | Metabolism: clinical and experimental | 35932995 | Metabolism | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35932995 |
| Pharmacological bypass of NAD(+) salvage pathway protects neurons from chemotherapy-induced degeneration. | Liu HW, Smith CB, Schmidt MS, Cambronne XA, Cohen MS, Migaud ME, Brenner C, Goodman RH | Proceedings of the National Academy of Sciences of the United States of America | 30257945 | Proc Natl Acad Sci U S A | 2018 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/30257945 |
| Flow Cytometry Analysis of Free Intracellular NAD(+) Using a Targeted Biosensor. | Eller JM, Stewart ML, Slepian AJ, Markwardt S, Wiedrick J, Cohen MS, Goodman RH, Cambronne XA | Current protocols in cytometry | 30556645 | Curr Protoc Cytom | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30556645 |
| Layered mechanisms regulating the human mitochondrial NAD+ transporter SLC25A51. | Goyal S, Cambronne XA | Biochemical Society transactions | 38108469 | Biochem Soc Trans | 2023 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/38108469 |
| Micron-scale geometrical features of microtubules as regulators of microtubule organization. | Mani N, Wijeratne SS, Subramanian R | eLife | 34114950 | Elife | 2021 Jun 11 | https://www.ncbi.nlm.nih.gov/pubmed/34114950 |
| Interplay between the Kinesin and Tubulin Mechanochemical Cycles Underlies Microtubule Tip Tracking by the Non-motile Ciliary Kinesin Kif7. | Jiang S, Mani N, Wilson-Kubalek EM, Ku PI, Milligan RA, Subramanian R | Developmental cell | 31031197 | Dev Cell | 2019 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/31031197 |
| Geometry of antiparallel microtubule bundles regulates relative sliding and stalling by PRC1 and Kif4A. | Wijeratne S, Subramanian R | eLife | 30353849 | Elife | 2018 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/30353849 |
| Active Microphase Separation in Mixtures of Microtubules and Tip-Accumulating Molecular Motors. | Lemma B, Mitchell NP, Subramanian R, Needleman DJ, Dogic Z | Physical review. X | 36643940 | Phys Rev X | 2022 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/36643940 |
| Simultaneous Visualization of the Dynamics of Crosslinked and Single Microtubules In Vitro by TIRF Microscopy. | Mani N, Marchan MF, Subramanian R | Journal of visualized experiments : JoVE | 35253794 | J Vis Exp | 2022 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/35253794 |
| Differential regulation of single microtubules and bundles by a three-protein module. | Mani N, Jiang S, Neary AE, Wijeratne SS, Subramanian R | Nature chemical biology | 34083810 | Nat Chem Biol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34083810 |
| Meeting report - Mitotic spindle: from living and synthetic systems to theory. | Simunić J, Subramanian R | Journal of cell science | 31477579 | J Cell Sci | 2019 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/31477579 |
| Motor guidance by long-range communication on the microtubule highway. | Wijeratne SS, Fiorenza SA, Neary AE, Subramanian R, Betterton MD | Proceedings of the National Academy of Sciences of the United States of America | 35867749 | Proc Natl Acad Sci U S A | 2022 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/35867749 |
| Atomic force microscopy reveals distinct protofilament-scale structural dynamics in depolymerizing microtubule arrays. | Wijeratne SS, Marchan MF, Tresback JS, Subramanian R | Proceedings of the National Academy of Sciences of the United States of America | 35101922 | Proc Natl Acad Sci U S A | 2022 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/35101922 |
| Real-Time Visualization of Microtubule and Protofilament-Scale Dynamics in Multi-Microtubule Arrays by Atomic Force Microscopy. | Wijeratne SS, Subramanian R | Current protocols | 37227098 | Curr Protoc | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37227098 |
| A commensal strain of Staphylococcus epidermidis protects against skin neoplasia. | Nakatsuji T, Chen TH, Butcher AM, Trzoss LL, Nam SJ, Shirakawa KT, Zhou W, Oh J, Otto M, Fenical W, Gallo RL | Science advances | 29507878 | Sci Adv | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29507878 |
| Resident risks. | Spoto M, Oh J | Nature microbiology | 30046171 | Nat Microbiol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30046171 |
| Using genome-wide expression compendia to study microorganisms. | Lee AJ, Reiter T, Doing G, Oh J, Hogan DA, Greene CS | Computational and structural biotechnology journal | 36016717 | Comput Struct Biotechnol J | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36016717 |
| Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults. | Larson PJ, Zhou W, Santiago A, Driscoll S, Fleming E, Voigt AY, Chun OK, Grady JJ, Kuchel GA, Robison JT, Oh J | Nature aging | 36398033 | Nat Aging | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36398033 |
| High-throughput bioprinting of the nasal epithelium using patient-derived nasal epithelial cells. | Deniz Derman I, Yeo M, Castaneda DC, Callender M, Horvath M, Mo Z, Xiong R, Fleming E, Chen P, Peeples ME, Palucka K, Oh J, Ozbolat IT | Biofabrication | 37536321 | Biofabrication | 2023 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/37536321 |
| Microbiome modulates immunotherapy response in cutaneous squamous cell carcinoma. | Voigt AY, Walter A, Young TH, Graham JP, Batista Bittencourt BM, de Mingo Pulido A, Prieto K, Tsai KY, Sundberg JP, Oh J | Experimental dermatology | 37350109 | Exp Dermatol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37350109 |
| Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. | Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J | Cell | 32004459 | Cell | 2020 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/32004459 |
| Recoding the metagenome: microbiome engineering in situ. | Whitfill T, Oh J | Current opinion in microbiology | 31622928 | Curr Opin Microbiol | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31622928 |
| Selective colonization ability of human fecal microbes in different mouse gut environments. | Zhou W, Chow KH, Fleming E, Oh J | The ISME journal | 30442907 | ISME J | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30442907 |
| Strains to go: interactions of the skin microbiome beyond its species. | Caldwell R, Zhou W, Oh J | Current opinion in microbiology | 36242896 | Curr Opin Microbiol | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36242896 |
| Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. | Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H | Nature communications | 34238936 | Nat Commun | 2021 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/34238936 |
| Metagenomic growth rate inferences of strains in situ. | Emiola A, Zhou W, Oh J | Science advances | 32494636 | Sci Adv | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32494636 |
| A host-microbiota interactome reveals extensive transkingdom connectivity. | Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW | Nature | 38509360 | Nature | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38509360 |
| BioMapAI: Artificial Intelligence Multi-Omics Modeling of Myalgic Encephalomyelitis / Chronic Fatigue Syndrome. | Xiong R, Aiken E, Caldwell R, Vernon SD, Kozhaya L, Gunter C, Bateman L, Unutmaz D, Oh J | bioRxiv : the preprint server for biology | 38979186 | bioRxiv | 2025 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/38979186 |
| Bioassay-Driven, Fractionation-Empowered, Focused Metabolomics for Discovering Bacterial Activators of Aryl Hydrocarbon Receptor. | Tian H, Wang L, Hardy R, Kozhaya L, Placek L, Fleming E, Oh J, Unutmaz D, Yao X | Journal of the American Society for Mass Spectrometry | 38308645 | J Am Soc Mass Spectrom | 2024 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/38308645 |
| Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients. | Xiong R, Gunter C, Fleming E, Vernon SD, Bateman L, Unutmaz D, Oh J | Cell host & microbe | 36758521 | Cell Host Microbe | 2023 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/36758521 |
| Genotype-environment-driven dysbiosis in the skin microbiome of ichthyosis. | Zhou W, Ring NG, Caldwell R, Milstone LM, Oh J | The Journal of investigative dermatology | 40571157 | J Invest Dermatol | 2025 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/40571157 |
| Differential Hairless Mouse Strain-Specific Susceptibility to Skin Cancer and Sunburn. | Voigt AY, Michaud M, Tsai KY, Oh J, Sundberg JP | The Journal of investigative dermatology | 30742806 | J Invest Dermatol | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30742806 |
| Challenges in Developing a Human Model System for Skin Microbiome Research. | Larson PJ, Chong D, Fleming E, Oh J | The Journal of investigative dermatology | 32522484 | J Invest Dermatol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32522484 |
| Skin Microbiome Variation with Cancer Progression in Human Cutaneous Squamous Cell Carcinoma. | Voigt AY, Emiola A, Johnson JS, Fleming ES, Nguyen H, Zhou W, Tsai KY, Fink C, Oh J | The Journal of investigative dermatology | 35390349 | J Invest Dermatol | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35390349 |
| State of Residency: Microbial Strain Diversity in the Skin. | Kong HH, Oh J | The Journal of investigative dermatology | 34688614 | J Invest Dermatol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/34688614 |
| Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota. | Fleming E, Pabst V, Scholar Z, Xiong R, Voigt AY, Zhou W, Hoyt A, Hardy R, Peterson A, Beach R, Ondouah-Nzutchi Y, Dong J, Bateman L, Vernon SD, Oh J | BMC microbiology | 34649516 | BMC Microbiol | 2021 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/34649516 |
| Network Topology of Biological Aging and Geroscience-Guided Approaches to COVID-19. | Landay A, Bartley J, Banerjee D, Hargis G, Haynes L, Keshavarzian A, Kuo CL, Kwon OS, Li S, Li S, Oh J, Ozbolat IT, Ucar D, Xu M, Yao X, Unutmaz D, Kuchel GA | Frontiers in aging | 35128530 | Front Aging | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35128530 |
| ReprDB and panDB: minimalist databases with maximal microbial representation. | Zhou W, Gay N, Oh J | Microbiome | 29347966 | Microbiome | 2018 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/29347966 |
| High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. | Emiola A, Oh J | Nature communications | 30470746 | Nat Commun | 2018 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/30470746 |
| A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes. | Spoto M, Guan C, Fleming E, Oh J | mSphere | 32051236 | mSphere | 2020 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/32051236 |
| Frailty-associated dysbiosis of human microbiotas in older adults in nursing homes. | Oh J, Robison J, Kuchel GA | Nature aging | 36909933 | Nat Aging | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36909933 |
| Engineering a "detect and destroy" skin probiotic to combat methicillin-resistant Staphylococcus aureus. | Guan C, Larson PJ, Fleming E, Tikhonov AP, Mootien S, Grossman TH, Golino C, Oh J | PloS one | 36520793 | PLoS One | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36520793 |
| Microbiome modulates immunotherapy response in cutaneous squamous cell carcinoma. | Voigt AY, Walter A, Young T, Graham JP, Batista Bittencourt BM, de Mingo Pulido A, Prieto K, Tsai KY, Sundberg JP, Oh J | bioRxiv : the preprint server for biology | 36747869 | bioRxiv | 2023 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/36747869 |
| Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility. | Spoto M, Riera Puma JP, Fleming E, Guan C, Ondouah Nzutchi Y, Kim D, Oh J | mBio | 36409086 | mBio | 2022 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/36409086 |
| Skin microbiome attributes associate with biophysical skin ageing. | Zhou W, Fleming E, Legendre G, Roux L, Latreille J, Gendronneau G, Forestier S, Oh J | Experimental dermatology | 37350224 | Exp Dermatol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37350224 |
| A multiplexed, electrochemical interface for gene-circuit-based sensors. | Sadat Mousavi P, Smith SJ, Chen JB, Karlikow M, Tinafar A, Robinson C, Liu W, Ma D, Green AA, Kelley SO, Pardee K | Nature chemistry | 31767994 | Nat Chem | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31767994 |
| De novo-designed translation-repressing riboregulators for multi-input cellular logic. | Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA | Nature chemical biology | 31686032 | Nat Chem Biol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31686032 |
| Low-cost detection of norovirus using paper-based cell-free systems and synbody-based viral enrichment. | Ma D, Shen L, Wu K, Diehnelt CW, Green AA | Synthetic biology (Oxford, England) | 30370338 | Synth Biol (Oxf) | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30370338 |
| Multi-arm RNA junctions encoding molecular logic unconstrained by input sequence for versatile cell-free diagnostics. | Ma D, Li Y, Wu K, Yan Z, Tang AA, Chaudhary S, Ticktin ZM, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Green AA | Nature biomedical engineering | 35288660 | Nat Biomed Eng | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35288660 |
| Design of RNA-Based Translational Repressors. | Hong S, Park D, Chaudhary S, McCutcheon G, Green AA, Kim J | Methods in molecular biology (Clifton, N.J.) | 35666438 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35666438 |
| Predictable control of RNA lifetime using engineered degradation-tuning RNAs. | Zhang Q, Ma D, Wu F, Standage-Beier K, Chen X, Wu K, Green AA, Wang X | Nature chemical biology | 34155402 | Nat Chem Biol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34155402 |
| Conditional RNA interference in mammalian cells via RNA transactivation. | Zhou Y, Sheng P, Li J, Li Y, Xie M, Green AA | Nature communications | 39127751 | Nat Commun | 2024 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/39127751 |
| Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches. | Yan Z, Tang AA, Eshed A, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA | medRxiv : the preprint server for health sciences | 37333364 | medRxiv | 2023 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/37333364 |
| Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. | Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA | Chem | 39036067 | Chem | 2024 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/39036067 |
| Synthetic bionanotechnology: synthetic biology finds a toehold in nanotechnology. | Green AA | Emerging topics in life sciences | 33523177 | Emerg Top Life Sci | 2019 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/33523177 |
| Precise and Programmable Detection of Mutations Using Ultraspecific Riboregulators. | Hong F, Ma D, Wu K, Mina LA, Luiten RC, Liu Y, Yan H, Green AA | Cell | 32109416 | Cell | 2020 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/32109416 |
| Design of Ribocomputing Devices for Complex Cellular Logic. | McCutcheon G, Chaudhary S, Hong S, Park D, Kim J, Green AA | Methods in molecular biology (Clifton, N.J.) | 35666439 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35666439 |
| Closing the loop on crowdsourced science. | Robson JM, Green AA | Proceedings of the National Academy of Sciences of the United States of America | 35687665 | Proc Natl Acad Sci U S A | 2022 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/35687665 |
| Design to Implementation Study for Development and Patient Validation of Paper-Based Toehold Switch Diagnostics. | Jaenes K, Ribeiro da Silva SJ, Vigar JRJ, Wu K, Norouzi M, Bayat P, Karlikow M, Cicek S, Guo Y, Green AA, Pena L, Pardee K | Journal of visualized experiments : JoVE | 35781278 | J Vis Exp | 2022 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/35781278 |
| A glucose meter interface for point-of-care gene circuit-based diagnostics. | Amalfitano E, Karlikow M, Norouzi M, Jaenes K, Cicek S, Masum F, Sadat Mousavi P, Guo Y, Tang L, Sydor A, Ma D, Pearson JD, Trcka D, Pinette M, Ambagala A, Babiuk S, Pickering B, Wrana J, Bremner R, Mazzulli T, Sinton D, Brumell JH, Green AA, Pardee K | Nature communications | 33526784 | Nat Commun | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33526784 |
| Field validation of the performance of paper-based tests for the detection of the Zika and chikungunya viruses in serum samples. | Karlikow M, da Silva SJR, Guo Y, Cicek S, Krokovsky L, Homme P, Xiong Y, Xu T, Calderón-Peláez MA, Camacho-Ortega S, Ma D, de Magalhães JJF, Souza BNRF, de Albuquerque Cabral DG, Jaenes K, Sutyrina P, Ferrante T, Benitez AD, Nipaz V, Ponce P, Rackus DG, Collins JJ, Paiva M, Castellanos JE, Cevallos V, Green AA, Ayres C, Pena L, Pardee K | Nature biomedical engineering | 35256758 | Nat Biomed Eng | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35256758 |
| Double emulsion flow cytometry with high-throughput single droplet isolation and nucleic acid recovery. | Brower KK, Carswell-Crumpton C, Klemm S, Cruz B, Kim G, Calhoun SGK, Nichols L, Fordyce PM | Lab on a chip | 32417874 | Lab Chip | 2020 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/32417874 |
| Double Emulsion Picoreactors for High-Throughput Single-Cell Encapsulation and Phenotyping via FACS. | Brower KK, Khariton M, Suzuki PH, Still C 2nd, Kim G, Calhoun SGK, Qi LS, Wang B, Fordyce PM | Analytical chemistry | 32900183 | Anal Chem | 2020 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/32900183 |
| MRBLES 2.0: High-throughput generation of chemically functionalized spectrally and magnetically encoded hydrogel beads using a simple single-layer microfluidic device. | Feng Y, White AK, Hein JB, Appel EA, Fordyce PM | Microsystems & nanoengineering | 33299601 | Microsyst Nanoeng | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33299601 |
| Machine learning for microfluidic design and control. | McIntyre D, Lashkaripour A, Fordyce P, Densmore D | Lab on a chip | 35904162 | Lab Chip | 2022 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/35904162 |
| An open-source software analysis package for Microspheres with Ratiometric Barcode Lanthanide Encoding (MRBLEs). | Harink B, Nguyen H, Thorn K, Fordyce P | PloS one | 30901328 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30901328 |
| micrIO: an open-source autosampler and fraction collector for automated microfluidic input-output. | Longwell SA, Fordyce PM | Lab on a chip | 31701110 | Lab Chip | 2020 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/31701110 |
| Versatility and stability optimization of flow-focusing droplet generators via quality metric-driven design automation. | McIntyre D, Lashkaripour A, Arguijo D, Fordyce P, Densmore D | Lab on a chip | 37909215 | Lab Chip | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/37909215 |
| Multi-step Variable Height Photolithography for Valved Multilayer Microfluidic Devices. | Brower K, White AK, Fordyce PM | Journal of visualized experiments : JoVE | 28190039 | J Vis Exp | 2017 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/28190039 |
| Design automation of microfluidic single and double emulsion droplets with machine learning. | Lashkaripour A, McIntyre DP, Calhoun SGK, Krauth K, Densmore DM, Fordyce PM | Nature communications | 38167827 | Nat Commun | 2024 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/38167827 |
| A microwell platform for high-throughput longitudinal phenotyping and selective retrieval of organoids. | Sockell A, Wong W, Longwell S, Vu T, Karlsson K, Mokhtari D, Schaepe J, Lo YH, Cornelius V, Kuo C, Van Valen D, Curtis C, Fordyce PM | Cell systems | 37734323 | Cell Syst | 2023 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/37734323 |
| An Open-Source, Programmable Pneumatic Setup for Operation and Automated Control of Single- and Multi-Layer Microfluidic Devices. | Brower K, Puccinelli R, Markin CJ, Shimko TC, Longwell SA, Cruz B, Gomez-Sjoberg R, Fordyce PM | HardwareX | 30221210 | HardwareX | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30221210 |
| Systematic characterization of effect of flow rates and buffer compositions on double emulsion droplet volumes and stability. | Calhoun SGK, Brower KK, Suja VC, Kim G, Wang N, McCully AL, Kusumaatmaja H, Fuller GG, Fordyce PM | Lab on a chip | 35593127 | Lab Chip | 2022 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/35593127 |
| Protocol for Peptide Synthesis on Spectrally Encoded Beads for MRBLE-pep Assays. | Hein JB, Nguyen HQ, Cyert M, Fordyce PM | Bio-protocol | 33659339 | Bio Protoc | 2020 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/33659339 |
| Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes. | Nguyen HQ, Baxter BC, Brower K, Diaz-Botia CA, DeRisi JL, Fordyce PM, Thorn KS | Advanced optical materials | 28936383 | Adv Opt Mater | 2017 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/28936383 |
| DeCoDe: degenerate codon design for complete protein-coding DNA libraries. | Shimko TC, Fordyce PM, Orenstein Y | Bioinformatics (Oxford, England) | 32176271 | Bioinformatics | 2020 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/32176271 |
| Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. | Nguyen HQ, Roy J, Harink B, Damle NP, Latorraca NR, Baxter BC, Brower K, Longwell SA, Kortemme T, Thorn KS, Cyert MS, Fordyce PM | eLife | 31282865 | Elife | 2019 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/31282865 |
| On the dependent recognition of some long zinc finger proteins. | Zuo Z, Billings T, Walker M, Petkov PM, Fordyce PM, Stormo GD | Nucleic acids research | 36951113 | Nucleic Acids Res | 2023 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/36951113 |
| MRBLE-pep Measurements Reveal Accurate Binding Affinities for B56, a PP2A Regulatory Subunit. | Hein JB, Cyert MS, Fordyce PM | ACS measurement science au | 35128539 | ACS Meas Sci Au | 2021 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/35128539 |
| A bead-based method for high-throughput mapping of the sequence- and force-dependence of T cell activation. | Feng Y, Zhao X, White AK, Garcia KC, Fordyce PM | Nature methods | 36064771 | Nat Methods | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36064771 |
| Tuning T cell receptor sensitivity through catch bond engineering. | Zhao X, Kolawole EM, Chan W, Feng Y, Yang X, Gee MH, Jude KM, Sibener LV, Fordyce PM, Germain RN, Evavold BD, Garcia KC | Science (New York, N.Y.) | 35389803 | Science | 2022 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/35389803 |
| Phosphatase specificity principles uncovered by MRBLE:Dephos and global substrate identification. | Hein JB, Nguyen HT, Garvanska DH, Nasa I, Kruse T, Feng Y, Lopez Mendez B, Davey N, Kettenbach AN, Fordyce PM, Nilsson J | Molecular systems biology | 37916966 | Mol Syst Biol | 2023 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/37916966 |
| Reprogramming progressive cells display low CAG promoter activity. | Hu X, Wu Q, Zhang J, Kim J, Chen X, Hartman AA, Eastman AE, Park IH, Guo S | Stem cells (Dayton, Ohio) | 33075202 | Stem Cells | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33075202 |
| The palette of techniques for cell cycle analysis. | Eastman AE, Guo S | FEBS letters | 32441778 | FEBS Lett | 2020 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/32441778 |
| Cell cycle dynamics in the reprogramming of cellular identity. | Hu X, Eastman AE, Guo S | FEBS letters | 31562821 | FEBS Lett | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31562821 |
| Targeting Fibrotic Signaling: A Review of Current Literature and Identification of Future Therapeutic Targets to Improve Wound Healing. | Hetzler PT 3rd, Dash BC, Guo S, Hsia HC | Annals of plastic surgery | 31246672 | Ann Plast Surg | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31246672 |
| MKL1-actin pathway restricts chromatin accessibility and prevents mature pluripotency activation. | Hu X, Liu ZZ, Chen X, Schulz VP, Kumar A, Hartman AA, Weinstein J, Johnston JF, Rodriguez EC, Eastman AE, Cheng J, Min L, Zhong M, Carroll C, Gallagher PG, Lu J, Schwartz M, King MC, Krause DS, Guo S | Nature communications | 30979898 | Nat Commun | 2019 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/30979898 |
| YAP Non-cell-autonomously Promotes Pluripotency Induction in Mouse Cells. | Hartman AA, Scalf SM, Zhang J, Hu X, Chen X, Eastman AE, Yang C, Guo S | Stem cell reports | 32243844 | Stem Cell Reports | 2020 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/32243844 |
| MLL-AF9 initiates transformation from fast-proliferating myeloid progenitors. | Chen X, Burkhardt DB, Hartman AA, Hu X, Eastman AE, Sun C, Wang X, Zhong M, Krishnaswamy S, Guo S | Nature communications | 31852898 | Nat Commun | 2019 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/31852898 |
| Resolving Cell Cycle Speed in One Snapshot with a Live-Cell Fluorescent Reporter. | Eastman AE, Chen X, Hu X, Hartman AA, Pearlman Morales AM, Yang C, Lu J, Kueh HY, Guo S | Cell reports | 32579930 | Cell Rep | 2020 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/32579930 |
| Serum Response Factor Reduces Gene Expression Noise and Confers Cell State Stability. | Zhang J, Wu Q, Hu X, Wang Y, Lu J, Chakraborty R, Martin KA, Guo S | Stem cells (Dayton, Ohio) | 37386941 | Stem Cells | 2023 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/37386941 |
| Dppa2/4 Facilitate Epigenetic Remodeling during Reprogramming to Pluripotency. | Hernandez C, Wang Z, Ramazanov B, Tang Y, Mehta S, Dambrot C, Lee YW, Tessema K, Kumar I, Astudillo M, Neubert TA, Guo S, Ivanova NB | Cell stem cell | 30146411 | Cell Stem Cell | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/30146411 |
| miR-125b promotes MLL-AF9-driven murine acute myeloid leukemia involving a VEGFA-mediated non-cell-intrinsic mechanism. | Liu J, Guo B, Chen Z, Wang N, Iacovino M, Cheng J, Roden C, Pan W, Khan S, Chen S, Kyba M, Fan R, Guo S, Lu J | Blood | 28053194 | Blood | 2017 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/28053194 |
| Engineered ACE2 receptor traps potently neutralize SARS-CoV-2. | Glasgow A, Glasgow J, Limonta D, Solomon P, Lui I, Zhang Y, Nix MA, Rettko NJ, Zha S, Yamin R, Kao K, Rosenberg OS, Ravetch JV, Wiita AP, Leung KK, Lim SA, Zhou XX, Hobman TC, Kortemme T, Wells JA | Proceedings of the National Academy of Sciences of the United States of America | 33093202 | Proc Natl Acad Sci U S A | 2020 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/33093202 |
| Integrated phosphoproteomics and transcriptional classifiers reveal hidden RAS signaling dynamics in multiple myeloma. | Lin YT, Way GP, Barwick BG, Mariano MC, Marcoulis M, Ferguson ID, Driessen C, Boise LH, Greene CS, Wiita AP | Blood advances | 31698452 | Blood Adv | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31698452 |
| Evaluating the efficacy of multiple myeloma cell lines as models for patient tumors via transcriptomic correlation analysis. | Sarin V, Yu K, Ferguson ID, Gugliemini O, Nix MA, Hann B, Sirota M, Wiita AP | Leukemia | 32123307 | Leukemia | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32123307 |
| Mitochondrial stress is relayed to the cytosol by an OMA1-DELE1-HRI pathway. | Guo X, Aviles G, Liu Y, Tian R, Unger BA, Lin YT, Wiita AP, Xu K, Correia MA, Kampmann M | Nature | 32132707 | Nature | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32132707 |
| CRISPR-based screens uncover determinants of immunotherapy response in multiple myeloma. | Ramkumar P, Abarientos AB, Tian R, Seyler M, Leong JT, Chen M, Choudhry P, Hechler T, Shah N, Wong SW, Martin TG, Wolf JL, Roybal KT, Pahl A, Taunton J, Wiita AP, Kampmann M | Blood advances | 32589729 | Blood Adv | 2020 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/32589729 |
| Proteasome inhibitor-induced modulation reveals the spliceosome as a specific therapeutic vulnerability in multiple myeloma. | Huang HH, Ferguson ID, Thornton AM, Bastola P, Lam C, Lin YT, Choudhry P, Mariano MC, Marcoulis MD, Teo CF, Malato J, Phojanakong PJ, Martin TG 3rd, Wolf JL, Wong SW, Shah N, Hann B, Brooks AN, Wiita AP | Nature communications | 32321912 | Nat Commun | 2020 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/32321912 |
| Seeking Convergence and Cure with New Myeloma Therapies. | Choudhry P, Galligan D, Wiita AP | Trends in cancer | 30064664 | Trends Cancer | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30064664 |
| DNA methyltransferase inhibitors upregulate CD38 protein expression and enhance daratumumab efficacy in multiple myeloma. | Choudhry P, Mariano MC, Geng H, Martin TG 3rd, Wolf JL, Wong SW, Shah N, Wiita AP | Leukemia | 31595037 | Leukemia | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31595037 |
| Surface Proteomics Reveals CD72 as a Target for In Vitro-Evolved Nanobody-Based CAR-T Cells in KMT2A/MLL1-Rearranged B-ALL. | Nix MA, Mandal K, Geng H, Paranjape N, Lin YT, Rivera JM, Marcoulis M, White KL, Whitman JD, Bapat SP, Parker KR, Ramirez J, Deucher A, Phojanokong P, Steri V, Fattahi F, Hann BC, Satpathy AT, Manglik A, Stieglitz E, Wiita AP | Cancer discovery | 33727310 | Cancer Discov | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33727310 |
| Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. | Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N | Genome biology | 33504367 | Genome Biol | 2021 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/33504367 |
| Voices of biotech research. | Annabi N, Baker M, Boettiger A, Chakraborty D, Chen Y, Corbett KS, Correia B, Dahlman J, de Oliveira T, Ertuerk A, Yanik MF, Henaff E, Huch M, Iliev ID, Jacobs T, Junca H, Keung A, Kolodkin-Gal I, Krishnaswamy S, Lancaster M, Macosko E, Martínez-Núñez MA, Miura K, Molloy J, Cruz AO, Platt RJ, Posey AD Jr, Shao H, Simunovic M, Slavov N, Takebe T, Vandenberghe LH, Varshney RK, Wang J | Nature biotechnology | 33692517 | Nat Biotechnol | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33692517 |
| Ribosome Stoichiometry: From Form to Function. | Emmott E, Jovanovic M, Slavov N | Trends in biochemical sciences | 30473427 | Trends Biochem Sci | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30473427 |
| SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation. | Budnik B, Levy E, Harmange G, Slavov N | Genome biology | 30343672 | Genome Biol | 2018 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/30343672 |
| Unpicking the proteome in single cells. | Slavov N | Science (New York, N.Y.) | 32001644 | Science | 2020 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/32001644 |
| New Views of Old Proteins: Clarifying the Enigmatic Proteome. | Burnum-Johnson KE, Conrads TP, Drake RR, Herr AE, Iyengar R, Kelly RT, Lundberg E, MacCoss MJ, Naba A, Nolan GP, Pevzner PA, Rodland KD, Sechi S, Slavov N, Spraggins JM, Van Eyk JE, Vidal M, Vogel C, Walt DR, Kelleher NL | Molecular & cellular proteomics : MCP | 35654359 | Mol Cell Proteomics | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35654359 |
| Optimizing Accuracy and Depth of Protein Quantification in Experiments Using Isobaric Carriers. | Specht H, Slavov N | Journal of proteome research | 33190502 | J Proteome Res | 2021 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/33190502 |
| DO-MS: Data-Driven Optimization of Mass Spectrometry Methods. | Huffman RG, Chen A, Specht H, Slavov N | Journal of proteome research | 31081635 | J Proteome Res | 2019 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/31081635 |
| Exploring functional protein covariation across single cells using nPOP. | Leduc A, Huffman RG, Cantlon J, Khan S, Slavov N | Genome biology | 36527135 | Genome Biol | 2022 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/36527135 |
| Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments. | Gatto L, Aebersold R, Cox J, Demichev V, Derks J, Emmott E, Franks AM, Ivanov AR, Kelly RT, Khoury L, Leduc A, MacCoss MJ, Nemes P, Perlman DH, Petelski AA, Rose CM, Schoof EM, Van Eyk J, Vanderaa C, Yates JR 3rd, Slavov N | Nature methods | 36864200 | Nat Methods | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36864200 |
| Kinase Activities of RIPK1 and RIPK3 Can Direct IFN-β Synthesis Induced by Lipopolysaccharide. | Saleh D, Najjar M, Zelic M, Shah S, Nogusa S, Polykratis A, Paczosa MK, Gough PJ, Bertin J, Whalen M, Fitzgerald KA, Slavov N, Pasparakis M, Balachandran S, Kelliher M, Mecsas J, Degterev A | Journal of immunology (Baltimore, Md. : 1950) | 28461567 | J Immunol | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28461567 |
| Integration of a multi-omics stem cell differentiation dataset using a dynamical model. | van den Berg PR, Bérenger-Currias NMLP, Budnik B, Slavov N, Semrau S | PLoS genetics | 37167320 | PLoS Genet | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37167320 |
| Single cell protein analysis for systems biology. | Levy E, Slavov N | Essays in biochemistry | 30072488 | Essays Biochem | 2018 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/30072488 |
| Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics. | Huffman RG, Leduc A, Wichmann C, Di Gioia M, Borriello F, Specht H, Derks J, Khan S, Khoury L, Emmott E, Petelski AA, Perlman DH, Cox J, Zanoni I, Slavov N | Nature methods | 37012480 | Nat Methods | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37012480 |
| Driving Single Cell Proteomics Forward with Innovation. | Slavov N | Journal of proteome research | 34597050 | J Proteome Res | 2021 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34597050 |
| Increasing proteomics throughput. | Slavov N | Nature biotechnology | 33767394 | Nat Biotechnol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33767394 |
| Analyzing Ribosome Remodeling in Health and Disease. | Petelski AA, Slavov N | Proteomics | 32820594 | Proteomics | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32820594 |
| Post-transcriptional regulation across human tissues. | Franks A, Airoldi E, Slavov N | PLoS computational biology | 28481885 | PLoS Comput Biol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28481885 |
| Single-cell protein analysis by mass spectrometry. | Slavov N | Current opinion in chemical biology | 32599342 | Curr Opin Chem Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32599342 |
| Transformative Opportunities for Single-Cell Proteomics. | Specht H, Slavov N | Journal of proteome research | 29945450 | J Proteome Res | 2018 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/29945450 |
| Voices in methods development. | Anikeeva P, Boyden E, Brangwynne C, Cissé II, Fiehn O, Fromme P, Gingras AC, Greene CS, Heard E, Hell SW, Hillman E, Jensen GJ, Karchin R, Kiessling LL, Kleinstiver BP, Knight R, Kukura P, Lancaster MA, Loman N, Looger L, Lundberg E, Luo Q, Miyawaki A, Myers EW Jr, Nolan GP, Picotti P, Reik W, Sauer M, Shalek AK, Shendure J, Slavov N, Tanay A, Troyanskaya O, van Valen D, Wang HW, Yi C, Yin P, Zernicka-Goetz M, Zhuang X | Nature methods | 31562479 | Nat Methods | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31562479 |
| Multiplexed single-cell proteomics using SCoPE2. | Petelski AA, Emmott E, Leduc A, Huffman RG, Specht H, Perlman DH, Slavov N | Nature protocols | 34716448 | Nat Protoc | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34716448 |
| DART-ID increases single-cell proteome coverage. | Chen AT, Franks A, Slavov N | PLoS computational biology | 31260443 | PLoS Comput Biol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31260443 |
| Approaches for Studying Ribosome Specialization. | Emmott E, Jovanovic M, Slavov N | Trends in biochemical sciences | 30792028 | Trends Biochem Sci | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30792028 |
| Increasing the throughput of sensitive proteomics by plexDIA. | Derks J, Leduc A, Wallmann G, Huffman RG, Willetts M, Khan S, Specht H, Ralser M, Demichev V, Slavov N | Nature biotechnology | 35835881 | Nat Biotechnol | 2023 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35835881 |
| Scaling Up Single-Cell Proteomics. | Slavov N | Molecular & cellular proteomics : MCP | 34808355 | Mol Cell Proteomics | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34808355 |
| Measuring Protein Shapes in Living Cells. | Slavov N | Journal of proteome research | 33988997 | J Proteome Res | 2021 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/33988997 |
| Quantifying Homologous Proteins and Proteoforms. | Malioutov D, Chen T, Airoldi E, Jaffe J, Budnik B, Slavov N | Molecular & cellular proteomics : MCP | 30282776 | Mol Cell Proteomics | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30282776 |
| Structural coordination between active sites of a CRISPR reverse transcriptase-integrase complex. | Wang JY, Hoel CM, Al-Shayeb B, Banfield JF, Brohawn SG, Doudna JA | Nature communications | 33958590 | Nat Commun | 2021 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/33958590 |
| Small molecule SWELL1 complex induction improves glycemic control and nonalcoholic fatty liver disease in murine Type 2 diabetes. | Gunasekar SK, Xie L, Kumar A, Hong J, Chheda PR, Kang C, Kern DM, My-Ta C, Maurer J, Heebink J, Gerber EE, Grzesik WJ, Elliot-Hudson M, Zhang Y, Key P, Kulkarni CA, Beals JW, Smith GI, Samuel I, Smith JK, Nau P, Imai Y, Sheldon RD, Taylor EB, Lerner DJ, Norris AW, Klein S, Brohawn SG, Kerns R, Sah R | Nature communications | 35145074 | Nat Commun | 2022 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/35145074 |
| Author Correction: Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. | Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG | Nature structural & molecular biology | 34285420 | Nat Struct Mol Biol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34285420 |
| The mechanosensitive ion channel TRAAK is localized to the mammalian node of Ranvier. | Brohawn SG, Wang W, Handler A, Campbell EB, Schwarz JR, MacKinnon R | eLife | 31674909 | Elife | 2019 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/31674909 |
| SARS-CoV-2 3a expression, purification, and reconstitution into lipid nanodiscs. | Kern DM, Brohawn SG | Methods in enzymology | 34099172 | Methods Enzymol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34099172 |
| Structural basis for pH gating of the two-pore domain K(+) channel TASK2. | Li B, Rietmeijer RA, Brohawn SG | Nature | 32999458 | Nature | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32999458 |
| Cryo-EM structure of the SARS-CoV-2 3a ion channel in lipid nanodiscs. | Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG | bioRxiv : the preprint server for biology | 32587976 | bioRxiv | 2021 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/32587976 |
| Studying Mechanosensitivity of Two-Pore Domain K(+) Channels in Cellular and Reconstituted Proteoliposome Membranes. | Del Mármol J, Rietmeijer RA, Brohawn SG | Methods in molecular biology (Clifton, N.J.) | 29058189 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29058189 |
| Cryo-EM structures of the DCPIB-inhibited volume-regulated anion channel LRRC8A in lipid nanodiscs. | Kern DM, Oh S, Hite RK, Brohawn SG | eLife | 30775971 | Elife | 2019 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/30775971 |
| Structural Basis for pH-gating of the K(+) channel TWIK1 at the selectivity filter. | Turney TS, Li V, Brohawn SG | Nature communications | 35680900 | Nat Commun | 2022 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/35680900 |
| Cryo-EM structures of the channelrhodopsin ChRmine in lipid nanodiscs. | Tucker K, Sridharan S, Adesnik H, Brohawn SG | Nature communications | 35977941 | Nat Commun | 2022 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/35977941 |
| Structure of the GOLD-domain seven-transmembrane helix protein family member TMEM87A. | Hoel CM, Zhang L, Brohawn SG | eLife | 36373655 | Elife | 2022 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/36373655 |
| Physical basis for distinct basal and mechanically gated activity of the human K(+) channel TRAAK. | Rietmeijer RA, Sorum B, Li B, Brohawn SG | Neuron | 34390650 | Neuron | 2021 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/34390650 |
| Structures of tweety homolog proteins TTYH2 and TTYH3 reveal a Ca(2+)-dependent switch from intra- to intermembrane dimerization. | Li B, Hoel CM, Brohawn SG | Nature communications | 34824283 | Nat Commun | 2021 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/34824283 |
| Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs. | Kern DM, Sorum B, Mali SS, Hoel CM, Sridharan S, Remis JP, Toso DB, Kotecha A, Bautista DM, Brohawn SG | Nature structural & molecular biology | 34158638 | Nat Struct Mol Biol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34158638 |
| Ultrasound activates mechanosensitive TRAAK K(+) channels through the lipid membrane. | Sorum B, Rietmeijer RA, Gopakumar K, Adesnik H, Brohawn SG | Proceedings of the National Academy of Sciences of the United States of America | 33542098 | Proc Natl Acad Sci U S A | 2021 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/33542098 |
| Cryo-EM structure of the potassium-chloride cotransporter KCC4 in lipid nanodiscs. | Reid MS, Kern DM, Brohawn SG | eLife | 32286222 | Elife | 2020 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/32286222 |
| Germline DNA replication timing shapes mammalian genome composition. | Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, Mansour Y, Baror-Sebban S, Masika H, Farago M, Berger M, Carmi S, Buganim Y, Koren A, Simon I | Nucleic acids research | 29986092 | Nucleic Acids Res | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/29986092 |
| Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics. | Caballero M, Boos D, Koren A | Cell genomics | 37388911 | Cell Genom | 2023 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37388911 |
| Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. | Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A | Genes | 30987063 | Genes (Basel) | 2019 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/30987063 |
| Cancer Mutational Processes Vary in Their Association with Replication Timing and Chromatin Accessibility. | Yaacov A, Vardi O, Blumenfeld B, Greenberg A, Massey DJ, Koren A, Adar S, Simon I, Rosenberg S | Cancer research | 34702725 | Cancer Res | 2021 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/34702725 |
| The genetic architecture of DNA replication timing in human pluripotent stem cells. | Ding Q, Edwards MM, Wang N, Zhu X, Bracci AN, Hulke ML, Hu Y, Tong Y, Hsiao J, Charvet CJ, Ghosh S, Handsaker RE, Eggan K, Merkle FT, Gerhardt J, Egli D, Clark AG, Koren A | Nature communications | 34799581 | Nat Commun | 2021 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/34799581 |
| Telomere-to-telomere human DNA replication timing profiles. | Massey DJ, Koren A | Scientific reports | 35688856 | Sci Rep | 2022 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/35688856 |
| Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. | Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A | Human molecular genetics | 35394024 | Hum Mol Genet | 2022 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/35394024 |
| Mutation Rate Variability across Human Y-Chromosome Haplogroups. | Ding Q, Hu Y, Koren A, Clark AG | Molecular biology and evolution | 33049047 | Mol Biol Evol | 2021 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/33049047 |
| Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. | Hulke ML, Siefert JC, Sansam CL, Koren A | Genome biology and evolution | 31076752 | Genome Biol Evol | 2019 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/31076752 |
| TIGER: inferring DNA replication timing from whole-genome sequence data. | Koren A, Massey DJ, Bracci AN | Bioinformatics (Oxford, England) | 33704387 | Bioinformatics | 2021 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/33704387 |
| Positive and Negative Regulation of DNA Replication Initiation. | Ding Q, Koren A | Trends in genetics : TIG | 32739030 | Trends Genet | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32739030 |
| Genomic methods for measuring DNA replication dynamics. | Hulke ML, Massey DJ, Koren A | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 31848781 | Chromosome Res | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31848781 |
| Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. | Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV | Molecular cell | 33545059 | Mol Cell | 2021 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/33545059 |
| High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control. | Massey DJ, Koren A | Nature communications | 35504890 | Nat Commun | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35504890 |
| Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. | Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J | Genetics | 34740250 | Genetics | 2021 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/34740250 |
| Cohesin Core Complex Gene Dosage Contributes to Germinal Center Derived Lymphoma Phenotypes and Outcomes. | Rivas MA, Durmaz C, Kloetgen A, Chin CR, Chen Z, Bhinder B, Koren A, Viny AD, Scharer CD, Boss JM, Elemento O, Mason CE, Melnick AM | Frontiers in immunology | 34621263 | Front Immunol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34621263 |
| Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. | Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J | Molecular cell | 36099913 | Mol Cell | 2022 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/36099913 |
| Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer. | Webster ALH, Sanders MA, Patel K, Dietrich R, Noonan RJ, Lach FP, White RR, Goldfarb A, Hadi K, Edwards MM, Donovan FX, Hoogenboezem RM, Jung M, Sridhar S, Wiley TF, Fedrigo O, Tian H, Rosiene J, Heineman T, Kennedy JA, Bean L, Rosti RO, Tryon R, Gonzalez AM, Rosenberg A, Luo JD, Carroll TS, Shroff S, Beaumont M, Velleuer E, Rastatter JC, Wells SI, Surrallés J, Bagby G, MacMillan ML, Wagner JE, Cancio M, Boulad F, Scognamiglio T, Vaughan R, Beaumont KG, Koren A, Imielinski M, Chandrasekharappa SC, Auerbach AD, Singh B, Kutler DI, Campbell PJ, Smogorzewska A | Nature | 36450981 | Nature | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36450981 |
| Replication timing alterations in leukemia affect clinically relevant chromosome domains. | Rivera-Mulia JC, Sasaki T, Trevilla-Garcia C, Nakamichi N, Knapp DJHF, Hammond CA, Chang BH, Tyner JW, Devidas M, Zimmerman J, Klein KN, Somasundaram V, Druker BJ, Gruber TA, Koren A, Eaves CJ, Gilbert DM | Blood advances | 31698451 | Blood Adv | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31698451 |
| The landscape of somatic mutations in lymphoblastoid cell lines. | Caballero M, Koren A | Cell genomics | 37388907 | Cell Genom | 2023 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37388907 |
| Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology. | Lopez-Garrido J, Ojkic N, Khanna K, Wagner FR, Villa E, Endres RG, Pogliano K | Cell | 29425492 | Cell | 2018 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/29425492 |
| The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. | Lu S, Ye Q, Singh D, Cao Y, Diedrich JK, Yates JR 3rd, Villa E, Cleveland DW, Corbett KD | Nature communications | 33479198 | Nat Commun | 2021 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/33479198 |
| Comprehensive structure and functional adaptations of the yeast nuclear pore complex. | Akey CW, Singh D, Ouch C, Echeverria I, Nudelman I, Varberg JM, Yu Z, Fang F, Shi Y, Wang J, Salzberg D, Song K, Xu C, Gumbart JC, Suslov S, Unruh J, Jaspersen SL, Chait BT, Sali A, Fernandez-Martinez J, Ludtke SJ, Villa E, Rout MP | Cell | 34982960 | Cell | 2022 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/34982960 |
| Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. | Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E | Nature protocols | 32405053 | Nat Protoc | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32405053 |
| The In Situ Structure of Parkinson's Disease-Linked LRRK2. | Watanabe R, Buschauer R, Böhning J, Audagnotto M, Lasker K, Lu TW, Boassa D, Taylor S, Villa E | Cell | 32783917 | Cell | 2020 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/32783917 |
| HSP70 chaperones RNA-free TDP-43 into anisotropic intranuclear liquid spherical shells. | Yu H, Lu S, Gasior K, Singh D, Vazquez-Sanchez S, Tapia O, Toprani D, Beccari MS, Yates JR 3rd, Da Cruz S, Newby JM, Lafarga M, Gladfelter AS, Villa E, Cleveland DW | Science (New York, N.Y.) | 33335017 | Science | 2021 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/33335017 |
| ExoSloNano: Multi-Modal Nanogold Tags for identification of Macromolecules in Live Cells & Cryo-Electron Tomograms. | Young LN, Sherrard A, Zhou H, Shaikh F, Hutchings J, Riggi M, Rosen MK, Giraldez AJ, Villa E | bioRxiv : the preprint server for biology | 39416124 | bioRxiv | 2024 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/39416124 |
| The SARS-CoV-2 Nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein. | Lu S, Ye Q, Singh D, Villa E, Cleveland DW, Corbett KD | bioRxiv : the preprint server for biology | 32766587 | bioRxiv | 2020 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/32766587 |
| Shaping an Endospore: Architectural Transformations During Bacillus subtilis Sporulation. | Khanna K, Lopez-Garrido J, Pogliano K | Annual review of microbiology | 32660383 | Annu Rev Microbiol | 2020 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/32660383 |
| Practical Approaches for Cryo-FIB Milling and Applications for Cellular Cryo-Electron Tomography. | Lam V, Villa E | Methods in molecular biology (Clifton, N.J.) | 33367999 | Methods Mol Biol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/33367999 |
| Assembly of a nucleus-like structure during viral replication in bacteria. | Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JK, Vavilina A, Newton GL, Buschauer R, Pogliano K, Villa E, Agard DA, Pogliano J | Science (New York, N.Y.) | 28082593 | Science | 2017 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/28082593 |
| The molecular architecture of engulfment during Bacillus subtilis sporulation. | Khanna K, Lopez-Garrido J, Zhao Z, Watanabe R, Yuan Y, Sugie J, Pogliano K, Villa E | eLife | 31282858 | Elife | 2019 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/31282858 |
| Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria. | Chaikeeratisak V, Khanna K, Nguyen KT, Sugie J, Egan ME, Erb ML, Vavilina A, Nonejuie P, Nieweglowska E, Pogliano K, Agard DA, Villa E, Pogliano J | Cell | 31199917 | Cell | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31199917 |
| Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps. | Gilbert BR, Thornburg ZR, Lam V, Rashid FM, Glass JI, Villa E, Dame RT, Luthey-Schulten Z | Frontiers in molecular biosciences | 34368224 | Front Mol Biosci | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34368224 |
| Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. | Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z | The journal of physical chemistry. B | 28291359 | J Phys Chem B | 2017 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/28291359 |
| Structure of LRRK2 in Parkinson's disease and model for microtubule interaction. | Deniston CK, Salogiannis J, Mathea S, Snead DM, Lahiri I, Matyszewski M, Donosa O, Watanabe R, Böhning J, Shiau AK, Knapp S, Villa E, Reck-Peterson SL, Leschziner AE | Nature | 32814344 | Nature | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32814344 |
| The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems. | Lasker K, Boeynaems S, Lam V, Scholl D, Stainton E, Briner A, Jacquemyn M, Daelemans D, Deniz A, Villa E, Holehouse AS, Gitler AD, Shapiro L | Nature communications | 36163138 | Nat Commun | 2022 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/36163138 |
| Entropy-regularized deconvolution of cellular cryotransmission electron tomograms. | Croxford M, Elbaum M, Arigovindan M, Kam Z, Agard D, Villa E, Sedat J | Proceedings of the National Academy of Sciences of the United States of America | 34876518 | Proc Natl Acad Sci U S A | 2021 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/34876518 |
| How TPX2 helps microtubules branch out. | Alfaro-Aco R, Petry S | Cell cycle (Georgetown, Tex.) | 28767311 | Cell Cycle | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28767311 |
| Building the Microtubule Cytoskeleton Piece by Piece. | Alfaro-Aco R, Petry S | The Journal of biological chemistry | 25957410 | J Biol Chem | 2015 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/25957410 |
| A hydrodynamic instability drives protein droplet formation on microtubules to nucleate branches. | Setru SU, Gouveia B, Alfaro-Aco R, Shaevitz JW, Stone HA, Petry S | Nature physics | 35211183 | Nat Phys | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35211183 |
| Microtubule nucleation for spindle assembly: one molecule at a time. | Kraus J, Alfaro-Aco R, Gouveia B, Petry S | Trends in biochemical sciences | 37482516 | Trends Biochem Sci | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37482516 |
| Acentrosomal spindles assemble from branching microtubule nucleation near chromosomes in Xenopus laevis egg extract. | Gouveia B, Setru SU, King MR, Hamlin A, Stone HA, Shaevitz JW, Petry S | Nature communications | 37344488 | Nat Commun | 2023 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/37344488 |
| Mechanism of how augmin directly targets the γ-tubulin ring complex to microtubules. | Song JG, King MR, Zhang R, Kadzik RS, Thawani A, Petry S | The Journal of cell biology | 29875259 | J Cell Biol | 2018 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/29875259 |
| Mechanisms of Mitotic Spindle Assembly. | Petry S | Annual review of biochemistry | 27145846 | Annu Rev Biochem | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27145846 |
| The transition state and regulation of γ-TuRC-mediated microtubule nucleation revealed by single molecule microscopy. | Thawani A, Rale MJ, Coudray N, Bhabha G, Stone HA, Shaevitz JW, Petry S | eLife | 32538784 | Elife | 2020 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/32538784 |
| Structural analysis of the role of TPX2 in branching microtubule nucleation. | Alfaro-Aco R, Thawani A, Petry S | The Journal of cell biology | 28264915 | J Cell Biol | 2017 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/28264915 |
| Phase Transitioning the Centrosome into a Microtubule Nucleator. | Rale MJ, Kadzik RS, Petry S | Biochemistry | 29256606 | Biochemistry | 2018 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/29256606 |
| Biochemical reconstitution of branching microtubule nucleation. | Alfaro-Aco R, Thawani A, Petry S | eLife | 31933480 | Elife | 2020 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/31933480 |
| Spatiotemporal organization of branched microtubule networks. | Thawani A, Stone HA, Shaevitz JW, Petry S | eLife | 31066674 | Elife | 2019 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/31066674 |
| Structural basis of protein condensation on microtubules underlying branching microtubule nucleation. | Guo C, Alfaro-Aco R, Zhang C, Russell RW, Petry S, Polenova T | Nature communications | 37344496 | Nat Commun | 2023 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/37344496 |
| Molecular insight into how γ-TuRC makes microtubules. | Thawani A, Petry S | Journal of cell science | 34297125 | J Cell Sci | 2021 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/34297125 |
| How Microtubules Build the Spindle Branch by Branch. | Travis SM, Mahon BP, Petry S | Annual review of cell and developmental biology | 35759800 | Annu Rev Cell Dev Biol | 2022 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/35759800 |
| Confinement size determines the architecture of Ran-induced microtubule networks. | Gai Y, Cook B, Setru S, Stone HA, Petry S | Soft matter | 34041514 | Soft Matter | 2021 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/34041514 |
| XMAP215 is a microtubule nucleation factor that functions synergistically with the γ-tubulin ring complex. | Thawani A, Kadzik RS, Petry S | Nature cell biology | 29695792 | Nat Cell Biol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29695792 |
| Dissecting Protein Complexes in Branching Microtubule Nucleation Using Meiotic Xenopus Egg Extracts. | Song JG, Petry S | Cold Spring Harbor protocols | 29321281 | Cold Spring Harb Protoc | 2018 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/29321281 |
| Phase separation of TPX2 enhances and spatially coordinates microtubule nucleation. | King MR, Petry S | Nature communications | 31937751 | Nat Commun | 2020 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/31937751 |
| Visualizing and Analyzing Branching Microtubule Nucleation Using Meiotic Xenopus Egg Extracts and TIRF Microscopy. | King M, Petry S | Methods in molecular biology (Clifton, N.J.) | 27193844 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27193844 |
| The conserved centrosomin motif, γTuNA, forms a dimer that directly activates microtubule nucleation by the γ-tubulin ring complex (γTuRC). | Rale MJ, Romer B, Mahon BP, Travis SM, Petry S | eLife | 36515268 | Elife | 2022 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/36515268 |
| Allosteric modulation of protein-protein interactions by individual lipid binding events. | Cong X, Liu Y, Liu W, Liang X, Laganowsky A | Nature communications | 29259178 | Nat Commun | 2017 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/29259178 |
| Allostery revealed within lipid binding events to membrane proteins. | Patrick JW, Boone CD, Liu W, Conover GM, Liu Y, Cong X, Laganowsky A | Proceedings of the National Academy of Sciences of the United States of America | 29507234 | Proc Natl Acad Sci U S A | 2018 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/29507234 |
| Variable-Temperature Native Mass Spectrometry for Studies of Protein Folding, Stabilities, Assembly, and Molecular Interactions. | Laganowsky A, Clemmer DE, Russell DH | Annual review of biophysics | 34932911 | Annu Rev Biophys | 2022 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/34932911 |
| Native IM-Orbitrap MS: Resolving What Was Hidden. | Poltash ML, McCabe JW, Shirzadeh M, Laganowsky A, Russell DH | Trends in analytical chemistry : TRAC | 32189816 | Trends Analyt Chem | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32189816 |
| Structural basis for lipid and copper regulation of the ABC transporter MsbA. | Lyu J, Liu C, Zhang T, Schrecke S, Elam NP, Packianathan C, Hochberg GKA, Russell D, Zhao M, Laganowsky A | Nature communications | 36435815 | Nat Commun | 2022 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/36435815 |
| Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. | Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A | bioRxiv : the preprint server for biology | 37461710 | bioRxiv | 2023 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/37461710 |
| Enhanced Characterization of Membrane Protein Complexes by Ultraviolet Photodissociation Mass Spectrometry. | Sipe SN, Patrick JW, Laganowsky A, Brodbelt JS | Analytical chemistry | 31765130 | Anal Chem | 2020 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/31765130 |
| Selective binding of a toxin and phosphatidylinositides to a mammalian potassium channel. | Liu Y, LoCaste CE, Liu W, Poltash ML, Russell DH, Laganowsky A | Nature communications | 30902995 | Nat Commun | 2019 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/30902995 |
| Generation of Charge-Reduced Ions of Membrane Protein Complexes for Native Ion Mobility Mass Spectrometry Studies. | Patrick JW, Laganowsky A | Journal of the American Society for Mass Spectrometry | 30887461 | J Am Soc Mass Spectrom | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30887461 |
| Small molecule peptidomimetic trypsin inhibitors: validation of an EKO binding mode, but with a twist. | Lyu RL, Joy S, Packianathan C, Laganowsky A, Burgess K | Organic & biomolecular chemistry | 35225309 | Org Biomol Chem | 2022 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/35225309 |
| Cupric Ions Selectively Modulate TRAAK-Phosphatidylserine Interactions. | Zhu Y, Schrecke S, Tang S, Odenkirk MT, Walker T, Stover L, Lyu J, Zhang T, Russell D, Baker ES, Yan X, Laganowsky A | Journal of the American Chemical Society | 35421309 | J Am Chem Soc | 2022 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/35421309 |
| Development of Native MS Capabilities on an Extended Mass Range Q-TOF MS. | Mallis CS, Zheng X, Qiu X, McCabe JW, Shirzadeh M, Lyu J, Laganowsky A, Russell DH | International journal of mass spectrometry | 33162786 | Int J Mass Spectrom | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33162786 |
| Variable-Temperature Electrospray Ionization for Temperature-Dependent Folding/Refolding Reactions of Proteins and Ligand Binding. | McCabe JW, Shirzadeh M, Walker TE, Lin CW, Jones BJ, Wysocki VH, Barondeau DP, Clemmer DE, Laganowsky A, Russell DH | Analytical chemistry | 33904705 | Anal Chem | 2021 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33904705 |
| Selective regulation of human TRAAK channels by biologically active phospholipids. | Schrecke S, Zhu Y, McCabe JW, Bartz M, Packianathan C, Zhao M, Zhou M, Russell D, Laganowsky A | Nature chemical biology | 32989299 | Nat Chem Biol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32989299 |
| THE IMS PARADOX: A PERSPECTIVE ON STRUCTURAL ION MOBILITY-MASS SPECTROMETRY. | McCabe JW, Hebert MJ, Shirzadeh M, Mallis CS, Denton JK, Walker TE, Russell DH | Mass spectrometry reviews | 32608033 | Mass Spectrom Rev | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/32608033 |
| Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. | Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A | Analytical chemistry | 32672445 | Anal Chem | 2020 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/32672445 |
| Surface induced dissociation as a tool to study membrane protein complexes. | Harvey SR, Liu Y, Liu W, Wysocki VH, Laganowsky A | Chemical communications (Cambridge, England) | 28243658 | Chem Commun (Camb) | 2017 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/28243658 |
| Development and Evaluation of a Reverse-Entry Ion Source Orbitrap Mass Spectrometer. | Poltash ML, McCabe JW, Patrick JW, Laganowsky A, Russell DH | Journal of the American Society for Mass Spectrometry | 29796735 | J Am Soc Mass Spectrom | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29796735 |
| Fourier Transform-Ion Mobility-Orbitrap Mass Spectrometer: A Next-Generation Instrument for Native Mass Spectrometry. | Poltash ML, McCabe JW, Shirzadeh M, Laganowsky A, Clowers BH, Russell DH | Analytical chemistry | 30091588 | Anal Chem | 2018 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/30091588 |
| Topological Analysis of Transthyretin Disassembly Mechanism: Surface-Induced Dissociation Reveals Hidden Reaction Pathways. | Shirzadeh M, Boone CD, Laganowsky A, Russell DH | Analytical chemistry | 30642177 | Anal Chem | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30642177 |
| Variable-Temperature ESI-IMS-MS Analysis of Myohemerythrin Reveals Ligand Losses, Unfolding, and a Non-Native Disulfide Bond. | Woodall DW, El-Baba TJ, Fuller DR, Liu W, Brown CJ, Laganowsky A, Russell DH, Clemmer DE | Analytical chemistry | 31038926 | Anal Chem | 2019 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/31038926 |
| Insight into the Phospholipid-Binding Preferences of Kir3.4. | Qiao P, Schrecke S, Lyu J, Zhu Y, Zhang T, Benavides A, Laganowsky A | Biochemistry | 34846128 | Biochemistry | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34846128 |
| Entropy in the Molecular Recognition of Membrane Protein-Lipid Interactions. | Qiao P, Schrecke S, Walker T, McCabe JW, Lyu J, Zhu Y, Zhang T, Kumar S, Clemmer D, Russell DH, Laganowsky A | The journal of physical chemistry letters | 34928154 | J Phys Chem Lett | 2021 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/34928154 |
| Implementing Digital-Waveform Technology for Extended m/z Range Operation on a Native Dual-Quadrupole FT-IM-Orbitrap Mass Spectrometer. | McCabe JW, Jones BJ, Walker TE, Schrader RL, Huntley AP, Lyu J, Hoffman NM, Anderson GA, Reilly PTA, Laganowsky A, Wysocki VH, Russell DH | Journal of the American Society for Mass Spectrometry | 34797072 | J Am Soc Mass Spectrom | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/34797072 |
| Intrinsic GTPase Activity of K-RAS Monitored by Native Mass Spectrometry. | Moghadamchargari Z, Huddleston J, Shirzadeh M, Zheng X, Clemmer DE, M Raushel F, Russell DH, Laganowsky A | Biochemistry | 31306575 | Biochemistry | 2019 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/31306575 |
| First-Principles Collision Cross Section Measurements of Large Proteins and Protein Complexes. | McCabe JW, Mallis CS, Kocurek KI, Poltash ML, Shirzadeh M, Hebert MJ, Fan L, Walker TE, Zheng X, Jiang T, Dong S, Lin CW, Laganowsky A, Russell DH | Analytical chemistry | 32662991 | Anal Chem | 2020 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/32662991 |
| A Sec14-like phosphatidylinositol transfer protein paralog defines a novel class of heme-binding proteins. | Khan D, Lee D, Gulten G, Aggarwal A, Wofford J, Krieger I, Tripathi A, Patrick JW, Eckert DM, Laganowsky A, Sacchettini J, Lindahl P, Bankaitis VA | eLife | 32780017 | Elife | 2020 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/32780017 |
| Evidence for Many Unique Solution Structures for Chymotrypsin Inhibitor 2: A Thermodynamic Perspective Derived from vT-ESI-IMS-MS Measurements. | Raab SA, El-Baba TJ, Woodall DW, Liu W, Liu Y, Baird Z, Hales DA, Laganowsky A, Russell DH, Clemmer DE | Journal of the American Chemical Society | 32866376 | J Am Chem Soc | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32866376 |
| Investigation of Protein-Lipid Interactions Using Native Mass Spectrometry. | Cong X, Patrick JW, Liu Y, Liang X, Liu W, Laganowsky A | Methods in molecular biology (Clifton, N.J.) | 34718990 | Methods Mol Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/34718990 |
| Protons Are Fast and Smart; Proteins Are Slow and Dumb: On the Relationship of Electrospray Ionization Charge States and Conformations. | Raab SA, El-Baba TJ, Laganowsky A, Russell DH, Valentine SJ, Clemmer DE | Journal of the American Society for Mass Spectrometry | 34151568 | J Am Soc Mass Spectrom | 2021 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/34151568 |
| Protonation state of glutamate 73 regulates the formation of a specific dimeric association of mVDAC1. | Bergdoll LA, Lerch MT, Patrick JW, Belardo K, Altenbach C, Bisignano P, Laganowsky A, Grabe M, Hubbell WL, Abramson J | Proceedings of the National Academy of Sciences of the United States of America | 29279396 | Proc Natl Acad Sci U S A | 2018 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/29279396 |
| Molecular assemblies of the catalytic domain of SOS with KRas and oncogenic mutants. | Moghadamchargari Z, Shirzadeh M, Liu C, Schrecke S, Packianathan C, Russell DH, Zhao M, Laganowsky A | Proceedings of the National Academy of Sciences of the United States of America | 33723061 | Proc Natl Acad Sci U S A | 2021 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/33723061 |
| Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions. | Lyu J, Zhang T, Marty MT, Clemmer D, Russell DH, Laganowsky A | eLife | 38252560 | Elife | 2024 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/38252560 |
| GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs. | Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A | Bioinformatics (Oxford, England) | 29554289 | Bioinformatics | 2018 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/29554289 |
| Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis. | Liu X, Sun T, Shcherbina A, Li Q, Jarmoskaite I, Kappel K, Ramaswami G, Das R, Kundaje A, Li JB | Nature communications | 33846332 | Nat Commun | 2021 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/33846332 |
| NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA. | Wang YXR, Sarkar P, Ursu O, Kundaje A, Bickel PJ | The annals of applied statistics | 32968472 | Ann Appl Stat | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32968472 |
| Opportunities and challenges for transcriptome-wide association studies. | Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A | Nature genetics | 30926968 | Nat Genet | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30926968 |
| Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts. | Nair S, Kim DS, Perricone J, Kundaje A | Bioinformatics (Oxford, England) | 31510655 | Bioinformatics | 2019 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/31510655 |
| Denoising genome-wide histone ChIP-seq with convolutional neural networks. | Koh PW, Pierson E, Kundaje A | Bioinformatics (Oxford, England) | 28881977 | Bioinformatics | 2017 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/28881977 |
| Opportunities and obstacles for deep learning in biology and medicine. | Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS | Journal of the Royal Society, Interface | 29618526 | J R Soc Interface | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29618526 |
| GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs. | Shrikumar A, Prakash E, Kundaje A | Bioinformatics (Oxford, England) | 31510661 | Bioinformatics | 2019 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/31510661 |
| Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. | Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM | Cancer discovery | 30228179 | Cancer Discov | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30228179 |
| The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. | Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, Chang HY, Snyder MP, Greenleaf WJ, Kundaje A, Khavari PA | Nature genetics | 34650237 | Nat Genet | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34650237 |
| Base-resolution models of transcription-factor binding reveal soft motif syntax. | Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J | Nature genetics | 33603233 | Nat Genet | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33603233 |
| Prediction of protein-ligand interactions from paired protein sequence motifs and ligand substructures. | Greenside P, Hillenmeyer M, Kundaje A | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 29218866 | Pac Symp Biocomput | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29218866 |
| Brief Report: Cell Cycle Dynamics of Human Pluripotent Stem Cells Primed for Differentiation. | Shcherbina A, Li J, Narayanan C, Greenleaf W, Kundaje A, Chetty S | Stem cells (Dayton, Ohio) | 31135093 | Stem Cells | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31135093 |
| Homogeneity in the association of body mass index with type 2 diabetes across the UK Biobank: A Mendelian randomization study. | Wainberg M, Mahajan A, Kundaje A, McCarthy MI, Ingelsson E, Sinnott-Armstrong N, Rivas MA | PLoS medicine | 31821322 | PLoS Med | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31821322 |
| ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. | Marinov GK, Kundaje A | Briefings in functional genomics | 29529131 | Brief Funct Genomics | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29529131 |
| Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays. | Movva R, Greenside P, Marinov GK, Nair S, Shrikumar A, Kundaje A | PloS one | 31206543 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31206543 |
| MTSplice predicts effects of genetic variants on tissue-specific splicing. | Cheng J, Çelik MH, Kundaje A, Gagneur J | Genome biology | 33789710 | Genome Biol | 2021 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/33789710 |
| Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. | Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ | Nature genetics | 33927397 | Nat Genet | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33927397 |
| Accelerating in silico saturation mutagenesis using compressed sensing. | Schreiber J, Nair S, Balsubramani A, Kundaje A | Bioinformatics (Oxford, England) | 35678521 | Bioinformatics | 2022 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/35678521 |
| Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. | Greenside P, Shimko T, Fordyce P, Kundaje A | Bioinformatics (Oxford, England) | 30423062 | Bioinformatics | 2018 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/30423062 |
| The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. | Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J | Nature biotechnology | 31138913 | Nat Biotechnol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31138913 |
| fastISM: performant in silico saturation mutagenesis for convolutional neural networks. | Nair S, Shrikumar A, Schreiber J, Kundaje A | Bioinformatics (Oxford, England) | 35238376 | Bioinformatics | 2022 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/35238376 |
| Domain-adaptive neural networks improve cross-species prediction of transcription factor binding. | Cochran K, Srivastava D, Shrikumar A, Balsubramani A, Hardison RC, Kundaje A, Mahony S | Genome research | 35042722 | Genome Res | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35042722 |
| Transparency and reproducibility in artificial intelligence. | Haibe-Kains B, Adam GA, Hosny A, Khodakarami F, Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL | Nature | 33057217 | Nature | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33057217 |
| The chromatin landscape of the euryarchaeon Haloferax volcanii. | Marinov GK, Bagdatli ST, Wu T, He C, Kundaje A, Greenleaf WJ | Genome biology | 37932847 | Genome Biol | 2023 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/37932847 |
| Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease. | Ameen M, Sundaram L, Shen M, Banerjee A, Kundu S, Nair S, Shcherbina A, Gu M, Wilson KD, Varadarajan A, Vadgama N, Balsubramani A, Wu JC, Engreitz JM, Farh K, Karakikes I, Wang KC, Quertermous T, Greenleaf WJ, Kundaje A | Cell | 36563664 | Cell | 2022 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/36563664 |
| Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stability. | Greenstein RA, Al-Sady B | Current genetics | 30390097 | Curr Genet | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30390097 |
| Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. | Kennedy DR, Lemiere J, Tan C, Simental E, Braxton J, Maxwell RA, Amine AA, Al-Sady B | bioRxiv : the preprint server for biology | 39554105 | bioRxiv | 2024 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/39554105 |
| Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability. | Greenstein RA, Jones SK, Spivey EC, Rybarski JR, Finkelstein IJ, Al-Sady B | eLife | 30020075 | Elife | 2018 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/30020075 |
| The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states. | Murawska M, Greenstein RA, Schauer T, Olsen KCF, Ng H, Ladurner AG, Al-Sady B, Braun S | Cell reports | 34731638 | Cell Rep | 2021 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/34731638 |
| Heterodimerization of H3K9 histone methyltransferases G9a and GLP activates methyl reading and writing capabilities. | Sanchez NA, Kallweit LM, Trnka MJ, Clemmer CL, Al-Sady B | The Journal of biological chemistry | 34619147 | J Biol Chem | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34619147 |
| Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction. | Greenstein RA, Ng H, Barrales RR, Tan C, Braun S, Al-Sady B | PLoS genetics | 35584134 | PLoS Genet | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35584134 |
| Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability. | Greenstein RA, Barrales RR, Sanchez NA, Bisanz JE, Braun S, Al-Sady B | Genes & development | 31805521 | Genes Dev | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31805521 |
| Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. | Barandun J, Hunziker M, Klinge S | Current opinion in structural biology | 29414516 | Curr Opin Struct Biol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29414516 |
| The complete structure of the small-subunit processome. | Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S | Nature structural & molecular biology | 28945246 | Nat Struct Mol Biol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28945246 |
| Assembly and early maturation of large subunit precursors. | Chaker-Margot M, Klinge S | RNA (New York, N.Y.) | 30670483 | RNA | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30670483 |
| Conformational switches control early maturation of the eukaryotic small ribosomal subunit. | Hunziker M, Barandun J, Buzovetsky O, Steckler C, Molina H, Klinge S | eLife | 31206356 | Elife | 2019 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/31206356 |
| Ribosome assembly coming into focus. | Klinge S, Woolford JL Jr | Nature reviews. Molecular cell biology | 30467428 | Nat Rev Mol Cell Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30467428 |
| Nucleolar maturation of the human small subunit processome. | Singh S, Vanden Broeck A, Miller L, Chaker-Margot M, Klinge S | Science (New York, N.Y.) | 34516797 | Science | 2021 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/34516797 |
| Modular assembly of the nucleolar pre-60S ribosomal subunit. | Sanghai ZA, Miller L, Molloy KR, Barandun J, Hunziker M, Chaker-Margot M, Wang J, Chait BT, Klinge S | Nature | 29512650 | Nature | 2018 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/29512650 |
| Evolutionary compaction and adaptation visualized by the structure of the dormant microsporidian ribosome. | Barandun J, Hunziker M, Vossbrinck CR, Klinge S | Nature microbiology | 31332387 | Nat Microbiol | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31332387 |
| Machine Learning Establishes Single-Cell Calcium Dynamics as an Early Indicator of Antibiotic Response. | Meyer CT, Jewell MP, Miller EJ, Kralj JM | Microorganisms | 34063175 | Microorganisms | 2021 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/34063175 |
| Membrane voltage dysregulation driven by metabolic dysfunction underlies bactericidal activity of aminoglycosides. | Bruni GN, Kralj JM | eLife | 32748785 | Elife | 2020 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/32748785 |
| A high-throughput and low-waste viability assay for microbes. | Meyer CT, Lynch GK, Stamo DF, Miller EJ, Chatterjee A, Kralj JM | Nature microbiology | 37919425 | Nat Microbiol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37919425 |
| High Throughput Viability Assay for Microbiology. | Meyer CT, Lynch GK, Stamo DF, Miller EJ, Chatterjee A, Kralj JM | bioRxiv : the preprint server for biology | 36712102 | bioRxiv | 2023 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/36712102 |
| Genome-Wide Functional Screen for Calcium Transients in Escherichia coli Identifies Increased Membrane Potential Adaptation to Persistent DNA Damage. | Luder R, Bruni GN, Kralj JM | Journal of bacteriology | 33199283 | J Bacteriol | 2021 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33199283 |
| Voltage-gated calcium flux mediates Escherichia coli mechanosensation. | Bruni GN, Weekley RA, Dodd BJT, Kralj JM | Proceedings of the National Academy of Sciences of the United States of America | 28808010 | Proc Natl Acad Sci U S A | 2017 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/28808010 |
| Live Cell Imaging Reveals pH Oscillations in Saccharomyces cerevisiae During Metabolic Transitions. | Dodd BJT, Kralj JM | Scientific reports | 29066766 | Sci Rep | 2017 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/29066766 |
| Finding the Spark. | Kralj JM | Bioelectricity | 34476390 | Bioelectricity | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/34476390 |
| Microbial predictors of healing and short-term effect of debridement on the microbiome of chronic wounds. | Verbanic S, Shen Y, Lee J, Deacon JM, Chen IA | NPJ biofilms and microbiomes | 32358500 | NPJ Biofilms Microbiomes | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32358500 |
| PacBio sequencing output increased through uniform and directional fivefold concatenation. | Kanwar N, Blanco C, Chen IA, Seelig B | Scientific reports | 34508117 | Sci Rep | 2021 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/34508117 |
| Rapid Colorimetric Detection of Bacterial Species through the Capture of Gold Nanoparticles by Chimeric Phages. | Peng H, Chen IA | ACS nano | 30586498 | ACS Nano | 2019 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/30586498 |
| Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes. | Janzen E, Shen Y, Vázquez-Salazar A, Liu Z, Blanco C, Kenchel J, Chen IA | Nature communications | 35752631 | Nat Commun | 2022 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/35752631 |
| Effects of Preservation and Propagation Methodology on Microcosms Derived from the Oral Microbiome. | Zhou B, Mobberley J, Shi K, Chen IA | Microorganisms | 36363738 | Microorganisms | 2022 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/36363738 |
| Biosourced Functional Hydroxybenzoate-co-Lactide Polymers with Antimicrobial Activity. | Salas-Ambrosio P, Vexler S, P Sivasankaran R, Vlahakis N, Lai RS, Johnson C, Baas-Maynard SI, Min DS, Lower H, Doyle AG, Tang Y, Rodriguez JA, Chen IA, Read de Alaniz J, Maynard HD | Journal of the American Chemical Society | 40380948 | J Am Chem Soc | 2025 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/40380948 |
| Phage therapy administered noninvasively could be effective in thin tubes subject to episodic flow despite washout: a simulation study. | Blanco C, Chen IA | Physical biology | 31266001 | Phys Biol | 2019 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/31266001 |
| Modulation of α-Synuclein Aggregation In Vitro by a DNA Aptamer. | Tran CH, Saha R, Blanco C, Bagchi D, Chen IA | Biochemistry | 35994742 | Biochemistry | 2022 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/35994742 |
| Vesicle encapsulation stabilizes intermolecular association and structure formation of functional RNA and DNA. | Peng H, Lelievre A, Landenfeld K, Müller S, Chen IA | Current biology : CB | 34762821 | Curr Biol | 2022 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/34762821 |
| A Bayesian nonparametric analysis for zero-inflated multivariate count data with application to microbiome study. | Shuler K, Verbanic S, Chen IA, Lee J | Journal of the Royal Statistical Society. Series C, Applied statistics | 37440868 | J R Stat Soc Ser C Appl Stat | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37440868 |
| Preparation of Bioconjugates of Chimeric M13 Phage and Gold Nanorods. | Peng H, Chen IA | Methods in molecular biology (Clifton, N.J.) | 38526728 | Methods Mol Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38526728 |
| Visualization of Engineered M13 Phages Bound to Bacterial Targets by Transmission Electron Microscopy. | Yang Y, Chen IA | Methods in molecular biology (Clifton, N.J.) | 38526731 | Methods Mol Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38526731 |
| High throughput sequencing of in vitro selections of mRNA-displayed peptides: data analysis and applications. | Blanco C , Verbanic S , Seelig B , Chen IA | Physical chemistry chemical physics : PCCP | 31967131 | Phys Chem Chem Phys | 2020 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/31967131 |
| Pharmacokinetics and Biodistribution of Phages and their Current Applications in Antimicrobial Therapy. | Kang D, Bagchi D, Chen IA | Advanced therapeutics | 38933919 | Adv Ther (Weinh) | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38933919 |
| Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution. | Janzen E, Blanco C, Peng H, Kenchel J, Chen IA | Chemical reviews | 32011135 | Chem Rev | 2020 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/32011135 |
| The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes. | Verbanic S, Deacon JM, Chen IA | Microbiology spectrum | 35435739 | Microbiol Spectr | 2022 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/35435739 |
| Self-cleaving ribozymes: substrate specificity and synthetic biology applications. | Peng H, Latifi B, Müller S, Lupták A, Chen IA | RSC chemical biology | 34704043 | RSC Chem Biol | 2021 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/34704043 |
| Kinetic sequencing (k-Seq) as a massively parallel assay for ribozyme kinetics: utility and critical parameters. | Shen Y, Pressman A, Janzen E, Chen IA | Nucleic acids research | 33772580 | Nucleic Acids Res | 2021 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/33772580 |
| Chimeric Phage Nanoparticles for Rapid Characterization of Bacterial Pathogens: Detection in Complex Biological Samples and Determination of Antibiotic Sensitivity. | Peng H, Borg RE, Nguyen ABN, Chen IA | ACS sensors | 32314570 | ACS Sens | 2020 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/32314570 |
| EasyDIVER: A Pipeline for Assembling and Counting High-Throughput Sequencing Data from In Vitro Evolution of Nucleic Acids or Peptides. | Blanco C, Verbanic S, Seelig B, Chen IA | Journal of molecular evolution | 32529275 | J Mol Evol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32529275 |
| Treatment of Wound Infections in a Mouse Model Using Zn(2+)-Releasing Phage Bound to Gold Nanorods. | Peng H, Rossetto D, Mansy SS, Jordan MC, Roos KP, Chen IA | ACS nano | 35239330 | ACS Nano | 2022 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/35239330 |
| Improved single-swab sample preparation for recovering bacterial and phage DNA from human skin and wound microbiomes. | Verbanic S, Kim CY, Deacon JM, Chen IA | BMC microbiology | 31488062 | BMC Microbiol | 2019 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/31488062 |
| Phage engineering and the evolutionary arms race. | Peng H, Chen IA | Current opinion in biotechnology | 33113495 | Curr Opin Biotechnol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33113495 |
| Controlled phage therapy by photothermal ablation of specific bacterial species using gold nanorods targeted by chimeric phages. | Peng H, Borg RE, Dow LP, Pruitt BL, Chen IA | Proceedings of the National Academy of Sciences of the United States of America | 31932441 | Proc Natl Acad Sci U S A | 2020 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/31932441 |
| Genetically engineered filamentous phage for bacterial detection using magnetic resonance imaging. | Borg RE, Ozbakir HF, Xu B, Li E, Fang X, Peng H, Chen IA, Mukherjee A | Sensors & diagnostics | 38405385 | Sens Diagn | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/38405385 |
| Expression of Foxp3 by T follicular helper cells in end-stage germinal centers. | Jacobsen JT, Hu W, R Castro TB, Solem S, Galante A, Lin Z, Allon SJ, Mesin L, Bilate AM, Schiepers A, Shalek AK, Rudensky AY, Victora GD | Science (New York, N.Y.) | 34437125 | Science | 2021 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/34437125 |
| Allergic inflammatory memory in human respiratory epithelial progenitor cells. | Ordovas-Montanes J, Dwyer DF, Nyquist SK, Buchheit KM, Vukovic M, Deb C, Wadsworth MH 2nd, Hughes TK, Kazer SW, Yoshimoto E, Cahill KN, Bhattacharyya N, Katz HR, Berger B, Laidlaw TM, Boyce JA, Barrett NA, Shalek AK | Nature | 30135581 | Nature | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30135581 |
| A Single Human V(H)-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood. | Sangesland M, Yousif AS, Ronsard L, Kazer SW, Zhu AL, Gatter GJ, Hayward MR, Barnes RM, Quirindongo-Crespo M, Rohrer D, Lonberg N, Kwon D, Shalek AK, Lingwood D | Cell reports | 32846123 | Cell Rep | 2020 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/32846123 |
| Circulating CXCR5(+)CXCR3(+)PD-1(lo) Tfh-like cells in HIV-1 controllers with neutralizing antibody breadth. | Martin-Gayo E, Cronin J, Hickman T, Ouyang Z, Lindqvist M, Kolb KE, Schulze Zur Wiesch J, Cubas R, Porichis F, Shalek AK, van Lunzen J, Haddad EK, Walker BD, Kaufmann DE, Lichterfeld M, Yu XG | JCI insight | 28138558 | JCI Insight | 2017 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/28138558 |
| Novel in vitro booster vaccination to rapidly generate antigen-specific human monoclonal antibodies. | Sanjuan Nandin I, Fong C, Deantonio C, Torreno-Pina JA, Pecetta S, Maldonado P, Gasparrini F, Ordovas-Montanes J, Kazer SW, Kjaer S, Borley DW, Nair U, Coleman JA, Lingwood D, Shalek AK, Meffre E, Poignard P, Burton DR, Batista FD | The Journal of experimental medicine | 28739603 | J Exp Med | 2017 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/28739603 |
| Antiviral CD8(+) T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion. | Ranasinghe S, Lamothe PA, Soghoian DZ, Kazer SW, Cole MB, Shalek AK, Yosef N, Jones RB, Donaghey F, Nwonu C, Jani P, Clayton GM, Crawford F, White J, Montoya A, Power K, Allen TM, Streeck H, Kaufmann DE, Picker LJ, Kappler JW, Walker BD | Immunity | 27760342 | Immunity | 2016 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/27760342 |
| Optofluidic real-time cell sorter for longitudinal CTC studies in mouse models of cancer. | Hamza B, Ng SR, Prakadan SM, Delgado FF, Chin CR, King EM, Yang LF, Davidson SM, DeGouveia KL, Cermak N, Navia AW, Winter PS, Drake RS, Tammela T, Li CM, Papagiannakopoulos T, Gupta AJ, Shaw Bagnall J, Knudsen SM, Vander Heiden MG, Wasserman SC, Jacks T, Shalek AK, Manalis SR | Proceedings of the National Academy of Sciences of the United States of America | 30674677 | Proc Natl Acad Sci U S A | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30674677 |
| Single-cell analyses to tailor treatments. | Shalek AK, Benson M | Science translational medicine | 28931656 | Sci Transl Med | 2017 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/28931656 |
| Identification of a Master Regulator of Differentiation in Toxoplasma. | Waldman BS, Schwarz D, Wadsworth MH 2nd, Saeij JP, Shalek AK, Lourido S | Cell | 31955846 | Cell | 2020 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/31955846 |
| PI3Kβ controls immune evasion in PTEN-deficient breast tumours. | Bergholz JS, Wang Q, Wang Q, Ramseier M, Prakadan S, Wang W, Fang R, Kabraji S, Zhou Q, Gray GK, Abell-Hart K, Xie S, Guo X, Gu H, Von T, Jiang T, Tang S, Freeman GJ, Kim HJ, Shalek AK, Roberts TM, Zhao JJ | Nature | 37076617 | Nature | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37076617 |
| Screening for modulators of the cellular composition of gut epithelia via organoid models of intestinal stem cell differentiation. | Mead BE, Hattori K, Levy L, Imada S, Goto N, Vukovic M, Sze D, Kummerlowe C, Matute JD, Duan J, Langer R, Blumberg RS, Ordovas-Montanes J, Yilmaz ÖH, Karp JM, Shalek AK | Nature biomedical engineering | 35314801 | Nat Biomed Eng | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35314801 |
| Single-Cell Analysis of the Liver Epithelium Reveals Dynamic Heterogeneity and an Essential Role for YAP in Homeostasis and Regeneration. | Pepe-Mooney BJ, Dill MT, Alemany A, Ordovas-Montanes J, Matsushita Y, Rao A, Sen A, Miyazaki M, Anakk S, Dawson PA, Ono N, Shalek AK, van Oudenaarden A, Camargo FD | Cell stem cell | 31080134 | Cell Stem Cell | 2019 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/31080134 |
| A validated single-cell-based strategy to identify diagnostic and therapeutic targets in complex diseases. | Gawel DR, Serra-Musach J, Lilja S, Aagesen J, Arenas A, Asking B, Bengnér M, Björkander J, Biggs S, Ernerudh J, Hjortswang H, Karlsson JE, Köpsen M, Lee EJ, Lentini A, Li X, Magnusson M, Martínez-Enguita D, Matussek A, Nestor CE, Schäfer S, Seifert O, Sonmez C, Stjernman H, Tjärnberg A, Wu S, Åkesson K, Shalek AK, Stenmarker M, Zhang H, Gustafsson M, Benson M | Genome medicine | 31358043 | Genome Med | 2019 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/31358043 |
| Seq-Well: A Sample-Efficient, Portable Picowell Platform for Massively Parallel Single-Cell RNA Sequencing. | Aicher TP, Carroll S, Raddi G, Gierahn T, Wadsworth MH 2nd, Hughes TK, Love C, Shalek AK | Methods in molecular biology (Clifton, N.J.) | 31028635 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31028635 |
| Inflammasomes within Hyperactive Murine Dendritic Cells Stimulate Long-Lived T Cell-Mediated Anti-tumor Immunity. | Zhivaki D, Borriello F, Chow OA, Doran B, Fleming I, Theisen DJ, Pallis P, Shalek AK, Sokol CL, Zanoni I, Kagan JC | Cell reports | 33207188 | Cell Rep | 2020 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/33207188 |
| Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. | Tirosh I, Izar B, Prakadan SM, Wadsworth MH 2nd, Treacy D, Trombetta JJ, Rotem A, Rodman C, Lian C, Murphy G, Fallahi-Sichani M, Dutton-Regester K, Lin JR, Cohen O, Shah P, Lu D, Genshaft AS, Hughes TK, Ziegler CG, Kazer SW, Gaillard A, Kolb KE, Villani AC, Johannessen CM, Andreev AY, Van Allen EM, Bertagnolli M, Sorger PK, Sullivan RJ, Flaherty KT, Frederick DT, Jané-Valbuena J, Yoon CH, Rozenblatt-Rosen O, Shalek AK, Regev A, Garraway LA | Science (New York, N.Y.) | 27124452 | Science | 2016 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/27124452 |
| A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages. | Kimmerling RJ, Lee Szeto G, Li JW, Genshaft AS, Kazer SW, Payer KR, de Riba Borrajo J, Blainey PC, Irvine DJ, Shalek AK, Manalis SR | Nature communications | 26732280 | Nat Commun | 2016 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/26732280 |
| Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction. | Genshaft AS, Li S, Gallant CJ, Darmanis S, Prakadan SM, Ziegler CG, Lundberg M, Fredriksson S, Hong J, Regev A, Livak KJ, Landegren U, Shalek AK | Genome biology | 27640647 | Genome Biol | 2016 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/27640647 |
| Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential. | Huang S, Ziegler CGK, Austin J, Mannoun N, Vukovic M, Ordovas-Montanes J, Shalek AK, von Andrian UH | Cell | 33333021 | Cell | 2021 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/33333021 |
| Distribution and storage of inflammatory memory in barrier tissues. | Ordovas-Montanes J, Beyaz S, Rakoff-Nahoum S, Shalek AK | Nature reviews. Immunology | 32015472 | Nat Rev Immunol | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32015472 |
| Tobacco smoke exposure recruits inflammatory airspace monocytes that establish permissive lung niches for Mycobacterium tuberculosis. | Corleis B, Tzouanas CN, Wadsworth MH 2nd, Cho JL, Linder AH, Schiff AE, Zessin B, Stei F, Dorhoi A, Dickey AK, Medoff BD, Shalek AK, Kwon DS | Science translational medicine | 38055798 | Sci Transl Med | 2023 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/38055798 |
| Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput. | Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK | Nature methods | 28192419 | Nat Methods | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28192419 |
| Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices. | Prakadan SM, Shalek AK, Weitz DA | Nature reviews. Genetics | 28392571 | Nat Rev Genet | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28392571 |
| Tuning of in vivo cognate B-T cell interactions by Intersectin 2 is required for effective anti-viral B cell immunity. | Burbage M, Gasparrini F, Aggarwal S, Gaya M, Arnold J, Nair U, Way M, Bruckbauer A, Batista FD | eLife | 29337666 | Elife | 2018 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/29337666 |
| Germline-Encoded Affinity for Cognate Antigen Enables Vaccine Amplification of a Human Broadly Neutralizing Response against Influenza Virus. | Sangesland M, Ronsard L, Kazer SW, Bals J, Boyoglu-Barnum S, Yousif AS, Barnes R, Feldman J, Quirindongo-Crespo M, McTamney PM, Rohrer D, Lonberg N, Chackerian B, Graham BS, Kanekiyo M, Shalek AK, Lingwood D | Immunity | 31563464 | Immunity | 2019 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/31563464 |
| TCR sequencing paired with massively parallel 3' RNA-seq reveals clonotypic T cell signatures. | Tu AA, Gierahn TM, Monian B, Morgan DM, Mehta NK, Ruiter B, Shreffler WG, Shalek AK, Love JC | Nature immunology | 31745340 | Nat Immunol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31745340 |
| Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. | Tsankov AM, Wadsworth MH 2nd, Akopian V, Charlton J, Allon SJ, Arczewska A, Mead BE, Drake RS, Smith ZD, Mikkelsen TS, Shalek AK, Meissner A | Development (Cambridge, England) | 31515224 | Development | 2019 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/31515224 |
| Mechanisms of Lymphoma Clearance Induced by High-Dose Alkylating Agents. | Lossos C, Liu Y, Kolb KE, Christie AL, Van Scoyk A, Prakadan SM, Shigemori K, Stevenson KE, Morrow S, Plana OD, Fraser C, Jones KL, Liu H, Pallasch CP, Modiste R, Nguyen QD, Craig JW, Morgan EA, Vega F, Aster JC, Sarosiek KA, Shalek AK, Hemann MT, Weinstock DM | Cancer discovery | 31040105 | Cancer Discov | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31040105 |
| Live cell tagging tracking and isolation for spatial transcriptomics using photoactivatable cell dyes. | Genshaft AS, Ziegler CGK, Tzouanas CN, Mead BE, Jaeger AM, Navia AW, King RP, Mana MD, Huang S, Mitsialis V, Snapper SB, Yilmaz ÖH, Jacks T, Van Humbeck JF, Shalek AK | Nature communications | 34404785 | Nat Commun | 2021 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/34404785 |
| Cyclin D3 drives inertial cell cycling in dark zone germinal center B cells. | Pae J, Ersching J, Castro TBR, Schips M, Mesin L, Allon SJ, Ordovas-Montanes J, Mlynarczyk C, Melnick A, Efeyan A, Shalek AK, Meyer-Hermann M, Victora GD | The Journal of experimental medicine | 33332554 | J Exp Med | 2021 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/33332554 |
| A Reproducibility-Based Computational Framework Identifies an Inducible, Enhanced Antiviral State in Dendritic Cells from HIV-1 Elite Controllers. | Martin-Gayo E, Cole MB, Kolb KE, Ouyang Z, Cronin J, Kazer SW, Ordovas-Montanes J, Lichterfeld M, Walker BD, Yosef N, Shalek AK, Yu XG | Genome biology | 29378643 | Genome Biol | 2018 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/29378643 |
| Distinct olfactory mucosal macrophage populations mediate neuronal maintenance and pathogen defense. | Wellford SA, Chen CW, Vukovic M, Batich KA, Lin E, Shalek AK, Ordovas-Montanes J, Moseman AP, Moseman EA | Mucosal immunology | 39074615 | Mucosal Immunol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39074615 |
| The mammalian kinetochore-microtubule interface: robust mechanics and computation with many microtubules. | Long AF, Kuhn J, Dumont S | Current opinion in cell biology | 31132675 | Curr Opin Cell Biol | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31132675 |
| Spindle assembly checkpoint satisfaction occurs via end-on but not lateral attachments under tension. | Kuhn J, Dumont S | The Journal of cell biology | 28536121 | J Cell Biol | 2017 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/28536121 |
| MYC Dysregulates Mitosis, Revealing Cancer Vulnerabilities. | Rohrberg J, Van de Mark D, Amouzgar M, Lee JV, Taileb M, Corella A, Kilinc S, Williams J, Jokisch ML, Camarda R, Balakrishnan S, Shankar R, Zhou A, Chang AN, Chen B, Rugo HS, Dumont S, Goga A | Cell reports | 32160543 | Cell Rep | 2020 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/32160543 |
| NuMA recruits dynein activity to microtubule minus-ends at mitosis. | Hueschen CL, Kenny SJ, Xu K, Dumont S | eLife | 29185983 | Elife | 2017 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/29185983 |
| The chromokinesin Klp3a and microtubules facilitate acentric chromosome segregation. | Karg T, Elting MW, Vicars H, Dumont S, Sullivan W | The Journal of cell biology | 28500183 | J Cell Biol | 2017 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/28500183 |
| Opposing motors provide mechanical and functional robustness in the human spindle. | Neahring L, Cho NH, Dumont S | Developmental cell | 34614397 | Dev Cell | 2021 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/34614397 |
| Hec1 Tail Phosphorylation Differentially Regulates Mammalian Kinetochore Coupling to Polymerizing and Depolymerizing Microtubules. | Long AF, Udy DB, Dumont S | Current biology : CB | 28552353 | Curr Biol | 2017 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/28552353 |
| The Spindle: Integrating Architecture and Mechanics across Scales. | Elting MW, Suresh P, Dumont S | Trends in cell biology | 30093097 | Trends Cell Biol | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30093097 |
| Increased lateral microtubule contact at the cell cortex is sufficient to drive mammalian spindle elongation. | Guild J, Ginzberg MB, Hueschen CL, Mitchison TJ, Dumont S | Molecular biology of the cell | 28468979 | Mol Biol Cell | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28468979 |
| Mapping Load-Bearing in the Mammalian Spindle Reveals Local Kinetochore Fiber Anchorage that Provides Mechanical Isolation and Redundancy. | Elting MW, Prakash M, Udy DB, Dumont S | Current biology : CB | 28690110 | Curr Biol | 2017 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/28690110 |
| The mitotic protein NuMA plays a spindle-independent role in nuclear formation and mechanics. | Serra-Marques A, Houtekamer R, Hintzen D, Canty JT, Yildiz A, Dumont S | The Journal of cell biology | 33044554 | J Cell Biol | 2020 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/33044554 |
| Microtubule End-Clustering Maintains a Steady-State Spindle Shape. | Hueschen CL, Galstyan V, Amouzgar M, Phillips R, Dumont S | Current biology : CB | 30744975 | Curr Biol | 2019 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/30744975 |
| Individual kinetochore-fibers locally dissipate force to maintain robust mammalian spindle structure. | Long AF, Suresh P, Dumont S | The Journal of cell biology | 32435797 | J Cell Biol | 2020 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/32435797 |
| Mammalian kinetochores count attached microtubules in a sensitive and switch-like manner. | Kuhn J, Dumont S | The Journal of cell biology | 31492713 | J Cell Biol | 2019 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/31492713 |
| Microneedle manipulation of the mammalian spindle reveals specialized, short-lived reinforcement near chromosomes. | Suresh P, Long AF, Dumont S | eLife | 32191206 | Elife | 2020 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/32191206 |
| The Astrin-SKAP complex reduces friction at the kinetochore-microtubule interface. | Rosas-Salvans M, Sutanto R, Suresh P, Dumont S | Current biology : CB | 35580605 | Curr Biol | 2022 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/35580605 |
| Progress and challenges for chemical probing of RNA structure inside living cells. | Kubota M, Tran C, Spitale RC | Nature chemical biology | 26575240 | Nat Chem Biol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26575240 |
| Assaying RNA solvent accessibility in living cells with LASER. | Feng C, Spitale RC | Methods in enzymology | 32713532 | Methods Enzymol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32713532 |
| Bioorthogonal Metabolic Labeling of Nascent RNA in Neurons Improves the Sensitivity of Transcriptome-Wide Profiling. | Zajaczkowski EL, Zhao QY, Zhang ZH, Li X, Wei W, Marshall PR, Leighton LJ, Nainar S, Feng C, Spitale RC, Bredy TW | ACS chemical neuroscience | 29874042 | ACS Chem Neurosci | 2018 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/29874042 |
| Protected pyrimidine nucleosides for cell-specific metabolic labeling of RNA. | Beasley S, Nguyen K, Fazio M, Spitale RC | Tetrahedron letters | 31031425 | Tetrahedron Lett | 2018 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/31031425 |
| Measuring RNA structure transcriptome-wide with icSHAPE. | Chan D, Feng C, Spitale RC | Methods (San Diego, Calif.) | 28336307 | Methods | 2017 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/28336307 |
| Human iPSC-derived microglia: A growing toolset to study the brain's innate immune cells. | Hasselmann J, Blurton-Jones M | Glia | 31926038 | Glia | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31926038 |
| Evolving insights into RNA modifications and their functional diversity in the brain. | Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW | Nature neuroscience | 27669990 | Nat Neurosci | 2016 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/27669990 |
| Defining Functional Structured RNA inside Living Cells. | Chan D, Spitale RC | Biochemistry | 29064690 | Biochemistry | 2017 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/29064690 |
| Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. | Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC | ACS chemical biology | 31310712 | ACS Chem Biol | 2019 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/31310712 |
| Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq. | Engel KL, Lo HG, Goering R, Li Y, Spitale RC, Taliaferro JM | Nucleic acids research | 34875090 | Nucleic Acids Res | 2022 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/34875090 |
| Biochemical Methods To Image and Analyze RNA Localization: From One to Many. | Li Y, Ke K, Spitale RC | Biochemistry | 30444114 | Biochemistry | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30444114 |
| Chemical Tools for Dissecting the Role of lncRNAs in Epigenetic Regulation. | Nainar S, Feng C, Spitale RC | ACS chemical biology | 27267401 | ACS Chem Biol | 2016 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/27267401 |
| Assaying RNA Structure Inside Living Cells with SHAPE. | Feng C, Chan D, Spitale RC | Methods in molecular biology (Clifton, N.J.) | 28766302 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28766302 |
| Photo-controlled cell-specific metabolic labeling of RNA. | Feng C, Li Y, Spitale RC | Organic & biomolecular chemistry | 28569333 | Org Biomol Chem | 2017 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/28569333 |
| Development of a Chimeric Model to Study and Manipulate Human Microglia In Vivo. | Hasselmann J, Coburn MA, England W, Figueroa Velez DX, Kiani Shabestari S, Tu CH, McQuade A, Kolahdouzan M, Echeverria K, Claes C, Nakayama T, Azevedo R, Coufal NG, Han CZ, Cummings BJ, Davtyan H, Glass CK, Healy LM, Gandhi SP, Spitale RC, Blurton-Jones M | Neuron | 31375314 | Neuron | 2019 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/31375314 |
| A Bump-Hole Strategy for Increased Stringency of Cell-Specific Metabolic Labeling of RNA. | Nguyen K, Kubota M, Arco JD, Feng C, Singha M, Beasley S, Sakr J, Gandhi SP, Blurton-Jones M, Fernández Lucas J, Spitale RC | ACS chemical biology | 33222436 | ACS Chem Biol | 2020 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/33222436 |
| Metabolic Incorporation of Azide Functionality into Cellular RNA. | Nainar S, Beasley S, Fazio M, Kubota M, Dai N, Corrêa IR Jr, Spitale RC | Chembiochem : a European journal of chemical biology | 27595557 | Chembiochem | 2016 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/27595557 |
| Assaying RNA Localization in Situ with Spatially Restricted Nucleobase Oxidation. | Li Y, Aggarwal MB, Nguyen K, Ke K, Spitale RC | ACS chemical biology | 28952711 | ACS Chem Biol | 2017 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/28952711 |
| Multiplex Aptamer Discovery through Apta-Seq and Its Application to ATP Aptamers Derived from Human-Genomic SELEX. | Abdelsayed MM, Ho BT, Vu MMK, Polanco J, Spitale RC, Lupták A | ACS chemical biology | 28661647 | ACS Chem Biol | 2017 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/28661647 |
| Halo-seq: An RNA Proximity Labeling Method for the Isolation and Analysis of Subcellular RNA Populations. | Lo HG, Engel KL, Goering R, Li Y, Spitale RC, Taliaferro JM | Current protocols | 35532287 | Curr Protoc | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35532287 |
| Cycloaddition enabled mutational profiling of 5-vinyluridine in RNA. | Gupta M, Wang J, Garfio CM, Vandewalle A, Spitale RC | Chemical communications (Cambridge, England) | 36815680 | Chem Commun (Camb) | 2023 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/36815680 |
| Comparative Analysis Reveals Furoyl in Vivo Selective Hydroxyl Acylation Analyzed by Primer Extension Reagents Form Stable Ribosyl Ester Adducts. | Chan D, Feng C, Zhen Y, Flynn RA, Spitale RC | Biochemistry | 28319368 | Biochemistry | 2017 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/28319368 |
| Facile synthesis and evaluation of a dual-functioning furoyl probe for in-cell SHAPE. | Chan D, Beasley S, Zhen Y, Spitale RC | Bioorganic & medicinal chemistry letters | 29398542 | Bioorg Med Chem Lett | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29398542 |
| Improved Analysis of RNA Localization by Spatially Restricted Oxidation of RNA-Protein Complexes. | Li Y, Aggarwal MB, Ke K, Nguyen K, Spitale RC | Biochemistry | 29474061 | Biochemistry | 2018 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/29474061 |
| Light-activated chemical probing of nucleobase solvent accessibility inside cells. | Feng C, Chan D, Joseph J, Muuronen M, Coldren WH, Dai N, Corrêa IR Jr, Furche F, Hadad CM, Spitale RC | Nature chemical biology | 29334380 | Nat Chem Biol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29334380 |
| Spatially Restricting Bioorthogonal Nucleoside Biosynthesis Enables Selective Metabolic Labeling of the Mitochondrial Transcriptome. | Nguyen K, Aggarwal MB, Feng C, Balderrama G, Fazio M, Mortazavi A, Spitale RC | ACS chemical biology | 29756767 | ACS Chem Biol | 2018 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/29756767 |
| Identification of Adenosine-to-Inosine RNA Editing with Acrylonitrile Reagents. | Li Y, Göhl M, Ke K, Vanderwal CD, Spitale RC | Organic letters | 31516001 | Org Lett | 2019 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/31516001 |
| Mutually Orthogonal DNA Replication Systems In Vivo. | Arzumanyan GA, Gabriel KN, Ravikumar A, Javanpour AA, Liu CC | ACS synthetic biology | 29969238 | ACS Synth Biol | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/29969238 |
| Genetic Compatibility and Extensibility of Orthogonal Replication. | Javanpour AA, Liu CC | ACS synthetic biology | 31095905 | ACS Synth Biol | 2019 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/31095905 |
| Automated Continuous Evolution of Proteins in Vivo. | Zhong Z, Wong BG, Ravikumar A, Arzumanyan GA, Khalil AS, Liu CC | ACS synthetic biology | 32374988 | ACS Synth Biol | 2020 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/32374988 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Hu VJ, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | Nature chemical biology | 34168368 | Nat Chem Biol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34168368 |
| Evolving Small-Molecule Biosensors with Improved Performance and Reprogrammed Ligand Preference Using OrthoRep. | Javanpour AA, Liu CC | ACS synthetic biology | 34597502 | ACS Synth Biol | 2021 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/34597502 |
| Tunable Expression Systems for Orthogonal DNA Replication. | Zhong Z, Ravikumar A, Liu CC | ACS synthetic biology | 30408954 | ACS Synth Biol | 2018 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/30408954 |
| Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. | Rix G, Watkins-Dulaney EJ, Almhjell PJ, Boville CE, Arnold FH, Liu CC | Nature communications | 33159067 | Nat Commun | 2020 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/33159067 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | bioRxiv : the preprint server for biology | 33200136 | bioRxiv | 2020 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/33200136 |
| Open-ended molecular recording of sequential cellular events into DNA. | Loveless TB, Carlson CK, Dentzel Helmy CA, Hu VJ, Ross SK, Demelo MC, Murtaza A, Liang G, Ficht M, Singhai A, Pajoh-Casco MJ, Liu CC | Nature chemical biology | 39543397 | Nat Chem Biol | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39543397 |
| Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds. | Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, Liu CC | Cell | 30415839 | Cell | 2018 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/30415839 |
| Toward an orthogonal central dogma. | Liu CC, Jewett MC, Chin JW, Voigt CA | Nature chemical biology | 29337969 | Nat Chem Biol | 2018 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/29337969 |
| Synthetic Epigenetics To Engineer Regulation. | Loveless TB, Liu CC | Biochemistry | 30860818 | Biochemistry | 2019 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/30860818 |
| Probing pathways of adaptation with continuous evolution. | Zhong Z, Liu CC | Current opinion in systems biology | 31608311 | Curr Opin Syst Biol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31608311 |
| Lineage tracing and analog recording in mammalian cells by single-site DNA writing. | Loveless TB, Grotts JH, Schechter MW, Forouzmand E, Carlson CK, Agahi BS, Liang G, Ficht M, Liu B, Xie X, Liu CC | Nature chemical biology | 33753928 | Nat Chem Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33753928 |
| An Adaptable Platform for Directed Evolution in Human Cells. | Berman CM, Papa LJ 3rd, Hendel SJ, Moore CL, Suen PH, Weickhardt AF, Doan ND, Kumar CM, Uil TG, Butty VL, Hoeben RC, Shoulders MD | Journal of the American Chemical Society | 30427676 | J Am Chem Soc | 2018 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/30427676 |
| Genetic Engineering by DNA Recombineering. | Papa LJ 3rd, Shoulders MD | Current protocols in chemical biology | 31483098 | Curr Protoc Chem Biol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31483098 |
| Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin. | Phillips AM, Doud MB, Gonzalez LO, Butty VL, Lin YS, Bloom JD, Shoulders MD | eLife | 30188321 | Elife | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/30188321 |
| Transportable, Chemical Genetic Methodology for the Small Molecule-Mediated Inhibition of Heat Shock Factor 1. | Moore CL, Dewal MB, Nekongo EE, Santiago S, Lu NB, Levine SS, Shoulders MD | ACS chemical biology | 26502114 | ACS Chem Biol | 2016 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/26502114 |
| Chemical Biology Framework to Illuminate Proteostasis. | Sebastian RM, Shoulders MD | Annual review of biochemistry | 32097570 | Annu Rev Biochem | 2020 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/32097570 |
| Multidimensional chemical control of CRISPR-Cas9. | Maji B, Moore CL, Zetsche B, Volz SE, Zhang F, Shoulders MD, Choudhary A | Nature chemical biology | 27820801 | Nat Chem Biol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27820801 |
| Host proteostasis modulates influenza evolution. | Phillips AM, Gonzalez LO, Nekongo EE, Ponomarenko AI, McHugh SM, Butty VL, Levine SS, Lin YS, Mirny LA, Shoulders MD | eLife | 28949290 | Elife | 2017 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/28949290 |
| A Processive Protein Chimera Introduces Mutations across Defined DNA Regions In Vivo. | Moore CL, Papa LJ 3rd, Shoulders MD | Journal of the American Chemical Society | 29991261 | J Am Chem Soc | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/29991261 |
| Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones. | Phillips AM, Ponomarenko AI, Chen K, Ashenberg O, Miao J, McHugh SM, Butty VL, Whittaker CA, Moore CL, Bloom JD, Lin YS, Shoulders MD | PLoS biology | 30222731 | PLoS Biol | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30222731 |
| The Path of Least Resistance: Mechanisms to Reduce Influenza's Sensitivity to Oseltamivir. | Phillips AM, Shoulders MD | Journal of molecular biology | 26748011 | J Mol Biol | 2016 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/26748011 |
| HSF1 Activation Can Restrict HIV Replication. | Nekongo EE, Ponomarenko AI, Dewal MB, Butty VL, Browne EP, Shoulders MD | ACS infectious diseases | 32502335 | ACS Infect Dis | 2020 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/32502335 |
| High-throughput Screening for Protein-based Inheritance in S. cerevisiae. | Byers JS, Jarosz DF | Journal of visualized experiments : JoVE | 28809826 | J Vis Exp | 2017 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/28809826 |
| A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program. | Chakravarty AK, Smejkal T, Itakura AK, Garcia DM, Jarosz DF | Molecular cell | 31757755 | Mol Cell | 2020 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/31757755 |
| Hsp90 shapes adaptation by controlling the fitness consequences of regulatory variation. | Jakobson CM, Aguilar-Rodríguez J, Jarosz DF | bioRxiv : the preprint server for biology | 37961536 | bioRxiv | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37961536 |
| Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. | Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF | Developmental cell | 38810654 | Dev Cell | 2024 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/38810654 |
| Massively parallel experimental interrogation of natural variants in ancient signaling pathways reveals both purifying selection and local adaptation. | Aguilar-Rodríguez J, Vila J, Chen SA, Razo-Mejia M, Ghosh O, Fraser HB, Jarosz DF, Petrov DA | bioRxiv : the preprint server for biology | 39553990 | bioRxiv | 2024 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/39553990 |
| The Hunt for Ancient Prions: Archaeal Prion-Like Domains Form Amyloid-Based Epigenetic Elements. | Zajkowski T, Lee MD, Mondal SS, Carbajal A, Dec R, Brennock PD, Piast RW, Snyder JE, Bense NB, Dzwolak W, Jarosz DF, Rothschild LJ | Molecular biology and evolution | 33480998 | Mol Biol Evol | 2021 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/33480998 |
| Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. | Itakura AK, Chakravarty AK, Jakobson CM, Jarosz DF | Molecular cell | 31757756 | Mol Cell | 2020 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/31757756 |
| What Has a Century of Quantitative Genetics Taught Us About Nature's Genetic Tool Kit? | Jakobson CM, Jarosz DF | Annual review of genetics | 32897739 | Annu Rev Genet | 2020 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/32897739 |
| Organizing biochemistry in space and time using prion-like self-assembly. | Jakobson CM, Jarosz DF | Current opinion in systems biology | 29725624 | Curr Opin Syst Biol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29725624 |
| It Pays To Be in Phase. | Itakura AK, Futia RA, Jarosz DF | Biochemistry | 29509425 | Biochemistry | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29509425 |
| A common bacterial metabolite elicits prion-based bypass of glucose repression. | Garcia DM, Dietrich D, Clardy J, Jarosz DF | eLife | 27906649 | Elife | 2016 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/27906649 |
| Protein self-assembly: A new frontier in cell signaling. | Saad S, Jarosz DF | Current opinion in cell biology | 33493989 | Curr Opin Cell Biol | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33493989 |
| Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships. | Jakobson CM, Jarosz DF | Cell systems | 31054809 | Cell Syst | 2019 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/31054809 |
| A prion accelerates proliferation at the expense of lifespan. | Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF | eLife | 34545808 | Elife | 2021 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/34545808 |
| Protein aggregation and the evolution of stress resistance in clinical yeast. | Chen YR, Ziv I, Swaminathan K, Elias JE, Jarosz DF | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 33866806 | Philos Trans R Soc Lond B Biol Sci | 2021 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/33866806 |
| A Prion Epigenetic Switch Establishes an Active Chromatin State. | Harvey ZH, Chakravarty AK, Futia RA, Jarosz DF | Cell | 32109413 | Cell | 2020 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/32109413 |
| Biomolecular Condensation: A New Phase in Cancer Research. | Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJH, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N | Cancer discovery | 35852417 | Cancer Discov | 2022 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/35852417 |
| The Hsp90 Molecular Chaperone as a Global Modifier of the Genotype-Phenotype-Fitness Map: An Evolutionary Perspective. | Aguilar-Rodríguez J, Jakobson CM, Jarosz DF | Journal of molecular biology | 39481633 | J Mol Biol | 2024 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/39481633 |
| Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits. | Chakrabortee S, Byers JS, Jones S, Garcia DM, Bhullar B, Chang A, She R, Lee L, Fremin B, Lindquist S, Jarosz DF | Cell | 27693355 | Cell | 2016 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/27693355 |
| Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome. | She R, Chakravarty AK, Layton CJ, Chircus LM, Andreasson JO, Damaraju N, McMahon PL, Buenrostro JD, Jarosz DF, Greenleaf WJ | Proceedings of the National Academy of Sciences of the United States of America | 28325876 | Proc Natl Acad Sci U S A | 2017 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/28325876 |
| Mutations, protein homeostasis, and epigenetic control of genome integrity. | Xie JL, Jarosz DF | DNA repair | 30181040 | DNA Repair (Amst) | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30181040 |
| More than Just a Phase: Prions at the Crossroads of Epigenetic Inheritance and Evolutionary Change. | Chakravarty AK, Jarosz DF | Journal of molecular biology | 30031007 | J Mol Biol | 2018 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/30031007 |
| Mapping Causal Variants with Single-Nucleotide Resolution Reveals Biochemical Drivers of Phenotypic Change. | She R, Jarosz DF | Cell | 29373829 | Cell | 2018 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/29373829 |
| Pervasive function and evidence for selection across standing genetic variation in S. cerevisiae. | Jakobson CM, She R, Jarosz DF | Nature communications | 30874558 | Nat Commun | 2019 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/30874558 |
| Protein-Based Inheritance: Epigenetics beyond the Chromosome. | Harvey ZH, Chen Y, Jarosz DF | Molecular cell | 29153393 | Mol Cell | 2018 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/29153393 |
| A genome-to-proteome atlas charts natural variants controlling proteome diversity and forecasts their fitness effects. | Jakobson CM, Hartl J, Trébulle P, Mülleder M, Jarosz DF, Ralser M | bioRxiv : the preprint server for biology | 39484408 | bioRxiv | 2024 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/39484408 |
| A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure. | Mendelsohn BA, Bennett NK, Darch MA, Yu K, Nguyen MK, Pucciarelli D, Nelson M, Horlbeck MA, Gilbert LA, Hyun W, Kampmann M, Nakamura JL, Nakamura K | PLoS biology | 30148842 | PLoS Biol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30148842 |
| Dual gene activation and knockout screen reveals directional dependencies in genetic networks. | Boettcher M, Tian R, Blau JA, Markegard E, Wagner RT, Wu D, Mo X, Biton A, Zaitlen N, Fu H, McCormick F, Kampmann M, McManus MT | Nature biotechnology | 29334369 | Nat Biotechnol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29334369 |
| Image-based pooled whole-genome CRISPRi screening for subcellular phenotypes. | Kanfer G, Sarraf SA, Maman Y, Baldwin H, Dominguez-Martin E, Johnson KR, Ward ME, Kampmann M, Lippincott-Schwartz J, Youle RJ | The Journal of cell biology | 33464298 | J Cell Biol | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33464298 |
| CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons. | Tian R, Gachechiladze MA, Ludwig CH, Laurie MT, Hong JY, Nathaniel D, Prabhu AV, Fernandopulle MS, Patel R, Abshari M, Ward ME, Kampmann M | Neuron | 31422865 | Neuron | 2019 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/31422865 |
| Compromised function of the ESCRT pathway promotes endolysosomal escape of tau seeds and propagation of tau aggregation. | Chen JJ, Nathaniel DL, Raghavan P, Nelson M, Tian R, Tse E, Hong JY, See SK, Mok SA, Hein MY, Southworth DR, Grinberg LT, Gestwicki JE, Leonetti MD, Kampmann M | The Journal of biological chemistry | 31578281 | J Biol Chem | 2019 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/31578281 |
| NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems. | Biebl MM, Delhommel F, Faust O, Zak KM, Agam G, Guo X, Mühlhofer M, Dahiya V, Hillebrand D, Popowicz GM, Kampmann M, Lamb DC, Rosenzweig R, Sattler M, Buchner J | Molecular cell | 35063133 | Mol Cell | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35063133 |
| A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states. | Dräger NM, Sattler SM, Huang CT, Teter OM, Leng K, Hashemi SH, Hong J, Aviles G, Clelland CD, Zhan L, Udeochu JC, Kodama L, Singleton AB, Nalls MA, Ichida J, Ward ME, Faghri F, Gan L, Kampmann M | Nature neuroscience | 35953545 | Nat Neurosci | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35953545 |
| CRISPRi and CRISPRa Screens in Mammalian Cells for Precision Biology and Medicine. | Kampmann M | ACS chemical biology | 29035510 | ACS Chem Biol | 2018 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/29035510 |
| Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. | Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS | eLife | 27661255 | Elife | 2016 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/27661255 |
| A CRISPR Approach to Neurodegenerative Diseases. | Kampmann M | Trends in molecular medicine | 28478951 | Trends Mol Med | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28478951 |
| Elucidating drug targets and mechanisms of action by genetic screens in mammalian cells. | Kampmann M | Chemical communications (Cambridge, England) | 28487920 | Chem Commun (Camb) | 2017 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/28487920 |
| An E3 ligase network engages GCN1 to promote the degradation of translation factors on stalled ribosomes. | Oltion K, Carelli JD, Yang T, See SK, Wang HY, Kampmann M, Taunton J | Cell | 36638793 | Cell | 2023 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/36638793 |
| The mTOR Complex Controls HIV Latency. | Besnard E, Hakre S, Kampmann M, Lim HW, Hosmane NN, Martin A, Bassik MC, Verschueren E, Battivelli E, Chan J, Svensson JP, Gramatica A, Conrad RJ, Ott M, Greene WC, Krogan NJ, Siliciano RF, Weissman JS, Verdin E | Cell host & microbe | 27978436 | Cell Host Microbe | 2016 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/27978436 |
| Tau Internalization is Regulated by 6-O Sulfation on Heparan Sulfate Proteoglycans (HSPGs). | Rauch JN, Chen JJ, Sorum AW, Miller GM, Sharf T, See SK, Hsieh-Wilson LC, Kampmann M, Kosik KS | Scientific reports | 29686391 | Sci Rep | 2018 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/29686391 |
| Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. | Mavor D, Barlow KA, Asarnow D, Birman Y, Britain D, Chen W, Green EM, Kenner LR, Mensa B, Morinishi LS, Nelson CA, Poss EM, Suresh P, Tian R, Arhar T, Ary BE, Bauer DP, Bergman ID, Brunetti RM, Chio CM, Dai SA, Dickinson MS, Elledge SK, Helsell CVM, Hendel NL, Kang E, Kern N, Khoroshkin MS, Kirkemo LL, Lewis GR, Lou K, Marin WM, Maxwell AM, McTigue PF, Myers-Turnbull D, Nagy TL, Natale AM, Oltion K, Pourmal S, Reder GK, Rettko NJ, Rohweder PJ, Schwarz DMC, Tan SK, Thomas PV, Tibble RW, Town JP, Tsai MK, Ugur FS, Wassarman DR, Wolff AM, Wu TS, Bogdanoff D, Li J, Thorn KS, O'Conchúir S, Swaney DL, Chow ED, Madhani HD, Redding S, Bolon DN, Kortemme T, DeRisi JL, Kampmann M, Fraser JS | Biology open | 30037883 | Biol Open | 2018 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/30037883 |
| CRISPulator: a discrete simulation tool for pooled genetic screens. | Nagy T, Kampmann M | BMC bioinformatics | 28732459 | BMC Bioinformatics | 2017 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/28732459 |
| Functional genomics screen identifies proteostasis targets that modulate prion protein (PrP) stability. | Abrams J, Arhar T, Mok SA, Taylor IR, Kampmann M, Gestwicki JE | Cell stress & chaperones | 33547632 | Cell Stress Chaperones | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33547632 |
| A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling. | Semesta KM, Tian R, Kampmann M, von Zastrow M, Tsvetanova NG | PLoS genetics | 33052901 | PLoS Genet | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33052901 |
| Defining the ATPome reveals cross-optimization of metabolic pathways. | Bennett NK, Nguyen MK, Darch MA, Nakaoka HJ, Cousineau D, Ten Hoeve J, Graeber TG, Schuelke M, Maltepe E, Kampmann M, Mendelsohn BA, Nakamura JL, Nakamura K | Nature communications | 32859923 | Nat Commun | 2020 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/32859923 |
| Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding. | Newberry RW, Arhar T, Costello J, Hartoularos GC, Maxwell AM, Naing ZZC, Pittman M, Reddy NR, Schwarz DMC, Wassarman DR, Wu TS, Barrero D, Caggiano C, Catching A, Cavazos TB, Estes LS, Faust B, Fink EA, Goldman MA, Gomez YK, Gordon MG, Gunsalus LM, Hoppe N, Jaime-Garza M, Johnson MC, Jones MG, Kung AF, Lopez KE, Lumpe J, Martyn C, McCarthy EE, Miller-Vedam LE, Navarro EJ, Palar A, Pellegrino J, Saylor W, Stephens CA, Strickland J, Torosyan H, Wankowicz SA, Wong DR, Wong G, Redding S, Chow ED, DeGrado WF, Kampmann M | ACS chemical biology | 32786289 | ACS Chem Biol | 2020 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/32786289 |
| CRISPR-based functional genomics for neurological disease. | Kampmann M | Nature reviews. Neurology | 32641861 | Nat Rev Neurol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32641861 |
| Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. | Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS | Cell | 33838111 | Cell | 2021 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/33838111 |
| Mapping the Genetic Landscape of Human Cells. | Horlbeck MA, Xu A, Wang M, Bennett NK, Park CY, Bogdanoff D, Adamson B, Chow ED, Kampmann M, Peterson TR, Nakamura K, Fischbach MA, Weissman JS, Gilbert LA | Cell | 30033366 | Cell | 2018 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/30033366 |
| The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. | Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ | Cell | 30053424 | Cell | 2018 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/30053424 |
| Heterochromatin anomalies and double-stranded RNA accumulation underlie C9orf72 poly(PR) toxicity. | Zhang YJ, Guo L, Gonzales PK, Gendron TF, Wu Y, Jansen-West K, O'Raw AD, Pickles SR, Prudencio M, Carlomagno Y, Gachechiladze MA, Ludwig C, Tian R, Chew J, DeTure M, Lin WL, Tong J, Daughrity LM, Yue M, Song Y, Andersen JW, Castanedes-Casey M, Kurti A, Datta A, Antognetti G, McCampbell A, Rademakers R, Oskarsson B, Dickson DW, Kampmann M, Ward ME, Fryer JD, Link CD, Shorter J, Petrucelli L | Science (New York, N.Y.) | 30765536 | Science | 2019 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/30765536 |
| LRP1 is a master regulator of tau uptake and spread. | Rauch JN, Luna G, Guzman E, Audouard M, Challis C, Sibih YE, Leshuk C, Hernandez I, Wegmann S, Hyman BT, Gradinaru V, Kampmann M, Kosik KS | Nature | 32296178 | Nature | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32296178 |
| Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast. | Eisenberg AR, Higdon AL, Hollerer I, Fields AP, Jungreis I, Diamond PD, Kellis M, Jovanovic M, Brar GA | Cell systems | 32710835 | Cell Syst | 2020 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/32710835 |
| Precise Post-translational Tuning Occurs for Most Protein Complex Components during Meiosis. | Eisenberg AR, Higdon A, Keskin A, Hodapp S, Jovanovic M, Brar GA | Cell reports | 30590036 | Cell Rep | 2018 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/30590036 |
| Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate. | Cheng Z, Mugler CF, Keskin A, Hodapp S, Chan LY, Weis K, Mertins P, Regev A, Jovanovic M, Brar GA | Molecular cell | 30503772 | Mol Cell | 2019 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/30503772 |
| Global Proteome Remodeling during ER Stress Involves Hac1-Driven Expression of Long Undecoded Transcript Isoforms. | Van Dalfsen KM, Hodapp S, Keskin A, Otto GM, Berdan CA, Higdon A, Cheunkarndee T, Nomura DK, Jovanovic M, Brar GA | Developmental cell | 30016623 | Dev Cell | 2018 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/30016623 |
| Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus in Drosophila melanogaster. | Jorgensen V, Chen J, Vander Wende H, Harris DE, McCarthy A, Breznak S, Wong-Deyrup SW, Chen Y, Rangan P, Brar GA, Sawyer EM, Chan LY, Ünal E | G3 (Bethesda, Md.) | 32213532 | G3 (Bethesda) | 2020 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/32213532 |
| Strategies and Challenges in Identifying Function for Thousands of sORF-Encoded Peptides in Meiosis. | Hollerer I, Higdon A, Brar GA | Proteomics | 28929627 | Proteomics | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/28929627 |
| Beyond the Triplet Code: Context Cues Transform Translation. | Brar GA | Cell | 27984720 | Cell | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27984720 |
| Pervasive, Coordinated Protein-Level Changes Driven by Transcript Isoform Switching during Meiosis. | Cheng Z, Otto GM, Powers EN, Keskin A, Mertins P, Carr SA, Jovanovic M, Brar GA | Cell | 29474919 | Cell | 2018 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/29474919 |
| Global mapping of translation initiation sites by TIS profiling in budding yeast. | Hollerer I, Powers EN, Brar GA | STAR protocols | 33458709 | STAR Protoc | 2021 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/33458709 |
| Evidence for an Integrated Gene Repression Mechanism Based on mRNA Isoform Toggling in Human Cells. | Hollerer I, Barker JC, Jorgensen V, Tresenrider A, Dugast-Darzacq C, Chan LY, Darzacq X, Tjian R, Ünal E, Brar GA | G3 (Bethesda, Md.) | 30723103 | G3 (Bethesda) | 2019 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/30723103 |
| Global translation inhibition yields condition-dependent de-repression of ribosome biogenesis mRNAs. | Cheng Z, Brar GA | Nucleic acids research | 30937450 | Nucleic Acids Res | 2019 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/30937450 |
| Increasing the uptake of carbon dioxide. | Franklin E, Jonikas M | eLife | 33270556 | Elife | 2020 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/33270556 |
| A Spatial Interactome Reveals the Protein Organization of the Algal CO(2)-Concentrating Mechanism. | Mackinder LCM, Chen C, Leib RD, Patena W, Blum SR, Rodman M, Ramundo S, Adams CM, Jonikas MC | Cell | 28938113 | Cell | 2017 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/28938113 |
| Rigidity enhances a magic-number effect in polymer phase separation. | Xu B, He G, Weiner BG, Ronceray P, Meir Y, Jonikas MC, Wingreen NS | Nature communications | 32214099 | Nat Commun | 2020 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/32214099 |
| Prospects for Engineering Biophysical CO(2) Concentrating Mechanisms into Land Plants to Enhance Yields. | Hennacy JH, Jonikas MC | Annual review of plant biology | 32151155 | Annu Rev Plant Biol | 2020 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/32151155 |
| A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis. | Li X, Patena W, Fauser F, Jinkerson RE, Saroussi S, Meyer MT, Ivanova N, Robertson JM, Yue R, Zhang R, Vilarrasa-Blasi J, Wittkopp TM, Ramundo S, Blum SR, Goh A, Laudon M, Srikumar T, Lefebvre PA, Grossman AR, Jonikas MC | Nature genetics | 30886426 | Nat Genet | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30886426 |
| Systematic characterization of gene function in the photosynthetic alga Chlamydomonas reinhardtii. | Fauser F, Vilarrasa-Blasi J, Onishi M, Ramundo S, Patena W, Millican M, Osaki J, Philp C, Nemeth M, Salomé PA, Li X, Wakao S, Kim RG, Kaye Y, Grossman AR, Niyogi KK, Merchant SS, Cutler SR, Walter P, Dinneny JR, Jonikas MC, Jinkerson RE | Nature genetics | 35513725 | Nat Genet | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35513725 |
| A Rubisco-binding protein is required for normal pyrenoid number and starch sheath morphology in Chlamydomonas reinhardtii. | Itakura AK, Chan KX, Atkinson N, Pallesen L, Wang L, Reeves G, Patena W, Caspari O, Roth R, Goodenough U, McCormick AJ, Griffiths H, Jonikas MC | Proceedings of the National Academy of Sciences of the United States of America | 31455733 | Proc Natl Acad Sci U S A | 2019 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/31455733 |
| Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts. | Küken A, Sommer F, Yaneva-Roder L, Mackinder LC, Höhne M, Geimer S, Jonikas MC, Schroda M, Stitt M, Nikoloski Z, Mettler-Altmann T | eLife | 30306890 | Elife | 2018 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/30306890 |
| Phase separation in biology and disease-a symposium report. | Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL | Annals of the New York Academy of Sciences | 31199001 | Ann N Y Acad Sci | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31199001 |
| Assembly of the algal CO(2)-fixing organelle, the pyrenoid, is guided by a Rubisco-binding motif. | Meyer MT, Itakura AK, Patena W, Wang L, He S, Emrich-Mills T, Lau CS, Yates G, Mackinder LCM, Jonikas MC | Science advances | 33177094 | Sci Adv | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33177094 |
| The Mars1 kinase confers photoprotection through signaling in the chloroplast unfolded protein response. | Perlaza K, Toutkoushian H, Boone M, Lam M, Iwai M, Jonikas MC, Walter P, Ramundo S | eLife | 31612858 | Elife | 2019 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/31612858 |
| Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments. | Vilarrasa-Blasi J, Vellosillo T, Jinkerson RE, Fauser F, Xiang T, Minkoff BB, Wang L, Kniazev K, Guzman M, Osaki J, Barrett-Wilt GA, Sussman MR, Jonikas MC, Dinneny JR | Nature communications | 39013881 | Nat Commun | 2024 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/39013881 |
| The structural basis of Rubisco phase separation in the pyrenoid. | He S, Chou HT, Matthies D, Wunder T, Meyer MT, Atkinson N, Martinez-Sanchez A, Jeffrey PD, Port SA, Patena W, He G, Chen VK, Hughson FM, McCormick AJ, Mueller-Cajar O, Engel BD, Yu Z, Jonikas MC | Nature plants | 33230314 | Nat Plants | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33230314 |
| A Polarizing Issue: Diversity in the Mechanisms Underlying Apico-Basolateral Polarization In Vivo. | Pickett MA, Naturale VF, Feldman JL | Annual review of cell and developmental biology | 31461314 | Annu Rev Cell Dev Biol | 2019 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/31461314 |
| Cytoskeletal variations in an asymmetric cell division support diversity in nematode sperm size and sex ratios. | Winter ES, Schwarz A, Fabig G, Feldman JL, Pires-daSilva A, Müller-Reichert T, Sadler PL, Shakes DC | Development (Cambridge, England) | 28827395 | Development | 2017 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28827395 |
| Efficient proximity labeling in living cells and organisms with TurboID. | Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY | Nature biotechnology | 30125270 | Nat Biotechnol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30125270 |
| Context matters: Lessons in epithelial polarity from the Caenorhabditis elegans intestine and other tissues. | Naturale VF, Pickett MA, Feldman JL | Current topics in developmental biology | 37100523 | Curr Top Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37100523 |
| Inherited apicobasal polarity defines the key features of axon-dendrite polarity in a sensory neuron. | Lee J, Magescas J, Fetter RD, Feldman JL, Shen K | Current biology : CB | 34270949 | Curr Biol | 2021 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/34270949 |
| Proximity labeling reveals non-centrosomal microtubule-organizing center components required for microtubule growth and localization. | Sanchez AD, Branon TC, Cote LE, Papagiannakis A, Liang X, Pickett MA, Shen K, Jacobs-Wagner C, Ting AY, Feldman JL | Current biology : CB | 34242576 | Curr Biol | 2021 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/34242576 |
| Tissue-specific degradation of essential centrosome components reveals distinct microtubule populations at microtubule organizing centers. | Sallee MD, Zonka JC, Skokan TD, Raftrey BC, Feldman JL | PLoS biology | 30080857 | PLoS Biol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30080857 |
| Growth cone-localized microtubule organizing center establishes microtubule orientation in dendrites. | Liang X, Kokes M, Fetter RD, Sallee MD, Moore AW, Feldman JL, Shen K | eLife | 32657271 | Elife | 2020 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/32657271 |
| Somatic polyploidy supports biosynthesis and tissue function by increasing transcriptional output. | Lessenger AT, Skotheim JM, Swaffer MP, Feldman JL | The Journal of cell biology | 39652010 | J Cell Biol | 2025 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/39652010 |
| Microtubule-organizing centers: from the centrosome to non-centrosomal sites. | Sanchez AD, Feldman JL | Current opinion in cell biology | 27666167 | Curr Opin Cell Biol | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27666167 |
| A two-step mechanism for the inactivation of microtubule organizing center function at the centrosome. | Magescas J, Zonka JC, Feldman JL | eLife | 31246171 | Elife | 2019 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/31246171 |
| Visualizing the metazoan proliferation-quiescence decision in vivo. | Adikes RC, Kohrman AQ, Martinez MAQ, Palmisano NJ, Smith JJ, Medwig-Kinney TN, Min M, Sallee MD, Ahmed OB, Kim N, Liu S, Morabito RD, Weeks N, Zhao Q, Zhang W, Feldman JL, Barkoulas M, Pani AM, Spencer SL, Martin BL, Matus DQ | eLife | 33350383 | Elife | 2020 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/33350383 |
| Apical PAR complex proteins protect against programmed epithelial assaults to create a continuous and functional intestinal lumen. | Sallee MD, Pickett MA, Feldman JL | eLife | 34137371 | Elife | 2021 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/34137371 |
| A proximity labeling protocol to probe proximity interactions in C. elegans. | Sanchez AD, Feldman JL | STAR protocols | 34927095 | STAR Protoc | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34927095 |
| Centriole-less pericentriolar material serves as a microtubule organizing center at the base of C. elegans sensory cilia. | Magescas J, Eskinazi S, Tran MV, Feldman JL | Current biology : CB | 33798428 | Curr Biol | 2021 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/33798428 |
| Persistent cell contacts enable E-cadherin/HMR-1- and PAR-3-based symmetry breaking within a developing C. elegans epithelium. | Naturale VF, Pickett MA, Feldman JL | Developmental cell | 37552986 | Dev Cell | 2023 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/37552986 |
| Separable mechanisms drive local and global polarity establishment in the Caenorhabditiselegans intestinal epithelium. | Pickett MA, Sallee MD, Cote L, Naturale VF, Akpinaroglu D, Lee J, Shen K, Feldman JL | Development (Cambridge, England) | 36264257 | Development | 2022 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/36264257 |
| CWL-Airflow: a lightweight pipeline manager supporting Common Workflow Language. | Kotliar M, Kartashov AV, Barski A | GigaScience | 31321430 | Gigascience | 2019 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/31321430 |
| Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. | Maezawa S, Sakashita A, Yukawa M, Chen X, Takahashi K, Alavattam KG, Nakata I, Weirauch MT, Barski A, Namekawa SH | Nature structural & molecular biology | 32895557 | Nat Struct Mol Biol | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32895557 |
| Endogenous retroviruses drive species-specific germline transcriptomes in mammals. | Sakashita A, Maezawa S, Takahashi K, Alavattam KG, Yukawa M, Hu YC, Kojima S, Parrish NF, Barski A, Pavlicev M, Namekawa SH | Nature structural & molecular biology | 32895553 | Nat Struct Mol Biol | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32895553 |
| Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. | Harley JB, Chen X, Pujato M, Miller D, Maddox A, Forney C, Magnusen AF, Lynch A, Chetal K, Yukawa M, Barski A, Salomonis N, Kaufman KM, Kottyan LC, Weirauch MT | Nature genetics | 29662164 | Nat Genet | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29662164 |
| Microbiota-sensitive epigenetic signature predicts inflammation in Crohn's disease. | Kelly D, Kotliar M, Woo V, Jagannathan S, Whitt J, Moncivaiz J, Aronow BJ, Dubinsky MC, Hyams JS, Markowitz JF, Baldassano RN, Stephens MC, Walters TD, Kugathasan S, Haberman Y, Sundaram N, Rosen MJ, Helmrath M, Karns R, Barski A, Denson LA, Alenghat T | JCI insight | 30232290 | JCI Insight | 2018 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/30232290 |
| Chromatin Preparation from Murine Eosinophils for Genome-Wide Analyses. | Bouffi C, Barski A, Fulkerson PC | Methods in molecular biology (Clifton, N.J.) | 29956158 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29956158 |
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| RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes. | Adams SR, Maezawa S, Alavattam KG, Abe H, Sakashita A, Shroder M, Broering TJ, Sroga Rios J, Thomas MA, Lin X, Price CM, Barski A, Andreassen PR, Namekawa SH | PLoS genetics | 29462142 | PLoS Genet | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29462142 |
| A rapidly evolved domain, the SCML2 DNA-binding repeats, contributes to chromatin binding of mouse SCML2†. | Maezawa S, Alavattam KG, Tatara M, Nagai R, Barski A, Namekawa SH | Biology of reproduction | 30137219 | Biol Reprod | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30137219 |
| TSLP signaling in CD4(+) T cells programs a pathogenic T helper 2 cell state. | Rochman Y, Dienger-Stambaugh K, Richgels PK, Lewkowich IP, Kartashov AV, Barski A, Khurana Hershey GK, Leonard WJ, Singh H | Science signaling | 29535264 | Sci Signal | 2018 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/29535264 |
| Genomic integration of Wnt/β-catenin and BMP/Smad1 signaling coordinates foregut and hindgut transcriptional programs. | Stevens ML, Chaturvedi P, Rankin SA, Macdonald M, Jagannathan S, Yukawa M, Barski A, Zorn AM | Development (Cambridge, England) | 28219948 | Development | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28219948 |
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| Nuclear Factor κB1/RelA Mediates Inflammation in Human Lung Epithelial Cells at Atmospheric Oxygen Levels. | Jagannathan L, Jose CC, Arita A, Kluz T, Sun H, Zhang X, Yao Y, Kartashov AV, Barski A, Costa M, Cuddapah S | Journal of cellular physiology | 26588041 | J Cell Physiol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26588041 |
| Polycomb protein SCML2 facilitates H3K27me3 to establish bivalent domains in the male germline. | Maezawa S, Hasegawa K, Yukawa M, Kubo N, Sakashita A, Alavattam KG, Sin HS, Kartashov AV, Sasaki H, Barski A, Namekawa SH | Proceedings of the National Academy of Sciences of the United States of America | 29686098 | Proc Natl Acad Sci U S A | 2018 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/29686098 |
| Analysis of ChIP-Seq and RNA-Seq Data with BioWardrobe. | Vallabh S, Kartashov AV, Barski A | Methods in molecular biology (Clifton, N.J.) | 29767371 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29767371 |
| AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. | Yukawa M, Jagannathan S, Vallabh S, Kartashov AV, Chen X, Weirauch MT, Barski A | The Journal of experimental medicine | 31653690 | J Exp Med | 2020 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/31653690 |
| Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. | Alavattam KG, Maezawa S, Sakashita A, Khoury H, Barski A, Kaplan N, Namekawa SH | Nature structural & molecular biology | 30778237 | Nat Struct Mol Biol | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30778237 |
| PRC1 suppresses a female gene regulatory network to ensure testicular differentiation. | Maezawa S, Yukawa M, Hasegawa K, Sugiyama R, Iizuka M, Hu M, Sakashita A, Vidal M, Koseki H, Barski A, DeFalco T, Namekawa SH | Cell death & disease | 37542070 | Cell Death Dis | 2023 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/37542070 |
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| Xist RNA repeat E is essential for ASH2L recruitment to the inactive X and regulates histone modifications and escape gene expression. | Yue M, Ogawa A, Yamada N, Charles Richard JL, Barski A, Ogawa Y | PLoS genetics | 28686623 | PLoS Genet | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28686623 |
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| Reuse of public, genome-wide, murine eosinophil expression data for hypotheses development. | Grace JO, Malik A, Reichman H, Munitz A, Barski A, Fulkerson PC | Journal of leukocyte biology | 29758095 | J Leukoc Biol | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29758095 |
| FOXF1 transcription factor promotes lung regeneration after partial pneumonectomy. | Bolte C, Flood HM, Ren X, Jagannathan S, Barski A, Kalin TV, Kalinichenko VV | Scientific reports | 28878348 | Sci Rep | 2017 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/28878348 |
| Site-specific DNA demethylation during spermatogenesis presets the sites of nucleosome retention in mouse sperm. | Maezawa S, Yukawa M, Sakashita A, Barski A, Namekawa SH | bioRxiv : the preprint server for biology | 39829778 | bioRxiv | 2025 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/39829778 |
| Genetically Encoded Toolbox for Glycocalyx Engineering: Tunable Control of Cell Adhesion, Survival, and Cancer Cell Behaviors. | Shurer CR, Colville MJ, Gupta VK, Head SE, Kai F, Lakins JN, Paszek MJ | ACS biomaterials science & engineering | 29805991 | ACS Biomater Sci Eng | 2018 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/29805991 |
| Mucin-coating technologies for protection and reduced aggregation of cellular production systems. | Shurer CR, Head SE, Goudge MC, Paszek MJ | Biotechnology and bioengineering | 30636317 | Biotechnol Bioeng | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30636317 |
| Tissue mechanics, an important regulator of development and disease. | Ayad NME, Kaushik S, Weaver VM | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 31431174 | Philos Trans R Soc Lond B Biol Sci | 2019 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/31431174 |
| Stable recombinant production of codon-scrambled lubricin and mucin in human cells. | Shurer CR, Wang Y, Feeney E, Head SE, Zhang VX, Su J, Cheng Z, Stark MA, Bonassar LJ, Reesink HL, Paszek MJ | Biotechnology and bioengineering | 30684357 | Biotechnol Bioeng | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30684357 |
| Litmus-Body: A Molecularly Targeted Sensor for Cell-Surface pH Measurements. | Kuo JC, Goudge MC, Metzloff AE, Huang LT, Colville MJ, Park S, Zipfel WR, Paszek MJ | ACS sensors | 32337979 | ACS Sens | 2020 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/32337979 |
| Glycocalyx Curving the Membrane: Forces Emerging from the Cell Exterior. | Kuo JC, Paszek MJ | Annual review of cell and developmental biology | 34613816 | Annu Rev Cell Dev Biol | 2021 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/34613816 |
| Equilibrium Modeling of the Mechanics and Structure of the Cancer Glycocalyx. | Gandhi JG, Koch DL, Paszek MJ | Biophysical journal | 30736980 | Biophys J | 2019 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/30736980 |
| Recombinant manufacturing of multispecies biolubricants. | Colville MJ, Huang LT, Schmidt S, Chen K, Vishwanath K, Su J, Williams RM, Bonassar LJ, Reesink HL, Paszek MJ | bioRxiv : the preprint server for biology | 38746339 | bioRxiv | 2024 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/38746339 |
| Nuclear Deformation Causes DNA Damage by Increasing Replication Stress. | Shah P, Hobson CM, Cheng S, Colville MJ, Paszek MJ, Superfine R, Lammerding J | Current biology : CB | 33326770 | Curr Biol | 2021 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/33326770 |
| Sequence-Specific Mucins for Glycocalyx Engineering. | Pan H, Colville MJ, Supekar NT, Azadi P, Paszek MJ | ACS synthetic biology | 31500407 | ACS Synth Biol | 2019 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/31500407 |
| Physical biology of the cancer cell glycocalyx. | Chin-Hun Kuo J, Gandhi JG, Zia RN, Paszek MJ | Nature physics | 33859716 | Nat Phys | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/33859716 |
| Physical Principles of Membrane Shape Regulation by the Glycocalyx. | Shurer CR, Kuo JC, Roberts LM, Gandhi JG, Colville MJ, Enoki TA, Pan H, Su J, Noble JM, Hollander MJ, O'Donnell JP, Yin R, Pedram K, Möckl L, Kourkoutis LF, Moerner WE, Bertozzi CR, Feigenson GW, Reesink HL, Paszek MJ | Cell | 31056282 | Cell | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31056282 |
| Immunoengineering can overcome the glycocalyx armour of cancer cells. | Park S, Colville MJ, Paek JH, Shurer CR, Singh A, Secor EJ, Sailer CJ, Huang LT, Kuo JC, Goudge MC, Su J, Kim M, DeLisa MP, Neelamegham S, Lammerding J, Zipfel WR, Fischbach C, Reesink HL, Paszek MJ | Nature materials | 38361041 | Nat Mater | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38361041 |
| The C-Terminal RGG Domain of Human Lsm4 Promotes Processing Body Formation Stimulated by Arginine Dimethylation. | Arribas-Layton M, Dennis J, Bennett EJ, Damgaard CK, Lykke-Andersen J | Molecular and cellular biology | 27247266 | Mol Cell Biol | 2016 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/27247266 |
| Distinct regulatory ribosomal ubiquitylation events are reversible and hierarchically organized. | Garshott DM, Sundaramoorthy E, Leonard M, Bennett EJ | eLife | 32011234 | Elife | 2020 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/32011234 |
| A Cdc48 "Retrochaperone" Function Is Required for the Solubility of Retrotranslocated, Integral Membrane Endoplasmic Reticulum-associated Degradation (ERAD-M) Substrates. | Neal S, Mak R, Bennett EJ, Hampton R | The Journal of biological chemistry | 28077573 | J Biol Chem | 2017 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/28077573 |
| iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation. | Garshott DM, An H, Sundaramoorthy E, Leonard M, Vicary A, Harper JW, Bennett EJ | Cell reports | 34469731 | Cell Rep | 2021 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/34469731 |
| An ERAD-independent role for rhomboid pseudoprotease Dfm1 in mediating sphingolipid homeostasis. | Bhaduri S, Aguayo A, Ohno Y, Proietto M, Jung J, Wang I, Kandel R, Singh N, Ibrahim I, Fulzele A, Bennett EJ, Kihara A, Neal SE | The EMBO journal | 36350249 | EMBO J | 2023 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/36350249 |
| Site-specific identification and quantitation of endogenous SUMO modifications under native conditions. | Lumpkin RJ, Gu H, Zhu Y, Leonard M, Ahmad AS, Clauser KR, Meyer JG, Bennett EJ, Komives EA | Nature communications | 29079793 | Nat Commun | 2017 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/29079793 |
| In vivo mapping of tissue- and subcellular-specific proteomes in Caenorhabditis elegans. | Reinke AW, Mak R, Troemel ER, Bennett EJ | Science advances | 28508060 | Sci Adv | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28508060 |
| Proteome complexity and the forces that drive proteome imbalance. | Harper JW, Bennett EJ | Nature | 27629639 | Nature | 2016 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/27629639 |
| Context-Dependent and Disease-Specific Diversity in Protein Interactions within Stress Granules. | Markmiller S, Soltanieh S, Server KL, Mak R, Jin W, Fang MY, Luo EC, Krach F, Yang D, Sen A, Fulzele A, Wozniak JM, Gonzalez DJ, Kankel MW, Gao FB, Bennett EJ, Lécuyer E, Yeo GW | Cell | 29373831 | Cell | 2018 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/29373831 |
| EDF1 coordinates cellular responses to ribosome collisions. | Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R | eLife | 32744497 | Elife | 2020 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/32744497 |
| Ribosome quality control activity potentiates vaccinia virus protein synthesis during infection. | Sundaramoorthy E, Ryan AP, Fulzele A, Leonard M, Daugherty MD, Bennett EJ | Journal of cell science | 33912921 | J Cell Sci | 2021 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33912921 |
| ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. | Sundaramoorthy E, Leonard M, Mak R, Liao J, Fulzele A, Bennett EJ | Molecular cell | 28132843 | Mol Cell | 2017 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/28132843 |
| Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction. | Gendron JM, Webb K, Yang B, Rising L, Zuzow N, Bennett EJ | Molecular & cellular proteomics : MCP | 27185884 | Mol Cell Proteomics | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27185884 |
| Mapping the mammalian ribosome quality control complex interactome using proximity labeling approaches. | Zuzow N, Ghosh A, Leonard M, Liao J, Yang B, Bennett EJ | Molecular biology of the cell | 29540532 | Mol Biol Cell | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29540532 |
| Ubiquitin diGLY Proteomics as an Approach to Identify and Quantify the Ubiquitin-Modified Proteome. | Fulzele A, Bennett EJ | Methods in molecular biology (Clifton, N.J.) | 30242721 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30242721 |
| Bombardier Enables Delivery of Short-Form Bomanins in the Drosophila Toll Response. | Lin SJH, Fulzele A, Cohen LB, Bennett EJ, Wasserman SA | Frontiers in immunology | 31998316 | Front Immunol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31998316 |
| Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics. | Markmiller S, Fulzele A, Higgins R, Leonard M, Yeo GW, Bennett EJ | Cell reports | 31042464 | Cell Rep | 2019 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/31042464 |
| Frequency-chirped dynamic nuclear polarization with magic angle spinning using a frequency-agile gyrotron. | Gao C, Alaniva N, Saliba EP, Sesti EL, Judge PT, Scott FJ, Halbritter T, Sigurdsson ST, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 31525550 | J Magn Reson | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31525550 |
| Dynamic Nuclear Polarization Nuclear Magnetic Resonance in Human Cells Using Fluorescent Polarizing Agents. | Albert BJ, Gao C, Sesti EL, Saliba EP, Alaniva N, Scott FJ, Sigurdsson ST, Barnes AB | Biochemistry | 29924582 | Biochemistry | 2018 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/29924582 |
| Electron Decoupling with Dynamic Nuclear Polarization in Rotating Solids. | Saliba EP, Sesti EL, Scott FJ, Albert BJ, Choi EJ, Alaniva N, Gao C, Barnes AB | Journal of the American Chemical Society | 28429936 | J Am Chem Soc | 2017 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/28429936 |
| Instrumentation for cryogenic magic angle spinning dynamic nuclear polarization using 90L of liquid nitrogen per day. | Albert BJ, Pahng SH, Alaniva N, Sesti EL, Rand PW, Saliba EP, Scott FJ, Choi EJ, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 28888182 | J Magn Reson | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28888182 |
| Magic angle spinning NMR with metallized rotors as cylindrical microwave resonators. | Scott FJ, Sesti EL, Choi EJ, Laut AJ, Sirigiri JR, Barnes AB | Magnetic resonance in chemistry : MRC | 29672916 | Magn Reson Chem | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29672916 |
| Magic angle spinning NMR below 6 K with a computational fluid dynamics analysis of fluid flow and temperature gradients. | Sesti EL, Alaniva N, Rand PW, Choi EJ, Albert BJ, Saliba EP, Scott FJ, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 29161649 | J Magn Reson | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29161649 |
| Dynamic Nuclear Polarization with Electron Decoupling in Intact Human Cells and Cell Lysates. | Judge PT, Sesti EL, Price LE, Albert BJ, Alaniva N, Saliba EP, Halbritter T, Sigurdsson ST, Kyei GB, Barnes AB | The journal of physical chemistry. B | 32083876 | J Phys Chem B | 2020 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/32083876 |
| Sensitivity analysis of magic angle spinning dynamic nuclear polarization below 6 K. | Judge PT, Sesti EL, Saliba EP, Alaniva N, Halbritter T, Sigurdsson ST, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 31212198 | J Magn Reson | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31212198 |
| Frequency swept microwaves for hyperfine decoupling and time domain dynamic nuclear polarization. | Hoff DE, Albert BJ, Saliba EP, Scott FJ, Choi EJ, Mardini M, Barnes AB | Solid state nuclear magnetic resonance | 26482131 | Solid State Nucl Magn Reson | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26482131 |
| Combinations of isoform-targeted histone deacetylase inhibitors and bryostatin analogues display remarkable potency to activate latent HIV without global T-cell activation. | Albert BJ, Niu A, Ramani R, Marshall GR, Wender PA, Williams RM, Ratner L, Barnes AB, Kyei GB | Scientific reports | 28785069 | Sci Rep | 2017 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/28785069 |
| A versatile custom cryostat for dynamic nuclear polarization supports multiple cryogenic magic angle spinning transmission line probes. | Scott FJ, Alaniva N, Golota NC, Sesti EL, Saliba EP, Price LE, Albert BJ, Chen P, O'Connor RD, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 30342370 | J Magn Reson | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30342370 |
| Magic angle spinning spheres. | Chen P, Albert BJ, Gao C, Alaniva N, Price LE, Scott FJ, Saliba EP, Sesti EL, Judge PT, Fisher EW, Barnes AB | Science advances | 30255153 | Sci Adv | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30255153 |
| Pulsed Electron Decoupling and Strategies for Time Domain Dynamic Nuclear Polarization with Magic Angle Spinning. | Saliba EP, Sesti EL, Alaniva N, Barnes AB | The journal of physical chemistry letters | 30180584 | J Phys Chem Lett | 2018 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/30180584 |
| Electron decoupling with cross polarization and dynamic nuclear polarization below 6 K. | Sesti EL, Saliba EP, Alaniva N, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 30077145 | J Magn Reson | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30077145 |
| Characterization of frequency-chirped dynamic nuclear polarization in rotating solids. | Judge PT, Sesti EL, Alaniva N, Saliba EP, Price LE, Gao C, Halbritter T, Sigurdsson ST, Kyei GB, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 32203923 | J Magn Reson | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32203923 |
| Fast electron paramagnetic resonance magic angle spinning simulations using analytical powder averaging techniques. | Saliba EP, Barnes AB | The Journal of chemical physics | 31542017 | J Chem Phys | 2019 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/31542017 |
| Frequency-agile gyrotron for electron decoupling and pulsed dynamic nuclear polarization. | Scott FJ, Saliba EP, Albert BJ, Alaniva N, Sesti EL, Gao C, Golota NC, Choi EJ, Jagtap AP, Wittmann JJ, Eckardt M, Harneit W, Corzilius B, Th Sigurdsson S, Barnes AB | Journal of magnetic resonance (San Diego, Calif. : 1997) | 29471275 | J Magn Reson | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29471275 |
| Akt3 is a privileged first responder in isozyme-specific electrophile response. | Long MJ, Parvez S, Zhao Y, Surya SL, Wang Y, Zhang S, Aye Y | Nature chemical biology | 28114274 | Nat Chem Biol | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28114274 |
| A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling. | Lin HY, Haegele JA, Disare MT, Lin Q, Aye Y | Journal of the American Chemical Society | 25909755 | J Am Chem Soc | 2015 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/25909755 |
| Cladribine and Fludarabine Nucleotides Induce Distinct Hexamers Defining a Common Mode of Reversible RNR Inhibition. | Wisitpitthaya S, Zhao Y, Long MJ, Li M, Fletcher EA, Blessing WA, Weiss RS, Aye Y | ACS chemical biology | 27159113 | ACS Chem Biol | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27159113 |
| T-REX on-demand redox targeting in live cells. | Parvez S, Long MJ, Lin HY, Zhao Y, Haegele JA, Pham VN, Lee DK, Aye Y | Nature protocols | 27809314 | Nat Protoc | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27809314 |
| Subcellular Redox Targeting: Bridging in Vitro and in Vivo Chemical Biology. | Long MJ, Poganik JR, Ghosh S, Aye Y | ACS chemical biology | 28068059 | ACS Chem Biol | 2017 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/28068059 |
| Cardiovascular Small Heat Shock Protein HSPB7 Is a Kinetically Privileged Reactive Electrophilic Species (RES) Sensor. | Surya SL, Long MJC, Urul DA, Zhao Y, Mercer EJ, EIsaid IM, Evans T, Aye Y | ACS chemical biology | 29397684 | ACS Chem Biol | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/29397684 |
| Modular Total Synthesis and Cell-Based Anticancer Activity Evaluation of Ouabagenin and Other Cardiotonic Steroids with Varying Degrees of Oxygenation. | Khatri HR, Bhattarai B, Kaplan W, Li Z, Curtis Long MJ, Aye Y, Nagorny P | Journal of the American Chemical Society | 30802047 | J Am Chem Soc | 2019 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/30802047 |
| Genie in a bottle: controlled release helps tame natural polypharmacology? | Long MJ, Liu X, Aye Y | Current opinion in chemical biology | 30913473 | Curr Opin Chem Biol | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30913473 |
| The Die Is Cast: Precision Electrophilic Modifications Contribute to Cellular Decision Making. | Long MJC, Aye Y | Chemical research in toxicology | 27617777 | Chem Res Toxicol | 2016 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/27617777 |
| Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1. | Poganik JR, Long MJC, Disare MT, Liu X, Chang SH, Hla T, Aye Y | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 31665914 | FASEB J | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31665914 |
| Empowering Global Chemical Biology at the Dawn of the New Decade. | Hoogendoorn S, Aye Y | ACS chemical biology | 32315151 | ACS Chem Biol | 2020 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/32315151 |
| Clofarabine Commandeers the RNR-α-ZRANB3 Nuclear Signaling Axis. | Long MJC, Zhao Y, Aye Y | Cell chemical biology | 31836351 | Cell Chem Biol | 2020 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/31836351 |
| Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities. | Long MJC, Zhao Y, Aye Y | RSC chemical biology | 34458747 | RSC Chem Biol | 2020 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/34458747 |
| Breaking the Fourth Wall: Modulating Quaternary Associations for Protein Regulation and Drug Discovery. | Long MJC, Hnedzko D, Kim BK, Aye Y | Chembiochem : a European journal of chemical biology | 30589188 | Chembiochem | 2019 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/30589188 |
| Redox Signaling by Reactive Electrophiles and Oxidants. | Parvez S, Long MJC, Poganik JR, Aye Y | Chemical reviews | 30148624 | Chem Rev | 2018 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/30148624 |
| Nuclear RNR-α antagonizes cell proliferation by directly inhibiting ZRANB3. | Fu Y, Long MJC, Wisitpitthaya S, Inayat H, Pierpont TM, Elsaid IM, Bloom JC, Ortega J, Weiss RS, Aye Y | Nature chemical biology | 30150681 | Nat Chem Biol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30150681 |
| Substoichiometric hydroxynonenylation of a single protein recapitulates whole-cell-stimulated antioxidant response. | Parvez S, Fu Y, Li J, Long MJ, Lin HY, Lee DK, Hu GS, Aye Y | Journal of the American Chemical Society | 25544059 | J Am Chem Soc | 2015 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/25544059 |
| Single-Protein-Specific Redox Targeting in Live Mammalian Cells and C. elegans. | Van Hall-Beauvais A, Zhao Y, Urul DA, Long MJC, Aye Y | Current protocols in chemical biology | 30085412 | Curr Protoc Chem Biol | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30085412 |
| Proteomics and Beyond: Cell Decision-Making Shaped by Reactive Electrophiles. | Liu X, Long MJC, Aye Y | Trends in biochemical sciences | 30327250 | Trends Biochem Sci | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30327250 |
| β-TrCP1 Is a Vacillatory Regulator of Wnt Signaling. | Long MJ, Lin HY, Parvez S, Zhao Y, Poganik JR, Huang P, Aye Y | Cell chemical biology | 28736239 | Cell Chem Biol | 2017 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/28736239 |
| Chemical Biology Gateways to Mapping Location, Association, and Pathway Responsivity. | Long MJC, Liu X, Aye Y | Frontiers in chemistry | 30949469 | Front Chem | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30949469 |
| Electrophile Signaling and Emerging Immuno- and Neuro-modulatory Electrophilic Pharmaceuticals. | Poganik JR, Aye Y | Frontiers in aging neuroscience | 32116644 | Front Aging Neurosci | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32116644 |
| REX technologies for profiling and decoding the electrophile signaling axes mediated by Rosetta Stone proteins. | Long MJC, Urul DA, Aye Y | Methods in enzymology | 32046846 | Methods Enzymol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32046846 |
| The mRNA-Binding Protein HuR Is a Kinetically-Privileged Electrophile Sensor. | Poganik JR, Van Hall-Beauvais AK, Long MJC, Disare MT, Zhao Y, Aye Y | Helvetica chimica acta | 34113045 | Helv Chim Acta | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/34113045 |
| On-Demand Targeting: Investigating Biology with Proximity-Directed Chemistry. | Long MJ, Poganik JR, Aye Y | Journal of the American Chemical Society | 26907082 | J Am Chem Soc | 2016 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/26907082 |
| Getting the Message? Native Reactive Electrophiles Pass Two Out of Three Thresholds to be Bona Fide Signaling Mediators. | Poganik JR, Long MJC, Aye Y | BioEssays : news and reviews in molecular, cellular and developmental biology | 29603288 | Bioessays | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29603288 |
| Privileged Electrophile Sensors: A Resource for Covalent Drug Development. | Long MJC, Aye Y | Cell chemical biology | 28648380 | Cell Chem Biol | 2017 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/28648380 |
| Getting the Right Grip? How Understanding Electrophile Selectivity Profiles Could Illuminate Our Understanding of Redox Signaling. | Long MJC, Wang L, Aye Y | Antioxidants & redox signaling | 31578876 | Antioxid Redox Signal | 2020 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/31578876 |
| The more the merrier: how homo-oligomerization alters the interactome and function of ribonucleotide reductase. | Long MJC, Van Hall-Beauvais A, Aye Y | Current opinion in chemical biology | 31734537 | Curr Opin Chem Biol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31734537 |
| Ube2V2 Is a Rosetta Stone Bridging Redox and Ubiquitin Codes, Coordinating DNA Damage Responses. | Zhao Y, Long MJC, Wang Y, Zhang S, Aye Y | ACS central science | 29532025 | ACS Cent Sci | 2018 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/29532025 |
| Weighing up the Selenocysteome Uncovers New Sec-rets. | Poganik JR, Aye Y | Cell chemical biology | 30445052 | Cell Chem Biol | 2018 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/30445052 |
| Optimal Design of Single-Cell Experiments within Temporally Fluctuating Environments. | Fox ZR, Neuert G, Munsky B | Complexity | 32982137 | Complexity | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32982137 |
| From analog to digital models of gene regulation. | Munsky B, Neuert G | Physical biology | 26086470 | Phys Biol | 2015 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/26086470 |
| Phenotypic consequences of logarithmic signaling in MAPK stress response. | Jashnsaz H, Neuert G | bioRxiv : the preprint server for biology | 38106069 | bioRxiv | 2023 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/38106069 |
| Modelling patient drug exposure profiles in vitro to narrow the valley of death. | Leasure CS, Neuert G | Nature reviews bioengineering | 38873361 | Nat Rev Bioeng | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38873361 |
| Automated cell boundary and 3D nuclear segmentation of cells in suspension. | Kesler B, Li G, Thiemicke A, Venkat R, Neuert G | Scientific reports | 31308458 | Sci Rep | 2019 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/31308458 |
| Multiplex RNA single molecule FISH of inducible mRNAs in single yeast cells. | Li G, Neuert G | Scientific data | 31209217 | Sci Data | 2019 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/31209217 |
| Integrating single-molecule experiments and discrete stochastic models to understand heterogeneous gene transcription dynamics. | Munsky B, Fox Z, Neuert G | Methods (San Diego, Calif.) | 26079925 | Methods | 2015 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/26079925 |
| A rate threshold mechanism regulates MAPK stress signaling and survival. | Johnson AN, Li G, Jashnsaz H, Thiemicke A, Kesler BK, Rogers DC, Neuert G | Proceedings of the National Academy of Sciences of the United States of America | 33443180 | Proc Natl Acad Sci U S A | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33443180 |
| Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments. | Thiemicke A, Neuert G | Frontiers in cell and developmental biology | 37025183 | Front Cell Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37025183 |
| TrueSpot: A robust automated tool for quantifying signal puncta in fluorescent imaging. | Hospelhorn BG, Kesler BK, Jashnsaz H, Neuert G | bioRxiv : the preprint server for biology | 39868229 | bioRxiv | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/39868229 |
| Distribution shapes govern the discovery of predictive models for gene regulation. | Munsky B, Li G, Fox ZR, Shepherd DP, Neuert G | Proceedings of the National Academy of Sciences of the United States of America | 29959206 | Proc Natl Acad Sci U S A | 2018 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/29959206 |
| Finite state projection based bounds to compare chemical master equation models using single-cell data. | Fox Z, Neuert G, Munsky B | The Journal of chemical physics | 27544081 | J Chem Phys | 2016 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/27544081 |
| Kinetics of osmotic stress regulate a cell fate switch of cell survival. | Thiemicke A, Neuert G | Science advances | 33608274 | Sci Adv | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33608274 |
| Generating kinetic environments to study dynamic cellular processes in single cells. | Thiemicke A, Jashnsaz H, Li G, Neuert G | Scientific reports | 31300695 | Sci Rep | 2019 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/31300695 |
| Diverse Cell Stimulation Kinetics Identify Predictive Signal Transduction Models. | Jashnsaz H, Fox ZR, Hughes JJ, Li G, Munsky B, Neuert G | iScience | 33083733 | iScience | 2020 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/33083733 |
| Substrate-Competitive Activity-Based Profiling of Ester Prodrug Activating Enzymes. | Xu H, Majmudar JD, Davda D, Ghanakota P, Kim KH, Carlson HA, Showalter HD, Martin BR, Amidon GL | Molecular pharmaceutics | 26262434 | Mol Pharm | 2015 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/26262434 |
| Enrichment of S-Palmitoylated Proteins for Mass Spectrometry Analysis. | Cheung See Kit M, Martin BR | Methods in molecular biology (Clifton, N.J.) | 31152396 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31152396 |
| Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry. | Borotto NB, McClory PJ, Martin BR, Håkansson K | Analytical chemistry | 28708386 | Anal Chem | 2017 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/28708386 |
| APT2 Inhibition Restores Scribble Localization and S-Palmitoylation in Snail-Transformed Cells. | Hernandez JL, Davda D, Cheung See Kit M, Majmudar JD, Won SJ, Gang M, Pasupuleti SC, Choi AI, Bartkowiak CM, Martin BR | Cell chemical biology | 28065656 | Cell Chem Biol | 2017 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/28065656 |
| Temporal Profiling Establishes a Dynamic S-Palmitoylation Cycle. | Won SJ, Martin BR | ACS chemical biology | 29733200 | ACS Chem Biol | 2018 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/29733200 |
| Protein depalmitoylases. | Won SJ, Cheung See Kit M, Martin BR | Critical reviews in biochemistry and molecular biology | 29239216 | Crit Rev Biochem Mol Biol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29239216 |
| HDAC8 Substrates Identified by Genetically Encoded Active Site Photocrosslinking. | Lopez JE, Haynes SE, Majmudar JD, Martin BR, Fierke CA | Journal of the American Chemical Society | 29035536 | J Am Chem Soc | 2017 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/29035536 |
| Chemoselective ratiometric imaging of protein S-sulfenylation. | Tom CTMB, Crellin JE, Motiwala HF, Stone MB, Davda D, Walker W, Kuo YH, Hernandez JL, Labby KJ, Gomez-Rodriguez L, Jenkins PM, Veatch SL, Martin BR | Chemical communications (Cambridge, England) | 28613292 | Chem Commun (Camb) | 2017 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/28613292 |
| DIA-SIFT: A Precursor and Product Ion Filter for Accurate Stable Isotope Data-Independent Acquisition Proteomics. | Haynes SE, Majmudar JD, Martin BR | Analytical chemistry | 29989796 | Anal Chem | 2018 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/29989796 |
| Free Radical Initiated Peptide Sequencing for Direct Site Localization of Sulfation and Phosphorylation with Negative Ion Mode Mass Spectrometry. | Borotto NB, Ileka KM, Tom CATMB, Martin BR, Håkansson K | Analytical chemistry | 30063332 | Anal Chem | 2018 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/30063332 |
| Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2). | Won SJ, Davda D, Labby KJ, Hwang SY, Pricer R, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL 3rd, Stuckey JA, Martin BR | ACS chemical biology | 27748579 | ACS Chem Biol | 2016 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/27748579 |
| Harnessing Redox Cross-Reactivity To Profile Distinct Cysteine Modifications. | Majmudar JD, Konopko AM, Labby KJ, Tom CT, Crellin JE, Prakash A, Martin BR | Journal of the American Chemical Society | 26780921 | J Am Chem Soc | 2016 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/26780921 |
| Variable-Velocity Traveling-Wave Ion Mobility Separation Enhancing Peak Capacity for Data-Independent Acquisition Proteomics. | Haynes SE, Polasky DA, Dixit SM, Majmudar JD, Neeson K, Ruotolo BT, Martin BR | Analytical chemistry | 28471653 | Anal Chem | 2017 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/28471653 |
| Affinity-Based Selectivity Profiling of an In-Class Selective Competitive Inhibitor of Acyl Protein Thioesterase 2. | Won SJ, Eschweiler JD, Majmudar JD, Chong FS, Hwang SY, Ruotolo BT, Martin BR | ACS medicinal chemistry letters | 28197315 | ACS Med Chem Lett | 2017 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/28197315 |
| Activated G Protein Gαs Samples Multiple Endomembrane Compartments. | Martin BR, Lambert NA | The Journal of biological chemistry | 27528603 | J Biol Chem | 2016 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/27528603 |
| Dimethyl Itaconate Is Not Metabolized into Itaconate Intracellularly. | ElAzzouny M, Tom CT, Evans CR, Olson LL, Tanga MJ, Gallagher KA, Martin BR, Burant CF | The Journal of biological chemistry | 28188288 | J Biol Chem | 2017 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/28188288 |
| Profiling Protein S-Sulfination with Maleimide-Linked Probes. | Kuo YH, Konopko AM, Borotto NB, Majmudar JD, Haynes SE, Martin BR | Chembiochem : a European journal of chemical biology | 28809078 | Chembiochem | 2017 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/28809078 |
| Global Analysis of Palmitoylated Proteins in Toxoplasma gondii. | Foe IT, Child MA, Majmudar JD, Krishnamurthy S, van der Linden WA, Ward GE, Martin BR, Bogyo M | Cell host & microbe | 26468752 | Cell Host Microbe | 2015 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/26468752 |
| Scribble sub-cellular localization modulates recruitment of YES1 to regulate YAP1 phosphorylation. | Zhao D, Yin Z, Soellner MB, Martin BR | Cell chemical biology | 33730553 | Cell Chem Biol | 2021 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/33730553 |
| Correlated S-palmitoylation profiling of Snail-induced epithelial to mesenchymal transition. | Hernandez JL, Davda D, Majmudar JD, Won SJ, Prakash A, Choi AI, Martin BR | Molecular bioSystems | 27030425 | Mol Biosyst | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27030425 |
| Tunable Heteroaromatic Sulfones Enhance in-Cell Cysteine Profiling. | Motiwala HF, Kuo YH, Stinger BL, Palfey BA, Martin BR | Journal of the American Chemical Society | 31881155 | J Am Chem Soc | 2020 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/31881155 |
| DNA Origami Rotaxanes: Tailored Synthesis and Controlled Structure Switching. | Powell JT, Akhuetie-Oni BO, Zhang Z, Lin C | Angewandte Chemie (International ed. in English) | 27527591 | Angew Chem Int Ed Engl | 2016 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/27527591 |
| FisB relies on homo-oligomerization and lipid binding to catalyze membrane fission in bacteria. | Landajuela A, Braun M, Rodrigues CDA, Martínez-Calvo A, Doan T, Horenkamp F, Andronicos A, Shteyn V, Williams ND, Lin C, Wingreen NS, Rudner DZ, Karatekin E | PLoS biology | 34185788 | PLoS Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34185788 |
| Fluorogenic DNA-PAINT for faster, low-background super-resolution imaging. | Chung KKH, Zhang Z, Kidd P, Zhang Y, Williams ND, Rollins B, Yang Y, Lin C, Baddeley D, Bewersdorf J | Nature methods | 35501386 | Nat Methods | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35501386 |
| Vesicle Tubulation with Self-Assembling DNA Nanosprings. | Grome MW, Zhang Z, Pincet F, Lin C | Angewandte Chemie (International ed. in English) | 29575478 | Angew Chem Int Ed Engl | 2018 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/29575478 |
| Directing reconfigurable DNA nanoarrays. | Yang Y, Lin C | Science (New York, N.Y.) | 28751594 | Science | 2017 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/28751594 |
| A programmable DNA-origami platform for studying lipid transfer between bilayers. | Bian X, Zhang Z, Xiong Q, De Camilli P, Lin C | Nature chemical biology | 31320758 | Nat Chem Biol | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31320758 |
| A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. | Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP | ACS nano | 29350911 | ACS Nano | 2018 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/29350911 |
| Placing and shaping liposomes with reconfigurable DNA nanocages. | Zhang Z, Yang Y, Pincet F, Llaguno MC, Lin C | Nature chemistry | 28644472 | Nat Chem | 2017 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/28644472 |
| DNA-Origami-Based Fluorescence Brightness Standards for Convenient and Fast Protein Counting in Live Cells. | Williams ND, Landajuela A, Kasula RK, Zhou W, Powell JT, Xi Z, Isaacs FJ, Berro J, Toomre D, Karatekin E, Lin C | Nano letters | 33164530 | Nano Lett | 2020 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/33164530 |
| Sorting sub-150-nm liposomes of distinct sizes by DNA-brick-assisted centrifugation. | Yang Y, Wu Z, Wang L, Zhou K, Xia K, Xiong Q, Liu L, Zhang Z, Chapman ER, Xiong Y, Melia TJ, Karatekin E, Gu H, Lin C | Nature chemistry | 33785892 | Nat Chem | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33785892 |
| Engineering Lipid Membranes with Programmable DNA Nanostructures. | Shen Q, Grome MW, Yang Y, Lin C | Advanced biosystems | 31934608 | Adv Biosyst | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31934608 |
| Stiffness and Membrane Anchor Density Modulate DNA-Nanospring-Induced Vesicle Tubulation. | Grome MW, Zhang Z, Lin C | ACS applied materials & interfaces | 31252462 | ACS Appl Mater Interfaces | 2019 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/31252462 |
| DNA Origami Post-Processing by CRISPR-Cas12a. | Xiong Q, Xie C, Zhang Z, Liu L, Powell JT, Shen Q, Lin C | Angewandte Chemie (International ed. in English) | 31883145 | Angew Chem Int Ed Engl | 2020 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/31883145 |
| Systematic identification of cis-regulatory variants that cause gene expression differences in a yeast cross. | Renganaath K, Chong R, Day L, Kosuri S, Kruglyak L, Albert FW | eLife | 33179598 | Elife | 2020 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/33179598 |
| Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically Encoded Multiplexed Reporter Assay in Escherichia coli. | Urtecho G, Tripp AD, Insigne KD, Kim H, Kosuri S | Biochemistry | 29388765 | Biochemistry | 2019 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/29388765 |
| A Scalable, Multiplexed Assay for Decoding GPCR-Ligand Interactions with RNA Sequencing. | Jones EM, Jajoo R, Cancilla D, Lubock NB, Wang J, Satyadi M, Chong R, de March C, Bloom JS, Matsunami H, Kosuri S | Cell systems | 30904378 | Cell Syst | 2019 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/30904378 |
| Highly parallel genome variant engineering with CRISPR-Cas9. | Sadhu MJ, Bloom JS, Day L, Siegel JJ, Kosuri S, Kruglyak L | Nature genetics | 29632376 | Nat Genet | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29632376 |
| Dissection of c-AMP Response Element Architecture by Using Genomic and Episomal Massively Parallel Reporter Assays. | Davis JE, Insigne KD, Jones EM, Hastings QA, Boldridge WC, Kosuri S | Cell systems | 32603702 | Cell Syst | 2020 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/32603702 |
| Metagenomic mining of regulatory elements enables programmable species-selective gene expression. | Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH | Nature methods | 30052624 | Nat Methods | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/30052624 |
| A Multiplexed Assay for Exon Recognition Reveals that an Unappreciated Fraction of Rare Genetic Variants Cause Large-Effect Splicing Disruptions. | Chong R, Insigne KD, Yao D, Burghard CP, Wang J, Hsiao YE, Jones EM, Goodman DB, Xiao X, Kosuri S | Molecular cell | 30503770 | Mol Cell | 2019 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/30503770 |
| A systematic comparison of error correction enzymes by next-generation sequencing. | Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S | Nucleic acids research | 28911123 | Nucleic Acids Res | 2017 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/28911123 |
| Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. | Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S | eLife | 33084570 | Elife | 2020 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/33084570 |
| Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems. | Yu TC, Liu WL, Brinck MS, Davis JE, Shek J, Bower G, Einav T, Insigne KD, Phillips R, Kosuri S, Urtecho G | Nature communications | 33436562 | Nat Commun | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33436562 |
| DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions. | Sidore AM, Plesa C, Samson JA, Lubock NB, Kosuri S | Nucleic acids research | 32692349 | Nucleic Acids Res | 2020 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/32692349 |
| Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. | Plesa C, Sidore AM, Lubock NB, Zhang D, Kosuri S | Science (New York, N.Y.) | 29301959 | Science | 2018 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/29301959 |
| A multiplexed bacterial two-hybrid for rapid characterization of protein-protein interactions and iterative protein design. | Boldridge WC, Ljubetič A, Kim H, Lubock N, Szilágyi D, Lee J, Brodnik A, Jerala R, Kosuri S | Nature communications | 37532706 | Nat Commun | 2023 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/37532706 |
| Comparative genomics of Steinernema reveals deeply conserved gene regulatory networks. | Dillman AR, Macchietto M, Porter CF, Rogers A, Williams B, Antoshechkin I, Lee MM, Goodwin Z, Lu X, Lewis EE, Goodrich-Blair H, Stock SP, Adams BJ, Sternberg PW, Mortazavi A | Genome biology | 26392177 | Genome Biol | 2015 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/26392177 |
| Single-nucleus RNA-seq of differentiating human myoblasts reveals the extent of fate heterogeneity. | Zeng W, Jiang S, Kong X, El-Ali N, Ball AR Jr, Ma CI, Hashimoto N, Yokomori K, Mortazavi A | Nucleic acids research | 27566152 | Nucleic Acids Res | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27566152 |
| Targeted demethylation at the CDKN1C/p57 locus induces human β cell replication. | Ou K, Yu M, Moss NG, Wang YJ, Wang AW, Nguyen SC, Jiang C, Feleke E, Kameswaran V, Joyce EF, Naji A, Glaser B, Avrahami D, Kaestner KH | The Journal of clinical investigation | 30352048 | J Clin Invest | 2019 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/30352048 |
| Integrating ChIP-seq with other functional genomics data. | Jiang S, Mortazavi A | Briefings in functional genomics | 29579165 | Brief Funct Genomics | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29579165 |
| Prevention of C5aR1 signaling delays microglial inflammatory polarization, favors clearance pathways and suppresses cognitive loss. | Hernandez MX, Jiang S, Cole TA, Chu SH, Fonseca MI, Fang MJ, Hohsfield LA, Torres MD, Green KN, Wetsel RA, Mortazavi A, Tenner AJ | Molecular neurodegeneration | 28923083 | Mol Neurodegener | 2017 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/28923083 |
| Activated entomopathogenic nematode infective juveniles release lethal venom proteins. | Lu D, Macchietto M, Chang D, Barros MM, Baldwin J, Mortazavi A, Dillman AR | PLoS pathogens | 28426766 | PLoS Pathog | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28426766 |
| Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network. | Longabaugh WJR, Zeng W, Zhang JA, Hosokawa H, Jansen CS, Li L, Romero-Wolf M, Liu P, Kueh HY, Mortazavi A, Rothenberg EV | Proceedings of the National Academy of Sciences of the United States of America | 28584128 | Proc Natl Acad Sci U S A | 2017 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/28584128 |
| A survey of best practices for RNA-seq data analysis. | Conesa A, Madrigal P, Tarazona S, Gomez-Cabrero D, Cervera A, McPherson A, Szcześniak MW, Gaffney DJ, Elo LL, Zhang X, Mortazavi A | Genome biology | 26813401 | Genome Biol | 2016 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/26813401 |
| Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. | Mortazavi A | Nature methods | 25825835 | Nat Methods | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25825835 |
| Dynamic Gene Regulatory Networks of Human Myeloid Differentiation. | Ramirez RN, El-Ali NC, Mager MA, Wyman D, Conesa A, Mortazavi A | Cell systems | 28365152 | Cell Syst | 2017 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/28365152 |
| Regeneration of fat cells from myofibroblasts during wound healing. | Plikus MV, Guerrero-Juarez CF, Ito M, Li YR, Dedhia PH, Zheng Y, Shao M, Gay DL, Ramos R, Hsi TC, Oh JW, Wang X, Ramirez A, Konopelski SE, Elzein A, Wang A, Supapannachart RJ, Lee HL, Lim CH, Nace A, Guo A, Treffeisen E, Andl T, Ramirez RN, Murad R, Offermanns S, Metzger D, Chambon P, Widgerow AD, Tuan TL, Mortazavi A, Gupta RK, Hamilton BA, Millar SE, Seale P, Pear WS, Lazar MA, Cotsarelis G | Science (New York, N.Y.) | 28059714 | Science | 2017 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/28059714 |
| Comparative Transcriptomics of Steinernema and Caenorhabditis Single Embryos Reveals Orthologous Gene Expression Convergence during Late Embryogenesis. | Macchietto M, Angdembey D, Heidarpour N, Serra L, Rodriguez B, El-Ali N, Mortazavi A | Genome biology and evolution | 29048526 | Genome Biol Evol | 2017 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/29048526 |
| Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. | Serra L, Chang DZ, Macchietto M, Williams K, Murad R, Lu D, Dillman AR, Mortazavi A | Bio-protocol | 29564372 | Bio Protoc | 2018 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/29564372 |
| MHC variation sculpts individualized microbial communities that control susceptibility to enteric infection. | Kubinak JL, Stephens WZ, Soto R, Petersen C, Chiaro T, Gogokhia L, Bell R, Ajami NJ, Petrosino JF, Morrison L, Potts WK, Jensen PE, O'Connell RM, Round JL | Nature communications | 26494419 | Nat Commun | 2015 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/26494419 |
| Antagonistic Interplay between MicroRNA-155 and IL-10 during Lyme Carditis and Arthritis. | Lochhead RB, Zachary JF, Dalla Rosa L, Ma Y, Weis JH, O'Connell RM, Weis JJ | PloS one | 26252010 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26252010 |
| T cell-mediated regulation of the microbiota protects against obesity. | Petersen C, Bell R, Klag KA, Lee SH, Soto R, Ghazaryan A, Buhrke K, Ekiz HA, Ost KS, Boudina S, O'Connell RM, Cox JE, Villanueva CJ, Stephens WZ, Round JL | Science (New York, N.Y.) | 31346040 | Science | 2019 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/31346040 |
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| Structural and mechanistic basis of the EMC-dependent biogenesis of distinct transmembrane clients. | Miller-Vedam LE, Bräuning B, Popova KD, Schirle Oakdale NT, Bonnar JL, Prabu JR, Boydston EA, Sevillano N, Shurtleff MJ, Stroud RM, Craik CS, Schulman BA, Frost A, Weissman JS | eLife | 33236988 | Elife | 2020 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/33236988 |
| In vitro analysis of RQC activities provides insights into the mechanism and function of CAT tailing. | Osuna BA, Howard CJ, Kc S, Frost A, Weinberg DE | eLife | 28718767 | Elife | 2017 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/28718767 |
| LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells. | Gu M, LaJoie D, Chen OS, von Appen A, Ladinsky MS, Redd MJ, Nikolova L, Bjorkman PJ, Sundquist WI, Ullman KS, Frost A | Proceedings of the National Academy of Sciences of the United States of America | 28242692 | Proc Natl Acad Sci U S A | 2017 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/28242692 |
| Structural basis of mitochondrial receptor binding and constriction by DRP1. | Kalia R, Wang RY, Yusuf A, Thomas PV, Agard DA, Shaw JM, Frost A | Nature | 29899447 | Nature | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29899447 |
| Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule. | Tsai JC, Miller-Vedam LE, Anand AA, Jaishankar P, Nguyen HC, Renslo AR, Frost A, Walter P | Science (New York, N.Y.) | 29599213 | Science | 2018 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/29599213 |
| Photocatalytic LPOR forms helical lattices that shape membranes for chlorophyll synthesis. | Nguyen HC, Melo AA, Kruk J, Frost A, Gabruk M | Nature plants | 33875834 | Nat Plants | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33875834 |
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| A Golgi rhomboid protease Rbd2 recruits Cdc48 to cleave yeast SREBP. | Hwang J, Ribbens D, Raychaudhuri S, Cairns L, Gu H, Frost A, Urban S, Espenshade PJ | The EMBO journal | 27655872 | EMBO J | 2016 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/27655872 |
| Structural basis of TRPV1 modulation by endogenous bioactive lipids. | Arnold WR, Mancino A, Moss FR 3rd, Frost A, Julius D, Cheng Y | Nature structural & molecular biology | 38698206 | Nat Struct Mol Biol | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38698206 |
| Vms1p is a release factor for the ribosome-associated quality control complex. | Zurita Rendón O, Fredrickson EK, Howard CJ, Van Vranken J, Fogarty S, Tolley ND, Kalia R, Osuna BA, Shen PS, Hill CP, Frost A, Rutter J | Nature communications | 29875445 | Nat Commun | 2018 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/29875445 |
| CAT-tailing as a fail-safe mechanism for efficient degradation of stalled nascent polypeptides. | Kostova KK, Hickey KL, Osuna BA, Hussmann JA, Frost A, Weinberg DE, Weissman JS | Science (New York, N.Y.) | 28751611 | Science | 2017 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/28751611 |
| Current outcomes when optimizing 'standard' sample preparation for single-particle cryo-EM. | Carragher B, Cheng Y, Frost A, Glaeser RM, Lander GC, Nogales E, Wang HW | Journal of microscopy | 31553060 | J Microsc | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31553060 |
| Exocyst structural changes associated with activation of tethering downstream of Rho/Cdc42 GTPases. | Rossi G, Lepore D, Kenner L, Czuchra AB, Plooster M, Frost A, Munson M, Brennwald P | The Journal of cell biology | 31904797 | J Cell Biol | 2020 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/31904797 |
| FDM 3D Printing of High-Pressure, Heat-Resistant, Transparent Microfluidic Devices. | Romanov V, Samuel R, Chaharlang M, Jafek AR, Frost A, Gale BK | Analytical chemistry | 30071717 | Anal Chem | 2018 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/30071717 |
| Brominated lipid probes expose structural asymmetries in constricted membranes. | Moss FR 3rd, Lincoff J, Tucker M, Mohammed A, Grabe M, Frost A | Nature structural & molecular biology | 36624348 | Nat Struct Mol Biol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36624348 |
| Interchangeable adaptors regulate mitochondrial dynamin assembly for membrane scission. | Koirala S, Guo Q, Kalia R, Bui HT, Eckert DM, Frost A, Shaw JM | Proceedings of the National Academy of Sciences of the United States of America | 23530241 | Proc Natl Acad Sci U S A | 2013 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/23530241 |
| Structures, Functions, and Dynamics of ESCRT-III/Vps4 Membrane Remodeling and Fission Complexes. | McCullough J, Frost A, Sundquist WI | Annual review of cell and developmental biology | 30095293 | Annu Rev Cell Dev Biol | 2018 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/30095293 |
| Cell biology: Double agents for mitochondrial division. | McBride HM, Frost A | Nature | 27880759 | Nature | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27880759 |
| Structural inhibition of dynamin-mediated membrane fission by endophilin. | Hohendahl A, Talledge N, Galli V, Shen PS, Humbert F, De Camilli P, Frost A, Roux A | eLife | 28933693 | Elife | 2017 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/28933693 |
| Membrane fission by dynamin: what we know and what we need to know. | Antonny B, Burd C, De Camilli P, Chen E, Daumke O, Faelber K, Ford M, Frolov VA, Frost A, Hinshaw JE, Kirchhausen T, Kozlov MM, Lenz M, Low HH, McMahon H, Merrifield C, Pollard TD, Robinson PJ, Roux A, Schmid S | The EMBO journal | 27670760 | EMBO J | 2016 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/27670760 |
| Subunit connectivity, assembly determinants and architecture of the yeast exocyst complex. | Heider MR, Gu M, Duffy CM, Mirza AM, Marcotte LL, Walls AC, Farrall N, Hakhverdyan Z, Field MC, Rout MP, Frost A, Munson M | Nature structural & molecular biology | 26656853 | Nat Struct Mol Biol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26656853 |
| Structure and membrane remodeling activity of ESCRT-III helical polymers. | McCullough J, Clippinger AK, Talledge N, Skowyra ML, Saunders MG, Naismith TV, Colf LA, Afonine P, Arthur C, Sundquist WI, Hanson PI, Frost A | Science (New York, N.Y.) | 26634441 | Science | 2015 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/26634441 |
| The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins. | Shurtleff MJ, Itzhak DN, Hussmann JA, Schirle Oakdale NT, Costa EA, Jonikas M, Weibezahn J, Popova KD, Jan CH, Sinitcyn P, Vembar SS, Hernandez H, Cox J, Burlingame AL, Brodsky JL, Frost A, Borner GH, Weissman JS | eLife | 29809151 | Elife | 2018 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/29809151 |
| Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. | Shen PS, Park J, Qin Y, Li X, Parsawar K, Larson MH, Cox J, Cheng Y, Lambowitz AM, Weissman JS, Brandman O, Frost A | Science (New York, N.Y.) | 25554787 | Science | 2015 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/25554787 |
| A Tunable Microfluidic Device Enables Cargo Encapsulation by Cell- or Organelle-Sized Lipid Vesicles Comprising Asymmetric Lipid Bilayers. | Romanov V, McCullough J, Gale BK, Frost A | Advanced biosystems | 31428671 | Adv Biosyst | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31428671 |
| LEM2 phase separation promotes ESCRT-mediated nuclear envelope reformation. | von Appen A, LaJoie D, Johnson IE, Trnka MJ, Pick SM, Burlingame AL, Ullman KS, Frost A | Nature | 32494070 | Nature | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32494070 |
| Membrane constriction and thinning by sequential ESCRT-III polymerization. | Nguyen HC, Talledge N, McCullough J, Sharma A, Moss FR 3rd, Iwasa JH, Vershinin MD, Sundquist WI, Frost A | Nature structural & molecular biology | 32251413 | Nat Struct Mol Biol | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32251413 |
| eIF2B-catalyzed nucleotide exchange and phosphoregulation by the integrated stress response. | Kenner LR, Anand AA, Nguyen HC, Myasnikov AG, Klose CJ, McGeever LA, Tsai JC, Miller-Vedam LE, Walter P, Frost A | Science (New York, N.Y.) | 31048491 | Science | 2019 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/31048491 |
| Functional role of PGAM5 multimeric assemblies and their polymerization into filaments. | Ruiz K, Thaker TM, Agnew C, Miller-Vedam L, Trenker R, Herrera C, Ingaramo M, Toso D, Frost A, Jura N | Nature communications | 30705304 | Nat Commun | 2019 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/30705304 |
| Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. | Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, Petersen KF, Kibbey RG, Goodman AL, Shulman GI | Nature | 27279214 | Nature | 2016 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/27279214 |
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| T cell receptor dwell times control the kinase activity of Zap70. | Klammt C, Novotná L, Li DT, Wolf M, Blount A, Zhang K, Fitchett JR, Lillemeier BF | Nature immunology | 26237552 | Nat Immunol | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26237552 |
| Superresolution imaging reveals nanometer- and micrometer-scale spatial distributions of T-cell receptors in lymph nodes. | Hu YS, Cang H, Lillemeier BF | Proceedings of the National Academy of Sciences of the United States of America | 27303041 | Proc Natl Acad Sci U S A | 2016 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/27303041 |
| A cycle of Zap70 kinase activation and release from the TCR amplifies and disperses antigenic stimuli. | Katz ZB, Novotná L, Blount A, Lillemeier BF | Nature immunology | 27869819 | Nat Immunol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27869819 |
| The Deubiquitylase MATH-33 Controls DAF-16 Stability and Function in Metabolism and Longevity. | Heimbucher T, Liu Z, Bossard C, McCloskey R, Carrano AC, Riedel CG, Tanasa B, Klammt C, Fonslow BR, Riera CE, Lillemeier BF, Kemphues K, Yates JR 3rd, O'Shea C, Hunter T, Dillin A | Cell metabolism | 26154057 | Cell Metab | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26154057 |
| Quantitative In Vivo Proteomics of Metformin Response in Liver Reveals AMPK-Dependent and -Independent Signaling Networks. | Stein BD, Calzolari D, Hellberg K, Hu YS, He L, Hung CM, Toyama EQ, Ross DS, Lillemeier BF, Cantley LC, Yates JR 3rd, Shaw RJ | Cell reports | 31801093 | Cell Rep | 2019 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/31801093 |
| The genomic architecture and molecular evolution of ant odorant receptors. | McKenzie SK, Kronauer DJC | Genome research | 30249741 | Genome Res | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30249741 |
| Fitness benefits and emergent division of labour at the onset of group living. | Ulrich Y, Saragosti J, Tokita CK, Tarnita CE, Kronauer DJC | Nature | 30135576 | Nature | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30135576 |
| Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor. | Libbrecht R, Oxley PR, Kronauer DJC | BMC biology | 30103762 | BMC Biol | 2018 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/30103762 |
| orco Mutagenesis Causes Loss of Antennal Lobe Glomeruli and Impaired Social Behavior in Ants. | Trible W, Olivos-Cisneros L, McKenzie SK, Saragosti J, Chang NC, Matthews BJ, Oxley PR, Kronauer DJC | Cell | 28802042 | Cell | 2017 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/28802042 |
| Ant genomics sheds light on the molecular regulation of social organization. | Libbrecht R, Oxley PR, Kronauer DJ, Keller L | Genome biology | 23895728 | Genome Biol | 2013 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/23895728 |
| Ant larvae regulate worker foraging behavior and ovarian activity in a dose-dependent manner. | Ulrich Y, Burns D, Libbrecht R, Kronauer DJ | Behavioral ecology and sociobiology | 27616809 | Behav Ecol Sociobiol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27616809 |
| The genome of the clonal raider ant Cerapachys biroi. | Oxley PR, Ji L, Fetter-Pruneda I, McKenzie SK, Li C, Hu H, Zhang G, Kronauer DJ | Current biology : CB | 24508170 | Curr Biol | 2014 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/24508170 |
| Comparative genomics and transcriptomics in ants provide new insights into the evolution and function of odorant binding and chemosensory proteins. | McKenzie SK, Oxley PR, Kronauer DJ | BMC genomics | 25159315 | BMC Genomics | 2014 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/25159315 |
| Robust DNA Methylation in the Clonal Raider Ant Brain. | Libbrecht R, Oxley PR, Keller L, Kronauer DJ | Current biology : CB | 26804553 | Curr Biol | 2016 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/26804553 |
| Transcriptomics and neuroanatomy of the clonal raider ant implicate an expanded clade of odorant receptors in chemical communication. | McKenzie SK, Fetter-Pruneda I, Ruta V, Kronauer DJ | Proceedings of the National Academy of Sciences of the United States of America | 27911792 | Proc Natl Acad Sci U S A | 2016 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/27911792 |
| Social regulation of insulin signaling and the evolution of eusociality in ants. | Chandra V, Fetter-Pruneda I, Oxley PR, Ritger AL, McKenzie SK, Libbrecht R, Kronauer DJC | Science (New York, N.Y.) | 30049879 | Science | 2018 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/30049879 |
| Srs2 prevents Rad51 filament formation by repetitive motion on DNA. | Qiu Y, Antony E, Doganay S, Koh HR, Lohman TM, Myong S | Nature communications | 23939144 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23939144 |
| The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. | Elbaum-Garfinkle S, Kim Y, Szczepaniak K, Chen CC, Eckmann CR, Myong S, Brangwynne CP | Proceedings of the National Academy of Sciences of the United States of America | 26015579 | Proc Natl Acad Sci U S A | 2015 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/26015579 |
| G-Quadruplex and Protein Binding by Single-Molecule FRET Microscopy. | Lee CY, McNerney C, Myong S | Methods in molecular biology (Clifton, N.J.) | 31444758 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31444758 |
| Single-molecule real-time detection of telomerase extension activity. | Hwang H, Opresko P, Myong S | Scientific reports | 25263700 | Sci Rep | 2014 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/25263700 |
| RNA Remodeling Activity of DEAD Box Proteins Tuned by Protein Concentration, RNA Length, and ATP. | Kim Y, Myong S | Molecular cell | 27546789 | Mol Cell | 2016 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/27546789 |
| Oxidative guanine base damage regulates human telomerase activity. | Fouquerel E, Lormand J, Bose A, Lee HT, Kim GS, Li J, Sobol RW, Freudenthal BD, Myong S, Opresko PL | Nature structural & molecular biology | 27820808 | Nat Struct Mol Biol | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27820808 |
| RNA stem structure governs coupling of dicing and gene silencing in RNA interference. | Koh HR, Ghanbariniaki A, Myong S | Proceedings of the National Academy of Sciences of the United States of America | 29133395 | Proc Natl Acad Sci U S A | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/29133395 |
| Dynamic profiling of double-stranded RNA binding proteins. | Wang X, Vukovic L, Koh HR, Schulten K, Myong S | Nucleic acids research | 26184879 | Nucleic Acids Res | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26184879 |
| Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. | Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S | Nucleic acids research | 27095201 | Nucleic Acids Res | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27095201 |
| ATP-independent diffusion of double-stranded RNA binding proteins. | Koh HR, Kidwell MA, Ragunathan K, Doudna JA, Myong S | Proceedings of the National Academy of Sciences of the United States of America | 23251028 | Proc Natl Acad Sci U S A | 2013 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/23251028 |
| Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing. | Koh HR, Xing L, Kleiman L, Myong S | Nucleic acids research | 24914047 | Nucleic Acids Res | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24914047 |
| Molecular mechanism of resolving trinucleotide repeat hairpin by helicases. | Qiu Y, Niu H, Vukovic L, Sung P, Myong S | Structure (London, England : 1993) | 26004439 | Structure | 2015 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/26004439 |
| Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36. | Chen MC, Tippana R, Demeshkina NA, Murat P, Balasubramanian S, Myong S, Ferré-D'Amaré AR | Nature | 29899445 | Nature | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29899445 |
| POT1-TPP1 regulates telomeric overhang structural dynamics. | Hwang H, Buncher N, Opresko PL, Myong S | Structure (London, England : 1993) | 22981946 | Structure | 2012 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/22981946 |
| RNA Scanning of a Molecular Machine with a Built-in Ruler. | Koh HR, Kidwell MA, Doudna J, Myong S | Journal of the American Chemical Society | 27958730 | J Am Chem Soc | 2017 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/27958730 |
| Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays. | Koh HR, Wang X, Myong S | Methods (San Diego, Calif.) | 27012177 | Methods | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27012177 |
| Single-molecule imaging reveals a common mechanism shared by G-quadruplex-resolving helicases. | Tippana R, Hwang H, Opresko PL, Bohr VA, Myong S | Proceedings of the National Academy of Sciences of the United States of America | 27407146 | Proc Natl Acad Sci U S A | 2016 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/27407146 |
| G-quadruplex formation in double strand DNA probed by NMM and CV fluorescence. | Kreig A, Calvert J, Sanoica J, Cullum E, Tipanna R, Myong S | Nucleic acids research | 26202971 | Nucleic Acids Res | 2015 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/26202971 |
| Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. | Bell RJ, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song JS, Costello JF | Science (New York, N.Y.) | 25977370 | Science | 2015 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/25977370 |
| Telomeric overhang length determines structural dynamics and accessibility to telomerase and ALT-associated proteins. | Hwang H, Kreig A, Calvert J, Lormand J, Kwon Y, Daley JM, Sung P, Opresko PL, Myong S | Structure (London, England : 1993) | 24836024 | Structure | 2014 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/24836024 |
| Substrate recognition and specificity of double-stranded RNA binding proteins. | Vuković L, Koh HR, Myong S, Schulten K | Biochemistry | 24801449 | Biochemistry | 2014 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/24801449 |
| G-quadruplex conformation and dynamics are determined by loop length and sequence. | Tippana R, Xiao W, Myong S | Nucleic acids research | 24920827 | Nucleic Acids Res | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24920827 |
| mRNA structure determines specificity of a polyQ-driven phase separation. | Langdon EM, Qiu Y, Ghanbari Niaki A, McLaughlin GA, Weidmann CA, Gerbich TM, Smith JA, Crutchley JM, Termini CM, Weeks KM, Myong S, Gladfelter AS | Science (New York, N.Y.) | 29650703 | Science | 2018 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/29650703 |
| Single-Cell Imaging Approaches for Studying Small-RNA-Induced Gene Regulation. | Koh HR, Myong S | Biophysical journal | 29970232 | Biophys J | 2018 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/29970232 |
| The Chd1 Chromatin Remodeler Shifts Nucleosomal DNA Bidirectionally as a Monomer. | Qiu Y, Levendosky RF, Chakravarthy S, Patel A, Bowman GD, Myong S | Molecular cell | 28943314 | Mol Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28943314 |
| CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog. | Pusapati GV, Kong JH, Patel BB, Krishnan A, Sagner A, Kinnebrew M, Briscoe J, Aravind L, Rohatgi R | Developmental cell | 29401421 | Dev Cell | 2018 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/29401421 |
| Lipid droplets can promote drug accumulation and activation. | Dubey R, Stivala CE, Nguyen HQ, Goo YH, Paul A, Carette JE, Trost BM, Rohatgi R | Nature chemical biology | 31932720 | Nat Chem Biol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31932720 |
| An essential role for Grk2 in Hedgehog signalling downstream of Smoothened. | Zhao Z, Lee RT, Pusapati GV, Iyu A, Rohatgi R, Ingham PW | EMBO reports | 27113758 | EMBO Rep | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27113758 |
| Chromatin-Remodeling Complex SWI/SNF Controls Multidrug Resistance by Transcriptionally Regulating the Drug Efflux Pump ABCB1. | Dubey R, Lebensohn AM, Bahrami-Nejad Z, Marceau C, Champion M, Gevaert O, Sikic BI, Carette JE, Rohatgi R | Cancer research | 27503929 | Cancer Res | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27503929 |
| Notch activity modulates the responsiveness of neural progenitors to sonic hedgehog signaling. | Kong JH, Yang L, Dessaud E, Chuang K, Moore DM, Rohatgi R, Briscoe J, Novitch BG | Developmental cell | 25936505 | Dev Cell | 2015 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/25936505 |
| Measuring Expression Levels of Endogenous Gli Genes by Immunoblotting and Real-Time PCR. | Niewiadomski P, Rohatgi R | Methods in molecular biology (Clifton, N.J.) | 26179041 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26179041 |
| G-protein-coupled receptors, Hedgehog signaling and primary cilia. | Mukhopadhyay S, Rohatgi R | Seminars in cell & developmental biology | 24845016 | Semin Cell Dev Biol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24845016 |
| Comparative genetic screens in human cells reveal new regulatory mechanisms in WNT signaling. | Lebensohn AM, Dubey R, Neitzel LR, Tacchelly-Benites O, Yang E, Marceau CD, Davis EM, Patel BB, Bahrami-Nejad Z, Travaglini KJ, Ahmed Y, Lee E, Carette JE, Rohatgi R | eLife | 27996937 | Elife | 2016 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/27996937 |
| CRISPR Screens Uncover Genes that Regulate Target Cell Sensitivity to the Morphogen Sonic Hedgehog. | Pusapati GV, Kong JH, Patel BB, Krishnan A, Sagner A, Kinnebrew M, Briscoe J, Aravind L, Rohatgi R | Developmental cell | 29290584 | Dev Cell | 2018 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/29290584 |
| G protein-coupled receptors control the sensitivity of cells to the morphogen Sonic Hedgehog. | Pusapati GV, Kong JH, Patel BB, Gouti M, Sagner A, Sircar R, Luchetti G, Ingham PW, Briscoe J, Rohatgi R | Science signaling | 29438014 | Sci Signal | 2018 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/29438014 |
| In Vivo Formation of Vacuolated Multi-phase Compartments Lacking Membranes. | Schmidt HB, Rohatgi R | Cell reports | 27452472 | Cell Rep | 2016 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/27452472 |
| Phase separation-deficient TDP43 remains functional in splicing. | Schmidt HB, Barreau A, Rohatgi R | Nature communications | 31653829 | Nat Commun | 2019 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/31653829 |
| Cholesterol accessibility at the ciliary membrane controls hedgehog signaling. | Kinnebrew M, Iverson EJ, Patel BB, Pusapati GV, Kong JH, Johnson KA, Luchetti G, Eckert KM, McDonald JG, Covey DF, Siebold C, Radhakrishnan A, Rohatgi R | eLife | 31657721 | Elife | 2019 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/31657721 |
| Measuring Gli2 Phosphorylation by Selected Reaction Monitoring Mass Spectrometry. | Ahrends R, Niewiadomski P, Teruel MN, Rohatgi R | Methods in molecular biology (Clifton, N.J.) | 26179043 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26179043 |
| Dynamic Remodeling of Membrane Composition Drives Cell Cycle through Primary Cilia Excision. | Phua SC, Chiba S, Suzuki M, Su E, Roberson EC, Pusapati GV, Schurmans S, Setou M, Rohatgi R, Reiter JF, Ikegami K, Inoue T | Cell | 28086093 | Cell | 2017 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/28086093 |
| R-spondins can potentiate WNT signaling without LGRs. | Lebensohn AM, Rohatgi R | eLife | 29405118 | Elife | 2018 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/29405118 |
| A single N-terminal phosphomimic disrupts TDP-43 polymerization, phase separation, and RNA splicing. | Wang A, Conicella AE, Schmidt HB, Martin EW, Rhoads SN, Reeb AN, Nourse A, Ramirez Montero D, Ryan VH, Rohatgi R, Shewmaker F, Naik MT, Mittag T, Ayala YM, Fawzi NL | The EMBO journal | 29438978 | EMBO J | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29438978 |
| Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens. | Patel BB, Lebensohn AM, Pusapati GV, Carette JE, Salzman J, Rohatgi R | PloS one | 30695034 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30695034 |
| TDP-43 α-helical structure tunes liquid-liquid phase separation and function. | Conicella AE, Dignon GL, Zerze GH, Schmidt HB, D'Ordine AM, Kim YC, Rohatgi R, Ayala YM, Mittal J, Fawzi NL | Proceedings of the National Academy of Sciences of the United States of America | 32132204 | Proc Natl Acad Sci U S A | 2020 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/32132204 |
| Rapid Screening of Gli2/3 Mutants Using the Flp-In System. | Niewiadomski P, Rohatgi R | Methods in molecular biology (Clifton, N.J.) | 26179044 | Methods Mol Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26179044 |
| Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling. | Hong SR, Wang CL, Huang YS, Chang YC, Chang YC, Pusapati GV, Lin CY, Hsu N, Cheng HC, Chiang YC, Huang WE, Shaner NC, Rohatgi R, Inoue T, Lin YC | Nature communications | 29712905 | Nat Commun | 2018 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/29712905 |
| Multiple ligand binding sites regulate the Hedgehog signal transducer Smoothened in vertebrates. | Byrne EF, Luchetti G, Rohatgi R, Siebold C | Current opinion in cell biology | 29268141 | Curr Opin Cell Biol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29268141 |
| EFCAB7 and IQCE regulate hedgehog signaling by tethering the EVC-EVC2 complex to the base of primary cilia. | Pusapati GV, Hughes CE, Dorn KV, Zhang D, Sugianto P, Aravind L, Rohatgi R | Developmental cell | 24582806 | Dev Cell | 2014 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/24582806 |
| Visualizing Dynamics of Cell Signaling In Vivo with a Phase Separation-Based Kinase Reporter. | Zhang Q, Huang H, Zhang L, Wu R, Chung CI, Zhang SQ, Torra J, Schepis A, Coughlin SR, Kornberg TB, Shu X | Molecular cell | 29307513 | Mol Cell | 2018 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/29307513 |
| Precision Optogenetic Tool for Selective Single- and Multiple-Cell Ablation in a Live Animal Model System. | Makhijani K, To TL, Ruiz-González R, Lafaye C, Royant A, Shu X | Cell chemical biology | 28065655 | Cell Chem Biol | 2017 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/28065655 |
| A rapid fluorogenic GPCR-β-arrestin interaction assay. | Zhang Q, Zheng YW, Coughlin SR, Shu X | Protein science : a publication of the Protein Society | 29411438 | Protein Sci | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29411438 |
| Dynamic Imaging of Small Molecule Induced Protein-Protein Interactions in Living Cells with a Fluorophore Phase Transition Based Approach. | Chung CI, Zhang Q, Shu X | Analytical chemistry | 30431263 | Anal Chem | 2018 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/30431263 |
| Singlet oxygen triplet energy transfer-based imaging technology for mapping protein-protein proximity in intact cells. | To TL, Fadul MJ, Shu X | Nature communications | 24905026 | Nat Commun | 2014 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/24905026 |
| Photoactivatable protein labeling by singlet oxygen mediated reactions. | To TL, Medzihradszky KF, Burlingame AL, DeGrado WF, Jo H, Shu X | Bioorganic & medicinal chemistry letters | 27220724 | Bioorg Med Chem Lett | 2016 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/27220724 |
| Structure-guided design of a reversible fluorogenic reporter of protein-protein interactions. | To TL, Zhang Q, Shu X | Protein science : a publication of the Protein Society | 26690964 | Protein Sci | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26690964 |
| Inhibitors of LexA Autoproteolysis and the Bacterial SOS Response Discovered by an Academic-Industry Partnership. | Mo CY, Culyba MJ, Selwood T, Kubiak JM, Hostetler ZM, Jurewicz AJ, Keller PM, Pope AJ, Quinn A, Schneck J, Widdowson KL, Kohli RM | ACS infectious diseases | 29275629 | ACS Infect Dis | 2018 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/29275629 |
| Non-equilibrium repressor binding kinetics link DNA damage dose to transcriptional timing within the SOS gene network. | Culyba MJ, Kubiak JM, Mo CY, Goulian M, Kohli RM | PLoS genetics | 29856734 | PLoS Genet | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29856734 |
| Targets for Combating the Evolution of Acquired Antibiotic Resistance. | Culyba MJ, Mo CY, Kohli RM | Biochemistry | 26016604 | Biochemistry | 2015 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/26016604 |
| Advancement of the 5-Amino-1-(Carbamoylmethyl)-1H-1,2,3-Triazole-4-Carboxamide Scaffold to Disarm the Bacterial SOS Response. | Selwood T, Larsen BJ, Mo CY, Culyba MJ, Hostetler ZM, Kohli RM, Reitz AB, Baugh SDP | Frontiers in microbiology | 30619111 | Front Microbiol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30619111 |
| Systematically Altering Bacterial SOS Activity under Stress Reveals Therapeutic Strategies for Potentiating Antibiotics. | Mo CY, Manning SA, Roggiani M, Culyba MJ, Samuels AN, Sniegowski PD, Goulian M, Kohli RM | mSphere | 27536734 | mSphere | 2016 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/27536734 |
| A Small-Molecule Inducible Synthetic Circuit for Control of the SOS Gene Network without DNA Damage. | Kubiak JM, Culyba MJ, Liu MY, Mo CY, Goulian M, Kohli RM | ACS synthetic biology | 28826208 | ACS Synth Biol | 2017 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/28826208 |
| Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis. | Mo CY, Birdwell LD, Kohli RM | Biochemistry | 24779472 | Biochemistry | 2014 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/24779472 |
| DNA Methyltransferases Demonstrate Reduced Activity against Arabinosylcytosine: Implications for Epigenetic Instability in Acute Myeloid Leukemia. | Nabel CS, DeNizio JE, Carroll M, Kohli RM | Biochemistry | 28394581 | Biochemistry | 2017 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/28394581 |
| Improving target amino acid selectivity in a permissive aminoacyl tRNA synthetase through counter-selection. | Sungwienwong I, Hostetler ZM, Blizzard RJ, Porter JJ, Driggers CM, Mbengi LZ, Villegas JA, Speight LC, Saven JG, Perona JJ, Kohli RM, Mehl RA, Petersson EJ | Organic & biomolecular chemistry | 28397914 | Org Biomol Chem | 2017 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/28397914 |
| A Single-Molecule Surface-Based Platform to Detect the Assembly and Function of the Human RNA Polymerase II Transcription Machinery. | Park SR, Hauver J, Zhang Y, Revyakin A, Coleman RA, Tjian R, Chu S, Pertsinidis A | Structure (London, England : 1993) | 32763141 | Structure | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/32763141 |
| Volumetric interferometric lattice light-sheet imaging. | Cao B, Coelho S, Li J, Wang G, Pertsinidis A | Nature biotechnology | 34635835 | Nat Biotechnol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34635835 |
| Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry. | Wang G, Hauver J, Thomas Z, Darst SA, Pertsinidis A | Cell | 27984731 | Cell | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27984731 |
| Single-gene imaging links genome topology, promoter-enhancer communication and transcription control. | Li J, Hsu A, Hua Y, Wang G, Cheng L, Ochiai H, Yamamoto T, Pertsinidis A | Nature structural & molecular biology | 32958948 | Nat Struct Mol Biol | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32958948 |
| Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos using CAS-LiveFISH. | Geng Y, Pertsinidis A | Scientific reports | 34108610 | Sci Rep | 2021 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/34108610 |
| Single-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells. | Li J, Dong A, Saydaminova K, Chang H, Wang G, Ochiai H, Yamamoto T, Pertsinidis A | Cell | 31155237 | Cell | 2019 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/31155237 |
| Topoisomerase III Acts at the Replication Fork To Remove Precatenanes. | Lee CM, Wang G, Pertsinidis A, Marians KJ | Journal of bacteriology | 30617245 | J Bacteriol | 2019 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/30617245 |
| Structural characterization of SpoIIIAB sporulation-essential protein in Bacillus subtilis. | Zeytuni N, Flanagan KA, Worrall LJ, Massoni SC, Camp AH, Strynadka NCJ | Journal of structural biology | 29288127 | J Struct Biol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29288127 |
| A Membrane-Embedded Amino Acid Couples the SpoIIQ Channel Protein to Anti-Sigma Factor Transcriptional Repression during Bacillus subtilis Sporulation. | Flanagan KA, Comber JD, Mearls E, Fenton C, Wang Erickson AF, Camp AH | Journal of bacteriology | 26929302 | J Bacteriol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26929302 |
| Structural and biochemical characterization of SpoIIIAF, a component of a sporulation-essential channel in Bacillus subtilis. | Zeytuni N, Flanagan KA, Worrall LJ, Massoni SC, Camp AH, Strynadka NCJ | Journal of structural biology | 29886194 | J Struct Biol | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29886194 |
| Structural Analysis of Bacillus subtilis Sigma Factors. | Collins KM, Evans NJ, Torpey JH, Harris JM, Haynes BA, Camp AH, Isaacson RL | Microorganisms | 37110501 | Microorganisms | 2023 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/37110501 |
| Near-atomic resolution cryoelectron microscopy structure of the 30-fold homooligomeric SpoIIIAG channel essential to spore formation in Bacillus subtilis. | Zeytuni N, Hong C, Flanagan KA, Worrall LJ, Theiltges KA, Vuckovic M, Huang RK, Massoni SC, Camp AH, Yu Z, Strynadka NC | Proceedings of the National Academy of Sciences of the United States of America | 28784753 | Proc Natl Acad Sci U S A | 2017 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/28784753 |
| Developmentally regulated proteolysis by MdfA and ClpCP mediates metabolic differentiation during Bacillus subtilis sporulation. | Riley EP, Lyda JA, Reyes-Matte O, Sugie J, Kasu IR, Enustun E, Armbruster EG, Ravishankar S, Isaacson RL, Camp AH, Lopez-Garrido J, Pogliano K | Genes & development | 40086876 | Genes Dev | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/40086876 |
| Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB. | Martínez-Lumbreras S, Alfano C, Evans NJ, Collins KM, Flanagan KA, Atkinson RA, Krysztofinska EM, Vydyanath A, Jackter J, Fixon-Owoo S, Camp AH, Isaacson RL | Structure (London, England : 1993) | 29526435 | Structure | 2018 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/29526435 |
| MdfA is a novel ClpC adaptor protein that functions in the developing Bacillus subtilis spore. | Massoni SC, Evans NJ, Hantke I, Fenton C, Torpey JH, Collins KM, Krysztofinska EM, Muench JH, Thapaliya A, Martínez-Lumbreras S, Hart Ferrell S, Slater C, Wang X, Fekade R, Obwar S, Yin S, Vazquez A, Prior CB, Turgay K, Isaacson RL, Camp AH | Genes & development | 40086879 | Genes Dev | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/40086879 |
| Liquid phase condensation in cell physiology and disease. | Shin Y, Brangwynne CP | Science (New York, N.Y.) | 28935776 | Science | 2017 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/28935776 |
| Coexisting Liquid Phases Underlie Nucleolar Subcompartments. | Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP | Cell | 27212236 | Cell | 2016 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/27212236 |
| RNA Controls PolyQ Protein Phase Transitions. | Zhang H, Elbaum-Garfinkle S, Langdon EM, Taylor N, Occhipinti P, Bridges AA, Brangwynne CP, Gladfelter AS | Molecular cell | 26474065 | Mol Cell | 2015 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/26474065 |
| Inverse size scaling of the nucleolus by a concentration-dependent phase transition. | Weber SC, Brangwynne CP | Current biology : CB | 25702583 | Curr Biol | 2015 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/25702583 |
| Hierarchical Size Scaling during Multicellular Growth and Development. | Uppaluri S, Weber SC, Brangwynne CP | Cell reports | 27705784 | Cell Rep | 2016 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/27705784 |
| Getting RNA and protein in phase. | Weber SC, Brangwynne CP | Cell | 22682242 | Cell | 2012 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/22682242 |
| Soft viscoelastic properties of nuclear actin age oocytes due to gravitational creep. | Feric M, Broedersz CP, Brangwynne CP | Scientific reports | 26577186 | Sci Rep | 2015 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/26577186 |
| Phase transitions and size scaling of membrane-less organelles. | Brangwynne CP | The Journal of cell biology | 24368804 | J Cell Biol | 2013 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/24368804 |
| A nuclear F-actin scaffold stabilizes ribonucleoprotein droplets against gravity in large cells. | Feric M, Brangwynne CP | Nature cell biology | 23995731 | Nat Cell Biol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23995731 |
| RNA transcription modulates phase transition-driven nuclear body assembly. | Berry J, Weber SC, Vaidya N, Haataja M, Brangwynne CP | Proceedings of the National Academy of Sciences of the United States of America | 26351690 | Proc Natl Acad Sci U S A | 2015 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/26351690 |
| Spatiotemporal Control of Intracellular Phase Transitions Using Light-Activated optoDroplets. | Shin Y, Berry J, Pannucci N, Haataja MP, Toettcher JE, Brangwynne CP | Cell | 28041848 | Cell | 2017 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/28041848 |
| Nuclear bodies: the emerging biophysics of nucleoplasmic phases. | Zhu L, Brangwynne CP | Current opinion in cell biology | 25942753 | Curr Opin Cell Biol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25942753 |
| The micro and macro of RNA function. | Brangwynne CP, Johnson TL | Molecular biology of the cell | 23486403 | Mol Biol Cell | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23486403 |
| Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles. | Wei MT, Elbaum-Garfinkle S, Holehouse AS, Chen CC, Feric M, Arnold CB, Priestley RD, Pappu RV, Brangwynne CP | Nature chemistry | 29064502 | Nat Chem | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29064502 |
| A size threshold governs Caenorhabditis elegans developmental progression. | Uppaluri S, Brangwynne CP | Proceedings. Biological sciences | 26290076 | Proc Biol Sci | 2015 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/26290076 |
| Remodeling nuclear architecture allows efficient transport of herpesvirus capsids by diffusion. | Bosse JB, Hogue IB, Feric M, Thiberge SY, Sodeik B, Brangwynne CP, Enquist LW | Proceedings of the National Academy of Sciences of the United States of America | 26438852 | Proc Natl Acad Sci U S A | 2015 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/26438852 |
| Biophysical characterization of organelle-based RNA/protein liquid phases using microfluidics. | Taylor N, Elbaum-Garfinkle S, Vaidya N, Zhang H, Stone HA, Brangwynne CP | Soft matter | 27791212 | Soft Matter | 2016 Nov 16 | https://www.ncbi.nlm.nih.gov/pubmed/27791212 |
| Farming and public goods production in Caenorhabditis elegans populations. | Thutupalli S, Uppaluri S, Constable GW, Levin SA, Stone HA, Tarnita CE, Brangwynne CP | Proceedings of the National Academy of Sciences of the United States of America | 28183799 | Proc Natl Acad Sci U S A | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28183799 |
| Worms under Pressure: Bulk Mechanical Properties of C. elegans Are Independent of the Cuticle. | Gilpin W, Uppaluri S, Brangwynne CP | Biophysical journal | 25902429 | Biophys J | 2015 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/25902429 |
| Interfacing Biocompatible Reactions with Engineered Escherichia coli. | Wallace S, Balskus EP | Methods in molecular biology (Clifton, N.J.) | 28470621 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28470621 |
| Rescuing auxotrophic microorganisms with nonenzymatic chemistry. | Lee Y, Umeano A, Balskus EP | Angewandte Chemie (International ed. in English) | 24115592 | Angew Chem Int Ed Engl | 2013 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/24115592 |
| Discovery of the lomaiviticin biosynthetic gene cluster in Salinispora pacifica. | Janso JE, Haltli BA, Eustáquio AS, Kulowski K, Waldman AJ, Zha L, Nakamura H, Bernan VS, He H, Carter GT, Koehn FE, Balskus EP | Tetrahedron | 25045187 | Tetrahedron | 2014 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/25045187 |
| The Cremeomycin Biosynthetic Gene Cluster Encodes a Pathway for Diazo Formation. | Waldman AJ, Pechersky Y, Wang P, Wang JX, Balskus EP | Chembiochem : a European journal of chemical biology | 26278892 | Chembiochem | 2015 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/26278892 |
| An N-nitrosating metalloenzyme constructs the pharmacophore of streptozotocin. | Ng TL, Rohac R, Mitchell AJ, Boal AK, Balskus EP | Nature | 30728519 | Nature | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30728519 |
| Discovery of the Azaserine Biosynthetic Pathway Uncovers a Biological Route for α-Diazoester Production. | Van Cura D, Ng TL, Huang J, Hager H, Hartwig JF, Keasling JD, Balskus EP | Angewandte Chemie (International ed. in English) | 37151182 | Angew Chem Int Ed Engl | 2023 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/37151182 |
| Designer Micelles Accelerate Flux Through Engineered Metabolism in E. coli and Support Biocompatible Chemistry. | Wallace S, Balskus EP | Angewandte Chemie (International ed. in English) | 27061024 | Angew Chem Int Ed Engl | 2016 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/27061024 |
| Using non-enzymatic chemistry to influence microbial metabolism. | Wallace S, Schultz EE, Balskus EP | Current opinion in chemical biology | 25579453 | Curr Opin Chem Biol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25579453 |
| Opportunities for merging chemical and biological synthesis. | Wallace S, Balskus EP | Current opinion in biotechnology | 24747284 | Curr Opin Biotechnol | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24747284 |
| A biocompatible alkene hydrogenation merges organic synthesis with microbial metabolism. | Sirasani G, Tong L, Balskus EP | Angewandte Chemie (International ed. in English) | 24916924 | Angew Chem Int Ed Engl | 2014 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/24916924 |
| Production of Stealthin C Involves an S-N-Type Smiles Rearrangement. | Wang P, Hong GJ, Wilson MR, Balskus EP | Journal of the American Chemical Society | 28191843 | J Am Chem Soc | 2017 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/28191843 |
| Discovery of a Diazo-Forming Enzyme in Cremeomycin Biosynthesis. | Waldman AJ, Balskus EP | The Journal of organic chemistry | 29771512 | J Org Chem | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/29771512 |
| Glutamic acid is a carrier for hydrazine during the biosyntheses of fosfazinomycin and kinamycin. | Wang KA, Ng TL, Wang P, Huang Z, Balskus EP, van der Donk WA | Nature communications | 30206228 | Nat Commun | 2018 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/30206228 |
| A Peroxodiiron(III/III) Intermediate Mediating Both N-Hydroxylation Steps in Biosynthesis of the N-Nitrosourea Pharmacophore of Streptozotocin by the Multi-domain Metalloenzyme SznF. | McBride MJ, Sil D, Ng TL, Crooke AM, Kenney GE, Tysoe CR, Zhang B, Balskus EP, Boal AK, Krebs C, Bollinger JM Jr | Journal of the American Chemical Society | 32511919 | J Am Chem Soc | 2020 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/32511919 |
| Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis. | Waldman AJ, Ng TL, Wang P, Balskus EP | Chemical reviews | 28375000 | Chem Rev | 2017 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/28375000 |
| Lomaiviticin biosynthesis employs a new strategy for starter unit generation. | Waldman AJ, Balskus EP | Organic letters | 24383813 | Org Lett | 2014 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/24383813 |
| Interfacing microbial styrene production with a biocompatible cyclopropanation reaction. | Wallace S, Balskus EP | Angewandte Chemie (International ed. in English) | 25925138 | Angew Chem Int Ed Engl | 2015 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/25925138 |
| The l-Alanosine Gene Cluster Encodes a Pathway for Diazeniumdiolate Biosynthesis. | Ng TL, McCallum ME, Zheng CR, Wang JX, Wu KJY, Balskus EP | Chembiochem : a European journal of chemical biology | 31643127 | Chembiochem | 2020 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/31643127 |
| Development of neural circuits for social motion perception in schooling fish. | Zada D, Schulze L, Yu JH, Tarabishi P, Napoli JL, Lovett-Barron M | bioRxiv : the preprint server for biology | 37961196 | bioRxiv | 2023 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/37961196 |
| Understanding collective behavior through neurobiology. | Yu JH, Napoli JL, Lovett-Barron M | Current opinion in neurobiology | 38852986 | Curr Opin Neurobiol | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38852986 |
| Development of neural circuits for social motion perception in schooling fish. | Zada D, Schulze L, Yu JH, Tarabishi P, Napoli JL, Milan J, Lovett-Barron M | Current biology : CB | 39025069 | Curr Biol | 2024 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/39025069 |
| A concentration of visual cortex-like neurons in prefrontal cortex. | Rose O, Ponce CR | Nature communications | 39143147 | Nat Commun | 2024 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/39143147 |
| Neuronal "parts list" and wiring diagram for a visual system. | Matsliah A, Yu SC, Kruk K, Bland D, Burke A, Gager J, Hebditch J, Silverman B, Willie K, Willie RW, Sorek M, Sterling AR, Kind E, Garner D, Sancer G, Wernet MF, Kim SS, Murthy M, Seung HS, FlyWire Consortium | bioRxiv : the preprint server for biology | 37873160 | bioRxiv | 2024 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/37873160 |
| Plasticity between visual input pathways and the head direction system. | Kim SS | Current opinion in neurobiology | 34619578 | Curr Opin Neurobiol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34619578 |
| Connectomic reconstruction predicts visual features used for navigation. | Garner D, Kind E, Lai JYH, Nern A, Zhao A, Houghton L, Sancer G, Wolff T, Rubin GM, Wernet MF, Kim SS | Nature | 39358517 | Nature | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39358517 |
| Connectomic reconstruction predicts the functional organization of visual inputs to the navigation center of the Drosophila brain. | Garner D, Kind E, Nern A, Houghton L, Zhao A, Sancer G, Rubin GM, Wernet MF, Kim SS | bioRxiv : the preprint server for biology | 38076786 | bioRxiv | 2023 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/38076786 |
| Neuronal parts list and wiring diagram for a visual system. | Matsliah A, Yu SC, Kruk K, Bland D, Burke AT, Gager J, Hebditch J, Silverman B, Willie KP, Willie R, Sorek M, Sterling AR, Kind E, Garner D, Sancer G, Wernet MF, Kim SS, Murthy M, Seung HS, FlyWire Consortium | Nature | 39358525 | Nature | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39358525 |
| LKB1 coordinates neurite remodeling to drive synapse layer emergence in the outer retina. | Burger CA, Alevy J, Casasent AK, Jiang D, Albrecht NE, Liang JH, Hirano AA, Brecha NC, Samuel MA | eLife | 32378514 | Elife | 2020 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/32378514 |
| Development and maintenance of vision's first synapse. | Burger CA, Jiang D, Mackin RD, Samuel MA | Developmental biology | 33848537 | Dev Biol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33848537 |
| Kctd7 deficiency induces myoclonic seizures associated with Purkinje cell death and microvascular defects. | Liang JH, Alevy J, Akhanov V, Seo R, Massey CA, Jiang D, Zhou J, Sillitoe RV, Noebels JL, Samuel MA | Disease models & mechanisms | 35972048 | Dis Model Mech | 2022 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/35972048 |
| Rapid and Integrative Discovery of Retina Regulatory Molecules. | Albrecht NE, Alevy J, Jiang D, Burger CA, Liu BI, Li F, Wang J, Kim SY, Hsu CW, Kalaga S, Udensi U, Asomugha C, Bohat R, Gaspero A, Justice MJ, Westenskow PD, Yamamoto S, Seavitt JR, Beaudet AL, Dickinson ME, Samuel MA | Cell reports | 30157441 | Cell Rep | 2018 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/30157441 |
| Neuronal signal-regulatory protein alpha drives microglial phagocytosis by limiting microglial interaction with CD47 in the retina. | Jiang D, Burger CA, Akhanov V, Liang JH, Mackin RD, Albrecht NE, Andrade P, Schafer DP, Samuel MA | Immunity | 36379210 | Immunity | 2022 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/36379210 |
| Progressive myoclonic epilepsy-associated gene Kctd7 regulates retinal neurovascular patterning and function. | Alevy J, Burger CA, Albrecht NE, Jiang D, Samuel MA | Neurochemistry international | 31175897 | Neurochem Int | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31175897 |
| Becoming a Principal Investigator: Designing and Navigating Your Academic Adventure. | Greer PL, Samuel MA | Neuron | 31557459 | Neuron | 2019 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/31557459 |
| Spatiotemporal gene expression patterns reveal molecular relatedness between retinal laminae. | Jiang D, Burger CA, Casasent AK, Albrecht NE, Li F, Samuel MA | The Journal of comparative neurology | 31609468 | J Comp Neurol | 2020 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/31609468 |
| LKB1 and AMPK instruct cone nuclear position to modify visual function. | Burger CA, Albrecht NE, Jiang D, Liang JH, Poché RA, Samuel MA | Cell reports | 33535040 | Cell Rep | 2021 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/33535040 |
| Single-cell RNA-Seq of Defined Subsets of Retinal Ganglion Cells. | Laboissonniere LA, Sonoda T, Lee SK, Trimarchi JM, Schmidt TM | Journal of visualized experiments : JoVE | 28570514 | J Vis Exp | 2017 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/28570514 |
| Divergent projection patterns of M1 ipRGC subtypes. | Li JY, Schmidt TM | The Journal of comparative neurology | 29888785 | J Comp Neurol | 2018 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/29888785 |
| M1 Intrinsically Photosensitive Retinal Ganglion Cells Integrate Rod and Melanopsin Inputs to Signal in Low Light. | Lee SK, Sonoda T, Schmidt TM | Cell reports | 31825819 | Cell Rep | 2019 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/31825819 |
| Diversity of intrinsically photosensitive retinal ganglion cells: circuits and functions. | Aranda ML, Schmidt TM | Cellular and molecular life sciences : CMLS | 32965515 | Cell Mol Life Sci | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32965515 |
| A noncanonical inhibitory circuit dampens behavioral sensitivity to light. | Sonoda T, Li JY, Hayes NW, Chan JC, Okabe Y, Belin S, Nawabi H, Schmidt TM | Science (New York, N.Y.) | 32355031 | Science | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32355031 |
| Overlapping morphological and functional properties between M4 and M5 intrinsically photosensitive retinal ganglion cells. | Sonoda T, Okabe Y, Schmidt TM | The Journal of comparative neurology | 31691279 | J Comp Neurol | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31691279 |
| Distinct ipRGC subpopulations mediate light's acute and circadian effects on body temperature and sleep. | Rupp AC, Ren M, Altimus CM, Fernandez DC, Richardson M, Turek F, Hattar S, Schmidt TM | eLife | 31333190 | Elife | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31333190 |
| Melanopsin phototransduction: beyond canonical cascades. | Contreras E, Nobleman AP, Robinson PR, Schmidt TM | The Journal of experimental biology | 34842918 | J Exp Biol | 2021 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/34842918 |
| The Retinal Basis of Light Aversion in Neonatal Mice. | Caval-Holme FS, Aranda ML, Chen AQ, Tiriac A, Zhang Y, Smith B, Birnbaumer L, Schmidt TM, Feller MB | The Journal of neuroscience : the official journal of the Society for Neuroscience | 35396331 | J Neurosci | 2022 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/35396331 |
| Cellular properties of intrinsically photosensitive retinal ganglion cells during postnatal development. | Lucas JA, Schmidt TM | Neural development | 31470901 | Neural Dev | 2019 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/31470901 |
| Melanopsin Phototransduction Is Repurposed by ipRGC Subtypes to Shape the Function of Distinct Visual Circuits. | Sonoda T, Lee SK, Birnbaumer L, Schmidt TM | Neuron | 30017393 | Neuron | 2018 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/30017393 |
| Flp-recombinase mouse line for genetic manipulation of ipRGCs. | Contreras E, Liang C, Mahoney HL, Javier JL, Luce ML, Labastida Medina K, Bozza T, Schmidt TM | bioRxiv : the preprint server for biology | 38766000 | bioRxiv | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38766000 |
| Melanopsin activates divergent phototransduction pathways in intrinsically photosensitive retinal ganglion cell subtypes. | Contreras E, Bhoi JD, Sonoda T, Birnbaumer L, Schmidt TM | eLife | 37937828 | Elife | 2023 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/37937828 |
| Electrical synapses convey orientation selectivity in the mouse retina. | Nath A, Schwartz GW | Nature communications | 29229967 | Nat Commun | 2017 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/29229967 |
| Cardinal Orientation Selectivity Is Represented by Two Distinct Ganglion Cell Types in Mouse Retina. | Nath A, Schwartz GW | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26985031 | J Neurosci | 2016 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/26985031 |
| Molecular signatures of retinal ganglion cells revealed through single cell profiling. | Laboissonniere LA, Goetz JJ, Martin GM, Bi R, Lund TJS, Ellson L, Lynch MR, Mooney B, Wickham H, Liu P, Schwartz GW, Trimarchi JM | Scientific reports | 31673015 | Sci Rep | 2019 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/31673015 |
| A Self-Regulating Gap Junction Network of Amacrine Cells Controls Nitric Oxide Release in the Retina. | Jacoby J, Nath A, Jessen ZF, Schwartz GW | Neuron | 30482690 | Neuron | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30482690 |
| Identification of retinal ganglion cell types and brain nuclei expressing the transcription factor Brn3c/Pou4f3 using a Cre recombinase knock-in allele. | Parmhans N, Fuller AD, Nguyen E, Chuang K, Swygart D, Wienbar SR, Lin T, Kozmik Z, Dong L, Schwartz GW, Badea TC | The Journal of comparative neurology | 33135183 | J Comp Neurol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33135183 |
| Three Small-Receptive-Field Ganglion Cells in the Mouse Retina Are Distinctly Tuned to Size, Speed, and Object Motion. | Jacoby J, Schwartz GW | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28100743 | J Neurosci | 2017 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/28100743 |
| Circuit Mechanisms of a Retinal Ganglion Cell with Stimulus-Dependent Response Latency and Activation Beyond Its Dendrites. | Mani A, Schwartz GW | Current biology : CB | 28132812 | Curr Biol | 2017 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/28132812 |
| Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression. | Goetz J, Jessen ZF, Jacobi A, Mani A, Cooler S, Greer D, Kadri S, Segal J, Shekhar K, Sanes JR, Schwartz GW | Cell reports | 35830791 | Cell Rep | 2022 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/35830791 |
| Differences in spike generation instead of synaptic inputs determine the feature selectivity of two retinal cell types. | Wienbar S, Schwartz GW | Neuron | 35508174 | Neuron | 2022 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/35508174 |
| Retinal patterns and the cellular repertoire of neuropsin (Opn5) retinal ganglion cells. | D'Souza SP, Swygart DI, Wienbar SR, Upton BA, Zhang KX, Mackin RD, Casasent AK, Samuel MA, Schwartz GW, Lang RA | The Journal of comparative neurology | 34743323 | J Comp Neurol | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34743323 |
| An Amacrine Cell Circuit for Signaling Steady Illumination in the Retina. | Jacoby J, Zhu Y, DeVries SH, Schwartz GW | Cell reports | 26711334 | Cell Rep | 2015 Dec 29 | https://www.ncbi.nlm.nih.gov/pubmed/26711334 |
| The dynamic receptive fields of retinal ganglion cells. | Wienbar S, Schwartz GW | Progress in retinal and eye research | 29944919 | Prog Retin Eye Res | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29944919 |
| An offset ON-OFF receptive field is created by gap junctions between distinct types of retinal ganglion cells. | Cooler S, Schwartz GW | Nature neuroscience | 33230322 | Nat Neurosci | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33230322 |
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| Learning to control the brain through adaptive closed-loop patterned stimulation. | Tafazoli S, MacDowell CJ, Che Z, Letai KC, Steinhardt CR, Buschman TJ | Journal of neural engineering | 32927437 | J Neural Eng | 2020 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/32927437 |
| Low-Dimensional Spatiotemporal Dynamics Underlie Cortex-wide Neural Activity. | MacDowell CJ, Buschman TJ | Current biology : CB | 32470366 | Curr Biol | 2020 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/32470366 |
| Rotational dynamics reduce interference between sensory and memory representations. | Libby A, Buschman TJ | Nature neuroscience | 33821001 | Nat Neurosci | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33821001 |
| Differences in the expression of cortex-wide neural dynamics are related to behavioral phenotype. | MacDowell CJ, Briones BA, Lenzi MJ, Gustison ML, Buschman TJ | Current biology : CB | 38417445 | Curr Biol | 2024 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/38417445 |
| High-fidelity optical excitation of cortico-cortical projections at physiological frequencies. | Hass CA, Glickfeld LL | Journal of neurophysiology | 27489370 | J Neurophysiol | 2016 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/27489370 |
| Contribution of Sensory Encoding to Measured Bias. | Jin M, Glickfeld LL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 31015339 | J Neurosci | 2019 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/31015339 |
| Magnitude, time course, and specificity of rapid adaptation across mouse visual areas. | Jin M, Glickfeld LL | Journal of neurophysiology | 32584636 | J Neurophysiol | 2020 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/32584636 |
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| GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation. | Terao C, Momozawa Y, Ishigaki K, Kawakami E, Akiyama M, Loh PR, Genovese G, Sugishita H, Ohta T, Hirata M, Perry JRB, Matsuda K, Murakami Y, Kubo M, Kamatani Y | Nature communications | 31624269 | Nat Commun | 2019 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/31624269 |
| A sequence of SVA retrotransposon insertions in ASIP shaped human pigmentation. | Kamitaki N, Hujoel MLA, Mukamel RE, Gebara E, McCarroll SA, Loh PR | Nature genetics | 39048794 | Nat Genet | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39048794 |
| Fusion of dysfunction muscle stem cells with myofibers induces sarcopenia in mice. | Wang X, Mishra P | bioRxiv : the preprint server for biology | 36711602 | bioRxiv | 2023 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/36711602 |
| Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis. | Shelton SD, House S, Martins Nascentes Melo L, Ramesh V, Chen Z, Wei T, Wang X, Llamas CB, Venigalla SSK, Menezes CJ, Allies G, Krystkiewicz J, Rösler J, Meckelmann SW, Zhao P, Rambow F, Schadendorf D, Zhao Z, Gill JG, DeBerardinis RJ, Morrison SJ, Tasdogan A, Mishra P | Science advances | 39485847 | Sci Adv | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39485847 |
| Pathogenic mitochondrial DNA mutations inhibit melanoma metastasis. | Shelton SD, House S, Ramesh V, Chen Z, Wei T, Wang X, Llamas CB, Venigalla SSK, Menezes CJ, Zhao Z, Gill JG, DeBerardinis RJ, Morrison SJ, Tasdogan A, Mishra P | bioRxiv : the preprint server for biology | 37732192 | bioRxiv | 2023 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/37732192 |
| Lactate metabolism is essential in early-onset mitochondrial myopathy. | Chen Z, Bordieanu B, Kesavan R, Lesner NP, Venigalla SSK, Shelton SD, DeBerardinis RJ, Mishra P | Science advances | 36598990 | Sci Adv | 2023 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/36598990 |
| Metabolic inflexibility promotes mitochondrial health during liver regeneration. | Wang X, Menezes CJ, Jia Y, Xiao Y, Venigalla SSK, Cai F, Hsieh MH, Gu W, Du L, Sudderth J, Kim D, Shelton SD, Llamas CB, Lin YH, Zhu M, Merchant S, Bezwada D, Kelekar S, Zacharias LG, Mathews TP, Hoxhaj G, Wynn RM, Tambar UK, DeBerardinis RJ, Zhu H, Mishra P | Science (New York, N.Y.) | 38870309 | Science | 2024 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/38870309 |
| Autosomal recessive progeroid syndrome due to homozygosity for a TOMM7 variant. | Garg A, Keng WT, Chen Z, Sathe AA, Xing C, Kailasam PD, Shao Y, Lesner NP, Llamas CB, Agarwal AK, Mishra P | The Journal of clinical investigation | 36282599 | J Clin Invest | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36282599 |
| The outer mitochondrial membrane protein TMEM11 demarcates spatially restricted BNIP3/BNIP3L-mediated mitophagy. | Gok MO, Connor OM, Wang X, Menezes CJ, Llamas CB, Mishra P, Friedman JR | The Journal of cell biology | 36795401 | J Cell Biol | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/36795401 |
| Scinderin promotes fusion of electron transport chain dysfunctional muscle stem cells with myofibers. | Wang X, Shelton SD, Bordieanu B, Frank AR, Yi Y, Venigalla SSK, Gu Z, Lenser NP, Glogauer M, Chandel NS, Zhao H, Zhao Z, McFadden DG, Mishra P | Nature aging | 35342888 | Nat Aging | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35342888 |
| A mitofusin 2/HIF1α axis sets a maturation checkpoint in regenerating skeletal muscle. | Wang X, Jia Y, Zhao J, Lesner NP, Menezes CJ, Shelton SD, Venigalla SSK, Xu J, Cai C, Mishra P | The Journal of clinical investigation | 36125902 | J Clin Invest | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/36125902 |
| Differential requirements for mitochondrial electron transport chain components in the adult murine liver. | Lesner NP, Wang X, Chen Z, Frank A, Menezes CJ, House S, Shelton SD, Lemoff A, McFadden DG, Wansapura J, DeBerardinis RJ, Mishra P | eLife | 36154948 | Elife | 2022 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/36154948 |
| Synthesis of push-pull-activated ynol ethers and their evaluation in the bioorthogonal hydroamination reaction. | Kang D, Wahl C, Kim J | Organic & biomolecular chemistry | 36367436 | Org Biomol Chem | 2022 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/36367436 |
| Bioorthogonally activated reactive species for target identification. | Siriwongsup S, Schmoker AM, Ficarro SB, Marto JA, Kim J | Chem | 38617077 | Chem | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38617077 |
| Bioorthogonal Click and Release: A General, Rapid, Chemically Revertible Bioconjugation Strategy Employing Enamine N-oxides. | Kang D, Lee S, Kim J | Chem | 36176744 | Chem | 2022 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/36176744 |
| Bioorthogonal Hydroamination of Push-Pull-Activated Linear Alkynes. | Kang D, Cheung ST, Kim J | Angewandte Chemie (International ed. in English) | 34019705 | Angew Chem Int Ed Engl | 2021 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/34019705 |
| Bioorthogonal Retro-Cope Elimination Reaction of N,N-Dialkylhydroxylamines and Strained Alkynes. | Kang D, Kim J | Journal of the American Chemical Society | 33829777 | J Am Chem Soc | 2021 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/33829777 |
| Enamine N-Oxides: Synthesis and Application to Hypoxia-Responsive Prodrugs and Imaging Agents. | Kang D, Cheung ST, Wong-Rolle A, Kim J | ACS central science | 34056093 | ACS Cent Sci | 2021 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/34056093 |
| Enamine N-oxides: Design, Synthesis, and Function in Bioorthogonal Reactions. | Kang D, Kim J | Synlett : accounts and rapid communications in synthetic organic chemistry | 38947226 | Synlett | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38947226 |
| Depolarization signatures map gold nanorods within biological tissue. | Lippok N, Villiger M, Albanese A, Meijer EFJ, Chung K, Padera TP, Bhatia SN, Bouma BE | Nature photonics | 29201136 | Nat Photonics | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29201136 |
| Npas4 Is a Critical Regulator of Learning-Induced Plasticity at Mossy Fiber-CA3 Synapses during Contextual Memory Formation. | Weng FJ, Garcia RI, Lutzu S, Alviña K, Zhang Y, Dushko M, Ku T, Zemoura K, Rich D, Garcia-Dominguez D, Hung M, Yelhekar TD, Sørensen AT, Xu W, Chung K, Castillo PE, Lin Y | Neuron | 29429933 | Neuron | 2018 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/29429933 |
| Basic principles of hydrogel-based tissue transformation technologies and their applications. | Choi SW, Guan W, Chung K | Cell | 34358468 | Cell | 2021 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/34358468 |
| Multiscale 3D phenotyping of human cerebral organoids. | Albanese A, Swaney JM, Yun DH, Evans NB, Antonucci JM, Velasco S, Sohn CH, Arlotta P, Gehrke L, Chung K | Scientific reports | 33293587 | Sci Rep | 2020 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/33293587 |
| Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition. | Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH | Cell | 30879788 | Cell | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30879788 |
| Integrated platform for multiscale molecular imaging and phenotyping of the human brain. | Park J, Wang J, Guan W, Gjesteby LA, Pollack D, Kamentsky L, Evans NB, Stirman J, Gu X, Zhao C, Marx S, Kim ME, Choi SW, Snyder M, Chavez D, Su-Arcaro C, Tian Y, Park CS, Zhang Q, Yun DH, Moukheiber M, Feng G, Yang XW, Keene CD, Hof PR, Ghosh SS, Frosch MP, Brattain LJ, Chung K | Science (New York, N.Y.) | 38870291 | Science | 2024 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/38870291 |
| Self-organized developmental patterning and differentiation in cerebral organoids. | Renner M, Lancaster MA, Bian S, Choi H, Ku T, Peer A, Chung K, Knoblich JA | The EMBO journal | 28283582 | EMBO J | 2017 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/28283582 |
| Brain-wide mapping reveals that engrams for a single memory are distributed across multiple brain regions. | Roy DS, Park YG, Kim ME, Zhang Y, Ogawa SK, DiNapoli N, Gu X, Cho JH, Choi H, Kamentsky L, Martin J, Mosto O, Aida T, Chung K, Tonegawa S | Nature communications | 35379803 | Nat Commun | 2022 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/35379803 |
| In situ expansion of engineered human liver tissue in a mouse model of chronic liver disease. | Stevens KR, Scull MA, Ramanan V, Fortin CL, Chaturvedi RR, Knouse KA, Xiao JW, Fung C, Mirabella T, Chen AX, McCue MG, Yang MT, Fleming HE, Chung K, de Jong YP, Chen CS, Rice CM, Bhatia SN | Science translational medicine | 28724577 | Sci Transl Med | 2017 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/28724577 |
| Label-free volumetric optical imaging of intact murine brains. | Ren J, Choi H, Chung K, Bouma BE | Scientific reports | 28401897 | Sci Rep | 2017 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/28401897 |
| Elasticizing tissues for reversible shape transformation and accelerated molecular labeling. | Ku T, Guan W, Evans NB, Sohn CH, Albanese A, Kim JG, Frosch MP, Chung K | Nature methods | 32424271 | Nat Methods | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32424271 |
| Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems. | Murray E, Cho JH, Goodwin D, Ku T, Swaney J, Kim SY, Choi H, Park YG, Park JY, Hubbert A, McCue M, Vassallo S, Bakh N, Frosch MP, Wedeen VJ, Seung HS, Chung K | Cell | 26638076 | Cell | 2015 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/26638076 |
| Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues. | Ku T, Swaney J, Park JY, Albanese A, Murray E, Cho JH, Park YG, Mangena V, Chen J, Chung K | Nature biotechnology | 27454740 | Nat Biotechnol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27454740 |
| Protection of tissue physicochemical properties using polyfunctional crosslinkers. | Park YG, Sohn CH, Chen R, McCue M, Yun DH, Drummond GT, Ku T, Evans NB, Oak HC, Trieu W, Choi H, Jin X, Lilascharoen V, Wang J, Truttmann MC, Qi HW, Ploegh HL, Golub TR, Chen SC, Frosch MP, Kulik HJ, Lim BK, Chung K | Nature biotechnology | 30556815 | Nat Biotechnol | 2018 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/30556815 |
| TISSUE CLEARING. | Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW | Nature reviews. Methods primers | 35128463 | Nat Rev Methods Primers | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35128463 |
| Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy. | Mano T, Albanese A, Dodt HU, Erturk A, Gradinaru V, Treweek JB, Miyawaki A, Chung K, Ueda HR | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30381424 | J Neurosci | 2018 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/30381424 |
| Tissue clearing and its applications in neuroscience. | Ueda HR, Ertürk A, Chung K, Gradinaru V, Chédotal A, Tomancak P, Keller PJ | Nature reviews. Neuroscience | 31896771 | Nat Rev Neurosci | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31896771 |
| Fetal and postnatal metal dysregulation in autism. | Arora M, Reichenberg A, Willfors C, Austin C, Gennings C, Berggren S, Lichtenstein P, Anckarsäter H, Tammimies K, Bölte S | Nature communications | 28569757 | Nat Commun | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28569757 |
| Exposure to environmental chemical mixtures is associated with nasal colonization by Staphylococcus aureus: NHANES 2001-2004. | Eggers S, Gennings C, Malecki KMC, Safdar N, Arora M | Environmental research | 32771801 | Environ Res | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32771801 |
| Uncovering system-specific stress signatures in primate teeth with multimodal imaging. | Austin C, Smith TM, Farahani RM, Hinde K, Carter EA, Lee J, Lay PA, Kennedy BJ, Sarrafpour B, Wright RJ, Wright RO, Arora M | Scientific reports | 26727334 | Sci Rep | 2016 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/26727334 |
| Wintertime stress, nursing, and lead exposure in Neanderthal children. | Smith TM, Austin C, Green DR, Joannes-Boyau R, Bailey S, Dumitriu D, Fallon S, Grün R, James HF, Moncel MH, Williams IS, Wood R, Arora M | Science advances | 30402544 | Sci Adv | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30402544 |
| Bayesian varying coefficient kernel machine regression to assess neurodevelopmental trajectories associated with exposure to complex mixtures. | Liu SH, Bobb JF, Claus Henn B, Gennings C, Schnaas L, Tellez-Rojo M, Bellinger D, Arora M, Wright RO, Coull BA | Statistics in medicine | 30277584 | Stat Med | 2018 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/30277584 |
| Lagged kernel machine regression for identifying time windows of susceptibility to exposures of complex mixtures. | Liu SH, Bobb JF, Lee KH, Gennings C, Claus Henn B, Bellinger D, Austin C, Schnaas L, Tellez-Rojo MM, Hu H, Wright RO, Arora M, Coull BA | Biostatistics (Oxford, England) | 28968676 | Biostatistics | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/28968676 |
| Extending the Distributed Lag Model framework to handle chemical mixtures. | Bello GA, Arora M, Austin C, Horton MK, Wright RO, Gennings C | Environmental research | 28371754 | Environ Res | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28371754 |
| Near-Infrared Intraoperative Chemiluminescence Imaging. | Büchel GE, Carney B, Shaffer TM, Tang J, Austin C, Arora M, Zeglis BM, Grimm J, Eppinger J, Reiner T | ChemMedChem | 27471800 | ChemMedChem | 2016 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/27471800 |
| Recent advances in simultaneous analysis of bisphenol A and its conjugates in human matrices: Exposure biomarker perspectives. | Andra SS, Austin C, Yang J, Patel D, Arora M | The Science of the total environment | 27586167 | Sci Total Environ | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27586167 |
| Comparison of multiple X-ray fluorescence techniques for elemental analysis of particulate matter collected on air filters. | Bilo F, Borgese L, Wambui A, Assi A, Zacco A, Federici S, Eichert DM, Tsuji K, Lucchini RG, Placidi D, Bontempi E, Depero LE | Journal of aerosol science | 30662085 | J Aerosol Sci | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30662085 |
| In utero metal exposures measured in deciduous teeth and birth outcomes in a racially-diverse urban cohort. | Cassidy-Bushrow AE, Wu KH, Sitarik AR, Park SK, Bielak LF, Austin C, Gennings C, Curtin P, Johnson CC, Arora M | Environmental research | 30735952 | Environ Res | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30735952 |
| Elemental signatures of Australopithecus africanus teeth reveal seasonal dietary stress. | Joannes-Boyau R, Adams JW, Austin C, Arora M, Moffat I, Herries AIR, Tonge MP, Benazzi S, Evans AR, Kullmer O, Wroe S, Dosseto A, Fiorenza L | Nature | 31308534 | Nature | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31308534 |
| Sex differences in sensitivity to prenatal and early childhood manganese exposure on neuromotor function in adolescents. | Chiu YM, Claus Henn B, Hsu HL, Pendo MP, Coull BA, Austin C, Cagna G, Fedrighi C, Placidi D, Smith DR, Wright RO, Lucchini RG, Arora M | Environmental research | 28858760 | Environ Res | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28858760 |
| Tooth matrix analysis for biomonitoring of organic chemical exposure: Current status, challenges, and opportunities. | Andra SS, Austin C, Arora M | Environmental research | 26219084 | Environ Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26219084 |
| Manganese in teeth and neurodevelopment in young Mexican-American children. | Gunier RB, Arora M, Jerrett M, Bradman A, Harley KG, Mora AM, Kogut K, Hubbard A, Austin C, Holland N, Eskenazi B | Environmental research | 26381693 | Environ Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26381693 |
| Tooth manganese as a biomarker of exposure and body burden in rats. | Austin C, Richardson C, Smith D, Arora M | Environmental research | 28279842 | Environ Res | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28279842 |
| Environmental exposures and pediatric kidney function and disease: A systematic review. | Zheng LY, Sanders AP, Saland JM, Wright RO, Arora M | Environmental research | 28727988 | Environ Res | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28727988 |
| Dysregulated biodynamics in metabolic attractor systems precede the emergence of amyotrophic lateral sclerosis. | Curtin P, Austin C, Curtin A, Gennings C, Figueroa-Romero C, Mikhail KA, Botero TM, Goutman SA, Feldman EL, Arora M | PLoS computational biology | 32294079 | PLoS Comput Biol | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32294079 |
| Effect of neonatal hyperoxia followed by concentrated ambient ultrafine particle exposure on cumulative learning in C57Bl/6J mice. | Morris-Schaffer K, Sobolewski M, Allen JL, Marvin E, Yee M, Arora M, O'Reilly MA, Cory-Slechta DA | Neurotoxicology | 29920326 | Neurotoxicology | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29920326 |
| Early-life dentine manganese concentrations and intrinsic functional brain connectivity in adolescents: A pilot study. | de Water E, Papazaharias DM, Ambrosi C, Mascaro L, Iannilli E, Gasparotti R, Lucchini RG, Austin C, Arora M, Tang CY, Smith DR, Wright RO, Horton MK | PloS one | 31412061 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31412061 |
| Dynamical features in fetal and postnatal zinc-copper metabolic cycles predict the emergence of autism spectrum disorder. | Curtin P, Austin C, Curtin A, Gennings C, Arora M, (for the Emergent Dynamical Systems Group), Tammimies K, Willfors C, Berggren S, Siper P, Rai D, Meyering K, Kolevzon A, Mollon J, David AS, Lewis G, Zammit S, Heilbrun L, Palmer RF, Wright RO, Bölte S, Reichenberg A | Science advances | 29854952 | Sci Adv | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29854952 |
| Stress exposure histories revealed by biochemical changes along accentuated lines in teeth. | Austin C, Kumar P, Carter EA, Lee J, Smith TM, Hinde K, Arora M, Lay PA | Chemosphere | 37054846 | Chemosphere | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37054846 |
| Critical windows of susceptibility in the association between manganese and neurocognition in Italian adolescents living near ferro-manganese industry. | Bauer JA, White RF, Coull BA, Austin C, Oppini M, Zoni S, Fedrighi C, Cagna G, Placidi D, Guazzetti S, Yang Q, Bellinger DC, Webster TF, Wright RO, Smith D, Horton M, Lucchini RG, Arora M, Claus Henn B | Neurotoxicology | 34478771 | Neurotoxicology | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34478771 |
| New Research Strategy for Measuring Pre- and Postnatal Metal Dysregulation in Psychotic Disorders. | Velthorst E, Smith L, Bello G, Austin C, Gennings C, Modabbernia A, Franke N, Frangou S, Wright R, de Haan L, Reichenberg A, Arora M | Schizophrenia bulletin | 28981868 | Schizophr Bull | 2017 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/28981868 |
| Uncovering neurodevelopmental windows of susceptibility to manganese exposure using dentine microspatial analyses. | Claus Henn B, Austin C, Coull BA, Schnaas L, Gennings C, Horton MK, Hernández-Ávila M, Hu H, Téllez-Rojo MM, Wright RO, Arora M | Environmental research | 29247915 | Environ Res | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29247915 |
| A multimodal imaging workflow to visualize metal mixtures in the human placenta and explore colocalization with biological response markers. | Niedzwiecki MM, Austin C, Remark R, Merad M, Gnjatic S, Estrada-Gutierrez G, Espejel-Nuñez A, Borboa-Olivares H, Guzman-Huerta M, Wright RJ, Wright RO, Arora M | Metallomics : integrated biometal science | 26987553 | Metallomics | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26987553 |
| Dentine biomarkers of prenatal and early childhood exposure to manganese, zinc and lead and childhood behavior. | Horton MK, Hsu L, Claus Henn B, Margolis A, Austin C, Svensson K, Schnaas L, Gennings C, Hu H, Wright R, Rojo MMT, Arora M | Environment international | 30205321 | Environ Int | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30205321 |
| Cross-sectional study of the association between serum perfluorinated alkyl acid concentrations and dental caries among US adolescents (NHANES 1999-2012). | Puttige Ramesh N, Arora M, Braun JM | BMJ open | 30782897 | BMJ Open | 2019 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/30782897 |
| Is poor oral health a risk marker for incident cardiovascular disease hospitalisation and all-cause mortality? Findings from 172 630 participants from the prospective 45 and Up Study. | Joshy G, Arora M, Korda RJ, Chalmers J, Banks E | BMJ open | 27577588 | BMJ Open | 2016 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/27577588 |
| Manganese in teeth and neurobehavior: Sex-specific windows of susceptibility. | Bauer JA, Claus Henn B, Austin C, Zoni S, Fedrighi C, Cagna G, Placidi D, White RF, Yang Q, Coull BA, Smith D, Lucchini RG, Wright RO, Arora M | Environment international | 28941415 | Environ Int | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28941415 |
| Cyclical nursing patterns in wild orangutans. | Smith TM, Austin C, Hinde K, Vogel ER, Arora M | Science advances | 28560319 | Sci Adv | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28560319 |
| Recurrence quantification analysis to characterize cyclical components of environmental elemental exposures during fetal and postnatal development. | Curtin P, Curtin A, Austin C, Gennings C, Tammimies K, Bölte S, Arora M | PloS one | 29112980 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29112980 |
| Tooth-Matrix Biomarkers to Reconstruct Critical Periods of Brain Plasticity. | Morishita H, Arora M | Trends in neurosciences | 28038829 | Trends Neurosci | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28038829 |
| Multielemental bioimaging of tissues in children's environmental health research. | Austinc C, Niedzwiecki MM, Arora M | Current opinion in pediatrics | 26845145 | Curr Opin Pediatr | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26845145 |
| Reconstructing pre-natal and early childhood exposure to multi-class organic chemicals using teeth: Towards a retrospective temporal exposome. | Andra SS, Austin C, Wright RO, Arora M | Environment international | 26134987 | Environ Int | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26134987 |
| The tooth exposome in children's health research. | Andra SS, Austin C, Arora M | Current opinion in pediatrics | 26859286 | Curr Opin Pediatr | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26859286 |
| Prenatal and postnatal manganese teeth levels and neurodevelopment at 7, 9, and 10.5 years in the CHAMACOS cohort. | Mora AM, Arora M, Harley KG, Kogut K, Parra K, Hernández-Bonilla D, Gunier RB, Bradman A, Smith DR, Eskenazi B | Environment international | 26209874 | Environ Int | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26209874 |
| Burden of higher lead exposure in African-Americans starts in utero and persists into childhood. | Cassidy-Bushrow AE, Sitarik AR, Havstad S, Park SK, Bielak LF, Austin C, Johnson CC, Arora M | Environment international | 28886415 | Environ Int | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28886415 |
| Polymorphisms in manganese transporters show developmental stage and sex specific associations with manganese concentrations in primary teeth. | Wahlberg K, Arora M, Curtin A, Curtin P, Wright RO, Smith DR, Lucchini RG, Broberg K, Austin C | Neurotoxicology | 28917719 | Neurotoxicology | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28917719 |
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| High-density transparent graphene arrays for predicting cellular calcium activity at depth from surface potential recordings. | Ramezani M, Kim JH, Liu X, Ren C, Alothman A, De-Eknamkul C, Wilson MN, Cubukcu E, Gilja V, Komiyama T, Kuzum D | Nature nanotechnology | 38212523 | Nat Nanotechnol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38212523 |
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| Multimodal neural recordings with Neuro-FITM uncover diverse patterns of cortical-hippocampal interactions. | Liu X, Ren C, Lu Y, Liu Y, Kim JH, Leutgeb S, Komiyama T, Kuzum D | Nature neuroscience | 33875893 | Nat Neurosci | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33875893 |
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| Microscale dynamics of electrophysiological markers of epilepsy. | Yang JC, Paulk AC, Salami P, Lee SH, Ganji M, Soper DJ, Cleary D, Simon M, Maus D, Lee JW, Nahed BV, Jones PS, Cahill DP, Cosgrove GR, Chu CJ, Williams Z, Halgren E, Dayeh S, Cash SS | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 34419344 | Clin Neurophysiol | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34419344 |
| Ultra-Sharp Nanowire Arrays Natively Permeate, Record, and Stimulate Intracellular Activity in Neuronal and Cardiac Networks. | Liu R, Lee J, Tchoe Y, Pre D, Bourhis AM, D'Antonio-Chronowska A, Robin G, Lee SH, Ro YG, Vatsyayan R, Tonsfeldt KJ, Hossain LA, Phipps ML, Yoo J, Nogan J, Martinez JS, Frazer KA, Bang AG, Dayeh SA | Advanced functional materials | 35603230 | Adv Funct Mater | 2022 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/35603230 |
| Scalable tactile sensor arrays on flexible substrates with high spatiotemporal resolution enabling slip and grip for closed-loop robotics. | Oh H, Yi GC, Yip M, Dayeh SA | Science advances | 33188031 | Sci Adv | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33188031 |
| Scalable Thousand Channel Penetrating Microneedle Arrays on Flex for Multimodal and Large Area Coverage BrainMachine Interfaces. | Lee SH, Thunemann M, Lee K, Cleary DR, Tonsfeldt KJ, Oh H, Azzazy F, Tchoe Y, Bourhis AM, Hossain L, Ro YG, Tanaka A, Kılıç K, Devor A, Dayeh SA | Advanced functional materials | 36381629 | Adv Funct Mater | 2022 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/36381629 |
| Constructing 2D maps of human spinal cord activity and isolating the functional midline with high-density microelectrode arrays. | Russman SM, Cleary DR, Tchoe Y, Bourhis AM, Stedelin B, Martin J, Brown EC, Zhang X, Kawamoto A, Ryu WHA, Raslan AM, Ciacci JD, Dayeh SA | Science translational medicine | 36170445 | Sci Transl Med | 2022 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/36170445 |
| Intraoperative application and early experience with novel high-resolution, high-channel-count thin-film electrodes for human microelectrocorticography. | Tan H, Paulk AC, Stedelin B, Cleary DR, Nerison C, Tchoe Y, Brown EC, Bourhis A, Russman S, Lee J, Tonsfeldt KJ, Yang JC, Oh H, Ro YG, Lee K, Ganji M, Galton I, Siler D, Han SJ, Collins KL, Ben-Haim S, Halgren E, Cash SS, Dayeh S, Raslan AM | Journal of neurosurgery | 37874692 | J Neurosurg | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/37874692 |
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| Flexible, scalable, high channel count stereo-electrode for recording in the human brain. | Lee K, Paulk AC, Ro YG, Cleary DR, Tonsfeldt KJ, Kfir Y, Pezaris JS, Tchoe Y, Lee J, Bourhis AM, Vatsyayan R, Martin JR, Russman SM, Yang JC, Baohan A, Richardson RM, Williams ZM, Fried SI, Hoi Sang U, Raslan AM, Ben-Haim S, Halgren E, Cash SS, Dayeh SA | Nature communications | 38233418 | Nat Commun | 2024 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/38233418 |
| Modular Phoneme Processing in Human Superior Temporal Gyrus. | Cleary DR, Tchoe Y, Bourhis A, Dickey CW, Stedelin B, Ganji M, Lee SH, Lee J, Siler DA, Brown EC, Rosen BQ, Kaestner E, Yang JC, Soper DJ, Han SJ, Paulk AC, Cash SS, Raslan AMT, Dayeh SA, Halgren E | bioRxiv : the preprint server for biology | 38293030 | bioRxiv | 2024 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/38293030 |
| Human brain mapping with multithousand-channel PtNRGrids resolves spatiotemporal dynamics. | Tchoe Y, Bourhis AM, Cleary DR, Stedelin B, Lee J, Tonsfeldt KJ, Brown EC, Siler DA, Paulk AC, Yang JC, Oh H, Ro YG, Lee K, Russman SM, Ganji M, Galton I, Ben-Haim S, Raslan AM, Dayeh SA | Science translational medicine | 35044788 | Sci Transl Med | 2022 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/35044788 |
| An Analytical Model for Dual Gate Piezoelectrically Sensitive ZnO Thin Film Transistors. | Oh H, Dayeh SA | Advanced materials technologies | 34485683 | Adv Mater Technol | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34485683 |
| Syllable processing is organized in discrete subregions of the human superior temporal gyrus. | Cleary DR, Tchoe Y, Bourhis A, Dickey CW, Stedelin B, Ganji M, Lee SH, Lee J, Siler DA, Brown EC, Rosen BQ, Kaestner E, Yang JC, Soper DJ, Han SJ, Paulk AC, Cash SS, Raslan AM, Dayeh SA, Halgren E | PLoS biology | 39241107 | PLoS Biol | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39241107 |
| Surface-Grafted Biocompatible Polymer Conductors for Stable and Compliant Electrodes for Brain Interfaces. | Blau R, Russman SM, Qie Y, Shipley W, Lim A, Chen AX, Nyayachavadi A, Ah L, Abdal A, Esparza GL, Edmunds SJ, Vatsyayan R, Dunfield SP, Halder M, Jokerst JV, Fenning DP, Tao AR, Dayeh SA, Lipomi DJ | Advanced healthcare materials | 39011811 | Adv Healthc Mater | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39011811 |
| Selective Formation of Porous Pt Nanorods for Highly Electrochemically Efficient Neural Electrode Interfaces. | Ganji M, Paulk AC, Yang JC, Vahidi NW, Lee SH, Liu R, Hossain L, Arneodo EM, Thunemann M, Shigyo M, Tanaka A, Ryu SB, Lee SW, Tchoe Y, Marsala M, Devor A, Cleary DR, Martin JR, Oh H, Gilja V, Gentner TQ, Fried SI, Halgren E, Cash SS, Dayeh SA | Nano letters | 31369283 | Nano Lett | 2019 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/31369283 |
| Electrochemical safety limits for clinical stimulation investigated using depth and strip electrodes in the pig brain. | Vatsyayan R, Cleary D, Martin JR, Halgren E, Dayeh SA | Journal of neural engineering | 34015769 | J Neural Eng | 2021 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/34015769 |
| Considerations and recent advances in nanoscale interfaces with neuronal and cardiac networks. | Tchoe Y, Lee J, Liu R, Bourhis AM, Vatsyayan R, Tonsfeldt KJ, Dayeh SA | Applied physics reviews | 34868443 | Appl Phys Rev | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34868443 |
| Spatially confined responses of mouse visual cortex to intracortical magnetic stimulation from micro-coils. | Ryu SB, Paulk AC, Yang JC, Ganji M, Dayeh SA, Cash SS, Fried SI, Lee SW | Journal of neural engineering | 32998116 | J Neural Eng | 2020 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/32998116 |
| Conductive electrospun polymer improves stem cell-derived cardiomyocyte function and maturation. | Gonzalez G, Nelson AC, Holman AR, Whitehead AJ, LaMontagne E, Lian R, Vatsyayan R, Dayeh SA, Engler AJ | Biomaterials | 37898021 | Biomaterials | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37898021 |
| A Low-Noise Low-Power 0.001Hz-1kHz Neural Recording System-on-Chip With Sample-Level Duty-Cycling. | Wu J, Akinin A, Somayajulu J, Lee MS, Paul A, Lu H, Park Y, Kim SJ, Mercier PP, Cauwenberghs G | IEEE transactions on biomedical circuits and systems | 38408002 | IEEE Trans Biomed Circuits Syst | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38408002 |
| An electroencephalogram microdisplay to visualize neuronal activity on the brain surface. | Tchoe Y, Wu T, U HS, Roth DM, Kim D, Lee J, Cleary DR, Pizarro P, Tonsfeldt KJ, Lee K, Chen PC, Bourhis AM, Galton I, Coughlin B, Yang JC, Paulk AC, Halgren E, Cash SS, Dayeh SA | Science translational medicine | 38657026 | Sci Transl Med | 2024 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/38657026 |
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| A Comprehensive Large Signal, Small Signal, and Noise Model for IGZO Thin Film Transistor Circuits. | Vatsyayan R, Dayeh SA | IEEE transactions on electron devices | 37680851 | IEEE Trans Electron Devices | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37680851 |
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| Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists. | Gallagher BR, Zhao Y | Neurobiology of disease | 33813047 | Neurobiol Dis | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33813047 |
| Expansion Microscopy: Toward Nanoscale Imaging of a Diverse Range of Biomolecules. | Klimas A, Zhao Y | ACS nano | 32628828 | ACS Nano | 2020 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/32628828 |
| MicroMagnify: A Multiplexed Expansion Microscopy Method for Pathogens and Infected Tissues. | Cheng Z, Stefani C, Skillman T, Klimas A, Lee A, DiBernardo EF, Brown KM, Milman T, Wang Y, Gallagher BR, Lagree K, Jena BP, Pulido JS, Filler SG, Mitchell AP, Hiller NL, Lacy-Hulbert A, Zhao Y | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 37658522 | Adv Sci (Weinh) | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37658522 |
| Magnify is a universal molecular anchoring strategy for expansion microscopy. | Klimas A, Gallagher BR, Wijesekara P, Fekir S, DiBernardo EF, Cheng Z, Stolz DB, Cambi F, Watkins SC, Brody SL, Horani A, Barth AL, Moore CI, Ren X, Zhao Y | Nature biotechnology | 36593399 | Nat Biotechnol | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36593399 |
| Super-Resolution Vibrational Imaging Using Expansion Stimulated Raman Scattering Microscopy. | Shi L, Klimas A, Gallagher B, Cheng Z, Fu F, Wijesekara P, Miao Y, Ren X, Zhao Y, Min W | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 35521971 | Adv Sci (Weinh) | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35521971 |
| A Novel Endocrine Role for the BAT-Released Lipokine 12,13-diHOME to Mediate Cardiac Function. | Pinckard KM, Shettigar VK, Wright KR, Abay E, Baer LA, Vidal P, Dewal RS, Das D, Duarte-Sanmiguel S, Hernández-Saavedra D, Arts PJ, Lehnig AC, Bussberg V, Narain NR, Kiebish MA, Yi F, Sparks LM, Goodpaster BH, Smith SR, Pratley RE, Lewandowski ED, Raman SV, Wold LE, Gallego-Perez D, Coen PM, Ziolo MT, Stanford KI | Circulation | 33106031 | Circulation | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33106031 |
| Nanotransfection-based vasculogenic cell reprogramming drives functional recovery in a mouse model of ischemic stroke. | Lemmerman LR, Balch MHH, Moore JT, Alzate-Correa D, Rincon-Benavides MA, Salazar-Puerta A, Gnyawali S, Harris HN, Lawrence W, Ortega-Pineda L, Wilch L, Risser IB, Maxwell AJ, Duarte-Sanmiguel S, Dodd D, Guio-Vega GP, McTigue DM, Arnold WD, Nimjee SM, Sen CK, Khanna S, Rink C, Higuita-Castro N, Gallego-Perez D | Science advances | 33741587 | Sci Adv | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33741587 |
| Injectable pulverized electrospun poly(lactic-co-glycolic acid) fibers improve human adipose tissue engraftment and volume retention. | Das D, Lawrence WR, Diaz-Starokozheva L, Salazar-Puerta AI, Ott N, Goebel ER, Damughatla A, Vidal P, Gallentine S, Moore JT, Kayuha D, Mendonca NC, Albert JB, Houser R, Johnson J, Powell H, Higuita-Castro N, Stanford KI, Gallego-Perez D | Journal of biomedical materials research. Part A | 37326365 | J Biomed Mater Res A | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37326365 |
| Engineered extracellular vesicles from human skin cells induce pro-β-cell conversions in pancreatic ductal cells. | Ortega-Pineda L, Guilfoyle E, Rincon-Benavides MA, Anaparthi AL, Lemmerman LR, Cuellar-Gaviria TZ, Lawrence W, Buss JL, Deng B, Blackstone BN, Salazar-Puerta A, McComb DW, Powell H, Gallego-Perez D, Higuita-Castro N | Advanced nanobiomed research | 38911285 | Adv Nanobiomed Res | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38911285 |
| Tissue nano-transfection of antimicrobial genes drives bacterial biofilm killing in wounds and is potentially mediated by extracellular vesicles. | Cuellar-Gaviria TZ, Rincon-Benavides MA, Halipci Topsakal HN, Salazar-Puerta AI, Jaramillo-Garrido S, Kordowski M, Vasquez-Martinez CA, Nguyen KT, Rima XY, Rana PSJB, Combita-Heredia O, Deng B, Dathathreya K, McComb DW, Reategui E, Wozniak D, Higuita-Castro N, Gallego-Perez D | Journal of controlled release : official journal of the Controlled Release Society | 39491627 | J Control Release | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39491627 |
| The Fifth Annual Symposium of the Midwest Aging Consortium. | Reader BF, Rosas L, Knopf BA, Liu Y, Alzate-Correa D, Bhat A, Carey A, Cuervo AM, Dayal S, Demarco RS, Elliehausen CJ, Englund DA, Hamilton HL, Johnston M, Kang P, Konopka AR, Lepola N, Presley CJ, Schafer MJ, Serrano J, Singer BD, Song MA, Stanford KI, Taylor J, Wei W, Yeh CY, Zhang L, Zhang L, Anderson RM, Bai H, Robbins PD, Lamming DW, Mihaylova MM, Rojas M, Mora AL | The journals of gerontology. Series A, Biological sciences and medical sciences | 39704343 | J Gerontol A Biol Sci Med Sci | 2025 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/39704343 |
| Engineered Extracellular Vesicle-Based Therapies for Valvular Heart Disease. | Salazar-Puerta AI, Kordowski M, Cuellar-Gaviria TZ, Rincon-Benavides MA, Hussein J, Flemister D, Mayoral-Andrade G, Barringer G, Guilfoyle E, Blackstone BN, Deng B, Zepeda-Orozco D, McComb DW, Powell H, Dasi LP, Gallego-Perez D, Higuita-Castro N | Cellular and molecular bioengineering | 37810997 | Cell Mol Bioeng | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37810997 |
| Nanotechnology-Driven Cell-Based Therapies in Regenerative Medicine. | Alzate-Correa D, Lawrence WR, Salazar-Puerta A, Higuita-Castro N, Gallego-Perez D | The AAPS journal.. | 35292878 | AAPS J | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/35292878 |
| Transient Middle Cerebral Artery Occlusion with an Intraluminal Suture Enables Reproducible Induction of Ischemic Stroke in Mice. | Lemmerman LR, Harris HN, Balch MHH, Rincon-Benavides MA, Higuita-Castro N, Arnold DW, Gallego-Perez D | Bio-protocol | 35284595 | Bio Protoc | 2022 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/35284595 |
| Early Intervention in Ischemic Tissue with Oxygen Nanocarriers Enables Successful Implementation of Restorative Cell Therapies. | Diaz-Starokozheva L, Das D, Gu X, Moore JT, Lemmerman LR, Valerio I, Powell HM, Higuita-Castro N, Go MR, Palmer AF, Gallego-Perez D | Cellular and molecular bioengineering | 33184576 | Cell Mol Bioeng | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33184576 |
| Nanochannel-Based Poration Drives Benign and Effective Nonviral Gene Delivery to Peripheral Nerve Tissue. | Moore JT, Wier CG, Lemmerman LR, Ortega-Pineda L, Dodd DJ, Lawrence WR, Duarte-Sanmiguel S, Dathathreya K, Diaz-Starokozheva L, Harris HN, Sen CK, Valerio IL, Higuita-Castro N, Arnold WD, Kolb SJ, Gallego-Perez D | Advanced biosystems | 32939985 | Adv Biosyst | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32939985 |
| Nanomedicine-Based Strategies for Diabetes: Diagnostics, Monitoring, and Treatment. | Lemmerman LR, Das D, Higuita-Castro N, Mirmira RG, Gallego-Perez D | Trends in endocrinology and metabolism: TEM | 32396845 | Trends Endocrinol Metab | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32396845 |
| Reciprocal Signaling between Myeloid Derived Suppressor and Tumor Cells Enhances Cellular Motility and is Mediated by Structural Cues in the Microenvironment. | Shukla VC, Duarte-Sanmiguel S, Panic A, Senthilvelan A, Moore J, Bobba C, Benner B, Carson WE 3rd, Ghadiali SN, Gallego-Perez D | Advanced biosystems | 32419350 | Adv Biosyst | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32419350 |
| Designer Extracellular Vesicles Modulate Pro-Neuronal Cell Responses and Improve Intracranial Retention. | Ortega-Pineda L, Sunyecz A, Salazar-Puerta AI, Rincon-Benavides MA, Alzate-Correa D, Anaparthi AL, Guilfoyle E, Mezache L, Struckman HL, Duarte-Sanmiguel S, Deng B, McComb DW, Dodd DJ, Lawrence WR, Moore J, Zhang J, Reátegui E, Veeraraghavan R, Nelson MT, Gallego-Perez D, Higuita-Castro N | Advanced healthcare materials | 35014204 | Adv Healthc Mater | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35014204 |
| In Situ Deployment of Engineered Extracellular Vesicles into the Tumor Niche via Myeloid-Derived Suppressor Cells. | Duarte-Sanmiguel S, Panic A, Dodd DJ, Salazar-Puerta A, Moore JT, Lawrence WR, Nairon K, Francis C, Zachariah N, McCoy W, Turaga R, Skardal A, Carson WE, Higuita-Castro N, Gallego-Perez D | Advanced healthcare materials | 34662497 | Adv Healthc Mater | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34662497 |
| Engineered Vasculogenic Extracellular Vesicles Drive Nonviral Direct Conversions of Human Dermal Fibroblasts into Induced Endothelial Cells and Improve Wound Closure. | Rincon-Benavides MA, Mendonca NC, Cuellar-Gaviria TZ, Salazar-Puerta AI, Ortega-Pineda L, Blackstone BN, Deng B, McComb DW, Gallego-Perez D, Powell HM, Higuita-Castro N | Advanced therapeutics | 37577183 | Adv Ther (Weinh) | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/37577183 |
| Engineered Extracellular Vesicles Derived from Dermal Fibroblasts Attenuate Inflammation in a Murine Model of Acute Lung Injury. | Salazar-Puerta AI, Rincon-Benavides MA, Cuellar-Gaviria TZ, Aldana J, Vasquez Martinez G, Ortega-Pineda L, Das D, Dodd D, Spencer CA, Deng B, McComb DW, Englert JA, Ghadiali S, Zepeda-Orozco D, Wold LE, Gallego-Perez D, Higuita-Castro N | Advanced materials (Deerfield Beach, Fla.) | 37119468 | Adv Mater | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37119468 |
| Guided migration analyses at the single-clone level uncover cellular targets of interest in tumor-associated myeloid-derived suppressor cell populations. | Duarte-Sanmiguel S, Shukla V, Benner B, Moore J, Lemmerman L, Lawrence W, Panic A, Wang S, Idzkowski N, Guio-Vega G, Higuita-Castro N, Ghadiali S, Carson WE, Gallego-Perez D | Scientific reports | 31988310 | Sci Rep | 2020 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/31988310 |
| ICAM-1-decorated extracellular vesicles loaded with miR-146a and Glut1 drive immunomodulation and hinder tumor progression in a murine model of breast cancer. | Duarte-Sanmiguel S, Salazar-Puerta AI, Panic A, Dodd D, Francis C, Alzate-Correa D, Ortega-Pineda L, Lemmerman L, Rincon-Benavides MA, Dathathreya K, Lawrence W, Ott N, Zhang J, Deng B, Wang S, Santander SP, McComb DW, Reategui E, Palmer AF, Carson WE, Higuita-Castro N, Gallego-Perez D | Biomaterials science | 37646133 | Biomater Sci | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37646133 |
| Self-assembled, ellipsoidal polymeric nanoparticles for intracellular delivery of therapeutics. | Desai P, Venkataramanan A, Schneider R, Jaiswal MK, Carrow JK, Purwada A, Singh A, Gaharwar AK | Journal of biomedical materials research. Part A | 29577576 | J Biomed Mater Res A | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29577576 |
| 3D Bioprinted Multicellular Vascular Models. | Gold KA, Saha B, Rajeeva Pandian NK, Walther BK, Palma JA, Jo J, Cooke JP, Jain A, Gaharwar AK | Advanced healthcare materials | 34310082 | Adv Healthc Mater | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34310082 |
| Nanoengineered Colloidal Inks for 3D Bioprinting. | Peak CW, Stein J, Gold KA, Gaharwar AK | Langmuir : the ACS journal of surfaces and colloids | 28981287 | Langmuir | 2018 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/28981287 |
| Photothermal modulation of human stem cells using light-responsive 2D nanomaterials. | Carrow JK, Singh KA, Jaiswal MK, Ramirez A, Lokhande G, Yeh AT, Sarkar TR, Singh I, Gaharwar AK | Proceedings of the National Academy of Sciences of the United States of America | 32461372 | Proc Natl Acad Sci U S A | 2020 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/32461372 |
| Conditioning of 3D Printed Nanoengineered Ionic-Covalent Entanglement Scaffolds with iP-hMSCs Derived Matrix. | Sears C, Mondragon E, Richards ZI, Sears N, Chimene D, McNeill EP, Gregory CA, Gaharwar AK, Kaunas R | Advanced healthcare materials | 32147960 | Adv Healthc Mater | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32147960 |
| Sustained and Prolonged Delivery of Protein Therapeutics from Two-Dimensional Nanosilicates. | Cross LM, Carrow JK, Ding X, Singh KA, Gaharwar AK | ACS applied materials & interfaces | 30676016 | ACS Appl Mater Interfaces | 2019 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/30676016 |
| Superhydrophobic states of 2D nanomaterials controlled by atomic defects can modulate cell adhesion. | Jaiswal MK , Singh KA , Lokhande G , Gaharwar AK | Chemical communications (Cambridge, England) | 31172998 | Chem Commun (Camb) | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31172998 |
| Organ-on-chips made of blood: endothelial progenitor cells from blood reconstitute vascular thromboinflammation in vessel-chips. | Mathur T, Singh KA, R Pandian NK, Tsai SH, Hein TW, Gaharwar AK, Flanagan JM, Jain A | Lab on a chip | 31246211 | Lab Chip | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31246211 |
| Comparison of Photo Cross Linkable Gelatin Derivatives and Initiators for Three-Dimensional Extrusion Bioprinting. | Tigner TJ, Rajput S, Gaharwar AK, Alge DL | Biomacromolecules | 31743018 | Biomacromolecules | 2020 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/31743018 |
| Animal models of postpartum hemorrhage. | Hargett SE, Leslie EF, Chapa HO, Gaharwar AK | Lab animal | 38528231 | Lab Anim (NY) | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38528231 |
| Nanobio Interface Between Proteins and 2D Nanomaterials. | Roy S, Aastha, Deo KA, Dey K, Gaharwar AK, Jaiswal A | ACS applied materials & interfaces | 37487195 | ACS Appl Mater Interfaces | 2023 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/37487195 |
| Dynamically crosslinked thermoresponsive granular hydrogels. | Lee HP, Cai KX, Wang TC, Davis R Jr, Deo K, Singh KA, Lele TP, Gaharwar AK | Journal of biomedical materials research. Part A | 37199446 | J Biomed Mater Res A | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37199446 |
| Nanoengineered Osteoinductive Bioink for 3D Bioprinting Bone Tissue. | Chimene D, Miller L, Cross LM, Jaiswal MK, Singh I, Gaharwar AK | ACS applied materials & interfaces | 32091189 | ACS Appl Mater Interfaces | 2020 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/32091189 |
| Dissociation of nanosilicates induces downstream endochondral differentiation gene expression program. | Brokesh AM, Cross LM, Kersey AL, Murali A, Richter C, Gregory CA, Singh I, Gaharwar AK | Science advances | 35476448 | Sci Adv | 2022 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/35476448 |
| Gradient nanocomposite hydrogels for interface tissue engineering. | Cross LM, Shah K, Palani S, Peak CW, Gaharwar AK | Nanomedicine : nanotechnology, biology, and medicine | 28554596 | Nanomedicine | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28554596 |
| Light-Responsive Inorganic Biomaterials for Biomedical Applications. | Lee HP, Gaharwar AK | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 32995121 | Adv Sci (Weinh) | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32995121 |
| Inorganic ions activate lineage-specific gene regulatory networks. | Kersey AL, Singh I, Gaharwar AK | Acta biomaterialia | 38552761 | Acta Biomater | 2024 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/38552761 |
| Atomic vacancies of molybdenum disulfide nanoparticles stimulate mitochondrial biogenesis. | Singh KA, Soukar J, Zulkifli M, Kersey A, Lokhande G, Ghosh S, Murali A, Garza NM, Kaur H, Keeney JN, Banavath R, Ceylan Koydemir H, Sitcheran R, Singh I, Gohil VM, Gaharwar AK | Nature communications | 39289340 | Nat Commun | 2024 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/39289340 |
| Inorganic Biomaterials Shape the Transcriptome Profile to Induce Endochondral Differentiation. | Murali A, Brokesh AM, Cross LM, Kersey AL, Jaiswal MK, Singh I, Gaharwar A | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 38738803 | Adv Sci (Weinh) | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38738803 |
| Organelle-Targeting Nanoparticles. | Soukar J, Peppas NA, Gaharwar AK | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 39806939 | Adv Sci (Weinh) | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39806939 |
| Effect of ionic strength on shear-thinning nanoclay-polymer composite hydrogels. | Sheikhi A , Afewerki S , Oklu R , Gaharwar AK , Khademhosseini A | Biomaterials science | 29944151 | Biomater Sci | 2018 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/29944151 |
| Printing Therapeutic Proteins in 3D using Nanoengineered Bioink to Control and Direct Cell Migration. | Peak CW, Singh KA, Adlouni M, Chen J, Gaharwar AK | Advanced healthcare materials | 31066517 | Adv Healthc Mater | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31066517 |
| 3D-printed bioactive scaffolds from nanosilicates and PEOT/PBT for bone tissue engineering. | Carrow JK, Di Luca A, Dolatshahi-Pirouz A, Moroni L, Gaharwar AK | Regenerative biomaterials | 30740240 | Regen Biomater | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30740240 |
| Emerging 2D Nanomaterials for Biomedical Applications. | Murali A, Lokhande G, Deo KA, Brokesh A, Gaharwar AK | Materials today (Kidlington, England) | 34970073 | Mater Today (Kidlington) | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34970073 |
| Polymer-Coated Extracellular Vesicles for Selective Codelivery of Chemotherapeutics and siRNA to Cancer Cells. | Jhan YY, Palou Zuniga G, Singh KA, Gaharwar AK, Alge DL, Bishop CJ | ACS applied bio materials | 35014481 | ACS Appl Bio Mater | 2021 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/35014481 |
| Nanoengineered Ink for Designing 3D Printable Flexible Bioelectronics. | Deo KA, Jaiswal MK, Abasi S, Lokhande G, Bhunia S, Nguyen TU, Namkoong M, Darvesh K, Guiseppi-Elie A, Tian L, Gaharwar AK | ACS nano | 35675588 | ACS Nano | 2022 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/35675588 |
| Clickable PEG hydrogel microspheres as building blocks for 3D bioprinting. | Xin S , Chimene D , Garza JE , Gaharwar AK , Alge DL | Biomaterials science | 30656307 | Biomater Sci | 2019 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/30656307 |
| Nano-bio interactions of 2D molybdenum disulfide. | Roy S, Deo KA, Singh KA, Lee HP, Jaiswal A, Gaharwar AK | Advanced drug delivery reviews | 35636569 | Adv Drug Deliv Rev | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35636569 |
| 2D layered nanomaterials for therapeutics delivery. | Davis R Jr, Urbanowski RA Jr, Gaharwar AK | Current opinion in biomedical engineering | 35814330 | Curr Opin Biomed Eng | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35814330 |
| 2D Covalent Organic Framework Direct Osteogenic Differentiation of Stem Cells. | Bhunia S, Jaiswal MK, Singh KA, Deo KA, Gaharwar AK | Advanced healthcare materials | 35104392 | Adv Healthc Mater | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35104392 |
| Generalizing hydrogel microparticles into a new class of bioinks for extrusion bioprinting. | Xin S, Deo KA, Dai J, Pandian NKR, Chimene D, Moebius RM, Jain A, Han A, Gaharwar AK, Alge DL | Science advances | 34652944 | Sci Adv | 2021 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/34652944 |
| Emerging trends in multiscale modeling of vascular pathophysiology: Organ-on-a-chip and 3D printing. | Gold K, Gaharwar AK, Jain A | Biomaterials | 30072038 | Biomaterials | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30072038 |
| 2D Nanoclay for Biomedical Applications: Regenerative Medicine, Therapeutic Delivery, and Additive Manufacturing. | Gaharwar AK, Cross LM, Peak CW, Gold K, Carrow JK, Brokesh A, Singh KA | Advanced materials (Deerfield Beach, Fla.) | 30941811 | Adv Mater | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30941811 |
| Nanoclay Reinforced Biomaterials for Mending Musculoskeletal Tissue Disorders. | Erezuma I, Eufrasio-da-Silva T, Golafshan N, Deo K, Mishra YK, Castilho M, Gaharwar AK, Leeuwenburgh S, Dolatshahi-Pirouz A, Orive G | Advanced healthcare materials | 34185438 | Adv Healthc Mater | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34185438 |
| Granular Biphasic Colloidal Hydrogels for 3D Bioprinting. | Deo KA, Murali A, Tronolone JJ, Mandrona C, Lee HP, Rajput S, Hargett SE, Selahi A, Sun Y, Alge DL, Jain A, Gaharwar AK | Advanced healthcare materials | 38749006 | Adv Healthc Mater | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38749006 |
| Intra-Articular Injectable Biomaterials for Cartilage Repair and Regeneration. | Kalairaj MS, Pradhan R, Saleem W, Smith MM, Gaharwar AK | Advanced healthcare materials | 38324655 | Adv Healthc Mater | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38324655 |
| Dynamically Cross-Linked Granular Hydrogels for 3D Printing and Therapeutic Delivery. | Lee HP, Davis R Jr, Wang TC, Deo KA, Cai KX, Alge DL, Lele TP, Gaharwar AK | ACS applied bio materials | 37584641 | ACS Appl Bio Mater | 2023 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/37584641 |
| Stiffness assisted cell-matrix remodeling trigger 3D mechanotransduction regulatory programs. | Kersey AL, Cheng DY, Deo KA, Dubell CR, Wang TC, Jaiswal MK, Kim MH, Murali A, Hargett SE, Mallick S, Lele TP, Singh I, Gaharwar AK | Biomaterials | 38335719 | Biomaterials | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38335719 |
| Screening a chemically defined extracellular matrix mimetic substrate library to identify substrates that enhance substrate-mediated transfection. | Hamann A, Thomas AK, Kozisek T, Farris E, Lück S, Zhang Y, Pannier AK | Experimental biology and medicine (Maywood, N.J.) | 32183552 | Exp Biol Med (Maywood) | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32183552 |
| Formulation of Chitosan-Zein Nano-in-Microparticles for Oral DNA Delivery. | Heck K, Farris E, Pannier AK | Methods in molecular biology (Clifton, N.J.) | 37775665 | Methods Mol Biol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/37775665 |
| Nucleic acid delivery to mesenchymal stem cells: a review of nonviral methods and applications. | Hamann A, Nguyen A, Pannier AK | Journal of biological engineering | 30675180 | J Biol Eng | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30675180 |
| High- and low-molecular-weight chitosan act as adjuvants during single-dose influenza A virus protein vaccination through distinct mechanisms. | Lampe AT, Farris EJ, Brown DM, Pannier AK | Biotechnology and bioengineering | 33289090 | Biotechnol Bioeng | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33289090 |
| Glucocorticoid Priming of Nonviral Gene Delivery to hMSCs Increases Transfection by Reducing Induced Stresses. | Hamann A, Kozisek T, Broad K, Pannier AK | Molecular therapy. Methods & clinical development | 32913879 | Mol Ther Methods Clin Dev | 2020 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/32913879 |
| High-throughput screening of clinically approved drugs that prime nonviral gene delivery to human Mesenchymal stem cells. | Kozisek T, Hamann A, Nguyen A, Miller M, Plautz S, Pannier AK | Journal of biological engineering | 32467728 | J Biol Eng | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32467728 |
| Mechanisms of unprimed and dexamethasone-primed nonviral gene delivery to human mesenchymal stem cells. | Hamann A, Broad K, Nguyen A, Pannier AK | Biotechnology and bioengineering | 30450542 | Biotechnol Bioeng | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30450542 |
| Oral Non-Viral Gene Delivery for Applications in DNA Vaccination and Gene Therapy. | Farris E, Sanderfer K, Lampe A, Brown DM, Ramer-Tait AE, Pannier AK | Current opinion in biomedical engineering | 31011691 | Curr Opin Biomed Eng | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31011691 |
| Systematic comparison of nonviral gene delivery strategies for efficient co-expression of two transgenes in human mesenchymal stem cells. | Kozisek T, Samuelson L, Hamann A, Pannier AK | Journal of biological engineering | 38062439 | J Biol Eng | 2023 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/38062439 |
| Free Polyethylenimine Enhances Substrate-Mediated Gene Delivery on Titanium Substrates Modified With RGD-Functionalized Poly(acrylic acid) Brushes. | Mantz A, Rosenthal A, Farris E, Kozisek T, Bittrich E, Nazari S, Schubert E, Schubert M, Stamm M, Uhlmann P, Pannier AK | Frontiers in chemistry | 30792979 | Front Chem | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30792979 |
| Surface- and Hydrogel-Mediated Delivery of Nucleic Acid Nanoparticles. | Pannier AK, Kozisek T, Segura T | Methods in molecular biology (Clifton, N.J.) | 30838617 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30838617 |
| Combined TLR4 and TLR9 agonists induce distinct phenotypic changes in innate immunity in vitro and in vivo. | Lampe AT, Puniya BL, Pannier AK, Helikar T, Brown DM | Cellular immunology | 32619809 | Cell Immunol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32619809 |
| Innovative nonviral gene delivery strategies for engineering human mesenchymal stem cell phenotypes toward clinical applications. | Hamann A, Pannier AK | Current opinion in biotechnology | 36274497 | Curr Opin Biotechnol | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36274497 |
| Comparison of promoter, DNA vector, and cationic carrier for efficient transfection of hMSCs from multiple donors and tissue sources. | Kozisek T, Hamann A, Samuelson L, Fudolig M, Pannier AK | Molecular therapy. Nucleic acids | 34513295 | Mol Ther Nucleic Acids | 2021 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/34513295 |
| Biomaterial substrate modifications that influence cell-material interactions to prime cellular responses to nonviral gene delivery. | Mantz A, Pannier AK | Experimental biology and medicine (Maywood, N.J.) | 30621454 | Exp Biol Med (Maywood) | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30621454 |
| Super-swelled lyotropic single crystals. | Kim H, Song Z, Leal C | Proceedings of the National Academy of Sciences of the United States of America | 28973884 | Proc Natl Acad Sci U S A | 2017 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/28973884 |
| Nanoscale partitioning of paclitaxel in hybrid lipid-polymer membranes. | Tuteja M , Kang M , Leal C , Centrone A | The Analyst | 29878001 | Analyst | 2018 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/29878001 |
| Wirelessly controlled, bioresorbable drug delivery device with active valves that exploit electrochemically triggered crevice corrosion. | Koo J, Kim SB, Choi YS, Xie Z, Bandodkar AJ, Khalifeh J, Yan Y, Kim H, Pezhouh MK, Doty K, Lee G, Chen YY, Lee SM, D'Andrea D, Jung K, Lee K, Li K, Jo S, Wang H, Kim JH, Kim J, Choi SG, Jang WJ, Oh YS, Park I, Kwak SS, Park JH, Hong D, Feng X, Lee CH, Banks A, Leal C, Lee HM, Huang Y, Franz CK, Ray WZ, MacEwan M, Kang SK, Rogers JA | Science advances | 32923633 | Sci Adv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32923633 |
| Open-air synthesis of oligo(ethylene glycol)-functionalized polypeptides from non-purified N-carboxyanhydrides. | Tan Z, Song Z, Xue T, Zheng L, Jiang L, Jiang Y, Fu Z, Nguyen A, Leal C, Cheng J | Biomaterials science | 33949455 | Biomater Sci | 2021 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/33949455 |
| Microfluidics Synthesis of Gene Silencing Cubosomes. | Kim H, Sung J, Chang Y, Alfeche A, Leal C | ACS nano | 30081623 | ACS Nano | 2018 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/30081623 |
| Self-organization of Nucleic Acids in Lipid Constructs. | Kang M, Kim H, Leal C | Current opinion in colloid & interface science | 28496379 | Curr Opin Colloid Interface Sci | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28496379 |
| Thermally Functional Liquid Crystal Networks by Magnetic Field Driven Molecular Orientation. | Shin J, Kang M, Tsai T, Leal C, Braun PV, Cahill DG | ACS macro letters | 35607211 | ACS Macro Lett | 2016 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/35607211 |
| Lipid-based Liquid Crystalline Films and Solutions for the Delivery of Cargo to Cells. | Porras-Gomez M, Leal C | Liquid crystals reviews | 31942262 | Liq Cryst Rev | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31942262 |
| Three-Dimensional Microphase Separation and Synergistic Permeability in Stacked Lipid-Polymer Hybrid Membranes. | Kang M, Lee B, Leal C | Chemistry of materials : a publication of the American Chemical Society | 31097879 | Chem Mater | 2017 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/31097879 |
| Lipid nanoparticle topology regulates endosomal escape and delivery of RNA to the cytoplasm. | Zheng L, Bandara SR, Tan Z, Leal C | Proceedings of the National Academy of Sciences of the United States of America | 37364130 | Proc Natl Acad Sci U S A | 2023 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/37364130 |
| Polymer-Lipid Hybrid Materials. | Go YK, Leal C | Chemical reviews | 34752064 | Chem Rev | 2021 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/34752064 |
| Graphene-based sensing of oxygen transport through pulmonary membranes. | Kim M, Porras-Gomez M, Leal C | Nature communications | 32107376 | Nat Commun | 2020 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/32107376 |
| Near-Infrared-Triggered Reversible Transformations of Gold Nanorod-Laden Lipid Assemblies: Implications for Cellular Delivery. | Rueben J, Jayaraman A, Mahanthappa MK, Leal C | ACS applied nano materials | 40115494 | ACS Appl Nano Mater | 2022 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/40115494 |
| Hybrid Unilamellar Vesicles of Phospholipids and Block Copolymers with Crystalline Domains. | Go YK, Kambar N, Leal C | Polymers | 32485809 | Polymers (Basel) | 2020 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/32485809 |
| The stabilization of primitive bicontinuous cubic phases with tunable swelling over a wide composition range. | Leung SSW , Leal C | Soft matter | 30462135 | Soft Matter | 2019 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/30462135 |
| Nanostructured Lipid-based Films for Substrate Mediated Applications in Biotechnology. | Kang M, Tuteja M, Centrone A, Topgaard D, Leal C | Advanced functional materials | 31080383 | Adv Funct Mater | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/31080383 |
| The structural fate of lipid nanoparticles in the extracellular matrix. | Bandara SR, Molley TG, Kim H, Bharath PA, Kilian KA, Leal C | Materials horizons | 31942243 | Mater Horiz | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31942243 |
| 3D Columnar Phase of Stacked Short DNA Organized by Coherent Membrane Undulations. | Bouxsein NF, Leal C, McAllister CS, Li Y, Ewert KK, Samuel CE, Safinya CR | Langmuir : the ACS journal of surfaces and colloids | 31408350 | Langmuir | 2019 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/31408350 |
| Optogenetic Reconstitution for Determining the Form and Function of Membraneless Organelles. | Dine E, Toettcher JE | Biochemistry | 29373016 | Biochemistry | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29373016 |
| Optogenetic regulation of engineered cellular metabolism for microbial chemical production. | Zhao EM, Zhang Y, Mehl J, Park H, Lalwani MA, Toettcher JE, Avalos JL | Nature | 29562237 | Nature | 2018 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/29562237 |
| Engineering combinatorial and dynamic decoders using synthetic immediate-early genes. | Ravindran PT, Wilson MZ, Jena SG, Toettcher JE | Communications biology | 32792645 | Commun Biol | 2020 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/32792645 |
| Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix. | Iuliano JN, Collado JT, Gil AA, Ravindran PT, Lukacs A, Shin S, Woroniecka HA, Adamczyk K, Aramini JM, Edupuganti UR, Hall CR, Greetham GM, Sazanovich IV, Clark IP, Daryaee T, Toettcher JE, French JB, Gardner KH, Simmerling CL, Meech SR, Tonge PJ | ACS chemical biology | 32880430 | ACS Chem Biol | 2020 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/32880430 |
| A Live-Cell Screen for Altered Erk Dynamics Reveals Principles of Proliferative Control. | Goglia AG, Wilson MZ, Jena SG, Silbert J, Basta LP, Devenport D, Toettcher JE | Cell systems | 32191874 | Cell Syst | 2020 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/32191874 |
| A synthetic gene circuit for imaging-free detection of signaling pulses. | Ravindran PT, McFann S, Thornton RH, Toettcher JE | Cell systems | 34739875 | Cell Syst | 2022 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/34739875 |
| Tracing Information Flow from Erk to Target Gene Induction Reveals Mechanisms of Dynamic and Combinatorial Control. | Wilson MZ, Ravindran PT, Lim WA, Toettcher JE | Molecular cell | 28826673 | Mol Cell | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28826673 |
| Erratum: Publisher Correction: Deconstructing and repurposing the light-regulated interplay between Arabidopsis phytochromes and interacting factors. | Golonka D, Fischbach P, Jena SG, Kleeberg JRW, Essen LO, Toettcher JE, Zurbriggen MD, Möglich A | Communications biology | 31872077 | Commun Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31872077 |
| Optogenetic Control of Ras/Erk Signaling Using the Phy-PIF System. | Goglia AG, Wilson MZ, DiGiorno DB, Toettcher JE | Methods in molecular biology (Clifton, N.J.) | 28730469 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28730469 |
| Membrane-proximal motifs encode differences in signaling strength between type I and III interferon receptors. | Mesev EV, Lin AE, Guare EG, Heller BL, Douam F, Adamson B, Toettcher JE, Ploss A | Science signaling | 37816090 | Sci Signal | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37816090 |
| Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. | Bracha D, Walls MT, Wei MT, Zhu L, Kurian M, Avalos JL, Toettcher JE, Brangwynne CP | Cell | 30500534 | Cell | 2018 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/30500534 |
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| The rod-shaped ATG2A-WIPI4 complex tethers membranes in vitro. | Otomo T, Chowdhury S, Lander GC | Contact (Thousand Oaks (Ventura County, Calif.)) | 30766969 | Contact (Thousand Oaks) | 2018 Jan-Dec | https://www.ncbi.nlm.nih.gov/pubmed/30766969 |
| Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome. | Bashore C, Dambacher CM, Goodall EA, Matyskiela ME, Lander GC, Martin A | Nature structural & molecular biology | 26301997 | Nat Struct Mol Biol | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26301997 |
| Exploring applications of crowdsourcing to cryo-EM. | Bruggemann J, Lander GC, Su AI | Journal of structural biology | 29486249 | J Struct Biol | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29486249 |
| Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis. | Wu M, Lander GC | Biophysical journal | 32919493 | Biophys J | 2020 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/32919493 |
| Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK:BMAL1 to control circadian timing. | Fribourgh JL, Srivastava A, Sandate CR, Michael AK, Hsu PL, Rakers C, Nguyen LT, Torgrimson MR, Parico GCG, Tripathi S, Zheng N, Lander GC, Hirota T, Tama F, Partch CL | eLife | 32101164 | Elife | 2020 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/32101164 |
| Structure of the mitochondrial inner membrane AAA+ protease YME1 gives insight into substrate processing. | Puchades C, Rampello AJ, Shin M, Giuliano CJ, Wiseman RL, Glynn SE, Lander GC | Science (New York, N.Y.) | 29097521 | Science | 2017 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/29097521 |
| Structure of the cold- and menthol-sensing ion channel TRPM8. | Yin Y, Wu M, Zubcevic L, Borschel WF, Lander GC, Lee SY | Science (New York, N.Y.) | 29217583 | Science | 2018 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/29217583 |
| Achieving better-than-3-Å resolution by single-particle cryo-EM at 200 keV. | Herzik MA Jr, Wu M, Lander GC | Nature methods | 28991891 | Nat Methods | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28991891 |
| Cryo-electron microscopy structure of the lysosomal calcium-permeable channel TRPML3. | Hirschi M, Herzik MA Jr, Wie J, Suo Y, Borschel WF, Ren D, Lander GC, Lee SY | Nature | 29019979 | Nature | 2017 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/29019979 |
| A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. | Herzik MA Jr, Fraser JS, Lander GC | Structure (London, England : 1993) | 30449687 | Structure | 2019 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/30449687 |
| Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. | Chowdhury S, Otomo C, Leitner A, Ohashi K, Aebersold R, Lander GC, Otomo T | Proceedings of the National Academy of Sciences of the United States of America | 30185561 | Proc Natl Acad Sci U S A | 2018 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/30185561 |
| A guided approach for subtomogram averaging of challenging macromolecular assemblies. | Basanta B, Chowdhury S, Lander GC, Grotjahn DA | Journal of structural biology: X | 33319208 | J Struct Biol X | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33319208 |
| AcrIF9 tethers non-sequence specific dsDNA to the CRISPR RNA-guided surveillance complex. | Hirschi M, Lu WT, Santiago-Frangos A, Wilkinson R, Golden SM, Davidson AR, Lander GC, Wiedenheft B | Nature communications | 32483187 | Nat Commun | 2020 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/32483187 |
| Site-specific labeling of proteins for electron microscopy. | Dambacher CM, Lander GC | Journal of structural biology | 26409249 | J Struct Biol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26409249 |
| Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition. | Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC | eLife | 26744777 | Elife | 2016 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/26744777 |
| Isolation of yeast complex IV in native lipid nanodiscs. | Smirnova IA, Sjöstrand D, Li F, Björck M, Schäfer J, Östbye H, Högbom M, von Ballmoos C, Lander GC, Ädelroth P, Brzezinski P | Biochimica et biophysica acta | 27620332 | Biochim Biophys Acta | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27620332 |
| The Pex1/Pex6 complex is a heterohexameric AAA+ motor with alternating and highly coordinated subunits. | Gardner BM, Chowdhury S, Lander GC, Martin A | Journal of molecular biology | 25659908 | J Mol Biol | 2015 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/25659908 |
| Structure Reveals Mechanisms of Viral Suppressors that Intercept a CRISPR RNA-Guided Surveillance Complex. | Chowdhury S, Carter J, Rollins MF, Golden SM, Jackson RN, Hoffmann C, Nosaka L, Bondy-Denomy J, Maxwell KL, Davidson AR, Fischer ER, Lander GC, Wiedenheft B | Cell | 28340349 | Cell | 2017 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/28340349 |
| Cryo-EM structure of a mitochondrial calcium uniporter. | Yoo J, Wu M, Yin Y, Herzik MA Jr, Lander GC, Lee SY | Science (New York, N.Y.) | 29954988 | Science | 2018 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/29954988 |
| Structural organization of the dynein-dynactin complex bound to microtubules. | Chowdhury S, Ketcham SA, Schroer TA, Lander GC | Nature structural & molecular biology | 25751425 | Nat Struct Mol Biol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25751425 |
| Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease. | Puchades C, Ding B, Song A, Wiseman RL, Lander GC, Glynn SE | Molecular cell | 31327635 | Mol Cell | 2019 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/31327635 |
| High-resolution structure determination of sub-100 kDa complexes using conventional cryo-EM. | Herzik MA Jr, Wu M, Lander GC | Nature communications | 30833564 | Nat Commun | 2019 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/30833564 |
| Structure Reveals a Mechanism of CRISPR-RNA-Guided Nuclease Recruitment and Anti-CRISPR Viral Mimicry. | Rollins MF, Chowdhury S, Carter J, Golden SM, Miettinen HM, Santiago-Frangos A, Faith D, Lawrence CM, Lander GC, Wiedenheft B | Molecular cell | 30872121 | Mol Cell | 2019 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/30872121 |
| The molecular principles governing the activity and functional diversity of AAA+ proteins. | Puchades C, Sandate CR, Lander GC | Nature reviews. Molecular cell biology | 31754261 | Nat Rev Mol Cell Biol | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31754261 |
| Conformational ensemble of the human TRPV3 ion channel. | Zubcevic L, Herzik MA Jr, Wu M, Borschel WF, Hirschi M, Song AS, Lander GC, Lee SY | Nature communications | 30429472 | Nat Commun | 2018 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/30429472 |
| Contact Line Pinning Is Not Required for Nanobubble Stability on Copolymer Brushes. | Bull DS, Nelson N, Konetski D, Bowman CN, Schwartz DK, Goodwin AP | The journal of physical chemistry letters | 30010342 | J Phys Chem Lett | 2018 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/30010342 |
| Surface-Templated Nanobubbles Protect Proteins from Surface-Mediated Denaturation. | Bull DS, Kienle DF, Chaparro Sosa AF, Nelson N, Roy S, Cha JN, Schwartz DK, Kaar JL, Goodwin AP | The journal of physical chemistry letters | 31067058 | J Phys Chem Lett | 2019 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/31067058 |
| Click Nucleic Acid Mediated Loading of Prodrug Activating Enzymes in PEG-PLGA Nanoparticles for Combination Chemotherapy. | Harguindey A, Roy S, Harris AW, Fairbanks BD, Goodwin AP, Bowman CN, Cha JN | Biomacromolecules | 30884222 | Biomacromolecules | 2019 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/30884222 |
| Depolymerizable Poly(O-vinyl carbamate-alt-sulfones) as Customizable Macromolecular Scaffolds for Mucosal Drug Delivery. | Kumar K, Castaño EJ, Weidner AR, Yildirim A, Goodwin AP | ACS macro letters | 28480130 | ACS Macro Lett | 2016 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/28480130 |
| DNA-Assembled Core-Satellite Upconverting-Metal-Organic Framework Nanoparticle Superstructures for Efficient Photodynamic Therapy. | He L, Brasino M, Mao C, Cho S, Park W, Goodwin AP, Cha JN | Small (Weinheim an der Bergstrasse, Germany) | 28481463 | Small | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28481463 |
| Understanding Acoustic Cavitation Initiation by Porous Nanoparticles: Toward Nanoscale Agents for Ultrasound Imaging and Therapy. | Yildirim A, Chattaraj R, Blum NT, Goodwin AP | Chemistry of materials : a publication of the American Chemical Society | 28484307 | Chem Mater | 2016 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/28484307 |
| Anti-EGFR Affibodies with Site-Specific Photo-Cross-Linker Incorporation Show Both Directed Target-Specific Photoconjugation and Increased Retention in Tumors. | Brasino M, Roy S, Erbse AH, He L, Mao C, Park W, Cha JN, Goodwin AP | Journal of the American Chemical Society | 30203972 | J Am Chem Soc | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/30203972 |
| Selective Vaporization of Superheated Nanodroplets for Rapid, Sensitive, Acoustic Biosensing. | Chattaraj R, Mohan P, Besmer JD, Goodwin AP | Advanced healthcare materials | 26084414 | Adv Healthc Mater | 2015 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/26084414 |
| Mutually-Reactive, Fluorogenic Hydrocyanine/Quinone Reporter Pairs for In-Solution Biosensing via Nanodroplet Association. | Chattaraj R, Mohan P, Livingston CM, Besmer JD, Kumar K, Goodwin AP | ACS applied materials & interfaces | 26710239 | ACS Appl Mater Interfaces | 2016 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/26710239 |
| Conversion of Ethanol to 2-Ethylhexenal at Ambient Conditions Using Tandem, Biphasic Catalysis. | Hafenstine GR, Harris AW, Ma K, Cha JN, Goodwin AP | ACS sustainable chemistry & engineering | 33224638 | ACS Sustain Chem Eng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/33224638 |
| Light-Driven Catalytic Upgrading of Butanol in a Biohybrid Photoelectrochemical System. | Harris AW, Yehezkeli O, Hafenstine GR, Goodwin AP, Cha JN | ACS sustainable chemistry & engineering | 33133786 | ACS Sustain Chem Eng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/33133786 |
| Solar Photocatalytic Phenol Polymerization and Hydrogen Generation for Flocculation of Wastewater Impurities. | Hafenstine GR, Patalano RE, Harris AW, Jiang G, Ma K, Goodwin AP, Cha JN | ACS applied polymer materials | 37206614 | ACS Appl Polym Mater | 2019 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37206614 |
| Alternating Sulfone Copolymers Depolymerize in Response to Both Chemical and Mechanical Stimuli. | Kumar K, Goodwin AP | ACS macro letters | 28480129 | ACS Macro Lett | 2015 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28480129 |
| Nanoparticles Formed by Acoustic Destruction of Microbubbles and Their Utilization for Imaging and Effects on Therapy by High Intensity Focused Ultrasound. | Blum NT, Yildirim A, Chattaraj R, Goodwin AP | Theranostics | 28255360 | Theranostics | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28255360 |
| Phospholipid Capped Mesoporous Nanoparticles for Targeted High Intensity Focused Ultrasound Ablation. | Yildirim A, Chattaraj R, Blum NT, Shi D, Kumar K, Goodwin AP | Advanced healthcare materials | 28699308 | Adv Healthc Mater | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28699308 |
| Phase Behavior of Mixed Lipid Monolayers on Perfluorocarbon Nanoemulsions and its Effect on Acoustic Contrast. | Chattaraj R, Goldscheitter GM, Yildirim A, Goodwin AP | RSC advances | 28603605 | RSC Adv | 2016 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/28603605 |
| Catalytic Upgrading in Bacteria-Compatible Conditions via a Biocompatible Aldol Condensation. | Domaille DW, Hafenstine GR, Greer MA, Goodwin AP, Cha JN | ACS sustainable chemistry & engineering | 28480149 | ACS Sustain Chem Eng | 2016 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/28480149 |
| Stable Encapsulation of Air in Mesoporous Silica Nanoparticles: Fluorocarbon-Free Nanoscale Ultrasound Contrast Agents. | Yildirim A, Chattaraj R, Blum NT, Goldscheitter GM, Goodwin AP | Advanced healthcare materials | 26990167 | Adv Healthc Mater | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26990167 |
| TiO(2)-Capped Gold Nanorods for Plasmon-Enhanced Production of Reactive Oxygen Species and Photothermal Delivery of Chemotherapeutic Agents. | He L, Mao C, Brasino M, Harguindey A, Park W, Goodwin AP, Cha JN | ACS applied materials & interfaces | 30044085 | ACS Appl Mater Interfaces | 2018 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/30044085 |
| Polyacrylamide Hydrogels Produce Hydrogen Peroxide from Osmotic Swelling in Aqueous Media. | Parameswar AV, Fitch KR, Bull DS, Duke VR, Goodwin AP | Biomacromolecules | 30052430 | Biomacromolecules | 2018 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/30052430 |
| Multicatalytic, Light-Driven Upgrading of Butanol to 2-Ethylhexenal and Hydrogen under Mild Aqueous Conditions. | Hafenstine GR, Ma K, Harris AW, Yehezkeli O, Park E, Domaille DW, Cha JN, Goodwin AP | ACS catalysis | 33133753 | ACS Catal | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/33133753 |
| Phospholipid-Coated Hydrophobic Mesoporous Silica Nanoparticles Enhance Thrombectomy by High-Intensity Focused Ultrasound with Low Production of Embolism-Inducing Clot Debris. | Blum NT, Gyorkos CM, Narowetz SJ, Mueller EN, Goodwin AP | ACS applied materials & interfaces | 31556582 | ACS Appl Mater Interfaces | 2019 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/31556582 |
| Design and Application of Stimulus-Responsive Droplets and Bubbles Stabilized by Phospholipid Monolayers. | Chattaraj R, Blum NT, Goodwin AP | Current opinion in colloid & interface science | 31086500 | Curr Opin Colloid Interface Sci | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/31086500 |
| Enzymes Photo-Cross-Linked to Live Cell Receptors Retain Activity and EGFR Inhibition after Both Internalization and Recycling. | Roy S, Brasino M, Beirne JM, Harguindey A, Chapnick DA, Liu X, Cha JN, Goodwin AP | Bioconjugate chemistry | 31840981 | Bioconjug Chem | 2020 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/31840981 |
| Temperature-Responsive Hydrophobic Silica Nanoparticle Ultrasound Contrast Agents Directed by Phospholipid Phase Behavior. | Blum NT, Yildirim A, Gyorkos C, Shi D, Cai A, Chattaraj R, Goodwin AP | ACS applied materials & interfaces | 31012297 | ACS Appl Mater Interfaces | 2019 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/31012297 |
| Nanoparticle-Mediated Acoustic Cavitation Enables High Intensity Focused Ultrasound Ablation Without Tissue Heating. | Yildirim A, Shi D, Roy S, Blum NT, Chattaraj R, Cha JN, Goodwin AP | ACS applied materials & interfaces | 30339360 | ACS Appl Mater Interfaces | 2018 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/30339360 |
| Color-Coded Super-Resolution Small-Molecule Imaging. | Beuzer P, La Clair JJ, Cang H | Chembiochem : a European journal of chemical biology | 26994590 | Chembiochem | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/26994590 |
| Single dish gradient screening of small molecule localization. | Beuzer P, Axelrod J, Trzoss L, Fenical W, Dasari R, Evidente A, Kornienko A, Cang H, La Clair JJ | Organic & biomolecular chemistry | 27530345 | Org Biomol Chem | 2016 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/27530345 |
| Glioma Stem Cell-Specific Superenhancer Promotes Polyunsaturated Fatty-Acid Synthesis to Support EGFR Signaling. | Gimple RC, Kidwell RL, Kim LJY, Sun T, Gromovsky AD, Wu Q, Wolf M, Lv D, Bhargava S, Jiang L, Prager BC, Wang X, Ye Q, Zhu Z, Zhang G, Dong Z, Zhao L, Lee D, Bi J, Sloan AE, Mischel PS, Brown JM, Cang H, Huan T, Mack SC, Xie Q, Rich JN | Cancer discovery | 31201181 | Cancer Discov | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31201181 |
| Ritterostatin G(N) 1(N) , a Cephalostatin-Ritterazine Bis-steroidal Pyrazine Hybrid, Selectively Targets GRP78. | Ambrose AJ, Santos EA, Jimenez PC, Rocha DD, Wilke DV, Beuzer P, Axelrod J, Kumar Kanduluru A, Fuchs PL, Cang H, Costa-Lotufo LV, Chapman E, La Clair JJ | Chembiochem : a European journal of chemical biology | 28074539 | Chembiochem | 2017 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/28074539 |
| Type I Interferon Regulates a Coordinated Gene Network to Enhance Cytotoxic T Cell-Mediated Tumor Killing. | Fan JB, Miyauchi S, Xu HZ, Liu D, Kim LJY, Burkart C, Cheng H, Arimoto KI, Yan M, Zhou Y, Győrffy B, Knobeloch KP, Rich JN, Cang H, Fu XD, Zhang DE | Cancer discovery | 31974171 | Cancer Discov | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31974171 |
| Molecular organization of mammalian meiotic chromosome axis revealed by expansion STORM microscopy. | Xu H, Tong Z, Ye Q, Sun T, Hong Z, Zhang L, Bortnick A, Cho S, Beuzer P, Axelrod J, Hu Q, Wang M, Evans SM, Murre C, Lu LF, Sun S, Corbett KD, Cang H | Proceedings of the National Academy of Sciences of the United States of America | 31444302 | Proc Natl Acad Sci U S A | 2019 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/31444302 |
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| Droplet-based transcriptome profiling of individual synapses. | Niu M, Cao W, Wang Y, Zhu Q, Luo J, Wang B, Zheng H, Weitz DA, Zong C | Nature biotechnology | 36646931 | Nat Biotechnol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36646931 |
| Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA). | Niu Y, Zhu Q, Zong C | Bio-protocol | 35434195 | Bio Protoc | 2022 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/35434195 |
| Single-cell total-RNA profiling unveils regulatory hubs of transcription factors. | Niu Y, Luo J, Zong C | Nature communications | 39009595 | Nat Commun | 2024 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/39009595 |
| Single-cell damagenome profiling unveils vulnerable genes and functional pathways in human genome toward DNA damage. | Zhu Q, Niu Y, Gundry M, Zong C | Science advances | 34215579 | Sci Adv | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34215579 |
| Fibroblast heterogeneity and its impact on extracellular matrix and immune landscape remodeling in cancer. | Yamauchi M, Gibbons DL, Zong C, Fradette JJ, Bota-Rabassedas N, Kurie JM | Matrix biology : journal of the International Society for Matrix Biology | 32442601 | Matrix Biol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32442601 |
| Single-PanIN-seq unveils that ARID1A deficiency promotes pancreatic tumorigenesis by attenuating KRAS-induced senescence. | Liu S, Cao W, Niu Y, Luo J, Zhao Y, Hu Z, Zong C | eLife | 33983114 | Elife | 2021 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/33983114 |
| Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1. | Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK | eLife | 31033441 | Elife | 2019 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/31033441 |
| Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. | Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF | Nature biotechnology | 27136077 | Nat Biotechnol | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27136077 |
| Circularly permuted and PAM-modified Cas9 variants broaden the targeting scope of base editors. | Huang TP, Zhao KT, Miller SM, Gaudelli NM, Oakes BL, Fellmann C, Savage DF, Liu DR | Nature biotechnology | 31110355 | Nat Biotechnol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31110355 |
| CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification. | Oakes BL, Fellmann C, Rishi H, Taylor KL, Ren SM, Nadler DC, Yokoo R, Arkin AP, Doudna JA, Savage DF | Cell | 30633905 | Cell | 2019 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/30633905 |
| Rapid and Programmable Protein Mutagenesis Using Plasmid Recombineering. | Higgins SA, Ouonkap SVY, Savage DF | ACS synthetic biology | 28707884 | ACS Synth Biol | 2017 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/28707884 |
| Rapid construction of metabolite biosensors using domain-insertion profiling. | Nadler DC, Morgan SA, Flamholz A, Kortright KE, Savage DF | Nature communications | 27470466 | Nat Commun | 2016 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/27470466 |
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| Cas14: Big Advances from Small CRISPR Proteins. | Savage DF | Biochemistry | 30740978 | Biochemistry | 2019 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/30740978 |
| Imaging and three-dimensional reconstruction of chemical groups inside a protein complex using atomic force microscopy. | Kim D, Sahin O | Nature nanotechnology | 25664622 | Nat Nanotechnol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25664622 |
| Calibration of T-shaped atomic force microscope cantilevers using the thermal noise method. | Kim Y, Mandriota N, Goodnight D, Sahin O | The Review of scientific instruments | 32872926 | Rev Sci Instrum | 2020 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/32872926 |
| Cellular nanoscale stiffness patterns governed by intracellular forces. | Mandriota N, Friedsam C, Jones-Molina JA, Tatem KV, Ingber DE, Sahin O | Nature materials | 31209386 | Nat Mater | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31209386 |
| Live-Cell Bioorthogonal Chemical Imaging: Stimulated Raman Scattering Microscopy of Vibrational Probes. | Wei L, Hu F, Chen Z, Shen Y, Zhang L, Min W | Accounts of chemical research | 27486796 | Acc Chem Res | 2016 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/27486796 |
| Spectral tracing of deuterium for imaging glucose metabolism. | Zhang L, Shi L, Shen Y, Miao Y, Wei M, Qian N, Liu Y, Min W | Nature biomedical engineering | 31036888 | Nat Biomed Eng | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31036888 |
| A ratiometric Raman probe for live-cell imaging of hydrogen sulfide in mitochondria by stimulated Raman scattering. | Zeng C , Hu F , Long R , Min W | The Analyst | 30246812 | Analyst | 2018 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/30246812 |
| Supermultiplexed optical imaging and barcoding with engineered polyynes. | Hu F, Zeng C, Long R, Miao Y, Wei L, Xu Q, Min W | Nature methods | 29334378 | Nat Methods | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29334378 |
| Two-color vibrational imaging of glucose metabolism using stimulated Raman scattering. | Long R, Zhang L, Shi L, Shen Y, Hu F, Zeng C, Min W | Chemical communications (Cambridge, England) | 29218356 | Chem Commun (Camb) | 2018 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/29218356 |
| Applications of vibrational tags in biological imaging by Raman microscopy. | Zhao Z, Shen Y, Hu F, Min W | The Analyst | 28875184 | Analyst | 2017 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/28875184 |
| Multicolor live-cell chemical imaging by isotopically edited alkyne vibrational palette. | Chen Z, Paley DW, Wei L, Weisman AL, Friesner RA, Nuckolls C, Min W | Journal of the American Chemical Society | 24849912 | J Am Chem Soc | 2014 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/24849912 |
| Operando and three-dimensional visualization of anion depletion and lithium growth by stimulated Raman scattering microscopy. | Cheng Q, Wei L, Liu Z, Ni N, Sang Z, Zhu B, Xu W, Chen M, Miao Y, Chen LQ, Min W, Yang Y | Nature communications | 30061610 | Nat Commun | 2018 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/30061610 |
| Vibrational Imaging of Glucose Uptake Activity in Live Cells and Tissues by Stimulated Raman Scattering. | Hu F, Chen Z, Zhang L, Shen Y, Wei L, Min W | Angewandte Chemie (International ed. in English) | 26207979 | Angew Chem Int Ed Engl | 2015 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/26207979 |
| Vibrational imaging of newly synthesized proteins in live cells by stimulated Raman scattering microscopy. | Wei L, Yu Y, Shen Y, Wang MC, Min W | Proceedings of the National Academy of Sciences of the United States of America | 23798434 | Proc Natl Acad Sci U S A | 2013 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/23798434 |
| Super-multiplex vibrational imaging. | Wei L, Chen Z, Shi L, Long R, Anzalone AV, Zhang L, Hu F, Yuste R, Cornish VW, Min W | Nature | 28424513 | Nature | 2017 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/28424513 |
| Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering. | Wei L, Hu F, Shen Y, Chen Z, Yu Y, Lin CC, Wang MC, Min W | Nature methods | 24584195 | Nat Methods | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24584195 |
| Live-cell vibrational imaging of choline metabolites by stimulated Raman scattering coupled with isotope-based metabolic labeling. | Hu F, Wei L, Zheng C, Shen Y, Min W | The Analyst | 24555181 | Analyst | 2014 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/24555181 |
| Imaging complex protein metabolism in live organisms by stimulated Raman scattering microscopy with isotope labeling. | Wei L, Shen Y, Xu F, Hu F, Harrington JK, Targoff KL, Min W | ACS chemical biology | 25560305 | ACS Chem Biol | 2015 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/25560305 |
| Optical imaging of metabolic dynamics in animals. | Shi L, Zheng C, Shen Y, Chen Z, Silveira ES, Zhang L, Wei M, Liu C, de Sena-Tomas C, Targoff K, Min W | Nature communications | 30082908 | Nat Commun | 2018 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/30082908 |
| Live-cell quantitative imaging of proteome degradation by stimulated Raman scattering. | Shen Y, Xu F, Wei L, Hu F, Min W | Angewandte Chemie (International ed. in English) | 24737659 | Angew Chem Int Ed Engl | 2014 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/24737659 |
| Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering. | Hu F, Lamprecht MR, Wei L, Morrison B, Min W | Scientific reports | 28000773 | Sci Rep | 2016 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/28000773 |
| Stimulated Raman scattering of polymer nanoparticles for multiplexed live-cell imaging. | Hu F, Brucks SD, Lambert TH, Campos LM, Min W | Chemical communications (Cambridge, England) | 28474031 | Chem Commun (Camb) | 2017 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/28474031 |
| Metabolic activity induces membrane phase separation in endoplasmic reticulum. | Shen Y, Zhao Z, Zhang L, Shi L, Shahriar S, Chan RB, Di Paolo G, Min W | Proceedings of the National Academy of Sciences of the United States of America | 29196526 | Proc Natl Acad Sci U S A | 2017 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/29196526 |
| Electronic Preresonance Stimulated Raman Scattering Microscopy. | Wei L, Min W | The journal of physical chemistry letters | 30001137 | J Phys Chem Lett | 2018 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/30001137 |
| Bioorthogonal chemical imaging of metabolic changes during epithelial-mesenchymal transition of cancer cells by stimulated Raman scattering microscopy. | Zhang L, Min W | Journal of biomedical optics | 29043713 | J Biomed Opt | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29043713 |
| Surface charge controlled nucleoli selective staining with nanoscale carbon dots. | Zhu Z, Li Q, Li P, Xun X, Zheng L, Ning D, Su M | PloS one | 31150413 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31150413 |
| Monte Carlo and analytic simulations in nanoparticle-enhanced radiation therapy. | Paro AD, Hossain M, Webster TJ, Su M | International journal of nanomedicine | 27695329 | Int J Nanomedicine | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27695329 |
| Enhanced radiation therapy with internalized polyelectrolyte modified nanoparticles. | Zhang P, Qiao Y, Wang C, Ma L, Su M | Nanoscale | 25032891 | Nanoscale | 2014 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/25032891 |
| Reducing X-Ray Induced Oxidative Damages in Fibroblasts with Graphene Oxide. | Qiao Y, Zhang P, Wang C, Ma L, Su M | Nanomaterials (Basel, Switzerland) | 25530873 | Nanomaterials (Basel) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25530873 |
| Multiplexed detection of molecular biomarkers with phase-change nanoparticles. | Su M | Nanomedicine (London, England) | 23394155 | Nanomedicine (Lond) | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23394155 |
| Cationic surface modification of gold nanoparticles for enhanced cellular uptake and X-ray radiation therapy. | Wang C, Sun A, Qiao Y, Zhang P, Ma L, Su M | Journal of materials chemistry. B | 26512323 | J Mater Chem B | 2015 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/26512323 |
| Three-dimensional microtissues as an in vitro model for personalized radiation therapy. | Qiu Y, Ning D, Zhang P, Curly S, Qiao Y, Ma L, Su M | The Analyst | 28812074 | Analyst | 2017 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/28812074 |
| Chip-scale alignment of long DNA nanofibers on a patterned self-assembled monolayer. | Xia J, Su M | Lab on a chip | 28820213 | Lab Chip | 2017 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/28820213 |
| Whole slide imaging of circulating tumor cells captured on a capillary microchannel device. | Zheng Y, Li Q, Hu W, Liao J, Zheng G, Su M | Lab on a chip | 31621763 | Lab Chip | 2019 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/31621763 |
| Nanoparticle location and material dependent dose enhancement in X-ray radiation therapy. | Hossain M, Su M | The journal of physical chemistry. C, Nanomaterials and interfaces | 23393610 | J Phys Chem C Nanomater Interfaces | 2012 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/23393610 |
| Polydopamine Nanoparticles for Combined Chemo- and Photothermal Cancer Therapy. | Zhu Z, Su M | Nanomaterials (Basel, Switzerland) | 28661423 | Nanomaterials (Basel) | 2017 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/28661423 |
| A noncanonical polyamine from bacteria antagonizes animal mitochondrial function. | Nauta KM, Gates DR, Weiland M, Mechan-Llontop ME, Wang X, Nguyen KP, Isaguirre C, Genjdar MR, Sheldon RD, Krawczyk CM, Burton NO | bioRxiv : the preprint server for biology | 38746390 | bioRxiv | 2025 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/38746390 |
| An ultrathin membrane mediates tissue-specific morphogenesis and barrier function in a human kidney chip. | Mou X, Shah J, Roye Y, Du C, Musah S | Science advances | 38838141 | Sci Adv | 2024 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/38838141 |
| Unleashing the power of biomaterials to enhance organoid differentiation and function. | Musah S, Arzaghi H | Nature methods | 39179910 | Nat Methods | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39179910 |
| Fenestrated Endothelial Cells across Organs: Insights into Kidney Function and Disease. | Mou X, Leeman SM, Roye Y, Miller C, Musah S | International journal of molecular sciences | 39201792 | Int J Mol Sci | 2024 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/39201792 |
| Kidney Disease Modeling with Organoids and Organs-on-Chips. | Musah S, Bhattacharya R, Himmelfarb J | Annual review of biomedical engineering | 38424088 | Annu Rev Biomed Eng | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38424088 |
| Engineered human iPS cell models reveal altered podocytogenesis and glomerular capillary wall in CHD-associated SMAD2 mutations. | Bhattacharya R, Ward T, Kalejaiye TD, Mishra A, Leeman S, Arzaghi H, Seidman JG, Seidman CE, Musah S | bioRxiv : the preprint server for biology | 39211233 | bioRxiv | 2024 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/39211233 |
| Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology. | Sharma SA, Oladejo SO, Kuang Z | Cell chemical biology | 38776923 | Cell Chem Biol | 2025 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/38776923 |
| Editorial: Environmental rhythms at the host-microbe interface. | Brooks JF, Heath-Heckman E, Kuang Z | Frontiers in genetics | 37811149 | Front Genet | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37811149 |
| HDAC3 integrates TGF-β and microbial cues to program tuft cell biogenesis and diurnal rhythms in mucosal immune surveillance. | Zhang J, Wang G, Ma J, Duan Y, Sharma SA, Oladejo S, Ma X, Arellano G, Orchard RC, Reese TA, Kuang Z | Science immunology | 39331726 | Sci Immunol | 2024 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/39331726 |
| A torpor-like state (TLS) in mice slows blood epigenetic aging and prolongs healthspan. | Jayne L, Lavin-Peter A, Roessler J, Tyshkovskiy A, Antoszewski M, Ren E, Markovski A, Sun S, Yao H, Sankaran VG, Gladyshev VN, Brooke RT, Horvath S, Griffith EC, Hrvatin S | bioRxiv : the preprint server for biology | 38585858 | bioRxiv | 2024 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/38585858 |
| Multi-species genome-wide CRISPR screens identify conserved suppressors of cold-induced cell death. | Lam B, Kajderowicz KM, Keys HR, Roessler JM, Frenkel EM, Kirkland A, Bisht P, El-Brolosy MA, Jaenisch R, Bell GW, Weissman JS, Griffith EC, Hrvatin S | bioRxiv : the preprint server for biology | 39091747 | bioRxiv | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39091747 |
| A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan. | Jayne L, Lavin-Peter A, Roessler J, Tyshkovskiy A, Antoszewski M, Ren E, Markovski A, Sun S, Yao H, Sankaran VG, Gladyshev VN, Brooke RT, Horvath S, Griffith EC, Hrvatin S | Nature aging | 40055478 | Nat Aging | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40055478 |
| Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease. | Huang B, Zeng Z, Kim S, Fausto CC, Koppitch K, Li H, Li Z, Chen X, Guo J, Zhang CC, Ma T, Medina P, Schreiber ME, Xia MW, Vonk AC, Xiang T, Patel T, Li Y, Parvez RK, Der B, Chen JH, Liu Z, Thornton ME, Grubbs BH, Diao Y, Dou Y, Gnedeva K, Ying Q, Pastor-Soler NM, Fei T, Hallows KR, Lindström NO, McMahon AP, Li Z | Cell stem cell | 38692273 | Cell Stem Cell | 2024 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/38692273 |
| Building a kidney tree: Functional collecting duct from human pluripotent stem cells. | Li Z, Lindström NO | Developmental cell | 36220079 | Dev Cell | 2022 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/36220079 |
| Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids. | Huang B, Zeng Z, Li H, Li Z, Chen X, Guo J, Zhang CC, Schreiber ME, Vonk AC, Xiang T, Patel T, Li Y, Parvez RK, Der B, Chen JH, Liu Z, Thornton ME, Grubbs BH, Diao Y, Dou Y, Gnedeva K, Lindström NO, Ying Q, Pastor-Soler NM, Fei T, Hallows KR, McMahon AP, Li Z | bioRxiv : the preprint server for biology | 37293038 | bioRxiv | 2023 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/37293038 |
| 3D kidney organoids for bench-to-bedside translation. | Gupta N, Dilmen E, Morizane R | Journal of molecular medicine (Berlin, Germany) | 33034708 | J Mol Med (Berl) | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33034708 |
| Live functional assays reveal longitudinal maturation of transepithelial transport in kidney organoids. | Rizki-Safitri A, Gupta N, Hiratsuka K, Kobayashi K, Zhang C, Ida K, Satlin LM, Morizane R | Frontiers in cell and developmental biology | 36046340 | Front Cell Dev Biol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36046340 |
| Navigating the kidney organoid: insights into assessment and enhancement of nephron function. | Tabibzadeh N, Satlin LM, Jain S, Morizane R | American journal of physiology. Renal physiology | 37767571 | Am J Physiol Renal Physiol | 2023 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/37767571 |
| Organoid-on-a-chip model of human ARPKD reveals mechanosensing pathomechanisms for drug discovery. | Hiratsuka K, Miyoshi T, Kroll KT, Gupta NR, Valerius MT, Ferrante T, Yamashita M, Lewis JA, Morizane R | Science advances | 36129975 | Sci Adv | 2022 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/36129975 |
| Engineering multicellular living systems-a Keystone Symposia report. | Cable J, Arlotta P, Parker KK, Hughes AJ, Goodwin K, Mummery CL, Kamm RD, Engle SJ, Tagle DA, Boj SF, Stanton AE, Morishita Y, Kemp ML, Norfleet DA, May EE, Lu A, Bashir R, Feinberg AW, Hull SM, Gonzalez AL, Blatchley MR, Montserrat Pulido N, Morizane R, McDevitt TC, Mishra D, Mulero-Russe A | Annals of the New York Academy of Sciences | 36177947 | Ann N Y Acad Sci | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36177947 |
| Cryopreservation of human kidney organoids. | Mashouf P, Tabibzadeh N, Kuraoka S, Oishi H, Morizane R | Cellular and molecular life sciences : CMLS | 39023560 | Cell Mol Life Sci | 2024 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/39023560 |
| Advancing preclinical drug evaluation through automated 3D imaging for high-throughput screening with kidney organoids. | Oishi H, Tabibzadeh N, Morizane R | Biofabrication | 38547531 | Biofabrication | 2024 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/38547531 |
| Epigenetic transcriptional reprogramming by WT1 mediates a repair response during podocyte injury. | Ettou S, Jung YL, Miyoshi T, Jain D, Hiratsuka K, Schumacher V, Taglienti ME, Morizane R, Park PJ, Kreidberg JA | Science advances | 32754639 | Sci Adv | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32754639 |
| 3D proximal tubule-on-chip model derived from kidney organoids with improved drug uptake. | Aceves JO, Heja S, Kobayashi K, Robinson SS, Miyoshi T, Matsumoto T, Schäffers OJM, Morizane R, Lewis JA | Scientific reports | 36056134 | Sci Rep | 2022 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/36056134 |
| A parathyroid hormone/salt-inducible kinase signaling axis controls renal vitamin D activation and organismal calcium homeostasis. | Yoon SH, Meyer MB, Arevalo C, Tekguc M, Zhang C, Wang JS, Castro Andrade CD, Strauss K, Sato T, Benkusky NA, Lee SM, Berdeaux R, Foretz M, Sundberg TB, Xavier RJ, Adelmann CH, Brooks DJ, Anselmo A, Sadreyev RI, Rosales IA, Fisher DE, Gupta N, Morizane R, Greka A, Pike JW, Mannstadt M, Wein MN | The Journal of clinical investigation | 36862513 | J Clin Invest | 2023 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/36862513 |
| Generation of glucocorticoid-producing cells derived from human pluripotent stem cells. | Ruiz-Babot G, Eceiza A, Abollo-Jiménez F, Malyukov M, Carlone DL, Borges K, Da Costa AR, Qarin S, Matsumoto T, Morizane R, Skarnes WC, Ludwig B, Chapple PJ, Guasti L, Storr HL, Bornstein SR, Breault DT | Cell reports methods | 37924815 | Cell Rep Methods | 2023 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/37924815 |
| Advancements in therapeutic development: kidney organoids and organs on a chip. | Tabibzadeh N, Morizane R | Kidney international | 38296026 | Kidney Int | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38296026 |
| Modeling injury and repair in kidney organoids reveals that homologous recombination governs tubular intrinsic repair. | Gupta N, Matsumoto T, Hiratsuka K, Garcia Saiz E, Galichon P, Miyoshi T, Susa K, Tatsumoto N, Yamashita M, Morizane R | Science translational medicine | 35235339 | Sci Transl Med | 2022 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/35235339 |
| Strategies for Improving Vascularization in Kidney Organoids: A Review of Current Trends. | Konoe R, Morizane R | Biology | 37106704 | Biology (Basel) | 2023 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/37106704 |
| ATP/ADP biosensor organoids for drug nephrotoxicity assessment. | Susa K, Kobayashi K, Galichon P, Matsumoto T, Tamura A, Hiratsuka K, Gupta NR, Yazdi IK, Bonventre JV, Morizane R | Frontiers in cell and developmental biology | 36936695 | Front Cell Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36936695 |
| Kidney organoids: a pioneering model for kidney diseases. | Tekguc M, Gaal RCV, Uzel SGM, Gupta N, Riella LV, Lewis JA, Morizane R | Translational research : the journal of laboratory and clinical medicine | 35750295 | Transl Res | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35750295 |
| Kidney development to kidney organoids and back again. | Gupta N, Morizane R | Seminars in cell & developmental biology | 34627669 | Semin Cell Dev Biol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34627669 |
| The NIH Somatic Cell Genome Editing program. | Saha K, Sontheimer EJ, Brooks PJ, Dwinell MR, Gersbach CA, Liu DR, Murray SA, Tsai SQ, Wilson RC, Anderson DG, Asokan A, Banfield JF, Bankiewicz KS, Bao G, Bulte JWM, Bursac N, Campbell JM, Carlson DF, Chaikof EL, Chen ZY, Cheng RH, Clark KJ, Curiel DT, Dahlman JE, Deverman BE, Dickinson ME, Doudna JA, Ekker SC, Emborg ME, Feng G, Freedman BS, Gamm DM, Gao G, Ghiran IC, Glazer PM, Gong S, Heaney JD, Hennebold JD, Hinson JT, Khvorova A, Kiani S, Lagor WR, Lam KS, Leong KW, Levine JE, Lewis JA, Lutz CM, Ly DH, Maragh S, McCray PB Jr, McDevitt TC, Mirochnitchenko O, Morizane R, Murthy N, Prather RS, Ronald JA, Roy S, Roy S, Sabbisetti V, Saltzman WM, Santangelo PJ, Segal DJ, Shimoyama M, Skala MC, Tarantal AF, Tilton JC, Truskey GA, Vandsburger M, Watts JK, Wells KD, Wolfe SA, Xu Q, Xue W, Yi G, Zhou J, SCGE Consortium | Nature | 33828315 | Nature | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33828315 |
| Kidney organoids in translational medicine: Disease modeling and regenerative medicine. | Miyoshi T, Hiratsuka K, Saiz EG, Morizane R | Developmental dynamics : an official publication of the American Association of Anatomists | 30843293 | Dev Dyn | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30843293 |
| Bioengineered Kidney Models: Methods and Functional Assessments. | Rizki-Safitri A, Traitteur T, Morizane R | Function (Oxford, England) | 35330622 | Function (Oxf) | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/35330622 |
| Functional maturation of kidney organoid tubules: PIEZO1-mediated Ca(2+) signaling. | Carrisoza-Gaytan R, Kroll KT, Hiratsuka K, Gupta NR, Morizane R, Lewis JA, Satlin LM | American journal of physiology. Cell physiology | 36745528 | Am J Physiol Cell Physiol | 2023 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/36745528 |
| Immune-infiltrated kidney organoid-on-chip model for assessing T cell bispecific antibodies. | Kroll KT, Mata MM, Homan KA, Micallef V, Carpy A, Hiratsuka K, Morizane R, Moisan A, Gubler M, Walz AC, Marrer-Berger E, Lewis JA | Proceedings of the National Academy of Sciences of the United States of America | 37603766 | Proc Natl Acad Sci U S A | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37603766 |
| Brain Defense of Glycemia in Health and Diabetes. | Mirzadeh Z, Faber C | Diabetes.. | 39401393 | Diabetes | 2024 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/39401393 |
| Central Nervous System Control of Glucose Homeostasis: A Therapeutic Target for Type 2 Diabetes? | Mirzadeh Z, Faber CL, Schwartz MW | Annual review of pharmacology and toxicology | 34990204 | Annu Rev Pharmacol Toxicol | 2022 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/34990204 |
| Leptin receptor neurons in the dorsomedial hypothalamus regulate diurnal patterns of feeding, locomotion, and metabolism. | Faber CL, Deem JD, Phan BA, Doan TP, Ogimoto K, Mirzadeh Z, Schwartz MW, Morton GJ | eLife | 33527893 | Elife | 2021 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/33527893 |
| COVID-19 Gastrointestinal Symptoms and Attenuation of the Immune Response to SARS-CoV-2. | Miller J, Yan KS | Gastroenterology | 33753106 | Gastroenterology | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33753106 |
| Presentation of the Julius M. Friedenwald Medal to Timothy C. Wang, MD, AGAF. | Abrams J, Camilleri M, Merchant J, Rustgi AK, Yan K | Gastroenterology | 35443933 | Gastroenterology | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35443933 |
| Modeling Oral-Esophageal Squamous Cell Carcinoma in 3D Organoids. | Flashner S, Martin C, Matsuura N, Shimonosono M, Tomita Y, Morimoto M, Okolo O, Yu VX, Parikh AS, Klein-Szanto AJP, Yan K, Gabre JT, Lu C, Momen-Heravi F, Rustgi AK, Nakagawa H | Journal of visualized experiments : JoVE | 36622034 | J Vis Exp | 2022 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/36622034 |
| Time-resolved fate mapping identifies the intestinal upper crypt zone as an origin of Lgr5+ crypt base columnar cells. | Capdevila C, Miller J, Cheng L, Kornberg A, George JJ, Lee H, Botella T, Moon CS, Murray JW, Lam S, Calderon RI, Malagola E, Whelan G, Lin CS, Han A, Wang TC, Sims PA, Yan KS | Cell | 38848677 | Cell | 2024 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/38848677 |
| Cellular origins and lineage relationships of the intestinal epithelium. | Capdevila C, Trifas M, Miller J, Anderson T, Sims PA, Yan KS | American journal of physiology. Gastrointestinal and liver physiology | 34431400 | Am J Physiol Gastrointest Liver Physiol | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34431400 |
| R-SPONDIN2(+) mesenchymal cells form the bud tip progenitor niche during human lung development. | Hein RFC, Wu JH, Holloway EM, Frum T, Conchola AS, Tsai YH, Wu A, Fine AS, Miller AJ, Szenker-Ravi E, Yan KS, Kuo CJ, Glass I, Reversade B, Spence JR | Developmental cell | 35679862 | Dev Cell | 2022 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/35679862 |
| Single-Cell Studies of Intestinal Stem Cell Heterogeneity During Homeostasis and Regeneration. | Norkin M, Capdevila C, Calderon RI, Su T, Trifas M, Ordóñez-Morán P, Yan KS | Methods in molecular biology (Clifton, N.J.) | 32705640 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32705640 |
| Microbial-Dependent Recruitment of Immature Myeloid Cells Promotes Intestinal Regeneration. | Jiang Z, Waterbury QT, Malagola E, Fu N, Kim W, Ochiai Y, Wu F, Guha C, Shawber CJ, Yan KS, Wang TC | Cellular and molecular gastroenterology and hepatology | 37898454 | Cell Mol Gastroenterol Hepatol | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/37898454 |
| Gluten induces rapid reprogramming of natural memory αβ and γδ intraepithelial T cells to induce cytotoxicity in celiac disease. | Kornberg A, Botella T, Moon CS, Rao S, Gelbs J, Cheng L, Miller J, Bacarella AM, García-Vilas JA, Vargas J, Yu X, Krupska I, Bush E, Garcia-Carrasquillo R, Lebwohl B, Krishnareddy S, Lewis S, Green PHR, Bhagat G, Yan KS, Han A | Science immunology | 37450575 | Sci Immunol | 2023 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/37450575 |
| Single-Cell Transcriptional Profiling of the Intestinal Epithelium. | Capdevila C, Calderon RI, Bush EC, Sheldon-Collins K, Sims PA, Yan KS | Methods in molecular biology (Clifton, N.J.) | 32705639 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32705639 |
| 3D Organoids: An Untapped Platform for Studying Host-Microbiome Interactions in Esophageal Cancers. | Flashner S, Yan KS, Nakagawa H | Microorganisms | 34835308 | Microorganisms | 2021 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/34835308 |
| Isthmus progenitor cells contribute to homeostatic cellular turnover and support regeneration following intestinal injury. | Malagola E, Vasciaveo A, Ochiai Y, Kim W, Zheng B, Zanella L, Wang ALE, Middelhoff M, Nienhüser H, Deng L, Wu F, Waterbury QT, Belin B, LaBella J, Zamechek LB, Wong MH, Li L, Guha C, Cheng CW, Yan KS, Califano A, Wang TC | Cell | 38848678 | Cell | 2024 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/38848678 |
| Epidermal-Derived Hedgehog Signaling Drives Mesenchymal Proliferation during Digit Tip Regeneration. | Maan ZN, Rinkevich Y, Barrera J, Chen K, Henn D, Foster D, Bonham CA, Padmanabhan J, Sivaraj D, Duscher D, Hu M, Yan K, Januszyk M, Longaker MT, Weissman IL, Gurtner GC | Journal of clinical medicine | 34575372 | J Clin Med | 2021 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/34575372 |
| Multiplexed single-cell analysis reveals prognostic and nonprognostic T cell types in human colorectal cancer. | Masuda K, Kornberg A, Miller J, Lin S, Suek N, Botella T, Secener KA, Bacarella AM, Cheng L, Ingham M, Rosario V, Al-Mazrou AM, Lee-Kong SA, Kiran RP, Stoeckius M, Smibert P, Del Portillo A, Oberstein PE, Sims PA, Yan KS, Han A | JCI insight | 35192548 | JCI Insight | 2022 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/35192548 |
| Xiphoid nucleus of the midline thalamus controls cold-induced food seeking. | Lal NK, Le P, Aggarwal S, Zhang A, Wang K, Qi T, Pang Z, Yang D, Nudell V, Yeo GW, Banks AS, Ye L | Nature | 37587337 | Nature | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37587337 |
| In situ identification of cellular drug targets in mammalian tissue. | Pang Z, Schafroth MA, Ogasawara D, Wang Y, Nudell V, Lal NK, Yang D, Wang K, Herbst DM, Ha J, Guijas C, Blankman JL, Cravatt BF, Ye L | Cell | 35483372 | Cell | 2022 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/35483372 |
| The Afferent Function of Adipose Innervation. | Wang Y, Ye L | Diabetes.. | 38377447 | Diabetes | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38377447 |
| Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope. | Lovelace JW, Ma J, Yadav S, Chhabria K, Shen H, Pang Z, Qi T, Sehgal R, Zhang Y, Bali T, Vaissiere T, Tan S, Liu Y, Rumbaugh G, Ye L, Kleinfeld D, Stringer C, Augustine V | Nature | 37914931 | Nature | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37914931 |
| HYBRiD: hydrogel-reinforced DISCO for clearing mammalian bodies. | Nudell V, Wang Y, Pang Z, Lal NK, Huang M, Shaabani N, Kanim W, Teijaro J, Maximov A, Ye L | Nature methods | 35347322 | Nat Methods | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/35347322 |
| Cortical Representations of Conspecific Sex Shape Social Behavior. | Kingsbury L, Huang S, Raam T, Ye LS, Wei D, Hu RK, Ye L, Hong W | Neuron | 32663438 | Neuron | 2020 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/32663438 |
| Xiphoid nucleus of the midline thalamus controls cold-induced food seeking. | Lal NK, Le P, Aggarwal S, Zhang A, Wang K, Qi T, Pang Z, Yang D, Nudell V, Yeo GW, Banks AS, Ye L | bioRxiv : the preprint server for biology | 36993706 | bioRxiv | 2023 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/36993706 |
| A protocol to visualize on-target specific drug binding in mammalian tissue with cellular resolution using tissue clearing and click chemistry. | Pang Z, Ye L | STAR protocols | 36313539 | STAR Protoc | 2022 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/36313539 |
| Illuminating spatial pharmacology with in situ drug imaging. | Pang Z, Ye L | Clinical and translational medicine | 36030504 | Clin Transl Med | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/36030504 |
| Somatosensory innervation of adipose tissues. | Wang Y, Ye L | Physiology & behavior | 36965573 | Physiol Behav | 2023 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/36965573 |
| Phosphorylation of pyruvate dehydrogenase inversely associates with neuronal activity. | Yang D, Wang Y, Qi T, Zhang X, Shen L, Ma J, Pang Z, Lal NK, McClatchy DB, Seradj SH, Leung VH, Wang K, Xie Y, Polli FS, Maximov A, Gonzalez OC, de Lecea L, Cline HT, Augustine V, Yates JR 3rd, Ye L | Neuron | 38266644 | Neuron | 2024 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/38266644 |
| Brainstem Dbh(+) neurons control allergen-induced airway hyperreactivity. | Su Y, Xu J, Zhu Z, Chin J, Xu L, Yu H, Nudell V, Dash B, Moya EA, Ye L, Nimmerjahn A, Sun X | Nature | 38987587 | Nature | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38987587 |
| TESOS: an integrated approach for uniform mesoscale imaging. | Wang Y, Ye L | Cell research | 38168641 | Cell Res | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38168641 |
| The role of somatosensory innervation of adipose tissues. | Wang Y, Leung VH, Zhang Y, Nudell VS, Loud M, Servin-Vences MR, Yang D, Wang K, Moya-Garzon MD, Li VL, Long JZ, Patapoutian A, Ye L | Nature | 36045288 | Nature | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36045288 |
| A key role of PIEZO2 mechanosensitive ion channel in adipose sensory innervation. | Wang Y, Zhang Y, Leung V, Seradj SH, Sonmez U, Servin-Vences R, Lipomi D, Ye L, Patapoutian A | bioRxiv : the preprint server for biology | 39605632 | bioRxiv | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39605632 |
| Acetylcholine-synthesizing macrophages in subcutaneous fat are regulated by β(2) -adrenergic signaling. | Knights AJ, Liu S, Ma Y, Nudell VS, Perkey E, Sorensen MJ, Kennedy RT, Maillard I, Ye L, Jun H, Wu J | The EMBO journal | 34459015 | EMBO J | 2021 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/34459015 |
| Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection. | Dobrindt K, Hoagland DA, Seah C, Kassim B, O'Shea CP, Iskhakova M, Fernando MB, Deans PJM, Powell SK, Javidfar B, Murphy A, Peter C, Møeller R, Garcia MF, Kimura M, Iwasawa K, Crary J, Kotton DN, Takebe T, Huckins LM, tenOever BR, Akbarian S, Brennand KJ | bioRxiv : the preprint server for biology | 32995783 | bioRxiv | 2020 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/32995783 |
| Narrative engineering of the liver. | Lee IS, Takebe T | Current opinion in genetics & development | 35700688 | Curr Opin Genet Dev | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35700688 |
| Synthetic augmentation of bilirubin metabolism in human pluripotent stem cell-derived liver organoids. | Reza HA, Farooqui Z, Reza AA, Conroy C, Iwasawa K, Ogura Y, Okita K, Osafune K, Takebe T | Stem cell reports | 37832542 | Stem Cell Reports | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/37832542 |
| Intercellular mRNA transfer alters the human pluripotent stem cell state. | Yoneyama Y, Zhang RR, Maezawa M, Masaki H, Kimura M, Cai Y, Adam M, Parameswaran S, Mizuno N, Bhadury J, Maezawa S, Ochiai H, Nakauchi H, Potter SS, Weirauch MT, Takebe T | Proceedings of the National Academy of Sciences of the United States of America | 39841146 | Proc Natl Acad Sci U S A | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39841146 |
| In toto biological framework: Modeling interconnectedness during human development. | Yoneyama Y, Wu Y, Mori K, Takebe T | Developmental cell | 39765224 | Dev Cell | 2025 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/39765224 |
| Organogenesis in vitro. | Iwasawa K, Takebe T | Current opinion in cell biology | 34352726 | Curr Opin Cell Biol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34352726 |
| Building consensus on definition and nomenclature of hepatic, pancreatic, and biliary organoids. | Marsee A, Roos FJM, Verstegen MMA, HPB Organoid Consortium, Gehart H, de Koning E, Lemaigre F, Forbes SJ, Peng WC, Huch M, Takebe T, Vallier L, Clevers H, van der Laan LJW, Spee B | Cell stem cell | 33961769 | Cell Stem Cell | 2021 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/33961769 |
| Engineering human hepato-biliary-pancreatic organoids from pluripotent stem cells. | Koike H, Iwasawa K, Ouchi R, Maezawa M, Kimura M, Kodaka A, Nishii S, Thompson WL, Takebe T | Nature protocols | 33432231 | Nat Protoc | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33432231 |
| Deciphering Endothelial and Mesenchymal Organ Specification in Vascularized Lung and Intestinal Organoids. | Miao Y, Tan C, Pek NM, Yu Z, Iwasawa K, Kechele DO, Sundaram N, Pastrana-Gomez V, Kishimoto K, Yang MC, Jiang C, Tchieu J, Whitsett JA, McCracken KW, Rottier RJ, Kotton DN, Helmrath MA, Wells JM, Takebe T, Zorn AM, Chen YW, Guo M, Gu M | bioRxiv : the preprint server for biology | 38370768 | bioRxiv | 2024 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/38370768 |
| Cellotype-phenotype associations using 'organoid villages'. | Kimura M, Takebe T | Trends in endocrinology and metabolism: TEM | 38575442 | Trends Endocrinol Metab | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38575442 |
| Three-dimensional matrix stiffness modulates mechanosensitive and phenotypic alterations in oral squamous cell carcinoma spheroids. | Sheth M, Sharma M, Lehn M, Reza H, Takebe T, Takiar V, Wise-Draper T, Esfandiari L | APL bioengineering | 39092008 | APL Bioeng | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39092008 |
| Inter-cellular mRNA Transfer Alters Human Pluripotent Stem Cell State. | Yoneyama Y, Zhang RR, Kimura M, Cai Y, Adam M, Parameswaran S, Masaki H, Mizuno N, Bhadury J, Maezawa S, Ochiai H, Nakauchi H, Potter SS, Weirauch MT, Takebe T | bioRxiv : the preprint server for biology | 38979277 | bioRxiv | 2024 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/38979277 |
| Self-Organization of Sinusoidal Vessels in Pluripotent Stem Cell-derived Human Liver Bud Organoids. | Saiki N, Nio Y, Yoneyama Y, Kawamura S, Iwasawa K, Kawakami E, Araki K, Fukumura J, Sakairi T, Kono T, Ohmura R, Koido M, Funata M, Thompson WL, Cruz-Encarnacion P, Chen YW, Takebe T | bioRxiv : the preprint server for biology | 39005378 | bioRxiv | 2024 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/39005378 |
| Eicosatetraynoic Acid Regulates Profibrotic Pathways in an Induced Pluripotent Stem Cell-Derived Macrophage-Human Intestinal Organoid Model of Crohn's Disease. | Jurickova I, Dreskin BW, Angerman E, Bonkowski E, Nguyen J, Villarreal R, Tominaga K, Iwasawa K, Braun T, Takebe T, Helmrath MA, Haberman Y, Wells JM, Denson LA | Journal of Crohn's & colitis | 39212594 | J Crohns Colitis | 2025 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/39212594 |
| Common Genetic Variation in Humans Impacts In Vitro Susceptibility to SARS-CoV-2 Infection. | Dobrindt K, Hoagland DA, Seah C, Kassim B, O'Shea CP, Murphy A, Iskhakova M, Fernando MB, Powell SK, Deans PJM, Javidfar B, Peter C, Møller R, Uhl SA, Garcia MF, Kimura M, Iwasawa K, Crary JF, Kotton DN, Takebe T, Huckins LM, tenOever BR, Akbarian S, Brennand KJ | Stem cell reports | 33636110 | Stem Cell Reports | 2021 Mar 9 | https://www.ncbi.nlm.nih.gov/pubmed/33636110 |
| Polygenic architecture informs potential vulnerability to drug-induced liver injury. | Koido M, Kawakami E, Fukumura J, Noguchi Y, Ohori M, Nio Y, Nicoletti P, Aithal GP, Daly AK, Watkins PB, Anayama H, Dragan Y, Shinozawa T, Takebe T | Nature medicine | 32895570 | Nat Med | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32895570 |
| Human liver model systems in a dish. | Thompson WL, Takebe T | Development, growth & differentiation | 33423319 | Dev Growth Differ | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33423319 |
| Fetal liver hematopoiesis: from development to delivery. | Lewis K, Yoshimoto M, Takebe T | Stem cell research & therapy | 33597015 | Stem Cell Res Ther | 2021 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/33597015 |
| Generation of multi-cellular human liver organoids from pluripotent stem cells. | Thompson WL, Takebe T | Methods in cell biology | 32586449 | Methods Cell Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32586449 |
| Organoid transplant approaches for the liver. | Reza HA, Okabe R, Takebe T | Transplant international : official journal of the European Society for Organ Transplantation | 34614263 | Transpl Int | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34614263 |
| Synthesis and application of POLYseq for profiling human liver organoids. | Dunn AW, Cai Y, Iwasawa K, Kimura M, Takebe T | STAR protocols | 34934958 | STAR Protoc | 2021 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/34934958 |
| Complement factor D targeting protects endotheliopathy in organoid and monkey models of COVID-19. | Kawakami E, Saiki N, Yoneyama Y, Moriya C, Maezawa M, Kawamura S, Kinebuchi A, Kono T, Funata M, Sakoda A, Kondo S, Ebihara T, Matsumoto H, Togami Y, Ogura H, Sugihara F, Okuzaki D, Kojima T, Deguchi S, Vallee S, McQuade S, Islam R, Natarajan M, Ishigaki H, Nakayama M, Nguyen CT, Kitagawa Y, Wu Y, Mori K, Hishiki T, Takasaki T, Itoh Y, Takayama K, Nio Y, Takebe T | Cell stem cell | 37802037 | Cell Stem Cell | 2023 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/37802037 |
| POLYseq: A poly(β-amino ester)-based vector for multifunctional cellular barcoding. | Dunn A, Cai Y, Iwasawa K, Kimura M, Takebe T | Stem cell reports | 34450040 | Stem Cell Reports | 2021 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/34450040 |
| En masse organoid phenotyping informs metabolic-associated genetic susceptibility to NASH. | Kimura M, Iguchi T, Iwasawa K, Dunn A, Thompson WL, Yoneyama Y, Chaturvedi P, Zorn AM, Wintzinger M, Quattrocelli M, Watanabe-Chailland M, Zhu G, Fujimoto M, Kumbaji M, Kodaka A, Gindin Y, Chung C, Myers RP, Subramanian GM, Hwa V, Takebe T | Cell | 36240780 | Cell | 2022 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/36240780 |
| Directed differentiation of human pluripotent stem cells into diverse organ-specific mesenchyme of the digestive and respiratory systems. | Kishimoto K, Iwasawa K, Sorel A, Ferran-Heredia C, Han L, Morimoto M, Wells JM, Takebe T, Zorn AM | Nature protocols | 35978039 | Nat Protoc | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/35978039 |
| In vitro human cell-based models: What can they do and what are their limitations? | Lutolf MP, Radisic M, Beekman J, Huh DD, Huch M, Turco MY, Tahmasebi Birgani ZN, Gao D, Yao R, Lin H, Takebe T | Cell | 39178827 | Cell | 2024 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/39178827 |
| ACMSD inhibition corrects fibrosis, inflammation, and DNA damage in MASLD/MASH. | Liu YJ, Kimura M, Li X, Sulc J, Wang Q, Rodríguez-López S, Scantlebery AML, Strotjohann K, Gallart-Ayala H, Vijayakumar A, Myers RP, Ivanisevic J, Houtkooper RH, Subramanian GM, Takebe T, Auwerx J | Journal of hepatology | 39181211 | J Hepatol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39181211 |
| Self-Assembled Generation of Multi-zonal Liver Organoids from Human Pluripotent Stem Cells. | Al Reza H, Santangelo C, Al Reza A, Iwasawa K, Sachiko S, Glaser K, Bondoc A, Merola J, Takebe T | bioRxiv : the preprint server for biology | 39257824 | bioRxiv | 2024 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/39257824 |
| Fetal Liver-like Organoids Recapitulate Blood-Liver Niche Development and Multipotent Hematopoiesis from Human Pluripotent Stem Cells. | Rezvani M, Lewis K, Quach S, Iwasawa K, Weihs J, Reza H, Cai Y, Kimura M, Zhang R, Milton Y, Chaturvedi P, Thorner K, Nayak RC, Munera JO, Kramer P, Davis B, Balamurugan A, Ait Ahmed Y, Finke M, Behncke RY, Guillot A, Haegerling R, Polansky J, Bufler P, Cancelas J, Wells J, Yoshimoto M, Takebe T | bioRxiv : the preprint server for biology | 39416072 | bioRxiv | 2024 Oct 12 | https://www.ncbi.nlm.nih.gov/pubmed/39416072 |
| The promise of human organoids in the digestive system. | Funata M, Nio Y, Erion DM, Thompson WL, Takebe T | Cell death and differentiation | 33204011 | Cell Death Differ | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33204011 |
| High-Fidelity Drug-Induced Liver Injury Screen Using Human Pluripotent Stem Cell-Derived Organoids. | Shinozawa T, Kimura M, Cai Y, Saiki N, Yoneyama Y, Ouchi R, Koike H, Maezawa M, Zhang RR, Dunn A, Ferguson A, Togo S, Lewis K, Thompson WL, Asai A, Takebe T | Gastroenterology | 33039464 | Gastroenterology | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33039464 |
| Organoid-guided precision hepatology for metabolic liver disease. | Osonoi S, Takebe T | Journal of hepatology | 38237864 | J Hepatol | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38237864 |
| A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis. | Kang SY, Kimura M, Shrestha S, Lewis P, Lee S, Cai Y, Joshi P, Acharya P, Liu J, Yang Y, Sanchez JG, Ayyagari S, Alsberg E, Wells JM, Takebe T, Lee MY | Advanced healthcare materials | 37616035 | Adv Healthc Mater | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37616035 |
| Within-host evolution of a gut pathobiont facilitates liver translocation. | Yang Y, Nguyen M, Khetrapal V, Sonnert ND, Martin AL, Chen H, Kriegel MA, Palm NW | Nature | 35831502 | Nature | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35831502 |
| Autoreactivity in naïve human fetal B cells is associated with commensal bacteria recognition. | Chen JW, Rice TA, Bannock JM, Bielecka AA, Strauss JD, Catanzaro JR, Wang H, Menard LC, Anolik JH, Palm NW, Meffre E | Science (New York, N.Y.) | 32675374 | Science | 2020 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/32675374 |
| Highly multiplexed bioactivity screening reveals human and microbiota metabolome-GPCRome interactions. | Chen H, Rosen CE, González-Hernández JA, Song D, Potempa J, Ring AM, Palm NW | Cell | 37321219 | Cell | 2023 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/37321219 |
| Small Molecule Metabolites at the Host-Microbiota Interface. | Bishai JD, Palm NW | Journal of immunology (Baltimore, Md. : 1950) | 34544815 | J Immunol | 2021 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/34544815 |
| Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. | Cao Y, Oh J, Xue M, Huh WJ, Wang J, Gonzalez-Hernandez JA, Rice TA, Martin AL, Song D, Crawford JM, Herzon SB, Palm NW | Science (New York, N.Y.) | 36302024 | Science | 2022 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/36302024 |
| Gut instincts in neuroimmunity from the eighteenth to twenty-first centuries. | Nguyen M, Palm NW | Seminars in immunopathology | 35786740 | Semin Immunopathol | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35786740 |
| Interspecies commensal interactions have nonlinear impacts on host immunity. | Rice TA, Bielecka AA, Nguyen MT, Rosen CE, Song D, Sonnert ND, Yang Y, Cao Y, Khetrapal V, Catanzaro JR, Martin AL, Rashed SA, Leopold SR, Hao L, Yu X, van Dijk D, Ring AM, Flavell RA, de Zoete MR, Palm NW | Cell host & microbe | 35640610 | Cell Host Microbe | 2022 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/35640610 |
| Kidney Disease-Associated APOL1 Variants Have Dose-Dependent, Dominant Toxic Gain-of-Function. | Datta S, Kataria R, Zhang JY, Moore S, Petitpas K, Mohamed A, Zahler N, Pollak MR, Olabisi OA | Journal of the American Society of Nephrology : JASN | 32675303 | J Am Soc Nephrol | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32675303 |
| Collapsing Glomerulopathy in Identical Twins With Lupus and High-Risk Apolipoprotein L1 (APOL1) Genotype. | DeOliveira M, Feeney C, Leahy C, Nystrom S, Howell DN, Farouk SS, Wu M, Olabisi OA, Sparks MA | Kidney international reports | 34514214 | Kidney Int Rep | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34514214 |
| JAK inhibitor blocks COVID-19 cytokine-induced JAK/STAT/APOL1 signaling in glomerular cells and podocytopathy in human kidney organoids. | Nystrom SE, Li G, Datta S, Soldano KL, Silas D, Weins A, Hall G, Thomas DB, Olabisi OA | JCI insight | 35472001 | JCI Insight | 2022 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/35472001 |
| APOL1-associated kidney disease in northern Nigerians with treated HIV infection. | Olabisi OA, Freedman BI | Kidney international | 34154709 | Kidney Int | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34154709 |
| APOL1 Variant and Kidney Disease-Reply. | Hopper T, Olabisi OA | JAMA | 39186317 | JAMA | 2024 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/39186317 |
| Diagnosis, Education, and Care of Patients with APOL1-Associated Nephropathy: A Delphi Consensus and Systematic Review. | Freedman BI, Burke W, Divers J, Eberhard L, Gadegbeku CA, Gbadegesin R, Hall ME, Jones-Smith T, Knight R, Kopp JB, Kovesdy CP, Norris KC, Olabisi OA, Roberts GV, Sedor JR, Blacksher E | Journal of the American Society of Nephrology : JASN | 33853887 | J Am Soc Nephrol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33853887 |
| APOL1-Mediated Kidney Disease. | Hopper T, Olabisi OA | JAMA | 38662391 | JAMA | 2024 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/38662391 |
| APOL1 High-Risk Genotype is Not Associated With New or Worsening of Proteinuria or Kidney Function Decline Following COVID-19 Vaccination. | Nystrom SE, Soldano KL, Rockett M, Datta S, Li G, Silas D, Garrett ME, Ashley-Koch AE, Olabisi OA | Kidney international reports | 39291186 | Kidney Int Rep | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39291186 |
| APOL1-mediated monovalent cation transport contributes to APOL1-mediated podocytopathy in kidney disease. | Datta S, Antonio BM, Zahler NH, Theile JW, Krafte D, Zhang H, Rosenberg PB, Chaves AB, Muoio DM, Zhang G, Silas D, Li G, Soldano K, Nystrom S, Ferreira D, Miller SE, Bain JR, Muehlbauer MJ, Ilkayeva O, Becker TC, Hohmeier HE, Newgard CB, Olabisi OA | The Journal of clinical investigation | 38227370 | J Clin Invest | 2024 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/38227370 |
| APOL1 channel blocker reduces proteinuria in FSGS. | Olabisi OA | Kidney international | 37224918 | Kidney Int | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37224918 |
| Prevalence and Impact of APOL1 Kidney Risk Variants in West Africa : Insights for Global Kidney Disease Assessment and Treatment. | Martinelli E, Westland R, Olabisi OA, Sanna-Cherchi S | Journal of the American Society of Nephrology : JASN | 39602366 | J Am Soc Nephrol | 2025 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/39602366 |
| The effect of size, charge, and peptide ligand length on kidney targeting by small, organic nanoparticles. | Huang Y, Jiang K, Zhang X, Chung EJ | Bioengineering & translational medicine | 33005739 | Bioeng Transl Med | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/33005739 |
| Targeting and therapeutic peptide-based strategies for polycystic kidney disease. | Wang J, Tripathy N, Chung EJ | Advanced drug delivery reviews | 32866560 | Adv Drug Deliv Rev | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32866560 |
| Overcoming physiological barriers by nanoparticles for intravenous drug delivery to the lymph nodes. | Trac N, Chung EJ | Experimental biology and medicine (Maywood, N.J.) | 33957802 | Exp Biol Med (Maywood) | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33957802 |
| Clinical progress of nanomedicine-based RNA therapies. | Lim SA, Cox A, Tung M, Chung EJ | Bioactive materials | 35310381 | Bioact Mater | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35310381 |
| Immunization using ApoB-100 peptide-linked nanoparticles reduces atherosclerosis. | Chyu KY, Zhao X, Zhou J, Dimayuga PC, Lio NW, Cercek B, Trac NT, Chung EJ, Shah PK | JCI insight | 35536648 | JCI Insight | 2022 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/35536648 |
| CCR2-targeted micelles for anti-cancer peptide delivery and immune stimulation. | Trac N, Chen LY, Zhang A, Liao CP, Poon C, Wang J, Ando Y, Joo J, Garri C, Shen K, Kani K, Gross ME, Chung EJ | Journal of controlled release : official journal of the Controlled Release Society | 33011241 | J Control Release | 2021 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/33011241 |
| Long-term, in vivo therapeutic effects of a single dose of miR-145 micelles for atherosclerosis. | Chin DD, Patel N, Lee W, Kanaya S, Cook J, Chung EJ | Bioactive materials | 37122900 | Bioact Mater | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37122900 |
| Oral delivery of nanomedicine for genetic kidney disease. | Huang Y, Wang J, Mancino V, Pham J, O'Grady C, Li H, Jiang K, Chin D, Poon C, Ho PY, Gyarmati G, Peti-Peterdi J, Hallows KR, Chung EJ | PNAS nexus | 38807632 | PNAS Nexus | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38807632 |
| Therapeutic potential of urinary extracellular vesicles in delivering functional proteins and modulating gene expression for genetic kidney disease. | Huang Y, Osouli A, Li H, Dudaney M, Pham J, Mancino V, Khan T, Chaudhuri B, Pastor-Soler NM, Hallows KR, Chung EJ | Biomaterials | 40158444 | Biomaterials | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40158444 |
| Oral delivery of metformin by chitosan nanoparticles for polycystic kidney disease. | Wang J, Chin D, Poon C, Mancino V, Pham J, Li H, Ho PY, Hallows KR, Chung EJ | Journal of controlled release : official journal of the Controlled Release Society | 33127449 | J Control Release | 2021 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/33127449 |
| Transdermal Delivery of Kidney-Targeting Nanoparticles Using Dissolvable Microneedles. | Tripathy N, Wang J, Tung M, Conway C, Chung EJ | Cellular and molecular bioengineering | 33184578 | Cell Mol Bioeng | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/33184578 |
| Hydroxyapatite-binding micelles for the detection of vascular calcification in atherosclerosis. | Chin DD, Wang J, Mel de Fontenay M, Plotkin A, Magee GA, Chung EJ | Journal of materials chemistry. B | 31553027 | J Mater Chem B | 2019 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/31553027 |
| Collagenase-Cleavable Peptide Amphiphile Micelles as a Novel Theranostic Strategy in Atherosclerosis. | Chin DD, Poon C, Trac N, Wang J, Cook J, Joo J, Jiang Z, Maria NSS, Jacobs RE, Chung EJ | Advanced therapeutics | 34295964 | Adv Ther (Weinh) | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34295964 |
| Strategies to deliver RNA by nanoparticles for therapeutic potential. | Cox A, Lim SA, Chung EJ | Molecular aspects of medicine | 34366123 | Mol Aspects Med | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34366123 |
| Spotlight on Genetic Kidney Diseases: A Call for Drug Delivery and Nanomedicine Solutions. | Trac N, Ashraf A, Giblin J, Prakash S, Mitragotri S, Chung EJ | ACS nano | 36988207 | ACS Nano | 2023 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/36988207 |
| CD70-Targeted Micelles Enhance HIF2α siRNA Delivery and Inhibit Oncogenic Functions in Patient-Derived Clear Cell Renal Carcinoma Cells. | Trac N, Oh HS, Jones LI, Caliliw R, Ohtake S, Shuch B, Chung EJ | Molecules (Basel, Switzerland) | 36500549 | Molecules | 2022 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/36500549 |
| Therapeutic Response of miR-145 Micelles on Patient-Derived Vascular Smooth Muscle Cells. | Patel N, Chin DD, Magee GA, Chung EJ | Frontiers in digital health | 35783597 | Front Digit Health | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35783597 |
| Improving kidney targeting: The influence of nanoparticle physicochemical properties on kidney interactions. | Huang Y, Wang J, Jiang K, Chung EJ | Journal of controlled release : official journal of the Controlled Release Society | 33892054 | J Control Release | 2021 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/33892054 |
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| Exosomes in Atherosclerosis, a Double-Edged Sword: Their Role in Disease Pathogenesis and Their Potential as Novel Therapeutics. | Patel N, Chin DD, Chung EJ | The AAPS journal.. | 34312734 | AAPS J | 2021 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/34312734 |
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