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 | Science advances | 40802757 | Sci Adv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40802757 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| In situ combinatorial synthesis of degradable branched lipidoids for systemic delivery of mRNA therapeutics and gene editors. | Han X, Xu J, Xu Y, Alameh MG, Xue L, Gong N, El-Mayta R, Palanki R, Warzecha CC, Zhao G, Vaughan AE, Wilson JM, Weissman D, Mitchell MJ | Nature communications | 38409275 | Nat Commun | 2024 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/38409275 |
| An immunosuppressive vascular niche drives macrophage polarization and immunotherapy resistance in glioblastoma. | Yang F, Akhtar MN, Zhang D, El-Mayta R, Shin J, Dorsey JF, Zhang L, Xu X, Guo W, Bagley SJ, Fuchs SY, Koumenis C, Lathia JD, Mitchell MJ, Gong Y, Fan Y | Science advances | 38416830 | Sci Adv | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38416830 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Peptide-Functionalized Lipid Nanoparticles for Targeted Systemic mRNA Delivery to the Brain. | Han EL, Tang S, Kim D, Murray AM, Swingle KL, Hamilton AG, Mrksich K, Padilla MS, Palanki R, Li JJ, Mitchell MJ | Nano letters | 39688915 | Nano Lett | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39688915 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Peptide-functionalized nanoparticles for brain-targeted therapeutics. | Tang S, Han EL, Mitchell MJ | Drug delivery and translational research | 40164912 | Drug Deliv Transl Res | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/40164912 |
| 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 |
| 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 |
| 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 |
| Elucidating lipid nanoparticle properties and structure through biophysical analyses. | 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 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/39763759 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| mRNA Lipid Nanoparticles for Ex Vivo Engineering of Immunosuppressive T Cells for Autoimmunity Therapies. | Thatte AS, Hamilton AG, Nachod BE, Mukalel AJ, Billingsley MM, Palanki R, Swingle KL, Mitchell MJ | Nano letters | 37906000 | Nano Lett | 2023 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/37906000 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Circular RNA lipid nanoparticle vaccine against SARS-CoV-2. | Swingle KL, Hamilton AG, Han X, Liao KC, Safford HC, Thatte AS, Geisler HC, Xu J, Saw TY, Wan Y, Mitchell MJ | Proceedings of the National Academy of Sciences of the United States of America | 40953267 | Proc Natl Acad Sci U S A | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/40953267 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanoparticle-Based Tolerogenic Vaccines: Next-Generation Strategies for Autoimmune and Allergic Disease Therapies. | Nachod BE, Thatte AS, Palanki R, Mitchell MJ | Angewandte Chemie (International ed. in English) | 41451511 | Angew Chem Int Ed Engl | 2026 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/41451511 |
| Prodrug-tethered lipid nanoparticles for synergistic messenger RNA cancer immunotherapy. | Shi Q, Gong N, Wang J, Palanki R, Zheng Q, Alameh MG, Dwivedi G, Davis B, Melamed J, Luo Z, Xu J, Figueroa-Espada CG, Xue L, Zeng Y, Han X, Kim D, Chen Q, Yamagata H, Geisler HC, El-Mayta R, Yoon IC, Weissman D, Mitchell MJ | Nature nanotechnology | 41851499 | Nat Nanotechnol | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41851499 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Imaging the lymphatic system. | Munn LL, Padera TP | Microvascular research | 24956510 | Microvasc Res | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24956510 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bioengineering kidneys for transplantation. | Madariaga ML, Ott HC | Seminars in nephrology | 25217267 | Semin Nephrol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25217267 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| Bacteria-surface interactions. | Tuson HH, Weibel DB | Soft matter | 23930134 | Soft Matter | 2013 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/23930134 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| (*) 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| CLARITY and PACT-based imaging of adult zebrafish and mouse for whole-animal analysis of infections. | Cronan MR, Rosenberg AF, Oehlers SH, Saelens JW, Sisk DM, Jurcic Smith KL, Lee S, Tobin DM | Disease models & mechanisms | 26449262 | Dis Model Mech | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26449262 |
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| Drug-Inducible, Cell-Specific Manipulation of Intracellular Calcium in Zebrafish Through Mammalian TRPV1 Expression. | Matty MA, Beerman RW, Tobin DM | Zebrafish | 27058231 | Zebrafish | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27058231 |
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| The Macrophage-Specific Promoter mfap4 Allows Live, Long-Term Analysis of Macrophage Behavior during Mycobacterial Infection in Zebrafish. | Walton EM, Cronan MR, Beerman RW, Tobin DM | PloS one | 26445458 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26445458 |
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| Direct In Vivo Manipulation and Imaging of Calcium Transients in Neutrophils Identify a Critical Role for Leading-Edge Calcium Flux. | Beerman RW, Matty MA, Au GG, Looger LL, Choudhury KR, Keller PJ, Tobin DM | Cell reports | 26673320 | Cell Rep | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26673320 |
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| Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. | Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, Shi W, Yang ZY, Doria-Rose NA, McKee K, O'Dell S, Schmidt SD, Chuang GY, Druz A, Soto C, Yang Y, Zhang B, Zhou T, Todd JP, Lloyd KE, Eudailey J, Roberts KE, Donald BR, Bailer RT, Ledgerwood J, NISC Comparative Sequencing Program, Mullikin JC, Shapiro L, Koup RA, Graham BS, Nason MC, Connors M, Haynes BF, Rao SS, Roederer M, Kwong PD, Mascola JR, Nabel GJ | Journal of virology | 25142607 | J Virol | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25142607 |
| Genome Engineering of Stem Cells for Autonomously Regulated, Closed-Loop Delivery of Biologic Drugs. | Brunger JM, Zutshi A, Willard VP, Gersbach CA, Guilak F | Stem cell reports | 28457885 | Stem Cell Reports | 2017 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/28457885 |
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| Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells. | Black JB, Adler AF, Wang HG, D'Ippolito AM, Hutchinson HA, Reddy TE, Pitt GS, Leong KW, Gersbach CA | Cell stem cell | 27524438 | Cell Stem Cell | 2016 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/27524438 |
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| Knockdown of the cell cycle inhibitor p21 enhances cartilage formation by induced pluripotent stem cells. | Diekman BO, Thakore PI, O'Connor SK, Willard VP, Brunger JM, Christoforou N, Leong KW, Gersbach CA, Guilak F | Tissue engineering. Part A | 25517798 | Tissue Eng Part A | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25517798 |
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| Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. | Kabadi AM, Gersbach CA | Methods (San Diego, Calif.) | 25010559 | Methods | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25010559 |
| Tissue-engineered cartilage with inducible and tunable immunomodulatory properties. | Glass KA, Link JM, Brunger JM, Moutos FT, Gersbach CA, Guilak F | Biomaterials | 24767790 | Biomaterials | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24767790 |
| Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector. | Kabadi AM, Ousterout DG, Hilton IB, Gersbach CA | Nucleic acids research | 25122746 | Nucleic Acids Res | 2014 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/25122746 |
| Light-inducible gene regulation with engineered zinc finger proteins. | Polstein LR, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 24718797 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24718797 |
| Reading frame correction by targeted genome editing restores dystrophin expression in cells from Duchenne muscular dystrophy patients. | Ousterout DG, Perez-Pinera P, Thakore PI, Kabadi AM, Brown MT, Qin X, Fedrigo O, Mouly V, Tremblay JP, Gersbach CA | Molecular therapy : the journal of the American Society of Gene Therapy | 23732986 | Mol Ther | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23732986 |
| Master Regulators and Cofactors of Human Neuronal Cell Fate Specification Identified by CRISPR Gene Activation Screens. | Black JB, McCutcheon SR, Dube S, Barrera A, Klann TS, Rice GA, Adkar SS, Soderling SH, Reddy TE, Gersbach CA | Cell reports | 33264623 | Cell Rep | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33264623 |
| Synergistic and tunable human gene activation by combinations of synthetic transcription factors. | Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA, Guilak F, Crawford GE, Hartemink AJ, Gersbach CA | Nature methods | 23377379 | Nat Methods | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23377379 |
| Highly active zinc-finger nucleases by extended modular assembly. | Bhakta MS, Henry IM, Ousterout DG, Das KT, Lockwood SH, Meckler JF, Wallen MC, Zykovich A, Yu Y, Leo H, Xu L, Gersbach CA, Segal DJ | Genome research | 23222846 | Genome Res | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23222846 |
| A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. | Polstein LR, Gersbach CA | Nature chemical biology | 25664691 | Nat Chem Biol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25664691 |
| An Engineered Optogenetic Switch for Spatiotemporal Control of Gene Expression, Cell Differentiation, and Tissue Morphogenesis. | Polstein LR, Juhas M, Hanna G, Bursac N, Gersbach CA | ACS synthetic biology | 28793186 | ACS Synth Biol | 2017 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/28793186 |
| CRISPR/Cas9 Editing of Murine Induced Pluripotent Stem Cells for Engineering Inflammation-Resistant Tissues. | Brunger JM, Zutshi A, Willard VP, Gersbach CA, Guilak F | Arthritis & rheumatology (Hoboken, N.J.) | 27813286 | Arthritis Rheumatol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/27813286 |
| Gene therapies that restore dystrophin expression for the treatment of Duchenne muscular dystrophy. | Robinson-Hamm JN, Gersbach CA | Human genetics | 27542949 | Hum Genet | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27542949 |
| Loss-of-function genetic tools for animal models: cross-species and cross-platform differences. | Housden BE, Muhar M, Gemberling M, Gersbach CA, Stainier DY, Seydoux G, Mohr SE, Zuber J, Perrimon N | Nature reviews. Genetics | 27795562 | Nat Rev Genet | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27795562 |
| RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors. | Thakore PI, Kwon JB, Nelson CE, Rouse DC, Gemberling MP, Oliver ML, Gersbach CA | Nature communications | 29700298 | Nat Commun | 2018 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/29700298 |
| Single-molecule analysis of myocyte differentiation reveals bimodal lineage commitment. | Gibson TM, Gersbach CA | Integrative biology : quantitative biosciences from nano to macro | 25953198 | Integr Biol (Camb) | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25953198 |
| Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage. | Brunger JM, Huynh NP, Guenther CM, Perez-Pinera P, Moutos FT, Sanchez-Adams J, Gersbach CA, Guilak F | Proceedings of the National Academy of Sciences of the United States of America | 24550481 | Proc Natl Acad Sci U S A | 2014 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/24550481 |
| Setting objective thresholds for rare event detection in flow cytometry. | Richards AJ, Staats J, Enzor J, McKinnon K, Frelinger J, Denny TN, Weinhold KJ, Chan C | Journal of immunological methods | 24727143 | J Immunol Methods | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24727143 |
| Genome engineering: the next genomic revolution. | Gersbach CA | Nature methods | 25264777 | Nat Methods | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25264777 |
| Enabling functional genomics with genome engineering. | Hilton IB, Gersbach CA | Genome research | 26430154 | Genome Res | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26430154 |
| The Development of TALE Nucleases for Biotechnology. | Ousterout DG, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 26443211 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26443211 |
| Design, Assembly, and Characterization of TALE-Based Transcriptional Activators and Repressors. | Thakore PI, Gersbach CA | Methods in molecular biology (Clifton, N.J.) | 26443215 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26443215 |
| Genome editing: the end of the beginning. | Doudna JA, Gersbach CA | Genome biology | 26700220 | Genome Biol | 2015 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/26700220 |
| Long-term evaluation of AAV-CRISPR genome editing for Duchenne muscular dystrophy. | Nelson CE, Wu Y, Gemberling MP, Oliver ML, Waller MA, Bohning JD, Robinson-Hamm JN, Bulaklak K, Castellanos Rivera RM, Collier JH, Asokan A, Gersbach CA | Nature medicine | 30778238 | Nat Med | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30778238 |
| Increasing the specificity of CRISPR systems with engineered RNA secondary structures. | Kocak DD, Josephs EA, Bhandarkar V, Adkar SS, Kwon JB, Gersbach CA | Nature biotechnology | 30988504 | Nat Biotechnol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30988504 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Insights into kidney stem cell development and regeneration using zebrafish. | Drummond BE, Wingert RA | World journal of stem cells | 26981168 | World J Stem Cells | 2016 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/26981168 |
| Renal progenitors: Roles in kidney disease and regeneration. | Chambers BE, Wingert RA | World journal of stem cells | 27928463 | World J Stem Cells | 2016 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/27928463 |
| 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 |
| Nephron proximal tubule patterning and corpuscles of Stannius formation are regulated by the sim1a transcription factor and retinoic acid in zebrafish. | Cheng CN, Wingert RA | Developmental biology | 25542995 | Dev Biol | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/25542995 |
| Temporal and spatial expression of tight junction genes during zebrafish pronephros development. | McKee R, Gerlach GF, Jou J, Cheng CN, Wingert RA | Gene expression patterns : GEP | 25460834 | Gene Expr Patterns | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25460834 |
| Flat mount preparation for observation and analysis of zebrafish embryo specimens stained by whole mount in situ hybridization. | Cheng CN, Li Y, Marra AN, Verdun V, Wingert RA | Journal of visualized experiments : JoVE | 25078510 | J Vis Exp | 2014 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/25078510 |
| Atlas of Cellular Dynamics during Zebrafish Adult Kidney Regeneration. | McCampbell KK, Springer KN, Wingert RA | Stem cells international | 26089919 | Stem Cells Int | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26089919 |
| Zebrafish Renal Pathology: Emerging Models of Acute Kidney Injury. | McKee RA, Wingert RA | Current pathobiology reports | 25973344 | Curr Pathobiol Rep | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25973344 |
| Roles of Iroquois Transcription Factors in Kidney Development. | Marra AN, Wingert RA | Cell & developmental biology | 24855634 | Cell Dev Biol | 2014 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/24855634 |
| Renal stem cells: fact or science fiction? | McCampbell KK, Wingert RA | The Biochemical journal | 22574774 | Biochem J | 2012 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/22574774 |
| Repopulating Decellularized Kidney Scaffolds: An Avenue for Ex Vivo Organ Generation. | McKee RA, Wingert RA | Materials (Basel, Switzerland) | 27375844 | Materials (Basel) | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27375844 |
| Renal stem cell reprogramming: Prospects in regenerative medicine. | Morales EE, Wingert RA | World journal of stem cells | 25258667 | World J Stem Cells | 2014 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/25258667 |
| Kidney organogenesis in the zebrafish: insights into vertebrate nephrogenesis and regeneration. | Gerlach GF, Wingert RA | Wiley interdisciplinary reviews. Developmental biology | 24014448 | Wiley Interdiscip Rev Dev Biol | 2013 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/24014448 |
| Congenital and Acute Kidney Disease: Translational Research Insights from Zebrafish Chemical Genetics. | Poureetezadi SJ, Wingert RA | General medicine (Los Angeles, Calif.) | 24653992 | Gen Med (Los Angel) | 2013 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24653992 |
| Analysis of nephron composition and function in the adult zebrafish kidney. | McCampbell KK, Springer KN, Wingert RA | Journal of visualized experiments : JoVE | 25145398 | J Vis Exp | 2014 Aug 9 | https://www.ncbi.nlm.nih.gov/pubmed/25145398 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Interactions between B lymphocytes and the osteoblast lineage in bone marrow. | Panaroni C, Wu JY | Calcified tissue international | 23839529 | Calcif Tissue Int | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23839529 |
| Mesenchymal progenitors and the osteoblast lineage in bone marrow hematopoietic niches. | Panaroni C, Tzeng YS, Saeed H, Wu JY | Current osteoporosis reports | 24477415 | Curr Osteoporos Rep | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24477415 |
| Induction of Osteoblasts by Direct Reprogramming of Mouse Fibroblasts. | Zhu H, Wu JY | Methods in molecular biology (Clifton, N.J.) | 32474879 | Methods Mol Biol | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32474879 |
| Myelopoiesis is regulated by osteocytes through Gsα-dependent signaling. | Fulzele K, Krause DS, Panaroni C, Saini V, Barry KJ, Liu X, Lotinun S, Baron R, Bonewald L, Feng JQ, Chen M, Weinstein LS, Wu JY, Kronenberg HM, Scadden DT, Divieti Pajevic P | Blood | 23160461 | Blood | 2013 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/23160461 |
| Pluripotent Stem Cells and Skeletal Regeneration--Promise and Potential. | Wu JY | Current osteoporosis reports | 26260198 | Curr Osteoporos Rep | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26260198 |
| Older Men With Anemia Have Increased Fracture Risk Independent of Bone Mineral Density. | Valderrábano RJ, Lee J, Lui LY, Hoffman AR, Cummings SR, Orwoll ES, Wu JY, Osteoporotic Fractures in Men (MrOS) Study Research Group | The Journal of clinical endocrinology and metabolism | 28368469 | J Clin Endocrinol Metab | 2017 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/28368469 |
| Pluripotent stem cells as a source of osteoblasts for bone tissue regeneration. | Zhu H, Kimura T, Swami S, Wu JY | Biomaterials | 29456164 | Biomaterials | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29456164 |
| Mesenchymal lineage cells and their importance in B lymphocyte niches. | Green AC, Rudolph-Stringer V, Chantry AD, Wu JY, Purton LE | Bone | 29183783 | Bone | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29183783 |
| Prevention of breast cancer skeletal metastases with parathyroid hormone. | Swami S, Johnson J, Bettinson LA, Kimura T, Zhu H, Albertelli MA, Johnson RW, Wu JY | JCI insight | 28878134 | JCI Insight | 2017 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/28878134 |
| 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 |
| Bone Density Loss Is Associated With Blood Cell Counts. | Valderrábano RJ, Lui LY, Lee J, Cummings SR, Orwoll ES, Hoffman AR, Wu JY, Osteoporotic Fractures in Men (MrOS) Study Research Group | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 27653240 | J Bone Miner Res | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27653240 |
| Bone and blood interactions in human health and disease. | Valderrábano RJ, Wu JY | Bone | 29476979 | Bone | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29476979 |
| 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 |
| Differential regulation of myeloid leukemias by the bone marrow microenvironment. | Krause DS, Fulzele K, Catic A, Sun CC, Dombkowski D, Hurley MP, Lezeau S, Attar E, Wu JY, Lin HY, Divieti-Pajevic P, Hasserjian RP, Schipani E, Van Etten RA, Scadden DT | Nature medicine | 24162813 | Nat Med | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24162813 |
| 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 |
| 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 |
| 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 |
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| Structure, bioactivity, and resistance mechanism of streptomonomicin, an unusual lasso Peptide from an understudied halophilic actinomycete. | Metelev M, Tietz JI, Melby JO, Blair PM, Zhu L, Livnat I, Severinov K, Mitchell DA | Chemistry & biology | 25601074 | Chem Biol | 2015 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/25601074 |
| Head-to-Head Prenyl Synthases in Pathogenic Bacteria. | Schwalen CJ, Feng X, Liu W, O-Dowd B, Ko TP, Shin CJ, Guo RT, Mitchell DA, Oldfield E | Chembiochem : a European journal of chemical biology | 28340291 | Chembiochem | 2017 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/28340291 |
| Selectivity, directionality, and promiscuity in peptide processing from a Bacillus sp. Al Hakam cyclodehydratase. | Melby JO, Dunbar KL, Trinh NQ, Mitchell DA | Journal of the American Chemical Society | 22401305 | J Am Chem Soc | 2012 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/22401305 |
| Crystal structure and absolute configuration of (3S,4aS,8aS)-N-tert-butyl-2-[(S)-3-(2-chloro-4-nitro-benzamido)-2-hy-droxy-prop-yl]deca-hydro-isoquinoline-3-carboxamide and (3S,4aS,8aS)-N-tert-butyl-2-{(S)-2-[(S)-1-(2-chloro-4-nitro-benzoyl)pyrrolidin-2-yl]-2-hy-droxy-eth-yl}deca-hydro-iso-quinoline-3-carboxamide. | Maxson T, Bertke JA, Gray DL, Mitchell DA | Acta crystallographica. Section E, Crystallographic communications | 26594520 | Acta Crystallogr E Crystallogr Commun | 2015 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/26594520 |
| In Vitro Biosynthesis of the Core Scaffold of the Thiopeptide Thiomuracin. | Hudson GA, Zhang Z, Tietz JI, Mitchell DA, van der Donk WA | Journal of the American Chemical Society | 26675417 | J Am Chem Soc | 2015 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/26675417 |
| A new genome-mining tool redefines the lasso peptide biosynthetic landscape. | Tietz JI, Schwalen CJ, Patel PS, Maxson T, Blair PM, Tai HC, Zakai UI, Mitchell DA | Nature chemical biology | 28244986 | Nat Chem Biol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28244986 |
| Targeted Treatment for Bacterial Infections: Prospects for Pathogen-Specific Antibiotics Coupled with Rapid Diagnostics. | Maxson T, Mitchell DA | Tetrahedron | 27429480 | Tetrahedron | 2016 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/27429480 |
| In Vitro Biosynthesis and Substrate Tolerance of the Plantazolicin Family of Natural Products. | Deane CD, Burkhart BJ, Saint-Vincent PMB, Tietz JI, Lin A, Mitchell DA | ACS chemical biology | 27248686 | ACS Chem Biol | 2016 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/27248686 |
| Structural and functional insight into an unexpectedly selective N-methyltransferase involved in plantazolicin biosynthesis. | Lee J, Hao Y, Blair PM, Melby JO, Agarwal V, Burkhart BJ, Nair SK, Mitchell DA | Proceedings of the National Academy of Sciences of the United States of America | 23878226 | Proc Natl Acad Sci U S A | 2013 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/23878226 |
| Synthesis of plantazolicin analogues enables dissection of ligand binding interactions of a highly selective methyltransferase. | Sharma A, Saint-Vincent PMB, Mitchell DA | Organic letters | 24063702 | Org Lett | 2013 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/24063702 |
| YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations. | Dunbar KL, Melby JO, Mitchell DA | Nature chemical biology | 22522320 | Nat Chem Biol | 2012 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/22522320 |
| Biological characterization of the hygrobafilomycin antibiotic JBIR-100 and bioinformatic insights into the hygrolide family of natural products. | Molloy EM, Tietz JI, Blair PM, Mitchell DA | Bioorganic & medicinal chemistry | 27234886 | Bioorg Med Chem | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27234886 |
| Nucleophilic 1,4-additions for natural product discovery. | Cox CL, Tietz JI, Sokolowski K, Melby JO, Doroghazi JR, Mitchell DA | ACS chemical biology | 24937678 | ACS Chem Biol | 2014 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/24937678 |
| Multitarget drug discovery for tuberculosis and other infectious diseases. | Li K, Schurig-Briccio LA, Feng X, Upadhyay A, Pujari V, Lechartier B, Fontes FL, Yang H, Rao G, Zhu W, Gulati A, No JH, Cintra G, Bogue S, Liu YL, Molohon K, Orlean P, Mitchell DA, Freitas-Junior L, Ren F, Sun H, Jiang T, Li Y, Guo RT, Cole ST, Gennis RB, Crick DC, Oldfield E | Journal of medicinal chemistry | 24568559 | J Med Chem | 2014 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/24568559 |
| Undecaprenyl diphosphate synthase inhibitors: antibacterial drug leads. | Sinko W, Wang Y, Zhu W, Zhang Y, Feixas F, Cox CL, Mitchell DA, Oldfield E, McCammon JA | Journal of medicinal chemistry | 24827744 | J Med Chem | 2014 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/24827744 |
| Identification of the minimal cytolytic unit for streptolysin S and an expansion of the toxin family. | Molloy EM, Casjens SR, Cox CL, Maxson T, Ethridge NA, Margos G, Fingerle V, Mitchell DA | BMC microbiology | 26204951 | BMC Microbiol | 2015 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/26204951 |
| Lessons learned from the transformation of natural product discovery to a genome-driven endeavor. | Deane CD, Mitchell DA | Journal of industrial microbiology & biotechnology | 24142337 | J Ind Microbiol Biotechnol | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24142337 |
| Engineering unnatural variants of plantazolicin through codon reprogramming. | Deane CD, Melby JO, Molohon KJ, Susarrey AR, Mitchell DA | ACS chemical biology | 23823732 | ACS Chem Biol | 2013 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/23823732 |
| Thiazole/oxazole-modified microcins: complex natural products from ribosomal templates. | Melby JO, Nard NJ, Mitchell DA | Current opinion in chemical biology | 21429787 | Curr Opin Chem Biol | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21429787 |
| HIV-1 Integrase Inhibitor-Inspired Antibacterials Targeting Isoprenoid Biosynthesis. | Zhang Y, Fu-Yang Lin, Li K, Zhu W, Liu YL, Cao R, Pang R, Lee E, Axelson J, Hensler M, Wang K, Molohon KJ, Wang Y, Mitchell DA, Nizet V, Oldfield E | ACS medicinal chemistry letters | 22662288 | ACS Med Chem Lett | 2012 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/22662288 |
| Insights into methyltransferase specificity and bioactivity of derivatives of the antibiotic plantazolicin. | Hao Y, Saint-Vincent PMB, Sharma A, Mitchell DA, Nair SK | ACS chemical biology | 25635336 | ACS Chem Biol | 2015 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/25635336 |
| Targeting Reactive Carbonyls for Identifying Natural Products and Their Biosynthetic Origins. | Maxson T, Tietz JI, Hudson GA, Guo XR, Tai HC, Mitchell DA | Journal of the American Chemical Society | 27797509 | J Am Chem Soc | 2016 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/27797509 |
| The genomic landscape of ribosomal peptides containing thiazole and oxazole heterocycles. | Cox CL, Doroghazi JR, Mitchell DA | BMC genomics | 26462797 | BMC Genomics | 2015 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/26462797 |
| YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. | Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA | Chemical reviews | 28256131 | Chem Rev | 2017 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/28256131 |
| Targeting the cell wall of Mycobacterium tuberculosis: structure and mechanism of L,D-transpeptidase 2. | Erdemli SB, Gupta R, Bishai WR, Lamichhane G, Amzel LM, Bianchet MA | Structure (London, England : 1993) | 23103390 | Structure | 2012 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/23103390 |
| An evolved oxazolidinone with selective potency against Mycobacterium tuberculosis and gram positive bacteria. | Kaushik A, Heuer AM, Bell DT, Culhane JC, Ebner DC, Parrish N, Ippoliti JT, Lamichhane G | Bioorganic & medicinal chemistry letters | 27329794 | Bioorg Med Chem Lett | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27329794 |
| Mutation in an Unannotated Protein Confers Carbapenem Resistance in Mycobacterium tuberculosis. | Kumar P, Kaushik A, Bell DT, Chauhan V, Xia F, Stevens RL, Lamichhane G | Antimicrobial agents and chemotherapy | 28069655 | Antimicrob Agents Chemother | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/28069655 |
| Structural and functional features of enzymes of Mycobacterium tuberculosis peptidoglycan biosynthesis as targets for drug development. | Moraes GL, Gomes GC, Monteiro de Sousa PR, Alves CN, Govender T, Kruger HG, Maguire GE, Lamichhane G, Lameira J | Tuberculosis (Edinburgh, Scotland) | 25701501 | Tuberculosis (Edinb) | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25701501 |
| Ldt(Mav2), a nonclassical transpeptidase and susceptibility of Mycobacterium avium to carbapenems. | Mattoo R, Lloyd EP, Kaushik A, Kumar P, Brunelle JL, Townsend CA, Lamichhane G | Future microbiology | 28555497 | Future Microbiol | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28555497 |
| In vitro and in vivo activity of biapenem against drug-susceptible and rifampicin-resistant Mycobacterium tuberculosis. | Kaushik A, Ammerman NC, Tasneen R, Story-Roller E, Dooley KE, Dorman SE, Nuermberger EL, Lamichhane G | The Journal of antimicrobial chemotherapy | 28575382 | J Antimicrob Chemother | 2017 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/28575382 |
| Carbapenems against Mycobacterium tuberculosis: a review of the evidence. | Jaganath D, Lamichhane G, Shah M | The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease | 27776583 | Int J Tuberc Lung Dis | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27776583 |
| Carbapenems and Rifampin Exhibit Synergy against Mycobacterium tuberculosis and Mycobacterium abscessus. | Kaushik A, Makkar N, Pandey P, Parrish N, Singh U, Lamichhane G | Antimicrobial agents and chemotherapy | 26259792 | Antimicrob Agents Chemother | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26259792 |
| Loss of a Functionally and Structurally Distinct ld-Transpeptidase, LdtMt5, Compromises Cell Wall Integrity in Mycobacterium tuberculosis. | Brammer Basta LA, Ghosh A, Pan Y, Jakoncic J, Lloyd EP, Townsend CA, Lamichhane G, Bianchet MA | The Journal of biological chemistry | 26304120 | J Biol Chem | 2015 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/26304120 |
| Intrabacterial Metabolism Obscures the Successful Prediction of an InhA Inhibitor of Mycobacterium tuberculosis. | Wang X, Perryman AL, Li SG, Paget SD, Stratton TP, Lemenze A, Olson AJ, Ekins S, Kumar P, Freundlich JS | ACS infectious diseases | 31625383 | ACS Infect Dis | 2019 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/31625383 |
| A screen for non-coding RNA in Mycobacterium tuberculosis reveals a cAMP-responsive RNA that is expressed during infection. | Pelly S, Bishai WR, Lamichhane G | Gene | 22446041 | Gene | 2012 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/22446041 |
| REMap: Operon map of M. tuberculosis based on RNA sequence data. | Pelly S, Winglee K, Xia FF, Stevens RL, Bishai WR, Lamichhane G | Tuberculosis (Edinburgh, Scotland) | 27450008 | Tuberculosis (Edinb) | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27450008 |
| Role of the Cys154Arg Substitution in Ribosomal Protein L3 in Oxazolidinone Resistance in Mycobacterium tuberculosis. | Makafe GG, Cao Y, Tan Y, Julius M, Liu Z, Wang C, Njire MM, Cai X, Liu T, Wang B, Pang W, Tan S, Zhang B, Yew WW, Lamichhane G, Guo J, Zhang T | Antimicrobial agents and chemotherapy | 26953211 | Antimicrob Agents Chemother | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26953211 |
| Pyrazinoic Acid Inhibits a Bifunctional Enzyme in Mycobacterium tuberculosis. | Njire M, Wang N, Wang B, Tan Y, Cai X, Liu Y, Mugweru J, Guo J, Hameed HMA, Tan S, Liu J, Yew WW, Nuermberger E, Lamichhane G, Liu J, Zhang T | Antimicrobial agents and chemotherapy | 28438933 | Antimicrob Agents Chemother | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28438933 |
| Non-classical transpeptidases yield insight into new antibacterials. | Kumar P, Kaushik A, Lloyd EP, Li SG, Mattoo R, Ammerman NC, Bell DT, Perryman AL, Zandi TA, Ekins S, Ginell SL, Townsend CA, Freundlich JS, Lamichhane G | Nature chemical biology | 27820797 | Nat Chem Biol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27820797 |
| A virtual screen discovers novel, fragment-sized inhibitors of Mycobacterium tuberculosis InhA. | Perryman AL, Yu W, Wang X, Ekins S, Forli S, Li SG, Freundlich JS, Tonge PJ, Olson AJ | Journal of chemical information and modeling | 25636146 | J Chem Inf Model | 2015 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/25636146 |
| Structural insight into the inactivation of Mycobacterium tuberculosis non-classical transpeptidase Ldt(Mt2) by biapenem and tebipenem. | Bianchet MA, Pan YH, Basta LAB, Saavedra H, Lloyd EP, Kumar P, Mattoo R, Townsend CA, Lamichhane G | BMC biochemistry | 28545389 | BMC Biochem | 2017 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/28545389 |
| Mycobacterium abscessus l,d-Transpeptidases Are Susceptible to Inactivation by Carbapenems and Cephalosporins but Not Penicillins. | Kumar P, Chauhan V, Silva JRA, Lameira J, d'Andrea FB, Li SG, Ginell SL, Freundlich JS, Alves CN, Bailey S, Cohen KA, Lamichhane G | Antimicrobial agents and chemotherapy | 28760902 | Antimicrob Agents Chemother | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28760902 |
| Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2. | Silva JR, Bishai WR, Govender T, Lamichhane G, Maguire GE, Kruger HG, Lameira J, Alves CN | Journal of biomolecular structure & dynamics | 25762064 | J Biomol Struct Dyn | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/25762064 |
| Nonclassical transpeptidases of Mycobacterium tuberculosis alter cell size, morphology, the cytosolic matrix, protein localization, virulence, and resistance to β-lactams. | Schoonmaker MK, Bishai WR, Lamichhane G | Journal of bacteriology | 24464457 | J Bacteriol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24464457 |
| Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk. | Tehranchi AK, Myrthil M, Martin T, Hie BL, Golan D, Fraser HB | Cell | 27087447 | Cell | 2016 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/27087447 |
| Adenovirus E4ORF1-induced MYC activation promotes host cell anabolic glucose metabolism and virus replication. | Thai M, Graham NA, Braas D, Nehil M, Komisopoulou E, Kurdistani SK, McCormick F, Graeber TG, Christofk HR | Cell metabolism | 24703700 | Cell Metab | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24703700 |
| Doxycycline alters metabolism and proliferation of human cell lines. | Ahler E, Sullivan WJ, Cass A, Braas D, York AG, Bensinger SJ, Graeber TG, Christofk HR | PloS one | 23741339 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23741339 |
| Asparagine promotes cancer cell proliferation through use as an amino acid exchange factor. | Krall AS, Xu S, Graeber TG, Braas D, Christofk HR | Nature communications | 27126896 | Nat Commun | 2016 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/27126896 |
| Metabolomics strategy reveals subpopulation of liposarcomas sensitive to gemcitabine treatment. | Braas D, Ahler E, Tam B, Nathanson D, Riedinger M, Benz MR, Smith KB, Eilber FC, Witte ON, Tap WD, Wu H, Christofk HR | Cancer discovery | 23230188 | Cancer Discov | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23230188 |
| MYC-induced reprogramming of glutamine catabolism supports optimal virus replication. | Thai M, Thaker SK, Feng J, Du Y, Hu H, Ting Wu T, Graeber TG, Braas D, Christofk HR | Nature communications | 26561297 | Nat Commun | 2015 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/26561297 |
| MCT1 Modulates Cancer Cell Pyruvate Export and Growth of Tumors that Co-express MCT1 and MCT4. | Hong CS, Graham NA, Gu W, Espindola Camacho C, Mah V, Maresh EL, Alavi M, Bagryanova L, Krotee PAL, Gardner BK, Behbahan IS, Horvath S, Chia D, Mellinghoff IK, Hurvitz SA, Dubinett SM, Critchlow SE, Kurdistani SK, Goodglick L, Braas D, Graeber TG, Christofk HR | Cell reports | 26876179 | Cell Rep | 2016 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/26876179 |
| Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota. | Bucci V, Bradde S, Biroli G, Xavier JB | PLoS computational biology | 22577356 | PLoS Comput Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22577356 |
| The ecological basis of morphogenesis: branching patterns in swarming colonies of bacteria. | Deng P, de Vargas Roditi L, van Ditmarsch D, Xavier JB | New journal of physics | 24587694 | New J Phys | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24587694 |
| Convergent evolution of hyperswarming leads to impaired biofilm formation in pathogenic bacteria. | van Ditmarsch D, Boyle KE, Sakhtah H, Oyler JE, Nadell CD, Déziel É, Dietrich LE, Xavier JB | Cell reports | 23954787 | Cell Rep | 2013 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/23954787 |
| Sociomicrobiology and Pathogenic Bacteria. | Xavier JB | Microbiology spectrum | 27337482 | Microbiol Spectr | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27337482 |
| Tumour-stromal interactions generate emergent persistence in collective cancer cell migration. | Chang WK, Carmona-Fontaine C, Xavier JB | Interface focus | 24511381 | Interface Focus | 2013 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/24511381 |
| Turning ecology and evolution against cancer. | Korolev KS, Xavier JB, Gore J | Nature reviews. Cancer | 24739582 | Nat Rev Cancer | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24739582 |
| Towards predictive models of the human gut microbiome. | Bucci V, Xavier JB | Journal of molecular biology | 24727124 | J Mol Biol | 2014 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/24727124 |
| Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. | Taur Y, Xavier JB, Lipuma L, Ubeda C, Goldberg J, Gobourne A, Lee YJ, Dubin KA, Socci ND, Viale A, Perales MA, Jenq RR, van den Brink MR, Pamer EG | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 22718773 | Clin Infect Dis | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22718773 |
| Multilevel selection analysis of a microbial social trait. | de Vargas Roditi L, Boyle KE, Xavier JB | Molecular systems biology | 23959025 | Mol Syst Biol | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/23959025 |
| Facultative control of matrix production optimizes competitive fitness in Pseudomonas aeruginosa PA14 biofilm models. | Madsen JS, Lin YC, Squyres GR, Price-Whelan A, de Santiago Torio A, Song A, Cornell WC, Sørensen SJ, Xavier JB, Dietrich LE | Applied and environmental microbiology | 26431965 | Appl Environ Microbiol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26431965 |
| Human symbionts inject and neutralize antibacterial toxins to persist in the gut. | Wexler AG, Bao Y, Whitney JC, Bobay LM, Xavier JB, Schofield WB, Barry NA, Russell AB, Tran BQ, Goo YA, Goodlett DR, Ochman H, Mougous JD, Goodman AL | Proceedings of the National Academy of Sciences of the United States of America | 26957597 | Proc Natl Acad Sci U S A | 2016 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/26957597 |
| Metabolism and the Evolution of Social Behavior. | Boyle KE, Monaco HT, Deforet M, Yan J, Wang Z, Rhee K, Xavier JB | Molecular biology and evolution | 28595344 | Mol Biol Evol | 2017 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/28595344 |
| Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile. | Buffie CG, Bucci V, Stein RR, McKenney PT, Ling L, Gobourne A, No D, Liu H, Kinnebrew M, Viale A, Littmann E, van den Brink MR, Jenq RR, Taur Y, Sander C, Cross JR, Toussaint NC, Xavier JB, Pamer EG | Nature | 25337874 | Nature | 2015 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/25337874 |
| Hyperswarming adaptations in a bacterium improve collective motility without enhancing single cell motility. | Deforet M, van Ditmarsch D, Carmona-Fontaine C, Xavier JB | Soft matter | 24622509 | Soft Matter | 2014 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/24622509 |
| Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait. | Boyle KE, Monaco H, van Ditmarsch D, Deforet M, Xavier JB | PLoS computational biology | 26102206 | PLoS Comput Biol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/26102206 |
| Emergence of spatial structure in the tumor microenvironment due to the Warburg effect. | Carmona-Fontaine C, Bucci V, Akkari L, Deforet M, Joyce JA, Xavier JB | Proceedings of the National Academy of Sciences of the United States of America | 24218566 | Proc Natl Acad Sci U S A | 2013 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/24218566 |
| Cutting through the complexity of cell collectives. | Nadell CD, Bucci V, Drescher K, Levin SA, Bassler BL, Xavier JB | Proceedings. Biological sciences | 23363630 | Proc Biol Sci | 2013 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/23363630 |
| Exploiting social evolution in biofilms. | Boyle KE, Heilmann S, van Ditmarsch D, Xavier JB | Current opinion in microbiology | 23357558 | Curr Opin Microbiol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23357558 |
| Cell-Size Homeostasis and the Incremental Rule in a Bacterial Pathogen. | Deforet M, van Ditmarsch D, Xavier JB | Biophysical journal | 26244734 | Biophys J | 2015 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/26244734 |
| Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota. | Stein RR, Bucci V, Toussaint NC, Buffie CG, Rätsch G, Pamer EG, Sander C, Xavier JB | PLoS computational biology | 24348232 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24348232 |
| Digital and analog gene circuits for biotechnology. | Roquet N, Lu TK | Biotechnology journal | 24677719 | Biotechnol J | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24677719 |
| 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 |
| 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 |
| Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing. | Ando H, Lemire S, Pires DP, Lu TK | Cell systems | 26973885 | Cell Syst | 2015 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/26973885 |
| Genetically Engineered Phages: a Review of Advances over the Last Decade. | Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK | Microbiology and molecular biology reviews : MMBR | 27250768 | Microbiol Mol Biol Rev | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27250768 |
| 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 |
| Engineering living functional materials. | Chen AY, Zhong C, Lu TK | ACS synthetic biology | 25592034 | ACS Synth Biol | 2015 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/25592034 |
| Single-molecule detection of protein efflux from microorganisms using fluorescent single-walled carbon nanotube sensor arrays. | Landry MP, Ando H, Chen AY, Cao J, Kottadiel VI, Chio L, Yang D, Dong J, Lu TK, Strano MS | Nature nanotechnology | 28114298 | Nat Nanotechnol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28114298 |
| Synthetic recombinase-based state machines in living cells. | Roquet N, Soleimany AP, Ferris AC, Aaronson S, Lu TK | Science (New York, N.Y.) | 27463678 | Science | 2016 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/27463678 |
| Synthetic mixed-signal computation in living cells. | Rubens JR, Selvaggio G, Lu TK | Nature communications | 27255669 | Nat Commun | 2016 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/27255669 |
| 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 |
| 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 |
| 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 |
| Synthesis and patterning of tunable multiscale materials with engineered cells. | Chen AY, Deng Z, Billings AN, Seker UO, Lu MY, Citorik RJ, Zakeri B, Lu TK | Nature materials | 24658114 | Nat Mater | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24658114 |
| Synthetic analog and digital circuits for cellular computation and memory. | Purcell O, Lu TK | Current opinion in biotechnology | 24794536 | Curr Opin Biotechnol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24794536 |
| 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 |
| 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 |
| Hydrogel-based biocontainment of bacteria for continuous sensing and computation. | Tang TC, Tham E, Liu X, Yehl K, Rovner AJ, Yuk H, de la Fuente-Nunez C, Isaacs FJ, Zhao X, Lu TK | Nature chemical biology | 33820990 | Nat Chem Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33820990 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| Microbiome therapeutics - Advances and challenges. | Mimee M, Citorik RJ, Lu TK | Advanced drug delivery reviews | 27158095 | Adv Drug Deliv Rev | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27158095 |
| 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 |
| A Modular Toolkit for Generating Pichia pastoris Secretion Libraries. | Obst U, Lu TK, Sieber V | ACS synthetic biology | 28252957 | ACS Synth Biol | 2017 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/28252957 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Corynebacterium glutamicum Metabolic Engineering with CRISPR Interference (CRISPRi). | Cleto S, Jensen JV, Wendisch VF, Lu TK | ACS synthetic biology | 26829286 | ACS Synth Biol | 2016 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/26829286 |
| Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota. | Mimee M, Tucker AC, Voigt CA, Lu TK | Cell systems | 26918244 | Cell Syst | 2015 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/26918244 |
| 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 |
| 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 |
| 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 |
| 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 |
| Full-colour Jabuticaba-like nanostructures via the multiplex and orthogonal self-assembly of protein-conjugated quantum dots with engineered biofilms. | Deng Z, Chen AY, Zakeri B, Zhong C, Lu TK | Materials horizons | 36786820 | Mater Horiz | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/36786820 |
| 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 |
| The LINC complex component Kms1 and CENP-B protein Cbp1 cooperate to enforce faithful homology-directed DNA repair at the nuclear periphery in S. pombe. | Laffitte A, Lin D, Tian YJ, Liu N, Lusk CP, Mochrie SGJ, King MC | Genes & development | 41436280 | Genes Dev | 2026 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/41436280 |
| 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 |
| 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 |
| 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 |
| 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 |
| The LINC complex component Kms1 and CENP-B protein Cbp1 cooperate to enforce faithful homology-directed DNA repair at the nuclear periphery in S. pombe. | Laffitte A, Lin D, Tian YJ, Liu N, Lusk CP, Mochrie SGJ, King MC | bioRxiv : the preprint server for biology | 41278860 | bioRxiv | 2025 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/41278860 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Vending Assessment and Program Implementation in Four Iowa Worksites. | Lillehoj CJ, Nothwehr F, Shipley K, Voss C | Health promotion practice | 26220278 | Health Promot Pract | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26220278 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| Two-Photon Polymerization as a Tool for Studying 3D Printed Topography-Induced Stem Cell Fate. | Worthington KS, Do AV, Smith R, Tucker BA, Salem AK | Macromolecular bioscience | 30430755 | Macromol Biosci | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30430755 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Wafer Scale Integration of CMOS Chips for Biomedical Applications via Self-Aligned Masking. | Uddin A, Milaninia K, Chen CH, Theogarajan L | IEEE transactions on components, packaging, and manufacturing technology | 22400126 | IEEE Trans Compon Packaging Manuf Technol | 2011 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/22400126 |
| Clickable Amphiphilic Triblock Copolymers. | Isaacman MJ, Barron KA, Theogarajan LS | Journal of polymer science. Part A, Polymer chemistry | 23100856 | J Polym Sci A Polym Chem | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23100856 |
| 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 |
| Solid-state nanopore based biomimetic voltage gated ion channels. | Pevarnik M, Cui W, Yemenicioglu S, Rofeh J, Theogarajan L | Bioinspiration & biomimetics | 28726670 | Bioinspir Biomim | 2017 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/28726670 |
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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 |
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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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| Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. | Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED | Stem cells (Dayton, Ohio) | 25826782 | Stem Cells | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25826782 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Diet-induced alterations in gut microflora contribute to lethal pulmonary damage in TLR2/TLR4-deficient mice. | Ji Y, Sun S, Goodrich JK, Kim H, Poole AC, Duhamel GE, Ley RE, Qi L | Cell reports | 24953658 | Cell Rep | 2014 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/24953658 |
| 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 |
| Shotgun Metagenomics of 250 Adult Twins Reveals Genetic and Environmental Impacts on the Gut Microbiome. | Xie H, Guo R, Zhong H, Feng Q, Lan Z, Qin B, Ward KJ, Jackson MA, Xia Y, Chen X, Chen B, Xia H, Xu C, Li F, Xu X, Al-Aama JY, Yang H, Wang J, Kristiansen K, Wang J, Steves CJ, Bell JT, Li J, Spector TD, Jia H | Cell systems | 27818083 | Cell Syst | 2016 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/27818083 |
| Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative. | Wang J, Kurilshikov A, Radjabzadeh D, Turpin W, Croitoru K, Bonder MJ, Jackson MA, Medina-Gomez C, Frost F, Homuth G, Rühlemann M, Hughes D, Kim HN, MiBioGen Consortium Initiative, Spector TD, Bell JT, Steves CJ, Timpson N, Franke A, Wijmenga C, Meyer K, Kacprowski T, Franke L, Paterson AD, Raes J, Kraaij R, Zhernakova A | Microbiome | 29880062 | Microbiome | 2018 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/29880062 |
| 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 |
| Detection of stable community structures within gut microbiota co-occurrence networks from different human populations. | Jackson MA, Bonder MJ, Kuncheva Z, Zierer J, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Bell JT, Spector TD, Steves CJ | PeerJ | 29441232 | PeerJ | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29441232 |
| Omega-3 fatty acids correlate with gut microbiome diversity and production of N-carbamylglutamate in middle aged and elderly women. | Menni C, Zierer J, Pallister T, Jackson MA, Long T, Mohney RP, Steves CJ, Spector TD, Valdes AM | Scientific reports | 28894110 | Sci Rep | 2017 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/28894110 |
| 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 |
| Genetic Determinants of the Gut Microbiome in UK Twins. | Goodrich JK, Davenport ER, Beaumont M, Jackson MA, Knight R, Ober C, Spector TD, Bell JT, Clark AG, Ley RE | Cell host & microbe | 27173935 | Cell Host Microbe | 2016 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/27173935 |
| Sphingolipids produced by gut bacteria enter host metabolic pathways impacting ceramide levels. | Johnson EL, Heaver SL, Waters JL, Kim BI, Bretin A, Goodman AL, Gewirtz AT, Worgall TS, Ley RE | Nature communications | 32424203 | Nat Commun | 2020 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/32424203 |
| 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 |
| Virome Diversity Correlates with Intestinal Microbiome Diversity in Adult Monozygotic Twins. | Moreno-Gallego JL, Chou SP, Di Rienzi SC, Goodrich JK, Spector TD, Bell JT, Youngblut ND, Hewson I, Reyes A, Ley RE | Cell host & microbe | 30763537 | Cell Host Microbe | 2019 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/30763537 |
| 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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| Innate and adaptive immunity interact to quench microbiome flagellar motility in the gut. | Cullender TC, Chassaing B, Janzon A, Kumar K, Muller CE, Werner JJ, Angenent LT, Bell ME, Hay AG, Peterson DA, Walter J, Vijay-Kumar M, Gewirtz AT, Ley RE | Cell host & microbe | 24237702 | Cell Host Microbe | 2013 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/24237702 |
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| 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 |
| Gut microbiota associations with common diseases and prescription medications in a population-based cohort. | Jackson MA, Verdi S, Maxan ME, Shin CM, Zierer J, Bowyer RCE, Martin T, Williams FMK, Menni C, Bell JT, Spector TD, Steves CJ | Nature communications | 29985401 | Nat Commun | 2018 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/29985401 |
| Signatures of early frailty in the gut microbiota. | Jackson MA, Jeffery IB, Beaumont M, Bell JT, Clark AG, Ley RE, O'Toole PW, Spector TD, Steves CJ | Genome medicine | 26822992 | Genome Med | 2016 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/26822992 |
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| Gut microbiome diversity and high-fibre intake are related to lower long-term weight gain. | Menni C, Jackson MA, Pallister T, Steves CJ, Spector TD, Valdes AM | International journal of obesity (2005) | 28286339 | Int J Obes (Lond) | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28286339 |
| The microbiome affects liver sphingolipids and plasma fatty acids in a murine model of the Western diet based on soybean oil. | Di Rienzi SC, Johnson EL, Waters JL, Kennedy EA, Jacobson J, Lawrence P, Wang DH, Worgall TS, Brenna JT, Ley RE | The Journal of nutritional biochemistry | 34186211 | J Nutr Biochem | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34186211 |
| Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome. | Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Falchi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD | BMC microbiology | 35114943 | BMC Microbiol | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35114943 |
| Sickle cell disease activates peripheral blood mononuclear cells to induce cathepsins k and v activity in endothelial cells. | Keegan PM, Surapaneni S, Platt MO | Anemia | 22550569 | Anemia | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22550569 |
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| Sickle Cell Anemia Mediates Carotid Artery Expansive Remodeling That Can Be Prevented by Inhibition of JNK (c-Jun N-Terminal Kinase). | Song H, Keegan PM, Anbazhakan S, Rivera CP, Feng Y, Omojola VO, Clark AA, Cai S, Selma J, Gleason RL Jr, Botchwey EA, Huo Y, Tan W, Platt MO | Arteriosclerosis, thrombosis, and vascular biology | 32160775 | Arterioscler Thromb Vasc Biol | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32160775 |
| Low-Cost Method to Monitor Patient Adherence to HIV Antiretroviral Therapy Using Multiplex Cathepsin Zymography. | Platt MO, Evans D, Keegan PM, McNamara L, Parker IK, Roberts LM, Caulk AW, Gleason RL Jr, Seifu D, Amogne W, Penny C | Molecular biotechnology | 26589706 | Mol Biotechnol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26589706 |
| Cathepsin Protease Inhibition Reduces Endometriosis Lesion Establishment. | Porter KM, Wieser FA, Wilder CL, Sidell N, Platt MO | Reproductive sciences (Thousand Oaks, Calif.) | 26482207 | Reprod Sci | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26482207 |
| Endothelial cells and cathepsins: Biochemical and biomechanical regulation. | Platt MO, Shockey WA | Biochimie | 26458976 | Biochimie | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26458976 |
| Patient specific proteolytic activity of monocyte-derived macrophages and osteoclasts predicted with temporal kinase activation states during differentiation. | Park KY, Li WA, Platt MO | Integrative biology : quantitative biosciences from nano to macro | 23114878 | Integr Biol (Camb) | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23114878 |
| Tumor necrosis factor alpha stimulates cathepsin K and V activity via juxtacrine monocyte-endothelial cell signaling and JNK activation. | Keegan PM, Wilder CL, Platt MO | Molecular and cellular biochemistry | 22562303 | Mol Cell Biochem | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22562303 |
| Cathepsin S cannibalism of cathepsin K as a mechanism to reduce type I collagen degradation. | Barry ZT, Platt MO | The Journal of biological chemistry | 22730330 | J Biol Chem | 2012 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/22730330 |
| Acid sphingomyelinase is activated in sickle cell erythrocytes and contributes to inflammatory microparticle generation in SCD. | Awojoodu AO, Keegan PM, Lane AR, Zhang Y, Lynch KR, Platt MO, Botchwey EA | Blood | 25075126 | Blood | 2014 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/25075126 |
| Biomechanical and biochemical regulation of cathepsin K expression in endothelial cells converge at AP-1 and NF-κB. | Keegan PM, Anbazhakan S, Kang B, Pace BS, Platt MO | Biological chemistry | 26760306 | Biol Chem | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26760306 |
| Pro-atherogenic shear stress and HIV proteins synergistically upregulate cathepsin K in endothelial cells. | Parker IK, Roberts LM, Hansen L, Gleason RL Jr, Sutliff RL, Platt MO | Annals of biomedical engineering | 24719048 | Ann Biomed Eng | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24719048 |
| Manipulating substrate and pH in zymography protocols selectively distinguishes cathepsins K, L, S, and V activity in cells and tissues. | Wilder CL, Park KY, Keegan PM, Platt MO | Archives of biochemistry and biophysics | 21982919 | Arch Biochem Biophys | 2011 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/21982919 |
| Original Research: Sickle cell anemia and pediatric strokes: Computational fluid dynamics analysis in the middle cerebral artery. | Rivera CP, Veneziani A, Ware RE, Platt MO | Experimental biology and medicine (Maywood, N.J.) | 26946534 | Exp Biol Med (Maywood) | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26946534 |
| PACMANS: A bioinformatically informed algorithm to predict, design, and disrupt protease-on-protease hydrolysis. | Ferrall-Fairbanks MC, Barry ZT, Affer M, Shuler MA, Moomaw EW, Platt MO | Protein science : a publication of the Protein Society | 28078782 | Protein Sci | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28078782 |
| Microarchitectural and mechanical characterization of the sickle bone. | Green M, Akinsami I, Lin A, Banton S, Ghosh S, Chen B, Platt M, Osunkwo I, Ofori-Acquah S, Guldberg R, Barabino G | Journal of the mechanical behavior of biomedical materials | 25957113 | J Mech Behav Biomed Mater | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25957113 |
| Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks. | Ferrall-Fairbanks MC, Kieslich CA, Platt MO | Proceedings of the National Academy of Sciences of the United States of America | 31980525 | Proc Natl Acad Sci U S A | 2020 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/31980525 |
| Age-dependent characterization of carotid and cerebral artery geometries in a transgenic mouse model of sickle cell anemia using ultrasound and microcomputed tomography. | Rivera CP, Li L, Cai S, Pei N, McAlear GE, Bollavaram K, Ariyo OV, Omojola VO, Song H, Alfonso AL, Tan W, Huo Y, Platt MO | Blood cells, molecules & diseases | 32841841 | Blood Cells Mol Dis | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32841841 |
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| Simultaneous mapping of membrane voltage and calcium in zebrafish heart in vivo reveals chamber-specific developmental transitions in ionic currents. | Hou JH, Kralj JM, Douglass AD, Engert F, Cohen AE | Frontiers in physiology | 25309445 | Front Physiol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25309445 |
| Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing. | Werley CA, Chien MP, Gaublomme J, Shekhar K, Butty V, Yi BA, Kralj JM, Bloxham BB, Boyer LA, Regev A, Cohen AE | PloS one | 28333933 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28333933 |
| A Bright and Fast Red Fluorescent Protein Voltage Indicator That Reports Neuronal Activity in Organotypic Brain Slices. | Abdelfattah AS, Farhi SL, Zhao Y, Brinks D, Zou P, Ruangkittisakul A, Platisa J, Pieribone VA, Ballanyi K, Cohen AE, Campbell RE | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26911693 | J Neurosci | 2016 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/26911693 |
| All-Optical Electrophysiology for High-Throughput Functional Characterization of a Human iPSC-Derived Motor Neuron Model of ALS. | Kiskinis E, Kralj JM, Zou P, Weinstein EN, Zhang H, Tsioras K, Wiskow O, Ortega JA, Eggan K, Cohen AE | Stem cell reports | 29779896 | Stem Cell Reports | 2018 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/29779896 |
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| Flash memory: photochemical imprinting of neuronal action potentials onto a microbial rhodopsin. | Venkatachalam V, Brinks D, Maclaurin D, Hochbaum D, Kralj J, Cohen AE | Journal of the American Chemical Society | 24428326 | J Am Chem Soc | 2014 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/24428326 |
| All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. | Hochbaum DR, Zhao Y, Farhi SL, Klapoetke N, Werley CA, Kapoor V, Zou P, Kralj JM, Maclaurin D, Smedemark-Margulies N, Saulnier JL, Boulting GL, Straub C, Cho YK, Melkonian M, Wong GK, Harrison DJ, Murthy VN, Sabatini BL, Boyden ES, Campbell RE, Cohen AE | Nature methods | 24952910 | Nat Methods | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24952910 |
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| Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage. | Brinks D, Klein AJ, Cohen AE | Biophysical journal | 26331249 | Biophys J | 2015 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/26331249 |
| All-Optical Interrogation of Neural Circuits. | Emiliani V, Cohen AE, Deisseroth K, Häusser M | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26468193 | J Neurosci | 2015 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/26468193 |
| Photostick: a method for selective isolation of target cells from culture. | Chien MP, Werley CA, Farhi SL, Cohen AE | Chemical science | 25705368 | Chem Sci | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25705368 |
| Optogenetics: Turning the Microscope on Its Head. | Cohen AE | Biophysical journal | 26958872 | Biophys J | 2016 Mar 8 | https://www.ncbi.nlm.nih.gov/pubmed/26958872 |
| Swimming motions evoke Piezo1-dependent Ca(2+) events in vascular endothelial cells of larval zebrafish. | Jia BZ, Tang X, Rossmann MP, Zon LI, Engert F, Cohen AE | Current biology : CB | 41237769 | Curr Biol | 2025 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/41237769 |
| Ultrasensitive measurements of microbial rhodopsin photocycles using photochromic FRET. | Bayraktar H, Fields AP, Kralj JM, Spudich JL, Rothschild KJ, Cohen AE | Photochemistry and photobiology | 22010969 | Photochem Photobiol | 2012 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/22010969 |
| Convex lens-induced confinement for imaging single molecules. | Leslie SR, Fields AP, Cohen AE | Analytical chemistry | 20557026 | Anal Chem | 2010 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/20557026 |
| Mechanism of voltage-sensitive fluorescence in a microbial rhodopsin. | Maclaurin D, Venkatachalam V, Lee H, Cohen AE | Proceedings of the National Academy of Sciences of the United States of America | 23530193 | Proc Natl Acad Sci U S A | 2013 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/23530193 |
| Optogenetic Approaches to Drug Discovery in Neuroscience and Beyond. | Zhang H, Cohen AE | Trends in biotechnology | 28552428 | Trends Biotechnol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28552428 |
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| A Low Affinity GCaMP3 Variant (GCaMPer) for Imaging the Endoplasmic Reticulum Calcium Store. | Henderson MJ, Baldwin HA, Werley CA, Boccardo S, Whitaker LR, Yan X, Holt GT, Schreiter ER, Looger LL, Cohen AE, Kim DS, Harvey BK | PloS one | 26451944 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26451944 |
| Screening fluorescent voltage indicators with spontaneously spiking HEK cells. | Park J, Werley CA, Venkatachalam V, Kralj JM, Dib-Hajj SD, Waxman SG, Cohen AE | PloS one | 24391999 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24391999 |
| Imaging GFP-based reporters in neurons with multiwavelength optogenetic control. | Venkatachalam V, Cohen AE | Biophysical journal | 25296307 | Biophys J | 2014 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/25296307 |
| Superoxide-mediated protection of Escherichia coli from antimicrobials. | Mosel M, Li L, Drlica K, Zhao X | Antimicrobial agents and chemotherapy | 23979754 | Antimicrob Agents Chemother | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23979754 |
| Lethal synergy involving bicyclomycin: an approach for reviving old antibiotics. | Malik M, Li L, Zhao X, Kerns RJ, Berger JM, Drlica K | The Journal of antimicrobial chemotherapy | 25085655 | J Antimicrob Chemother | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25085655 |
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| YihE kinase is a central regulator of programmed cell death in bacteria. | Dorsey-Oresto A, Lu T, Mosel M, Wang X, Salz T, Drlica K, Zhao X | Cell reports | 23416055 | Cell Rep | 2013 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/23416055 |
| Inhibitors of reactive oxygen species accumulation delay and/or reduce the lethality of several antistaphylococcal agents. | Liu Y, Liu X, Qu Y, Wang X, Li L, Zhao X | Antimicrobial agents and chemotherapy | 22948880 | Antimicrob Agents Chemother | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22948880 |
| Dimethyl Sulfoxide Protects Escherichia coli from Rapid Antimicrobial-Mediated Killing. | Mi H, Wang D, Xue Y, Zhang Z, Niu J, Hong Y, Drlica K, Zhao X | Antimicrobial agents and chemotherapy | 27246776 | Antimicrob Agents Chemother | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27246776 |
| Post-stress bacterial cell death mediated by reactive oxygen species. | Hong Y, Zeng J, Wang X, Drlica K, Zhao X | Proceedings of the National Academy of Sciences of the United States of America | 30948634 | Proc Natl Acad Sci U S A | 2019 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/30948634 |
| Resveratrol Antagonizes Antimicrobial Lethality and Stimulates Recovery of Bacterial Mutants. | Liu Y, Zhou J, Qu Y, Yang X, Shi G, Wang X, Hong Y, Drlica K, Zhao X | PloS one | 27045517 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27045517 |
| Suppression of Reactive Oxygen Species Accumulation Accounts for Paradoxical Bacterial Survival at High Quinolone Concentration. | Luan G, Hong Y, Drlica K, Zhao X | Antimicrobial agents and chemotherapy | 29229642 | Antimicrob Agents Chemother | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29229642 |
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| Contribution of reactive oxygen species to thymineless death in Escherichia coli. | Hong Y, Li L, Luan G, Drlica K, Zhao X | Nature microbiology | 28970486 | Nat Microbiol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28970486 |
| Involvement of Holliday junction resolvase in fluoroquinolone-mediated killing of Mycobacterium smegmatis. | Long Q, Du Q, Fu T, Drlica K, Zhao X, Xie J | Antimicrobial agents and chemotherapy | 25534729 | Antimicrob Agents Chemother | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25534729 |
| Humans put their eggs in more than one basket. | Laird DJ | Nature cell biology | 23263370 | Nat Cell Biol | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23263370 |
| A miR-372/let-7 Axis Regulates Human Germ Versus Somatic Cell Fates. | Tran ND, Kissner M, Subramanyam D, Parchem RJ, Laird DJ, Blelloch RH | Stem cells (Dayton, Ohio) | 27066911 | Stem Cells | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27066911 |
| Meiotic onset is reliant on spatial distribution but independent of germ cell number in the mouse ovary. | Arora R, Abby E, Ross AD, Cantu AV, Kissner MD, Castro V, Ho HY, Livera G, Laird DJ | Journal of cell science | 27199373 | J Cell Sci | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/27199373 |
| Patterning of sharp cellular interfaces with a reconfigurable elastic substrate. | Curtis A, Li DJ, DeVeale B, Onishi K, Kim MY, Blelloch R, Laird DJ, Hui EE | Integrative biology : quantitative biosciences from nano to macro | 28001149 | Integr Biol (Camb) | 2017 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/28001149 |
| Sustained fertility from first-wave follicle oocytes that pause their growth. | Soygur B, Gaylord EA, Foecke MH, Cincotta SA, Horan TS, Wood A, Cohen PE, Laird DJ | bioRxiv : the preprint server for biology | 39253445 | bioRxiv | 2024 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/39253445 |
| Ror2 enhances polarity and directional migration of primordial germ cells. | Laird DJ, Altshuler-Keylin S, Kissner MD, Zhou X, Anderson KV | PLoS genetics | 22216013 | PLoS Genet | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22216013 |
| Wnt and Bmp fit germ cells to a T. | Cantú AV, Laird DJ | Developmental cell | 24331924 | Dev Cell | 2013 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/24331924 |
| Follicle dynamics and global organization in the intact mouse ovary. | Faire M, Skillern A, Arora R, Nguyen DH, Wang J, Chamberlain C, German MS, Fung JC, Laird DJ | Developmental biology | 25889274 | Dev Biol | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/25889274 |
| Smad4 regulates growth plate matrix production and chondrocyte polarity. | Whitaker AT, Berthet E, Cantu A, Laird DJ, Alliston T | Biology open | 28167493 | Biol Open | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28167493 |
| Kinesin superfamily protein Kif26b links Wnt5a-Ror signaling to the control of cell and tissue behaviors in vertebrates. | Susman MW, Karuna EP, Kunz RC, Gujral TS, Cantú AV, Choi SS, Jong BY, Okada K, Scales MK, Hum J, Hu LS, Kirschner MW, Nishinakamura R, Yamada S, Laird DJ, Jao LE, Gygi SP, Greenberg ME, Ho HH | eLife | 28885975 | Elife | 2017 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/28885975 |
| Insights from imaging the implanting embryo and the uterine environment in three dimensions. | Arora R, Fries A, Oelerich K, Marchuk K, Sabeur K, Giudice LC, Laird DJ | Development (Cambridge, England) | 27836961 | Development | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27836961 |
| Comprehensive profiling of migratory primordial germ cells reveals niche-specific differences in non-canonical Wnt and Nodal-Lefty signaling in anterior vs posterior migrants. | Jaszczak RG, Zussman JW, Wagner DE, Laird DJ | bioRxiv : the preprint server for biology | 39257761 | bioRxiv | 2025 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/39257761 |
| Primordial germ cells and gastrointestinal stromal tumors respond distinctly to a cKit overactivating allele. | Chen L, Faire M, Kissner MD, Laird DJ | Human molecular genetics | 23077213 | Hum Mol Genet | 2013 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/23077213 |
| Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. | Blaschke K, Ebata KT, Karimi MM, Zepeda-Martínez JA, Goyal P, Mahapatra S, Tam A, Laird DJ, Hirst M, Rao A, Lorincz MC, Ramalho-Santos M | Nature | 23812591 | Nature | 2013 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/23812591 |
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| Cryopreservation and recovery of human endometrial epithelial cells with high viability, purity, and functional fidelity. | Chen JC, Hoffman JR, Arora R, Perrone LA, Gonzalez-Gomez CJ, Vo KC, Laird DJ, Irwin JC, Giudice LC | Fertility and sterility | 26515378 | Fertil Steril | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26515378 |
| Natural selection at the cellular level: insights from male germ cell differentiation. | Nguyen DH, Laird DJ | Cell death and differentiation | 34079077 | Cell Death Differ | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34079077 |
| Apoptosis in the fetal testis eliminates developmentally defective germ cell clones. | Nguyen DH, Soygur B, Peng SP, Malki S, Hu G, Laird DJ | Nature cell biology | 33199844 | Nat Cell Biol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33199844 |
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| The p23 molecular chaperone and GCN5 acetylase jointly modulate protein-DNA dynamics and open chromatin status. | Zelin E, Zhang Y, Toogun OA, Zhong S, Freeman BC | Molecular cell | 23022381 | Mol Cell | 2012 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/23022381 |
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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 |
| Affinity-based proteomics reveal cancer-specific networks coordinated by Hsp90. | Moulick K, Ahn JH, Zong H, Rodina A, Cerchietti L, Gomes DaGama EM, Caldas-Lopes E, Beebe K, Perna F, Hatzi K, Vu LP, Zhao X, Zatorska D, Taldone T, Smith-Jones P, Alpaugh M, Gross SS, Pillarsetty N, Ku T, Lewis JS, Larson SM, Levine R, Erdjument-Bromage H, Guzman ML, Nimer SD, Melnick A, Neckers L, Chiosis G | Nature chemical biology | 21946277 | Nat Chem Biol | 2011 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/21946277 |
| Novel mTOR inhibitory activity of ciclopirox enhances parthenolide antileukemia activity. | Sen S, Hassane DC, Corbett C, Becker MW, Jordan CT, Guzman ML | Experimental hematology | 23660068 | Exp Hematol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23660068 |
| Dehydroleucodine, a Sesquiterpene Lactone from Gynoxys verrucosa, Demonstrates Cytotoxic Activity against Human Leukemia Cells. | Ordóñez PE, Sharma KK, Bystrom LM, Alas MA, Enriquez RG, Malagón O, Jones DE, Guzman ML, Compadre CM | Journal of natural products | 27057812 | J Nat Prod | 2016 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/27057812 |
| Cranberry A-type proanthocyanidins selectively target acute myeloid leukemia cells. | Bystrom LM, Bezerra DP, Hsu HT, Zong H, Lara-Martínez LA, De Leon JP, Emmanuel M, Méry D, Gardenghi S, Hassane D, Neto CC, Cunningham-Rundles S, Becker MW, Rivella S, Guzman ML | Blood advances | 31698457 | Blood Adv | 2019 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/31698457 |
| Integrative epigenomic analysis identifies biomarkers and therapeutic targets in adult B-acute lymphoblastic leukemia. | Geng H, Brennan S, Milne TA, Chen WY, Li Y, Hurtz C, Kweon SM, Zickl L, Shojaee S, Neuberg D, Huang C, Biswas D, Xin Y, Racevskis J, Ketterling RP, Luger SM, Lazarus H, Tallman MS, Rowe JM, Litzow MR, Guzman ML, Allis CD, Roeder RG, Müschen M, Paietta E, Elemento O, Melnick AM | Cancer discovery | 23107779 | Cancer Discov | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23107779 |
| Discovery of 1,2,4-thiadiazolidine-3,5-dione analogs that exhibit unusual and selective rapid cell death kinetics against acute myelogenous leukemia cells in culture. | Nasim S, Guzman ML, Jordan CT, Crooks PA | Bioorganic & medicinal chemistry letters | 21757349 | Bioorg Med Chem Lett | 2011 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/21757349 |
| Single-cell mass cytometry reveals intracellular survival/proliferative signaling in FLT3-ITD-mutated AML stem/progenitor cells. | Han L, Qiu P, Zeng Z, Jorgensen JL, Mak DH, Burks JK, Schober W, McQueen TJ, Cortes J, Tanner SD, Roboz GJ, Kantarjian HM, Kornblau SM, Guzman ML, Andreeff M, Konopleva M | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 25598437 | Cytometry A | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25598437 |
| Synthesis and evaluation of a series of resveratrol analogues as potent anti-cancer agents that target tubulin. | Madadi NR, Zong H, Ketkar A, Zheng C, Penthala NR, Janganati V, Bommagani S, Eoff RL, Guzman ML, Crooks PA | MedChemComm | 26257861 | Medchemcomm | 2015 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/26257861 |
| Chemical biology. A small-molecule inhibitor of the aberrant transcription factor CBFβ-SMMHC delays leukemia in mice. | Illendula A, Pulikkan JA, Zong H, Grembecka J, Xue L, Sen S, Zhou Y, Boulton A, Kuntimaddi A, Gao Y, Rajewski RA, Guzman ML, Castilla LH, Bushweller JH | Science (New York, N.Y.) | 25678665 | Science | 2015 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/25678665 |
| Synthesis, anticancer activity and molecular docking studies on a series of heterocyclic trans-cyanocombretastatin analogues as antitubulin agents. | Penthala NR, Zong H, Ketkar A, Madadi NR, Janganati V, Eoff RL, Guzman ML, Crooks PA | European journal of medicinal chemistry | 25557492 | Eur J Med Chem | 2015 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/25557492 |
| Small Molecule Inhibitor of CBFβ-RUNX Binding for RUNX Transcription Factor Driven Cancers. | Illendula A, Gilmour J, Grembecka J, Tirumala VSS, Boulton A, Kuntimaddi A, Schmidt C, Wang L, Pulikkan JA, Zong H, Parlak M, Kuscu C, Pickin A, Zhou Y, Gao Y, Mishra L, Adli M, Castilla LH, Rajewski RA, Janes KA, Guzman ML, Bonifer C, Bushweller JH | EBioMedicine | 27428424 | EBioMedicine | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27428424 |
| Menin inhibitor MI-3454 induces remission in MLL1-rearranged and NPM1-mutated models of leukemia. | Klossowski S, Miao H, Kempinska K, Wu T, Purohit T, Kim E, Linhares BM, Chen D, Jih G, Perkey E, Huang H, He M, Wen B, Wang Y, Yu K, Lee SC, Danet-Desnoyers G, Trotman W, Kandarpa M, Cotton A, Abdel-Wahab O, Lei H, Dou Y, Guzman M, Peterson L, Gruber T, Choi S, Sun D, Ren P, Li LS, Liu Y, Burrows F, Maillard I, Cierpicki T, Grembecka J | The Journal of clinical investigation | 31855575 | J Clin Invest | 2020 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/31855575 |
| Acute myelogenous leukemia stem cells: from Bench to Bedside. | Felipe Rico J, Hassane DC, Guzman ML | Cancer letters | 22713929 | Cancer Lett | 2013 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/22713929 |
| In vivo targeting of leukemia stem cells by directing parthenolide-loaded nanoparticles to the bone marrow niche. | Zong H, Sen S, Zhang G, Mu C, Albayati ZF, Gorenstein DG, Liu X, Ferrari M, Crooks PA, Roboz GJ, Shen H, Guzman ML | Leukemia | 26669973 | Leukemia | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26669973 |
| Phase I trial of plerixafor combined with decitabine in newly diagnosed older patients with acute myeloid leukemia. | Roboz GJ, Ritchie EK, Dault Y, Lam L, Marshall DC, Cruz NM, Hsu HC, Hassane DC, Christos PJ, Ippoliti C, Scandura JM, Guzman ML | Haematologica | 29724902 | Haematologica | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29724902 |
| The epichaperome is an integrated chaperome network that facilitates tumour survival. | Rodina A, Wang T, Yan P, Gomes ED, Dunphy MP, Pillarsetty N, Koren J, Gerecitano JF, Taldone T, Zong H, Caldas-Lopes E, Alpaugh M, Corben A, Riolo M, Beattie B, Pressl C, Peter RI, Xu C, Trondl R, Patel HJ, Shimizu F, Bolaender A, Yang C, Panchal P, Farooq MF, Kishinevsky S, Modi S, Lin O, Chu F, Patil S, Erdjument-Bromage H, Zanzonico P, Hudis C, Studer L, Roboz GJ, Cesarman E, Cerchietti L, Levine R, Melnick A, Larson SM, Lewis JS, Guzman ML, Chiosis G | Nature | 27706135 | Nature | 2016 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/27706135 |
| Concise review: Leukemia stem cells in personalized medicine. | Guzman ML, Allan JN | Stem cells (Dayton, Ohio) | 24214290 | Stem Cells | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24214290 |
| Acute myeloid leukemia stem cells: seek and destroy. | Roboz GJ, Guzman M | Expert review of hematology | 21082958 | Expert Rev Hematol | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21082958 |
| Is minimal residual disease monitoring clinically relevant in adults with acute myelogenous leukemia? | Carlson KS, Guzman ML | Current hematologic malignancy reports | 23563936 | Curr Hematol Malig Rep | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23563936 |
| A phase I study using bortezomib with weekly idarubicin for treatment of elderly patients with acute myeloid leukemia. | Howard DS, Liesveld J, Phillips GL 2nd, Hayslip J, Weiss H, Jordan CT, Guzman ML | Leukemia research | 24075534 | Leuk Res | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24075534 |
| A Hyperactive Signalosome in Acute Myeloid Leukemia Drives Addiction to a Tumor-Specific Hsp90 Species. | Zong H, Gozman A, Caldas-Lopes E, Taldone T, Sturgill E, Brennan S, Ochiana SO, Gomes-DaGama EM, Sen S, Rodina A, Koren J 3rd, Becker MW, Rudin CM, Melnick A, Levine RL, Roboz GJ, Nimer SD, Chiosis G, Guzman ML | Cell reports | 26628369 | Cell Rep | 2015 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/26628369 |
| Selective activity of the histone deacetylase inhibitor AR-42 against leukemia stem cells: a novel potential strategy in acute myelogenous leukemia. | Guzman ML, Yang N, Sharma KK, Balys M, Corbett CA, Jordan CT, Becker MW, Steidl U, Abdel-Wahab O, Levine RL, Marcucci G, Roboz GJ, Hassane DC | Molecular cancer therapeutics | 24934933 | Mol Cancer Ther | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24934933 |
| 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 |
| 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 |
| In vitro cytocompatibility of one-dimensional and two-dimensional nanostructure-reinforced biodegradable polymeric nanocomposites. | Farshid B, Lalwani G, Sitharaman B | Journal of biomedical materials research. Part A | 25367032 | J Biomed Mater Res A | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25367032 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Detection, mapping, and quantification of single walled carbon nanotubes in histological specimens with photoacoustic microscopy. | Avti PK, Hu S, Favazza C, Mikos AG, Jansen JA, Shroyer KR, Wang LV, Sitharaman B | PloS one | 22496892 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22496892 |
| 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 |
| 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 |
| A novel nanoparticle-enhanced photoacoustic stimulus for bone tissue engineering. | Sitharaman B, Avti PK, Schaefer K, Talukdar Y, Longtin JP | Tissue engineering. Part A | 21395444 | Tissue Eng Part A | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21395444 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Vasoactive effects of stable aqueous suspensions of single walled carbon nanotubes in hamsters and mice. | Frame MD, Dewar AM, Mullick Chowdhury S, Sitharaman B | Nanotoxicology | 23992463 | Nanotoxicology | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23992463 |
| Toward single-walled carbon nanotube-gadolinium complex as advanced MRI contrast agents: pharmacodynamics and global genomic response in small animals. | Avti PK, Talukdar Y, Sirotkin MV, Shroyer KR, Sitharaman B | Journal of biomedical materials research. Part B, Applied biomaterials | 23559429 | J Biomed Mater Res B Appl Biomater | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23559429 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The effects of graphene nanostructures on mesenchymal stem cells. | Talukdar Y, Rashkow J, Lalwani G, Kanakia S, Sitharaman B | Biomaterials | 24674462 | Biomaterials | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24674462 |
| 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 |
| 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 |
| 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 |
| Titanium-enhanced Raman microcavity laser. | Deka N, Maker AJ, Armani AM | Optics letters | 24690786 | Opt Lett | 2014 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/24690786 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Recycling microcavity optical biosensors. | Hunt HK, Armani AM | Optics letters | 21478993 | Opt Lett | 2011 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/21478993 |
| 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 |
| 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 |
| Monitoring DNA hybridization using optical microcavities. | Hawk RM, Chistiakova MV, Armani AM | Optics letters | 24322107 | Opt Lett | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/24322107 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A rationally designed nanoparticle for RNA interference therapy in B-lineage lymphoid malignancies. | Uckun FM, Qazi S, Ma H, Yin L, Cheng J | EBioMedicine | 25599086 | EBioMedicine | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25599086 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| CD19-antigen specific nanoscale liposomal formulation of a SYK P-site inhibitor causes apoptotic destruction of human B-precursor leukemia cells. | Myers DE, Yiv S, Qazi S, Ma H, Cely I, Shahidzadeh A, Arellano M, Finestone E, Gaynon PS, Termuhlen A, Cheng J, Uckun FM | Integrative biology : quantitative biosciences from nano to macro | 24910947 | Integr Biol (Camb) | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24910947 |
| Redox-responsive, reversibly-crosslinked thiolated cationic helical polypeptides for efficient siRNA encapsulation and delivery. | Zheng N, Song Z, Liu Y, Zhang R, Zhang R, Yao C, Uckun FM, Yin L, Cheng J | Journal of controlled release : official journal of the Controlled Release Society | 25683619 | J Control Release | 2015 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/25683619 |
| Biodegradable micelles capable of mannose-mediated targeted drug delivery to cancer cells. | Yin L, Chen Y, Zhang Z, Yin Q, Zheng N, Cheng J | Macromolecular rapid communications | 25619623 | Macromol Rapid Commun | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25619623 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| Three-dimensional continuous particle focusing in a microfluidic channel via standing surface acoustic waves (SSAW). | Shi J, Yazdi S, Lin SC, Ding X, Chiang IK, Sharp K, Huang TJ | Lab on a chip | 21709881 | Lab Chip | 2011 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/21709881 |
| A reconfigurable plasmofluidic lens. | Zhao C, Liu Y, Zhao Y, Fang N, Huang TJ | Nature communications | 23929463 | Nat Commun | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23929463 |
| Microfluidic opportunities in the field of nutrition. | Li S, Kiehne J, Sinoway LI, Cameron CE, Huang TJ | Lab on a chip | 24056522 | Lab Chip | 2013 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/24056522 |
| 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 |
| Immunological analyses of whole blood via "microfluidic drifting" based flow cytometric chip. | Nawaz AA, Nissly RH, Li P, Chen Y, Guo F, Li S, Shariff YM, Qureshi AN, Wang L, Huang TJ | Annals of biomedical engineering | 24893596 | Ann Biomed Eng | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24893596 |
| Theory and experiment on particle trapping and manipulation via optothermally generated bubbles. | Zhao C, Xie Y, Mao Z, Zhao Y, Rufo J, Yang S, Guo F, Mai JD, Huang TJ | Lab on a chip | 24276624 | Lab Chip | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24276624 |
| Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions. | Zhao Y, Chen D, Yue H, Spiering MM, Zhao C, Benkovic SJ, Huang TJ | Nano letters | 24628474 | Nano Lett | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24628474 |
| 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 |
| On-chip manipulation of single microparticles, cells, and organisms using surface acoustic waves. | Ding X, Lin SC, Kiraly B, Yue H, Li S, Chiang IK, Shi J, Benkovic SJ, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 22733731 | Proc Natl Acad Sci U S A | 2012 Jul 10 | https://www.ncbi.nlm.nih.gov/pubmed/22733731 |
| Fabrication and characterization of beaded SiC quantum rings with anomalous red spectral shift. | Yang S, Kiraly B, Wang WY, Shang S, Cao B, Zeng H, Zhao Y, Li W, Liu ZK, Cai W, Huang TJ | Advanced materials (Deerfield Beach, Fla.) | 22911493 | Adv Mater | 2012 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/22911493 |
| A single-layer, planar, optofluidic switch powered by acoustically driven, oscillating microbubbles. | Huang PH, Ian Lapsley M, Ahmed D, Chen Y, Wang L, Jun Huang T | Applied physics letters | 23112348 | Appl Phys Lett | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/23112348 |
| Optofluidic tunable microlens by manipulating the liquid meniscus using a flared microfluidic structure. | Mao X, Stratton ZI, Nawaz AA, Lin SC, Huang TJ | Biomicrofluidics | 21267439 | Biomicrofluidics | 2010 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/21267439 |
| Optoacoustic tweezers: a programmable, localized cell concentrator based on opto-thermally generated, acoustically activated, surface bubbles. | Xie Y, Zhao C, Zhao Y, Li S, Rufo J, Yang S, Guo F, Huang TJ | Lab on a chip | 23511348 | Lab Chip | 2013 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/23511348 |
| Tunable nanowire patterning using standing surface acoustic waves. | Chen Y, Ding X, Steven Lin SC, Yang S, Huang PH, Nama N, Zhao Y, Nawaz AA, Guo F, Wang W, Gu Y, Mallouk TE, Huang TJ | ACS nano | 23540330 | ACS Nano | 2013 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/23540330 |
| 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 |
| Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves. | Guo F, Zhou W, Li P, Mao Z, Yennawar NH, French JB, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 25641793 | Small | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25641793 |
| Combining the Masking and Scaffolding Modalities of Colloidal Crystal Templates: Plasmonic Nanoparticle Arrays with Multiple Periodicities. | Yang S, Slotcavage D, Mai JD, Liang W, Xie Y, Chen Y, Huang TJ | Chemistry of materials : a publication of the American Chemical Society | 25620849 | Chem Mater | 2014 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/25620849 |
| 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 |
| Cell separation using tilted-angle standing surface acoustic waves. | Ding X, Peng Z, Lin SC, Geri M, Li S, Li P, Chen Y, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25157150 | Proc Natl Acad Sci U S A | 2014 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/25157150 |
| A reliable and programmable acoustofluidic pump powered by oscillating sharp-edge structures. | Huang PH, Nama N, Mao Z, Li P, Rufo J, Chen Y, Xie Y, Wei CH, Wang L, Huang TJ | Lab on a chip | 25188786 | Lab Chip | 2014 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/25188786 |
| Lab-on-a-chip technologies for single-molecule studies. | Zhao Y, Chen D, Yue H, French JB, Rufo J, Benkovic SJ, Huang TJ | Lab on a chip | 23670195 | Lab Chip | 2013 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/23670195 |
| Unconventional microfluidics: expanding the discipline. | Nawaz AA, Mao X, Stratton ZS, Huang TJ | Lab on a chip | 23478651 | Lab Chip | 2013 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/23478651 |
| 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 |
| 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 |
| An acoustofluidic micromixer based on oscillating sidewall sharp-edges. | Huang PH, Xie Y, Ahmed D, Rufo J, Nama N, Chen Y, Chan CY, Huang TJ | Lab on a chip | 23896797 | Lab Chip | 2013 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/23896797 |
| Standing surface acoustic wave (SSAW) based multichannel cell sorting. | Ding X, Lin SC, Lapsley MI, Li S, Guo X, Chan CY, Chiang IK, Wang L, McCoy JP, Huang TJ | Lab on a chip | 22992833 | Lab Chip | 2012 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/22992833 |
| 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 |
| Revisiting lab-on-a-chip technology for drug discovery. | Neuži P, Giselbrecht S, Länge K, Huang TJ, Manz A | Nature reviews. Drug discovery | 22850786 | Nat Rev Drug Discov | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22850786 |
| Optofluidic imaging: now and beyond. | Zhao Y, Stratton ZS, Guo F, Lapsley MI, Chan CY, Lin SC, Huang TJ | Lab on a chip | 23138193 | Lab Chip | 2013 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/23138193 |
| 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 |
| An on-chip, multichannel droplet sorter using standing surface acoustic waves. | Li S, Ding X, Guo F, Chen Y, Lapsley MI, Lin SC, Wang L, McCoy JP, Cameron CE, Huang TJ | Analytical chemistry | 23647057 | Anal Chem | 2013 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/23647057 |
| Tunable, pulsatile chemical gradient generation via acoustically driven oscillating bubbles. | Ahmed D, Chan CY, Lin SC, Muddana HS, Nama N, Benkovic SJ, Huang TJ | Lab on a chip | 23254861 | Lab Chip | 2013 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/23254861 |
| Probing circulating tumor cells in microfluidics. | Li P, Stratton ZS, Dao M, Ritz J, Huang TJ | Lab on a chip | 23306378 | Lab Chip | 2013 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/23306378 |
| Investigation of acoustic streaming patterns around oscillating sharp edges. | Nama N, Huang PH, Huang TJ, Costanzo F | Lab on a chip | 24903475 | Lab Chip | 2014 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/24903475 |
| All-Optical Modulation of Localized Surface Plasmon Coupling in a Hybrid System Composed of Photo-Switchable Gratings and Au Nanodisk Arrays. | Liu YJ, Zheng YB, Liou J, Chiang IK, Khoo IC, Huang TJ | The journal of physical chemistry. C, Nanomaterials and interfaces | 21643480 | J Phys Chem C Nanomater Interfaces | 2011 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/21643480 |
| A single-layer, planar, optofluidic Mach-Zehnder interferometer for label-free detection. | Lapsley MI, Chiang IK, Zheng YB, Ding X, Mao X, Huang TJ | Lab on a chip | 21479332 | Lab Chip | 2011 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/21479332 |
| Tunable patterning of microparticles and cells using standing surface acoustic waves. | Ding X, Shi J, Lin SC, Yazdi S, Kiraly B, Huang TJ | Lab on a chip | 22648600 | Lab Chip | 2012 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/22648600 |
| Surface acoustic wave (SAW) acoustophoresis: now and beyond. | Lin SC, Mao X, Huang TJ | Lab on a chip | 22781941 | Lab Chip | 2012 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/22781941 |
| 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 |
| Single-shot characterization of enzymatic reaction constants Km and kcat by an acoustic-driven, bubble-based fast micromixer. | Xie Y, Ahmed D, Lapsley MI, Lin SC, Nawaz AA, Wang L, Huang TJ | Analytical chemistry | 22880882 | Anal Chem | 2012 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/22880882 |
| Exploiting mechanical biomarkers in microfluidics. | Mao X, Huang TJ | Lab on a chip | 22968689 | Lab Chip | 2012 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/22968689 |
| Molecular plasmonics for biology and nanomedicine. | Zheng YB, Kiraly B, Weiss PS, Huang TJ | Nanomedicine (London, England) | 22630155 | Nanomedicine (Lond) | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22630155 |
| Selectively manipulable acoustic-powered microswimmers. | Ahmed D, Lu M, Nourhani A, Lammert PE, Stratton Z, Muddana HS, Crespi VH, Huang TJ | Scientific reports | 25993314 | Sci Rep | 2015 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/25993314 |
| Standing surface acoustic wave (SSAW)-based cell washing. | Li S, Ding X, Mao Z, Chen Y, Nama N, Guo F, Li P, Wang L, Cameron CE, Huang TJ | Lab on a chip | 25372273 | Lab Chip | 2015 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/25372273 |
| 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 |
| Acoustic propulsion of nanorod motors inside living cells. | Wang W, Li S, Mair L, Ahmed S, Huang TJ, Mallouk TE | Angewandte Chemie (International ed. in English) | 24677393 | Angew Chem Int Ed Engl | 2014 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/24677393 |
| Controlling cell-cell interactions using surface acoustic waves. | Guo F, Li P, French JB, Mao Z, Zhao H, Li S, Nama N, Fick JR, Benkovic SJ, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25535339 | Proc Natl Acad Sci U S A | 2015 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/25535339 |
| Acoustic separation of circulating tumor cells. | Li P, Mao Z, Peng Z, Zhou L, Chen Y, Huang PH, Truica CI, Drabick JJ, El-Deiry WS, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25848039 | Proc Natl Acad Sci U S A | 2015 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/25848039 |
| Standing surface acoustic wave (SSAW)-based microfluidic cytometer. | Chen Y, Nawaz AA, Zhao Y, Huang PH, McCoy JP, Levine SJ, Wang L, Huang TJ | Lab on a chip | 24406848 | Lab Chip | 2014 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/24406848 |
| Rare cell isolation and analysis in microfluidics. | Chen Y, Li P, Huang PH, Xie Y, Mai JD, Wang L, Nguyen NT, Huang TJ | Lab on a chip | 24406985 | Lab Chip | 2014 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/24406985 |
| Acoustofluidic relay: sequential trapping and transporting of microparticles via acoustically excited oscillating bubbles. | Xie Y, Ahmed D, Lapsley MI, Lu M, Li S, Huang TJ | Journal of laboratory automation | 23592570 | J Lab Autom | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23592570 |
| Holographically formed, acoustically switchable gratings based on polymer-dispersed liquid crystals. | Liu YJ, Lu M, Ding X, Leong ES, Lin SC, Shi J, Teng JH, Wang L, Bunning TJ, Huang TJ | Journal of laboratory automation | 22909448 | J Lab Autom | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22909448 |
| An integrated, multiparametric flow cytometry chip using "microfluidic drifting" based three-dimensional hydrodynamic focusing. | Mao X, Nawaz AA, Lin SC, Lapsley MI, Zhao Y, McCoy JP, El-Deiry WS, Huang TJ | Biomicrofluidics | 22567082 | Biomicrofluidics | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22567082 |
| Scalable manufacturing of plasmonic nanodisk dimers and cusp nanostructures using salting-out quenching method and colloidal lithography. | Juluri BK, Chaturvedi N, Hao Q, Lu M, Velegol D, Jensen L, Huang TJ | ACS nano | 21692473 | ACS Nano | 2011 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/21692473 |
| An acoustofluidic micromixer via bubble inception and cavitation from microchannel sidewalls. | Ozcelik A, Ahmed D, Xie Y, Nama N, Qu Z, Nawaz AA, Huang TJ | Analytical chemistry | 24754496 | Anal Chem | 2014 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/24754496 |
| Superhydrophobic Surface Enhanced Raman Scattering Sensing using Janus Particle Arrays Realized by Site-Specific Electrochemical Growth. | Yang S, Hricko PJ, Huang PH, Li S, Zhao Y, Xie Y, Guo F, Wang L, Huang TJ | Journal of materials chemistry. C | 24748991 | J Mater Chem C Mater | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24748991 |
| 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 |
| 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 |
| Sub-micrometer-precision, three-dimensional (3D) hydrodynamic focusing via "microfluidic drifting". | Nawaz AA, Zhang X, Mao X, Rufo J, Lin SC, Guo F, Zhao Y, Lapsley M, Li P, McCoy JP, Levine SJ, Huang TJ | Lab on a chip | 24287742 | Lab Chip | 2014 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/24287742 |
| 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 |
| 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 |
| 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 |
| Electrochemically Created Highly Surface Roughened Ag Nanoplate Arrays for SERS Biosensing Applications. | Yang S, Slotcavage D, Mai JD, Guo F, Li S, Zhao Y, Lei Y, Cameron CE, Huang TJ | Journal of materials chemistry. C | 25383191 | J Mater Chem C Mater | 2014 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/25383191 |
| High-speed optical humidity sensors based on chiral sculptured thin films. | Liu YJ, Shi J, Zhang F, Liang H, Xu J, Lakhtakia A, Fonash SJ, Huang TJ | Sensors and actuators. B, Chemical | 30739999 | Sens Actuators B Chem | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30739999 |
| Large-Scale Fabrication of Three-Dimensional Surface Patterns Using Template-Defined Electrochemical Deposition. | Yang S, Lapsley MI, Cao B, Zhao C, Zhao Y, Hao Q, Kiraly B, Scott J, Li W, Wang L, Lei Y, Huang TJ | Advanced functional materials | 31588203 | Adv Funct Mater | 2013 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/31588203 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| Statistical metamodeling for revealing synergistic antimicrobial interactions. | Chen HC, Gau V, Zhang DD, Liao JC, Wang FY, Wong PK | PloS one | 21124958 | PLoS One | 2010 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/21124958 |
| 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 |
| 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 |
| AC Electrokinetics of Physiological Fluids for Biomedical Applications. | Lu Y, Liu T, Lamanda AC, Sin ML, Gau V, Liao JC, Wong PK | Journal of laboratory automation | 25487557 | J Lab Autom | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25487557 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Oncogenic KRAS confers chemoresistance by upregulating NRF2. | Tao S, Wang S, Moghaddam SJ, Ooi A, Chapman E, Wong PK, Zhang DD | Cancer research | 25339352 | Cancer Res | 2014 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/25339352 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cervical and Tumor-Associated Microbiomes in Botswana Women With and Without HIV With Carcinoma of the Cervix Before and After Definitive Chemoradiation. | Sims TT, Yoshida-Court K, El Alam MB, Ramatlho P, Ketlametswe R, Ning MS, Robertson ES, Schmeler KM, Colbert LE, Klopp AH, Grover S | JCO global oncology | 41160784 | JCO Glob Oncol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41160784 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Variants in Solute Carrier SLC26A9 Modify Prenatal Exocrine Pancreatic Damage in Cystic Fibrosis. | Miller MR, Soave D, Li W, Gong J, Pace RG, Boëlle PY, Cutting GR, Drumm ML, Knowles MR, Sun L, Rommens JM, Accurso F, Durie PR, Corvol H, Levy H, Sontag MK, Strug LJ | The Journal of pediatrics | 25771386 | J Pediatr | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25771386 |
| Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. | Levy H, Wang X, Kaldunski M, Jia S, Kramer J, Pavletich SJ, Reske M, Gessel T, Yassai M, Quasney MW, Dahmer MK, Gorski J, Hessner MJ | Genes and immunity | 22972474 | Genes Immun | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22972474 |
| Risk factors for the progression of cystic fibrosis lung disease throughout childhood. | Sanders DB, Li Z, Laxova A, Rock MJ, Levy H, Collins J, Ferec C, Farrell PM | Annals of the American Thoracic Society | 24261460 | Ann Am Thorac Soc | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24261460 |
| Genome-wide association meta-analysis identifies five modifier loci of lung disease severity in cystic fibrosis. | Corvol H, Blackman SM, Boëlle PY, Gallins PJ, Pace RG, Stonebraker JR, Accurso FJ, Clement A, Collaco JM, Dang H, Dang AT, Franca A, Gong J, Guillot L, Keenan K, Li W, Lin F, Patrone MV, Raraigh KS, Sun L, Zhou YH, O'Neal WK, Sontag MK, Levy H, Durie PR, Rommens JM, Drumm ML, Wright FA, Strug LJ, Cutting GR, Knowles MR | Nature communications | 26417704 | Nat Commun | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26417704 |
| Changing incidence of cystic fibrosis in Wisconsin, USA. | Parker-McGill K, Nugent M, Bersie R, Hoffman G, Rock M, Baker M, Farrell PM, Simpson P, Levy H | Pediatric pulmonology | 26258862 | Pediatr Pulmonol | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26258862 |
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| Transcriptional consequences of impaired immune cell responses induced by cystic fibrosis plasma characterized via dual RNA sequencing. | Ideozu JE, Rangaraj V, Abdala-Valencia H, Zhang X, Kandpal M, Sala MA, Davuluri RV, Levy H | BMC medical genomics | 31118097 | BMC Med Genomics | 2019 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/31118097 |
| Refining the continuum of CFTR-associated disorders in the era of newborn screening. | Levy H, Nugent M, Schneck K, Stachiw-Hietpas D, Laxova A, Lakser O, Rock M, Dahmer MK, Biller J, Nasr SZ, Baker M, McColley SA, Simpson P, Farrell PM | Clinical genetics | 26671754 | Clin Genet | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26671754 |
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| CFTR-mediated monocyte/macrophage dysfunction revealed by cystic fibrosis proband-parent comparisons. | Zhang X, Moore CM, Harmacek LD, Domenico J, Rangaraj VR, Ideozu JE, Knapp JR, Woods KJ, Jump S, Jia S, Prokop JW, Bowler R, Hessner MJ, Gelfand EW, Levy H | JCI insight | 35315363 | JCI Insight | 2022 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/35315363 |
| Cystic fibrosis mutations for p.F508del compound heterozygotes predict sweat chloride levels and pancreatic sufficiency. | Sebro R, Levy H, Schneck K, Dimmock D, Raby BA, Cannon CL, Broeckel U, Risch NJ | Clinical genetics | 22035343 | Clin Genet | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22035343 |
| Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. | Levy H, Jia S, Pan A, Zhang X, Kaldunski M, Nugent ML, Reske M, Feliciano RA, Quintero D, Renda MM, Woods KJ, Murkowski K, Johnson K, Verbsky J, Dasu T, Ideozu JE, McColley S, Quasney MW, Dahmer MK, Avner E, Farrell PM, Cannon CL, Jacob H, Simpson PM, Hessner MJ | Physiological genomics | 30540547 | Physiol Genomics | 2019 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/30540547 |
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| New challenges in the diagnosis and management of cystic fibrosis. | Levy H, Farrell PM | The Journal of pediatrics | 26008169 | J Pediatr | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26008169 |
| Association of cystic fibrosis transmembrane conductance regulator gene variants with acute lung injury in African American children with pneumonia*. | Baughn JM, Quasney MW, Simpson P, Merchant D, Li SH, Levy H, Dahmer MK | Critical care medicine | 22890249 | Crit Care Med | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22890249 |
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| Increased Expression of Plasma-Induced ABCC1 mRNA in Cystic Fibrosis. | Ideozu JE, Zhang X, Pan A, Ashrafi Z, Woods KJ, Hessner MJ, Simpson P, Levy H | International journal of molecular sciences | 28800122 | Int J Mol Sci | 2017 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/28800122 |
| Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci. | Gong J, Wang F, Xiao B, Panjwani N, Lin F, Keenan K, Avolio J, Esmaeili M, Zhang L, He G, Soave D, Mastromatteo S, Baskurt Z, Kim S, O'Neal WK, Polineni D, Blackman SM, Corvol H, Cutting GR, Drumm M, Knowles MR, Rommens JM, Sun L, Strug LJ | PLoS genetics | 30807572 | PLoS Genet | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30807572 |
| Systems-based technologies in profiling the stem cell molecular framework for cardioregenerative medicine. | Wyles SP, Faustino RS, Li X, Terzic A, Nelson TJ | Stem cell reviews and reports | 25218144 | Stem Cell Rev Rep | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25218144 |
| Inhibition of DNA topoisomerase II selectively reduces the threat of tumorigenicity following induced pluripotent stem cell-based myocardial therapy. | Wyles SP, Yamada S, Oommen S, Maleszewski JJ, Beraldi R, Martinez-Fernandez A, Terzic A, Nelson TJ | Stem cells and development | 25036735 | Stem Cells Dev | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/25036735 |
| Stem cells: the pursuit of genomic stability. | Wyles SP, Brandt EB, Nelson TJ | International journal of molecular sciences | 25405730 | Int J Mol Sci | 2014 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/25405730 |
| Natural cardiogenesis-based template predicts cardiogenic potential of induced pluripotent stem cell lines. | Martinez-Fernandez A, Li X, Hartjes KA, Terzic A, Nelson TJ | Circulation. Cardiovascular genetics | 24036272 | Circ Cardiovasc Genet | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24036272 |
| Modeling structural and functional deficiencies of RBM20 familial dilated cardiomyopathy using human induced pluripotent stem cells. | Wyles SP, Li X, Hrstka SC, Reyes S, Oommen S, Beraldi R, Edwards J, Terzic A, Olson TM, Nelson TJ | Human molecular genetics | 26604136 | Hum Mol Genet | 2016 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/26604136 |
| Disease-causing mitochondrial heteroplasmy segregated within induced pluripotent stem cell clones derived from a patient with MELAS. | Folmes CD, Martinez-Fernandez A, Perales-Clemente E, Li X, McDonald A, Oglesbee D, Hrstka SC, Perez-Terzic C, Terzic A, Nelson TJ | Stem cells (Dayton, Ohio) | 23553816 | Stem Cells | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23553816 |
| Apoptotic susceptibility to DNA damage of pluripotent stem cells facilitates pharmacologic purging of teratoma risk. | Smith AJ, Nelson NG, Oommen S, Hartjes KA, Folmes CD, Terzic A, Nelson TJ | Stem cells translational medicine | 23197662 | Stem Cells Transl Med | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23197662 |
| The science and ethics of induced pluripotency: what will become of embryonic stem cells? | Zacharias DG, Nelson TJ, Mueller PS, Hook CC | Mayo Clinic proceedings | 21719620 | Mayo Clin Proc | 2011 Jul | https://www.ncbi.nlm.nih.gov/pubmed/21719620 |
| Transcriptional atlas of cardiogenesis maps congenital heart disease interactome. | Li X, Martinez-Fernandez A, Hartjes KA, Kocher JP, Olson TM, Terzic A, Nelson TJ | Physiological genomics | 24803680 | Physiol Genomics | 2014 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/24803680 |
| Pharmacological Modulation of Calcium Homeostasis in Familial Dilated Cardiomyopathy: An In Vitro Analysis From an RBM20 Patient-Derived iPSC Model. | Wyles SP, Hrstka SC, Reyes S, Terzic A, Olson TM, Nelson TJ | Clinical and translational science | 27105042 | Clin Transl Sci | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27105042 |
| Natural underlying mtDNA heteroplasmy as a potential source of intra-person hiPSC variability. | Perales-Clemente E, Cook AN, Evans JM, Roellinger S, Secreto F, Emmanuele V, Oglesbee D, Mootha VK, Hirano M, Schon EA, Terzic A, Nelson TJ | The EMBO journal | 27436875 | EMBO J | 2016 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/27436875 |
| Rbm20-deficient cardiogenesis reveals early disruption of RNA processing and sarcomere remodeling establishing a developmental etiology for dilated cardiomyopathy. | Beraldi R, Li X, Martinez Fernandez A, Reyes S, Secreto F, Terzic A, Olson TM, Nelson TJ | Human molecular genetics | 24584570 | Hum Mol Genet | 2014 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/24584570 |
| Selection via pluripotency-related transcriptional screen minimizes the influence of somatic origin on iPSC differentiation propensity. | Hartjes KA, Li X, Martinez-Fernandez A, Roemmich AJ, Larsen BT, Terzic A, Nelson TJ | Stem cells (Dayton, Ohio) | 24802033 | Stem Cells | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24802033 |
| Human umbilical cord blood-derived mononuclear cells improve murine ventricular function upon intramyocardial delivery in right ventricular chronic pressure overload. | Oommen S, Yamada S, Cantero Peral S, Campbell KA, Bruinsma ES, Terzic A, Nelson TJ | Stem cell research & therapy | 25890300 | Stem Cell Res Ther | 2015 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/25890300 |
| Induced pluripotent stem cells for cardiovascular disease: from product-focused disease modeling to process-focused disease discovery. | Campbell KA, Terzic A, Nelson TJ | Regenerative medicine | 26439809 | Regen Med | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26439809 |
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| Adipose circadian clocks: coordination of metabolic rhythms by clock genes, steroid hormones, and PPARs. | Krueger KC, Feldman BJ | Hormone molecular biology and clinical investigation | 25436716 | Horm Mol Biol Clin Investig | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25436716 |
| Cell-autonomous regulation of brown fat identity gene UCP1 by unliganded vitamin D receptor. | Malloy PJ, Feldman BJ | Molecular endocrinology (Baltimore, Md.) | 23906633 | Mol Endocrinol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23906633 |
| Using SRM-MS to quantify nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice. | Ota A, Kovary KM, Wu OH, Ahrends R, Shen WJ, Costa MJ, Feldman BJ, Kraemer FB, Teruel MN | Journal of lipid research | 25840986 | J Lipid Res | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25840986 |
| The Circadian Clock Regulates Adipogenesis by a Per3 Crosstalk Pathway to Klf15. | Aggarwal A, Costa MJ, Rivero-Gutiérrez B, Ji L, Morgan SL, Feldman BJ | Cell reports | 29186676 | Cell Rep | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/29186676 |
| Circadian rhythm gene period 3 is an inhibitor of the adipocyte cell fate. | Costa MJ, So AY, Kaasik K, Krueger KC, Pillsbury ML, Fu YH, Ptacek LJ, Yamamoto KR, Feldman BJ | The Journal of biological chemistry | 21228270 | J Biol Chem | 2011 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/21228270 |
| A plasmonic chip for biomarker discovery and diagnosis of type 1 diabetes. | Zhang B, Kumar RB, Dai H, Feldman BJ | Nature medicine | 25038825 | Nat Med | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25038825 |
| Vitamin D Regulates Fatty Acid Composition in Subcutaneous Adipose Tissue Through Elovl3. | Ji L, Gupta M, Feldman BJ | Endocrinology | 26488808 | Endocrinology | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26488808 |
| Inhibition of Mouse Breast Tumor-Initiating Cells by Calcitriol and Dietary Vitamin D. | Jeong Y, Swami S, Krishnan AV, Williams JD, Martin S, Horst RL, Albertelli MA, Feldman BJ, Feldman D, Diehn M | Molecular cancer therapeutics | 25934710 | Mol Cancer Ther | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25934710 |
| Tumor Autonomous Effects of Vitamin D Deficiency Promote Breast Cancer Metastasis. | Williams JD, Aggarwal A, Swami S, Krishnan AV, Ji L, Albertelli MA, Feldman BJ | Endocrinology | 26934299 | Endocrinology | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26934299 |
| Global survey of cell death mechanisms reveals metabolic regulation of ferroptosis. | Shimada K, Skouta R, Kaplan A, Yang WS, Hayano M, Dixon SJ, Brown LM, Valenzuela CA, Wolpaw AJ, Stockwell BR | Nature chemical biology | 27159577 | Nat Chem Biol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27159577 |
| A glucocorticoid- and diet-responsive pathway toggles adipocyte precursor cell activity in vivo. | Wong JC, Krueger KC, Costa MJ, Aggarwal A, Du H, McLaughlin TL, Feldman BJ | Science signaling | 27811141 | Sci Signal | 2016 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/27811141 |
| Macrophage-released ADAMTS1 promotes muscle stem cell activation. | Du H, Shih CH, Wosczyna MN, Mueller AA, Cho J, Aggarwal A, Rando TA, Feldman BJ | Nature communications | 28939843 | Nat Commun | 2017 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/28939843 |
| BMPR2 preserves mitochondrial function and DNA during reoxygenation to promote endothelial cell survival and reverse pulmonary hypertension. | Diebold I, Hennigs JK, Miyagawa K, Li CG, Nickel NP, Kaschwich M, Cao A, Wang L, Reddy S, Chen PI, Nakahira K, Alcazar MA, Hopper RK, Ji L, Feldman BJ, Rabinovitch M | Cell metabolism | 25863249 | Cell Metab | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25863249 |
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| The development of next-generation screening and diagnostic platforms will change diabetes care. | Kumar RB, Gupta M, Feldman BJ | Expert review of molecular diagnostics | 25583407 | Expert Rev Mol Diagn | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25583407 |
| A minimal fate-selection switch. | Weinberger LS | Current opinion in cell biology | 26611210 | Curr Opin Cell Biol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26611210 |
| RanDeL-Seq: a High-Throughput Method to Map Viral cis- and trans-Acting Elements. | Notton T, Glazier JJ, Saykally VR, Thompson CE, Weinberger LS | mBio | 33468683 | mBio | 2021 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/33468683 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Application of fiber-optic attenuated total reflection-FT-IR methods for in situ characterization of protein delivery systems in real time. | McFearin CL, Sankaranarayanan J, Almutairi A | Analytical chemistry | 21476582 | Anal Chem | 2011 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/21476582 |
| Photochemical mechanisms of light-triggered release from nanocarriers. | Fomina N, Sankaranarayanan J, Almutairi A | Advanced drug delivery reviews | 22386560 | Adv Drug Deliv Rev | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22386560 |
| Nanogels from metal-chelating crosslinkers as versatile platforms applied to copper-64 PET imaging of tumors and metastases. | Lux J, White AG, Chan M, Anderson CJ, Almutairi A | Theranostics | 25553115 | Theranostics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25553115 |
| Light-responsive nanoparticle depot to control release of a small molecule angiogenesis inhibitor in the posterior segment of the eye. | Huu VA, Luo J, Zhu J, Zhu J, Patel S, Boone A, Mahmoud E, McFearin C, Olejniczak J, de Gracia Lux C, Lux J, Fomina N, Huynh M, Zhang K, Almutairi A | Journal of controlled release : official journal of the Controlled Release Society | 25571784 | J Control Release | 2015 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/25571784 |
| Collective activation of MRI agents via encapsulation and disease-triggered release. | Viger ML, Sankaranarayanan J, de Gracia Lux C, Chan M, Almutairi A | Journal of the American Chemical Society | 23672342 | J Am Chem Soc | 2013 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/23672342 |
| Highest Efficiency Two-Photon Degradable Copolymer for Remote Controlled Release. | Olejniczak J, Sankaranarayanan J, Viger ML, Almutairi A | ACS macro letters | 24044102 | ACS Macro Lett | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/24044102 |
| 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 |
| 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 |
| Nanogels as imaging agents for modalities spanning the electromagnetic spectrum. | Chan M, Almutairi A | Materials horizons | 27398218 | Mater Horiz | 2016 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/27398218 |
| Light-triggered chemical amplification to accelerate degradation and release from polymeric particles. | Olejniczak J, Nguyen Huu VA, Lux J, Grossman M, He S, Almutairi A | Chemical communications (Cambridge, England) | 26445896 | Chem Commun (Camb) | 2015 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/26445896 |
| Density gradient multilayer polymerization for creating complex tissue. | Karpiak JV, Ner Y, Almutairi A | Advanced materials (Deerfield Beach, Fla.) | 22318771 | Adv Mater | 2012 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/22318771 |
| Iron oxide nanoparticle-based magnetic resonance method to monitor release kinetics from polymeric particles with high resolution. | Chan M, Schopf E, Sankaranarayanan J, Almutairi A | Analytical chemistry | 22891894 | Anal Chem | 2012 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/22891894 |
| An extracellular MRI polymeric contrast agent that degrades at physiological pH. | Schopf E, Sankaranarayanan J, Chan M, Mattrey R, Almutairi A | Molecular pharmaceutics | 22657107 | Mol Pharm | 2012 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/22657107 |
| Metal Chelating Crosslinkers Form Nanogels with High Chelation Stability. | Lux J, Chan M, Elst LV, Schopf E, Mahmoud E, Laurent S, Almutairi A | Journal of materials chemistry. B | 24505553 | J Mater Chem B | 2013 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/24505553 |
| 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 |
| Tunable protein release from acetalated dextran microparticles: a platform for delivery of protein therapeutics to the heart post-MI. | Suarez S, Grover GN, Braden RL, Christman KL, Almutairi A | Biomacromolecules | 24053580 | Biomacromolecules | 2013 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/24053580 |
| Intramyocardial injection of hydrogel with high interstitial spread does not impact action potential propagation. | Suarez SL, Rane AA, Muñoz A, Wright AT, Zhang SX, Braden RL, Almutairi A, McCulloch AD, Christman KL | Acta biomaterialia | 26265060 | Acta Biomater | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26265060 |
| Low power, biologically benign NIR light triggers polymer disassembly. | Fomina N, McFearin CL, Sermsakdi M, Morachis JM, Almutairi A | Macromolecules | 22096258 | Macromolecules | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22096258 |
| Increasing materials' response to two-photon NIR light via self-immolative dendritic scaffolds. | Fomina N, McFearin CL, Almutairi A | Chemical communications (Cambridge, England) | 22475792 | Chem Commun (Camb) | 2012 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/22475792 |
| 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 |
| Application of time-resolved fluorescence for direct and continuous probing of release from polymeric delivery vehicles. | Viger ML, Sheng W, McFearin CL, Berezin MY, Almutairi A | Journal of controlled release : official journal of the Controlled Release Society | 23792808 | J Control Release | 2013 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/23792808 |
| Intramolecular Cyclization for Stimuli-Controlled Depolymerization of Polycaprolactone Particles Leading to Disassembly and Payload Release. | de Gracia Lux C, Almutairi A | ACS macro letters | 23814697 | ACS Macro Lett | 2013 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/23814697 |
| Layered hydrogels accelerate iPSC-derived neuronal maturation and reveal migration defects caused by MeCP2 dysfunction. | Zhang ZN, Freitas BC, Qian H, Lux J, Acab A, Trujillo CA, Herai RH, Nguyen Huu VA, Wen JH, Joshi-Barr S, Karpiak JV, Engler AJ, Fu XD, Muotri AR, Almutairi A | Proceedings of the National Academy of Sciences of the United States of America | 26944080 | Proc Natl Acad Sci U S A | 2016 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/26944080 |
| Gold Nanoparticle-assisted Selective Photothermolysis of Adipose Tissue (NanoLipo). | Sheng W, Alhasan AH, DiBernardo G, Almutairi KM, Rubin JP, DiBernardo BE, Almutairi A | Plastic and reconstructive surgery. Global open | 25587517 | Plast Reconstr Surg Glob Open | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25587517 |
| Exploiting oxidative microenvironments in the body as triggers for drug delivery systems. | Joshi-Barr S, de Gracia Lux C, Mahmoud E, Almutairi A | Antioxidants & redox signaling | 24328819 | Antioxid Redox Signal | 2014 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/24328819 |
| 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 |
| Near-infrared-induced heating of confined water in polymeric particles for efficient payload release. | Viger ML, Sheng W, Doré K, Alhasan AH, Carling CJ, Lux J, de Gracia Lux C, Grossman M, Malinow R, Almutairi A | ACS nano | 24717072 | ACS Nano | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24717072 |
| Antigen-loaded pH-sensitive hydrogel microparticles are taken up by dendritic cells with no requirement for targeting antibodies. | Ruff LE, Mahmoud EA, Sankaranarayanan J, Morachis JM, Katayama CD, Corr M, Hedrick SM, Almutairi A | Integrative biology : quantitative biosciences from nano to macro | 23060228 | Integr Biol (Camb) | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23060228 |
| Density gradient multilayered polymerization (DGMP): a novel technique for creating multi-compartment, customizable scaffolds for tissue engineering. | Joshi-Barr S, Karpiak JV, Ner Y, Wen JH, Engler AJ, Almutairi A | Journal of visualized experiments : JoVE | 23426045 | J Vis Exp | 2013 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/23426045 |
| 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 Visible Light-Triggered Drug Release From an Implanted Depot. | Carling CJ, Viger ML, Huu VA, Garcia AV, Almutairi A | Chemical science | 25598962 | Chem Sci | 2015 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/25598962 |
| Multiresponse strategies to modulate burst degradation and release from nanoparticles. | Sankaranarayanan J, Mahmoud EA, Kim G, Morachis JM, Almutairi A | ACS nano | 20828178 | ACS Nano | 2010 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/20828178 |
| Long-Lasting and Efficient Tumor Imaging Using a High Relaxivity Polysaccharide Nanogel Magnetic Resonance Imaging Contrast Agent. | Chan M, Lux J, Nishimura T, Akiyoshi K, Almutairi A | Biomacromolecules | 26278775 | Biomacromolecules | 2015 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/26278775 |
| Photocontrolled release using one-photon absorption of visible or NIR light. | Olejniczak J, Carling CJ, Almutairi A | Journal of controlled release : official journal of the Controlled Release Society | 26394063 | J Control Release | 2015 Dec 10 | https://www.ncbi.nlm.nih.gov/pubmed/26394063 |
| Spatial self-organization favors heterotypic cooperation over cheating. | Momeni B, Waite AJ, Shou W | eLife | 24220506 | Elife | 2013 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/24220506 |
| Simulations reveal challenges to artificial community selection and possible strategies for success. | Xie L, Yuan AE, Shou W | PLoS biology | 31237866 | PLoS Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31237866 |
| Disentangling strictly self-serving mutations from win-win mutations in a mutualistic microbial community. | Hart SFM, Pineda JMB, Chen CC, Green R, Shou W | eLife | 31162049 | Elife | 2019 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/31162049 |
| Adaptation to a new environment allows cooperators to purge cheaters stochastically. | Waite AJ, Shou W | Proceedings of the National Academy of Sciences of the United States of America | 23091010 | Proc Natl Acad Sci U S A | 2012 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/23091010 |
| Strong inter-population cooperation leads to partner intermixing in microbial communities. | Momeni B, Brileya KA, Fields MW, Shou W | eLife | 23359860 | Elife | 2013 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/23359860 |
| Constructing synthetic microbial communities to explore the ecology and evolution of symbiosis. | Waite AJ, Shou W | Methods in molecular biology (Clifton, N.J.) | 24838876 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24838876 |
| Defectors Can Create Conditions That Rescue Cooperation. | Waite AJ, Cannistra C, Shou W | PLoS computational biology | 26690946 | PLoS Comput Biol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26690946 |
| Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth. | Skelding D, Hart SFM, Vidyasagar T, Pozhitkov AE, Shou W | Quantitative biology (Beijing, China) | 31598380 | Quant Biol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31598380 |
| Metabolic excretion associated with nutrient-growth dysregulation promotes the rapid evolution of an overt metabolic defect. | Green R, Sonal, Wang L, Hart SFM, Lu W, Skelding D, Burton JC, Mi H, Capel A, Chen HA, Lin A, Subramaniam AR, Rabinowitz JD, Shou W | PLoS biology | 32833957 | PLoS Biol | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32833957 |
| Pleiotropic mutations can rapidly evolve to directly benefit self and cooperative partner despite unfavorable conditions. | Hart SFM, Chen CC, Shou W | eLife | 33501915 | Elife | 2021 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/33501915 |
| Modeling community population dynamics with the open-source language R. | Green R, Shou W | Methods in molecular biology (Clifton, N.J.) | 24838889 | Methods Mol Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24838889 |
| Using artificial systems to explore the ecology and evolution of symbioses. | Momeni B, Chen CC, Hillesland KL, Waite A, Shou W | Cellular and molecular life sciences : CMLS | 21424911 | Cell Mol Life Sci | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21424911 |
| High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy. | Hart SFM, Skelding D, Waite AJ, Burton JC, Shou W | Quantitative biology (Beijing, China) | 31598381 | Quant Biol | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31598381 |
| Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells. | Hart SFM, Mi H, Green R, Xie L, Pineda JMB, Momeni B, Shou W | PLoS biology | 30794534 | PLoS Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30794534 |
| L1 retrotransposition in neurons is modulated by MeCP2. | Muotri AR, Marchetto MC, Coufal NG, Oefner R, Yeo G, Nakashima K, Gage FH | Nature | 21085180 | Nature | 2010 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/21085180 |
| 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 |
| Severe Hypoxia: Consequences to Neural Stem Cells and Neurons. | Felfly H, Zambon AC, Xue J, Muotri A, Zhou D, Snyder EY, Haddad GG | Journal of neurology research | 24348887 | J Neurol Res | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/24348887 |
| 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 |
| 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 |
| LINE-1 retrotransposition in the nervous system. | Thomas CA, Paquola AC, Muotri AR | Annual review of cell and developmental biology | 23057747 | Annu Rev Cell Dev Biol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23057747 |
| 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 |
| 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 |
| Pharmacological reversal of synaptic and network pathology in human MECP2-KO neurons and cortical organoids. | Trujillo CA, Adams JW, Negraes PD, Carromeu C, Tejwani L, Acab A, Tsuda B, Thomas CA, Sodhi N, Fichter KM, Romero S, Zanella F, Sejnowski TJ, Ulrich H, Muotri AR | EMBO molecular medicine | 33501759 | EMBO Mol Med | 2021 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/33501759 |
| A human neurodevelopmental model for Williams syndrome. | Chailangkarn T, Trujillo CA, Freitas BC, Hrvoj-Mihic B, Herai RH, Yu DX, Brown TT, Marchetto MC, Bardy C, McHenry L, Stefanacci L, Järvinen A, Searcy YM, DeWitt M, Wong W, Lai P, Ard MC, Hanson KL, Romero S, Jacobs B, Dale AM, Dai L, Korenberg JR, Gage FH, Bellugi U, Halgren E, Semendeferi K, Muotri AR | Nature | 27509850 | Nature | 2016 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/27509850 |
| Proteomic analyses reveal misregulation of LIN28 expression and delayed timing of glial differentiation in human iPS cells with MECP2 loss-of-function. | Kim JJ, Savas JN, Miller MT, Hu X, Carromeu C, Lavallée-Adam M, Freitas BCG, Muotri AR, Yates JR 3rd, Ghosh A | PloS one | 30789962 | PLoS One | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30789962 |
| Loss of GTF2I promotes neuronal apoptosis and synaptic reduction in human cellular models of neurodevelopment. | Adams JW, Vinokur A, de Souza JS, Austria C, Guerra BS, Herai RH, Wahlin KJ, Muotri AR | Cell reports | 38416640 | Cell Rep | 2024 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/38416640 |
| Evidence for premature aging due to oxidative stress in iPSCs from Cockayne syndrome. | Andrade LN, Nathanson JL, Yeo GW, Menck CF, Muotri AR | Human molecular genetics | 22661500 | Hum Mol Genet | 2012 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/22661500 |
| Modeling neurodevelopmental disorders using human neurons. | Chailangkarn T, Acab A, Muotri AR | Current opinion in neurobiology | 22717528 | Curr Opin Neurobiol | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22717528 |
| Altered neuronal network and rescue in a human MECP2 duplication model. | Nageshappa S, Carromeu C, Trujillo CA, Mesci P, Espuny-Camacho I, Pasciuto E, Vanderhaeghen P, Verfaillie CM, Raitano S, Kumar A, Carvalho CM, Bagni C, Ramocki MB, Araujo BH, Torres LB, Lupski JR, Van Esch H, Muotri AR | Molecular psychiatry | 26347316 | Mol Psychiatry | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26347316 |
| Modeling non-syndromic autism and the impact of TRPC6 disruption in human neurons. | Griesi-Oliveira K, Acab A, Gupta AR, Sunaga DY, Chailangkarn T, Nicol X, Nunez Y, Walker MF, Murdoch JD, Sanders SJ, Fernandez TV, Ji W, Lifton RP, Vadasz E, Dietrich A, Pradhan D, Song H, Ming GL, Gu X, Haddad G, Marchetto MC, Spitzer N, Passos-Bueno MR, State MW, Muotri AR | Molecular psychiatry | 25385366 | Mol Psychiatry | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25385366 |
| 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 |
| Cockayne syndrome-derived neurons display reduced synapse density and altered neural network synchrony. | Vessoni AT, Herai RH, Karpiak JV, Leal AM, Trujillo CA, Quinet A, Agnez Lima LF, Menck CF, Muotri AR | Human molecular genetics | 26755826 | Hum Mol Genet | 2016 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/26755826 |
| 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 |
| 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 |
| Astroglial cells regulate the developmental timeline of human neurons differentiated from induced pluripotent stem cells. | Tang X, Zhou L, Wagner AM, Marchetto MC, Muotri AR, Gage FH, Chen G | Stem cell research | 23759711 | Stem Cell Res | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23759711 |
| KCC2 rescues functional deficits in human neurons derived from patients with Rett syndrome. | Tang X, Kim J, Zhou L, Wengert E, Zhang L, Wu Z, Carromeu C, Muotri AR, Marchetto MC, Gage FH, Chen G | Proceedings of the National Academy of Sciences of the United States of America | 26733678 | Proc Natl Acad Sci U S A | 2016 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/26733678 |
| Bradykinin promotes neuron-generating division of neural progenitor cells through ERK activation. | Pillat MM, Lameu C, Trujillo CA, Glaser T, Cappellari AR, Negraes PD, Battastini AM, Schwindt TT, Muotri AR, Ulrich H | Journal of cell science | 27528403 | J Cell Sci | 2016 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/27528403 |
| 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 |
| Micro RNA detection in long-term fixed tissue of cortical glutamatergic pyramidal neurons after targeted laser-capture neuroanatomical microdissection. | Herai RR, Stefanacci L, Hrvoj-Mihic B, Chailangkarn T, Hanson K, Semendeferi K, Muotri AR | Journal of neuroscience methods | 24992573 | J Neurosci Methods | 2014 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/24992573 |
| Polyglutamine-expanded androgen receptor interferes with TFEB to elicit autophagy defects in SBMA. | Cortes CJ, Miranda HC, Frankowski H, Batlevi Y, Young JE, Le A, Ivanov N, Sopher BL, Carromeu C, Muotri AR, Garden GA, La Spada AR | Nature neuroscience | 25108912 | Nat Neurosci | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25108912 |
| 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 |
| Novel tools, classic techniques: evolutionary studies using primate pluripotent stem cells. | Hrvoj-Mihic B, Marchetto MC, Gage FH, Semendeferi K, Muotri AR | Biological psychiatry | 24041506 | Biol Psychiatry | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24041506 |
| 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 |
| Altered iPSC-derived neurons' sodium channel properties in subjects with Monge's disease. | Zhao HW, Gu XQ, Chailangkarn T, Perkins G, Callacondo D, Appenzeller O, Poulsen O, Zhou D, Muotri AR, Haddad GG | Neuroscience | 25559931 | Neuroscience | 2015 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/25559931 |
| Ataxia telangiectasia mutated (ATM) modulates long interspersed element-1 (L1) retrotransposition in human neural stem cells. | Coufal NG, Garcia-Perez JL, Peng GE, Marchetto MC, Muotri AR, Mu Y, Carson CT, Macia A, Moran JV, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 22159035 | Proc Natl Acad Sci U S A | 2011 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/22159035 |
| L1 Retrotransposition in Neural Progenitor Cells. | Muotri AR | Methods in molecular biology (Clifton, N.J.) | 26895053 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26895053 |
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| 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 |
| De novo self-assembling collagen heterotrimers using explicit positive and negative design. | Xu F, Zhang L, Koder RL, Nanda V | Biochemistry | 20170197 | Biochemistry | 2010 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/20170197 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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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 |
| 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 |
| Empirical estimation of local dielectric constants: Toward atomistic design of collagen mimetic peptides. | Pike DH, Nanda V | Biopolymers | 25784456 | Biopolymers | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25784456 |
| 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 |
| Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides. | Maeda Y, Fang J, Ikezoe Y, Pike DH, Nanda V, Matsui H | PloS one | 27116246 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27116246 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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: 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 |
| 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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| Nanoparticle surface charge mediates the cellular receptors used by protein-nanoparticle complexes. | Fleischer CC, Payne CK | The journal of physical chemistry. B | 22774860 | J Phys Chem B | 2012 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/22774860 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| Magnetoencephalography correlate of EEG POSTS (positive occipital sharp transients of sleep). | Kakisaka Y, Wang ZI, Enatsu R, Dubarry AS, Mosher JC, Alexopoulos AV, Burgess RC | Journal of clinical neurophysiology : official publication of the American Electroencephalographic Society | 23733086 | J Clin Neurophysiol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23733086 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Bacterial cell widening alters periplasmic size and activates envelope stress responses. | Zietek M, Miguel A, Shi H, Khusainov I, Asmar AT, Ram S, Wartel M, Sueki A, Schorb M, Goulian M, Collet JF, Beck M, Huang KC, Typas A | The EMBO journal | 40903550 | EMBO J | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40903550 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| A Programmable DNA Origami Platform to Organize SNAREs for Membrane Fusion. | Xu W, Nathwani B, Lin C, Wang J, Karatekin E, Pincet F, Shih W, Rothman JE | Journal of the American Chemical Society | 26938705 | J Am Chem Soc | 2016 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/26938705 |
| Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. | Perrault SD, Shih WM | ACS nano | 24694301 | ACS Nano | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24694301 |
| Two design strategies for enhancement of multilayer-DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. | Ke Y, Bellot G, Voigt NV, Fradkov E, Shih WM | Chemical science | 24653832 | Chem Sci | 2012 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/24653832 |
| Designing DNA Nanotube Liquid Crystals as a Weak-Alignment Medium for NMR Structure Determination of Membrane Proteins. | Min J, Shih WM, Bellot G | Methods in molecular biology (Clifton, N.J.) | 27813010 | Methods Mol Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/27813010 |
| Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. | Ducani C, Kaul C, Moche M, Shih WM, Högberg B | Nature methods | 23727986 | Nat Methods | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23727986 |
| Disruption of helix-capping residues 671 and 674 reveals a role in HIV-1 entry for a specialized hinge segment of the membrane proximal external region of gp41. | Sun ZY, Cheng Y, Kim M, Song L, Choi J, Kudahl UJ, Brusic V, Chowdhury B, Yu L, Seaman MS, Bellot G, Shih WM, Wagner G, Reinherz EL | Journal of molecular biology | 24075869 | J Mol Biol | 2014 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/24075869 |
| Self-assembly of DNA into nanoscale three-dimensional shapes. | Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM | Nature | 19458720 | Nature | 2009 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/19458720 |
| Multilayer DNA origami packed on hexagonal and hybrid lattices. | Ke Y, Voigt NV, Gothelf KV, Shih WM | Journal of the American Chemical Society | 22187940 | J Am Chem Soc | 2012 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/22187940 |
| Aldolase provides an unusual binding site for thrombospondin-related anonymous protein in the invasion machinery of the malaria parasite. | Bosch J, Buscaglia CA, Krumm B, Ingason BP, Lucas R, Roach C, Cardozo T, Nussenzweig V, Hol WG | Proceedings of the National Academy of Sciences of the United States of America | 17426153 | Proc Natl Acad Sci U S A | 2007 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/17426153 |
| Recombinant derivatives of botulinum neurotoxin A engineered for trafficking studies and neuronal delivery. | Band PA, Blais S, Neubert TA, Cardozo TJ, Ichtchenko K | Protein expression and purification | 20045734 | Protein Expr Purif | 2010 May | https://www.ncbi.nlm.nih.gov/pubmed/20045734 |
| Inhibitors of SCF-Skp2/Cks1 E3 ligase block estrogen-induced growth stimulation and degradation of nuclear p27kip1: therapeutic potential for endometrial cancer. | Pavlides SC, Huang KT, Reid DA, Wu L, Blank SV, Mittal K, Guo L, Rothenberg E, Rueda B, Cardozo T, Gold LI | Endocrinology | 24035998 | Endocrinology | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24035998 |
| Vaccine focusing to cross-subtype HIV-1 gp120 variable loop epitopes. | Cardozo T, Wang S, Jiang X, Kong XP, Hioe C, Krachmarov C | Vaccine | 25045827 | Vaccine | 2014 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/25045827 |
| Specific increase in potency via structure-based design of a TCR. | Malecek K, Grigoryan A, Zhong S, Gu WJ, Johnson LA, Rosenberg SA, Cardozo T, Krogsgaard M | Journal of immunology (Baltimore, Md. : 1950) | 25070852 | J Immunol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25070852 |
| Specific small molecule inhibitors of Skp2-mediated p27 degradation. | Wu L, Grigoryan AV, Li Y, Hao B, Pagano M, Cardozo TJ | Chemistry & biology | 23261596 | Chem Biol | 2012 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/23261596 |
| Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate. | Goyanka R, Das S, Samuels HH, Cardozo T | Protein engineering, design & selection : PEDS | 20817759 | Protein Eng Des Sel | 2010 Nov | https://www.ncbi.nlm.nih.gov/pubmed/20817759 |
| Triazolo[4,5-d]pyrimidines as Validated General Control Nonderepressible 2 (GCN2) Protein Kinase Inhibitors Reduce Growth of Leukemia Cells. | Lough L, Sherman D, Beccera-Flores M, Lavinda O, Ni E, Wang H, Tibes R, Cardozo T | Computational and structural biotechnology journal | 30364637 | Comput Struct Biotechnol J | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30364637 |
| Translational induction of ATF4 during integrated stress response requires noncanonical initiation factors eIF2D and DENR. | Vasudevan D, Neuman SD, Yang A, Lough L, Brown B, Bashirullah A, Cardozo T, Ryoo HD | Nature communications | 32938929 | Nat Commun | 2020 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/32938929 |
| Inhibition by stabilization: targeting the Plasmodium falciparum aldolase-TRAP complex. | Nemetski SM, Cardozo TJ, Bosch G, Weltzer R, O'Malley K, Ejigiri I, Kumar KA, Buscaglia CA, Nussenzweig V, Sinnis P, Levitskaya J, Bosch J | Malaria journal | 26289816 | Malar J | 2015 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/26289816 |
| Quantitative assessment of masking of neutralization epitopes in HIV-1. | Agarwal A, Hioe CE, Swetnam J, Zolla-Pazner S, Cardozo T | Vaccine | 21216319 | Vaccine | 2011 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/21216319 |
| Tagetitoxin inhibits RNA polymerase through trapping of the trigger loop. | Artsimovitch I, Svetlov V, Nemetski SM, Epshtein V, Cardozo T, Nudler E | The Journal of biological chemistry | 21976682 | J Biol Chem | 2011 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/21976682 |
| Wrenches in the works: drug discovery targeting the SCF ubiquitin ligase and APC/C complexes. | Cardozo T, Pagano M | BMC biochemistry | 18047746 | BMC Biochem | 2007 Nov 22 | https://www.ncbi.nlm.nih.gov/pubmed/18047746 |
| Structural Model of the Extracellular Assembly of the TCR-CD3 Complex. | Natarajan A, Nadarajah V, Felsovalyi K, Wang W, Jeyachandran VR, Wasson RA, Cardozo T, Bracken C, Krogsgaard M | Cell reports | 26997265 | Cell Rep | 2016 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/26997265 |
| Visualizing the phage T4 activated transcription complex of DNA and E. coli RNA polymerase. | James TD, Cardozo T, Abell LE, Hsieh ML, Jenkins LM, Jha SS, Hinton DM | Nucleic acids research | 27458207 | Nucleic Acids Res | 2016 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/27458207 |
| HIV's Nef interacts with β-catenin of the Wnt signaling pathway in HEK293 cells. | Weiser K, Barton M, Gershoony D, Dasgupta R, Cardozo T | PloS one | 24130899 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24130899 |
| Identification and characterization of small molecules that inhibit nonsense-mediated RNA decay and suppress nonsense p53 mutations. | Martin L, Grigoryan A, Wang D, Wang J, Breda L, Rivella S, Cardozo T, Gardner LB | Cancer research | 24662918 | Cancer Res | 2014 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/24662918 |
| Indirect detection of an epitope-specific response to HIV-1 gp120 immunization in human subjects. | Shmelkov E, Nadas A, Swetnam J, Zolla-Pazner S, Cardozo T | PloS one | 22076145 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22076145 |
| Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies. | Almond D, Krachmarov C, Swetnam J, Zolla-Pazner S, Cardozo T | Advances in virology | 22548061 | Adv Virol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22548061 |
| Assessment of immunologically relevant dynamic tertiary structural features of the HIV-1 V3 loop crown R2 sequence by ab initio folding. | Almond D, Cardozo T | Journal of visualized experiments : JoVE | 20864931 | J Vis Exp | 2010 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/20864931 |
| Can the energy gap in the protein-ligand binding energy landscape be used as a descriptor in virtual ligand screening? | Grigoryan AV, Wang H, Cardozo TJ | PloS one | 23071584 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23071584 |
| Statins Increase Plasminogen Activator Inhibitor Type 1 Gene Transcription through a Pregnane X Receptor Regulated Element. | Stanley FM, Linder KM, Cardozo TJ | PloS one | 26379245 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26379245 |
| An Improved Method for Modeling Voltage-Gated Ion Channels at Atomic Accuracy Applied to Human Ca(v) Channels. | Martinez-Ortiz W, Cardozo TJ | Cell reports | 29719253 | Cell Rep | 2018 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/29719253 |
| Quantitative analysis of T cell receptor complex interaction sites using genetically encoded photo-cross-linkers. | Wang W, Li T, Felsovalyi K, Chen C, Cardozo T, Krogsgaard M | ACS chemical biology | 25061810 | ACS Chem Biol | 2014 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/25061810 |
| Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design. | Zolla-Pazner S, Cardozo T | Nature reviews. Immunology | 20577269 | Nat Rev Immunol | 2010 Jul | https://www.ncbi.nlm.nih.gov/pubmed/20577269 |
| Structural determinants of PERK inhibitor potency and selectivity. | Wang H, Blais J, Ron D, Cardozo T | Chemical biology & drug design | 21070610 | Chem Biol Drug Des | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21070610 |
| Worldwide distribution of HIV type 1 epitopes recognized by human anti-V3 monoclonal antibodies. | Cardozo T, Swetnam J, Pinter A, Krachmarov C, Nadas A, Almond D, Zolla-Pazner S | AIDS research and human retroviruses | 19320565 | AIDS Res Hum Retroviruses | 2009 Apr | https://www.ncbi.nlm.nih.gov/pubmed/19320565 |
| Modulation of Macrophage Gene Expression via Liver X Receptor α Serine 198 Phosphorylation. | Wu C, Hussein MA, Shrestha E, Leone S, Aiyegbo MS, Lambert WM, Pourcet B, Cardozo T, Gustafson JA, Fisher EA, Pineda-Torra I, Garabedian MJ | Molecular and cellular biology | 25825525 | Mol Cell Biol | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/25825525 |
| Assessing quality and completeness of human transcriptional regulatory pathways on a genome-wide scale. | Shmelkov E, Tang Z, Aifantis I, Statnikov A | Biology direct | 21356087 | Biol Direct | 2011 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/21356087 |
| The architecture of CopA from Archeaoglobus fulgidus studied by cryo-electron microscopy and computational docking. | Allen GS, Wu CC, Cardozo T, Stokes DL | Structure (London, England : 1993) | 21820315 | Structure | 2011 Sep 7 | https://www.ncbi.nlm.nih.gov/pubmed/21820315 |
| Ro52 autoantibodies arise from self-reactive progenitors in a mother of a child with neonatal lupus. | Reed JH, Gorny MK, Li L, Cardozo T, Buyon JP, Clancy RM | Journal of autoimmunity | 28118945 | J Autoimmun | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28118945 |
| TRF2, but not TBP, mediates the transcription of ribosomal protein genes. | Wang YL, Duttke SH, Chen K, Johnston J, Kassavetis GA, Zeitlinger J, Kadonaga JT | Genes & development | 24958592 | Genes Dev | 2014 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/24958592 |
| Drosophila poised enhancers are generated during tissue patterning with the help of repression. | Koenecke N, Johnston J, He Q, Meier S, Zeitlinger J | Genome research | 27979994 | Genome Res | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27979994 |
| Hippo Reprograms the Transcriptional Response to Ras Signaling. | Pascual J, Jacobs J, Sansores-Garcia L, Natarajan M, Zeitlinger J, Aerts S, Halder G, Hamaratoglu F | Developmental cell | 28950103 | Dev Cell | 2017 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/28950103 |
| TATA and paused promoters active in differentiated tissues have distinct expression characteristics. | Ramalingam V, Natarajan M, Johnston J, Zeitlinger J | Molecular systems biology | 33543829 | Mol Syst Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33543829 |
| ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. | He Q, Johnston J, Zeitlinger J | Nature biotechnology | 25751057 | Nat Biotechnol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25751057 |
| Identification of transcription factor binding sites from ChIP-seq data at high resolution. | Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A | Bioinformatics (Oxford, England) | 23980024 | Bioinformatics | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/23980024 |
| Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development. | Ramalingam V, Yu X, Slaughter BD, Unruh JR, Brennan KJ, Onyshchenko A, Lange JJ, Natarajan M, Buck M, Zeitlinger J | Nature communications | 37735176 | Nat Commun | 2023 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/37735176 |
| Poised RNA polymerase II changes over developmental time and prepares genes for future expression. | Gaertner B, Johnston J, Chen K, Wallaschek N, Paulson A, Garruss AS, Gaudenz K, De Kumar B, Krumlauf R, Zeitlinger J | Cell reports | 23260668 | Cell Rep | 2012 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/23260668 |
| A global change in RNA polymerase II pausing during the Drosophila midblastula transition. | Chen K, Johnston J, Shao W, Meier S, Staber C, Zeitlinger J | eLife | 23951546 | Elife | 2013 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/23951546 |
| Zelda overcomes the high intrinsic nucleosome barrier at enhancers during Drosophila zygotic genome activation. | Sun Y, Nien CY, Chen K, Liu HY, Johnston J, Zeitlinger J, Rushlow C | Genome research | 26335633 | Genome Res | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26335633 |
| Hibernating squirrel muscle activates the endurance exercise pathway despite prolonged immobilization. | Xu R, Andres-Mateos E, Mejias R, MacDonald EM, Leinwand LA, Merriman DK, Fink RH, Cohn RD | Experimental neurology | 23333568 | Exp Neurol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23333568 |
| One size may not fit all: anti-aging therapies and sarcopenia. | Burks TN, Cohn RD | Aging | 22184279 | Aging (Albany NY) | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22184279 |
| Loss of sarcolemmal nNOS is common in acquired and inherited neuromuscular disorders. | Finanger Hedderick EL, Simmers JL, Soleimani A, Andres-Mateos E, Marx R, Files DC, King L, Crawford TO, Corse AM, Cohn RD | Neurology | 21403107 | Neurology | 2011 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/21403107 |
| Regulation of muscle mass by follistatin and activins. | Lee SJ, Lee YS, Zimmers TA, Soleimani A, Matzuk MM, Tsuchida K, Cohn RD, Barton ER | Molecular endocrinology (Baltimore, Md.) | 20810712 | Mol Endocrinol | 2010 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20810712 |
| TGFβ signaling: its role in fibrosis formation and myopathies. | MacDonald EM, Cohn RD | Current opinion in rheumatology | 22918531 | Curr Opin Rheumatol | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22918531 |
| Activation of serum/glucocorticoid-induced kinase 1 (SGK1) is important to maintain skeletal muscle homeostasis and prevent atrophy. | Andres-Mateos E, Brinkmeier H, Burks TN, Mejias R, Files DC, Steinberger M, Soleimani A, Marx R, Simmers JL, Lin B, Finanger Hedderick E, Marr TG, Lin BM, Hourdé C, Leinwand LA, Kuhl D, Föller M, Vogelsang S, Hernandez-Diaz I, Vaughan DK, Alvarez de la Rosa D, Lang F, Cohn RD | EMBO molecular medicine | 23161797 | EMBO Mol Med | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23161797 |
| Losartan restores skeletal muscle remodeling and protects against disuse atrophy in sarcopenia. | Burks TN, Andres-Mateos E, Marx R, Mejias R, Van Erp C, Simmers JL, Walston JD, Ward CW, Cohn RD | Science translational medicine | 21562229 | Sci Transl Med | 2011 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/21562229 |
| Impaired skeletal muscle regeneration in the absence of fibrosis during hibernation in 13-lined ground squirrels. | Andres-Mateos E, Mejias R, Soleimani A, Lin BM, Burks TN, Marx R, Lin B, Zellars RC, Zhang Y, Huso DL, Marr TG, Leinwand LA, Merriman DK, Cohn RD | PloS one | 23155423 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23155423 |
| Denervation atrophy is independent from Akt and mTOR activation and is not rescued by myostatin inhibition. | MacDonald EM, Andres-Mateos E, Mejias R, Simmers JL, Mi R, Park JS, Ying S, Hoke A, Lee SJ, Cohn RD | Disease models & mechanisms | 24504412 | Dis Model Mech | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24504412 |
| Maintaining skeletal muscle mass: lessons learned from hibernation. | Ivakine EA, Cohn RD | Experimental physiology | 24443348 | Exp Physiol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24443348 |
| The Prp19 WD40 domain contains a conserved protein interaction region essential for its function. | Vander Kooi CW, Ren L, Xu P, Ohi MD, Gould KL, Chazin WJ | Structure (London, England : 1993) | 20462492 | Structure | 2010 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/20462492 |
| Systematic two-hybrid and comparative proteomic analyses reveal novel yeast pre-mRNA splicing factors connected to Prp19. | Ren L, McLean JR, Hazbun TR, Fields S, Vander Kooi C, Ohi MD, Gould KL | PloS one | 21386897 | PLoS One | 2011 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/21386897 |
| Cdk1 phosphorylation of the kinetochore protein Nsk1 prevents error-prone chromosome segregation. | Chen JS, Lu LX, Ohi MD, Creamer KM, English C, Partridge JF, Ohi R, Gould KL | The Journal of cell biology | 22065639 | J Cell Biol | 2011 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/22065639 |
| Structural and functional insights into the N-terminus of Schizosaccharomyces pombe Cdc5. | Collier SE, Voehler M, Peng D, Ohi R, Gould KL, Reiter NJ, Ohi MD | Biochemistry | 25263959 | Biochemistry | 2014 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/25263959 |
| Tailoring of membrane proteins by alternative splicing of pre-mRNA. | Mittendorf KF, Deatherage CL, Ohi MD, Sanders CR | Biochemistry | 22708632 | Biochemistry | 2012 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/22708632 |
| Structural and functional characterization of the N terminus of Schizosaccharomyces pombe Cwf10. | Livesay SB, Collier SE, Bitton DA, Bähler J, Ohi MD | Eukaryotic cell | 24014766 | Eukaryot Cell | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24014766 |
| Glycolytic enzymes localize to ribonucleoprotein granules in Drosophila germ cells, bind Tudor and protect from transposable elements. | Gao M, Thomson TC, Creed TM, Tu S, Loganathan SN, Jackson CA, McCluskey P, Lin Y, Collier SE, Weng Z, Lasko P, Ohi MD, Arkov AL | EMBO reports | 25600116 | EMBO Rep | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25600116 |
| Gle1 functions during mRNA export in an oligomeric complex that is altered in human disease. | Folkmann AW, Collier SE, Zhan X, Aditi, Ohi MD, Wente SR | Cell | 24243016 | Cell | 2013 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/24243016 |
| Ank3-dependent SVZ niche assembly is required for the continued production of new neurons. | Paez-Gonzalez P, Abdi K, Luciano D, Liu Y, Soriano-Navarro M, Rawlins E, Bennett V, Garcia-Verdugo JM, Kuo CT | Neuron | 21745638 | Neuron | 2011 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/21745638 |
| Protective astrogenesis from the SVZ niche after injury is controlled by Notch modulator Thbs4. | Benner EJ, Luciano D, Jo R, Abdi K, Paez-Gonzalez P, Sheng H, Warner DS, Liu C, Eroglu C, Kuo CT | Nature | 23615612 | Nature | 2013 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/23615612 |
| Cysteine proteinase-1 and cut protein isoform control dendritic innervation of two distinct sensory fields by a single neuron. | Lyons GR, Andersen RO, Abdi K, Song WS, Kuo CT | Cell reports | 24582961 | Cell Rep | 2014 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/24582961 |
| Identification of distinct ChAT⁺ neurons and activity-dependent control of postnatal SVZ neurogenesis. | Paez-Gonzalez P, Asrican B, Rodriguez E, Kuo CT | Nature neuroscience | 24880216 | Nat Neurosci | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24880216 |
| Reduced hippocampal volume and verbal memory performance associated with interleukin-6 and tumor necrosis factor-alpha levels in chemotherapy-treated breast cancer survivors. | Kesler S, Janelsins M, Koovakkattu D, Palesh O, Mustian K, Morrow G, Dhabhar FS | Brain, behavior, and immunity | 22698992 | Brain Behav Immun | 2013 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22698992 |
| Prefrontal cortex and executive function impairments in primary breast cancer. | Kesler SR, Kent JS, O'Hara R | Archives of neurology | 22084128 | Arch Neurol | 2011 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22084128 |
| Comparing connectivity pattern and small-world organization between structural correlation and resting-state networks in healthy adults. | Hosseini SM, Kesler SR | NeuroImage | 23603348 | Neuroimage | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23603348 |
| Neurotoxic Effects of Anthracycline- vs Nonanthracycline-Based Chemotherapy on Cognition in Breast Cancer Survivors. | Kesler SR, Blayney DW | JAMA oncology | 26633037 | JAMA Oncol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26633037 |
| Brain network alterations and vulnerability to simulated neurodegeneration in breast cancer. | Kesler SR, Watson CL, Blayney DW | Neurobiology of aging | 26004016 | Neurobiol Aging | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26004016 |
| Evidence of compensatory neural hyperactivity in a subgroup of chemotherapy-treated breast cancer survivors and its association with brain aging. | Mulholland MM, Stuifbergen A, De La Torre Schutz A, Franco Rocha OY, Blayney DW, Kesler SR | medRxiv : the preprint server for health sciences | 38712178 | medRxiv | 2024 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/38712178 |
| Task-based neurofeedback training: A novel approach toward training executive functions. | Hosseini SMH, Pritchard-Berman M, Sosa N, Ceja A, Kesler SR | NeuroImage | 27015711 | Neuroimage | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/27015711 |
| Default mode network connectivity distinguishes chemotherapy-treated breast cancer survivors from controls. | Kesler SR, Wefel JS, Hosseini SM, Cheung M, Watson CL, Hoeft F | Proceedings of the National Academy of Sciences of the United States of America | 23798392 | Proc Natl Acad Sci U S A | 2013 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/23798392 |
| Predicting clinical outcome using brain activation associated with set-shifting and central coherence skills in Anorexia Nervosa. | Garrett AS, Lock J, Datta N, Beenhaker J, Kesler SR, Reiss AL | Journal of psychiatric research | 25027478 | J Psychiatr Res | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25027478 |
| Default mode network as a potential biomarker of chemotherapy-related brain injury. | Kesler SR | Neurobiology of aging | 24913897 | Neurobiol Aging | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24913897 |
| Evidence of compensatory neural hyperactivity in a subgroup of breast cancer survivors treated with chemotherapy and its association with brain aging. | Mulholland MM, Stuifbergen A, De La Torre Schutz A, Franco Rocha OY, Blayney DW, Kesler SR | Frontiers in aging neuroscience | 39723153 | Front Aging Neurosci | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39723153 |
| GAT: a graph-theoretical analysis toolbox for analyzing between-group differences in large-scale structural and functional brain networks. | Hosseini SM, Hoeft F, Kesler SR | PloS one | 22808240 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22808240 |
| Regional brain activation during verbal declarative memory in metastatic breast cancer. | Kesler SR, Bennett FC, Mahaffey ML, Spiegel D | Clinical cancer research : an official journal of the American Association for Cancer Research | 19843664 | Clin Cancer Res | 2009 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/19843664 |
| Altered small-world properties of gray matter networks in breast cancer. | Hosseini SM, Koovakkattu D, Kesler SR | BMC neurology | 22632066 | BMC Neurol | 2012 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/22632066 |
| Anomalous gray matter structural networks in major depressive disorder. | Singh MK, Kesler SR, Hadi Hosseini SM, Kelley RG, Amatya D, Hamilton JP, Chen MC, Gotlib IH | Biological psychiatry | 23601854 | Biol Psychiatry | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23601854 |
| Elevated prefrontal myo-inositol and choline following breast cancer chemotherapy. | Kesler SR, Watson C, Koovakkattu D, Lee C, O'Hara R, Mahaffey ML, Wefel JS | Brain imaging and behavior | 23536015 | Brain Imaging Behav | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23536015 |
| Cognitive training for improving executive function in chemotherapy-treated breast cancer survivors. | Kesler S, Hadi Hosseini SM, Heckler C, Janelsins M, Palesh O, Mustian K, Morrow G | Clinical breast cancer | 23647804 | Clin Breast Cancer | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23647804 |
| Multivariate pattern analysis of FMRI in breast cancer survivors and healthy women. | Hosseini SM, Kesler SR | Journal of the International Neuropsychological Society : JINS | 24135221 | J Int Neuropsychol Soc | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24135221 |
| The association of genetic polymorphisms with neuroconnectivity in breast cancer patients. | Harrison RA, Rao V, Kesler SR | Scientific reports | 33731765 | Sci Rep | 2021 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/33731765 |
| Functional connectome biotypes of chemotherapy-related cognitive impairment. | Kesler SR, Petersen ML, Rao V, Harrison RA, Palesh O | Journal of cancer survivorship : research and practice | 32157609 | J Cancer Surviv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32157609 |
| Exploring Relationships Among Peripheral Amyloid Beta, Tau, Cytokines, Cognitive Function, and Psychosomatic Symptoms in Breast Cancer Survivors. | Henneghan A, Haley AP, Kesler S | Biological research for nursing | 31707784 | Biol Res Nurs | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31707784 |
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| Piwi/PRG-1 Argonaute and TGF-β Mediate Transgenerational Learned Pathogenic Avoidance. | Moore RS, Kaletsky R, Murphy CT | Cell | 31178117 | Cell | 2019 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/31178117 |
| Insulin Signaling Regulates Oocyte Quality Maintenance with Age via Cathepsin B Activity. | Templeman NM, Luo S, Kaletsky R, Shi C, Ashraf J, Keyes W, Murphy CT | Current biology : CB | 29478855 | Curr Biol | 2018 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/29478855 |
| Surface association and the MreB cytoskeleton regulate pilus production, localization and function in Pseudomonas aeruginosa. | Cowles KN, Gitai Z | Molecular microbiology | 20398206 | Mol Microbiol | 2010 Jun | https://www.ncbi.nlm.nih.gov/pubmed/20398206 |
| Image analysis in fluorescence microscopy: bacterial dynamics as a case study. | van Teeffelen S, Shaevitz JW, Gitai Z | BioEssays : news and reviews in molecular, cellular and developmental biology | 22415868 | Bioessays | 2012 May | https://www.ncbi.nlm.nih.gov/pubmed/22415868 |
| Diverse functions for six glycosyltransferases in Caulobacter crescentus cell wall assembly. | Yakhnina AA, Gitai Z | Journal of bacteriology | 23935048 | J Bacteriol | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23935048 |
| Specific control of Pseudomonas aeruginosa surface-associated behaviors by two c-di-GMP diguanylate cyclases. | Merritt JH, Ha DG, Cowles KN, Lu W, Morales DK, Rabinowitz J, Gitai Z, O'Toole GA | mBio | 20978535 | mBio | 2010 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/20978535 |
| Enzyme clustering accelerates processing of intermediates through metabolic channeling. | Castellana M, Wilson MZ, Xu Y, Joshi P, Cristea IM, Rabinowitz JD, Gitai Z, Wingreen NS | Nature biotechnology | 25262299 | Nat Biotechnol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25262299 |
| Surface attachment induces Pseudomonas aeruginosa virulence. | Siryaporn A, Kuchma SL, O'Toole GA, Gitai Z | Proceedings of the National Academy of Sciences of the United States of America | 25385640 | Proc Natl Acad Sci U S A | 2014 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/25385640 |
| Mode of action and resistance studies unveil new roles for tropodithietic acid as an anticancer agent and the γ-glutamyl cycle as a proton sink. | Wilson MZ, Wang R, Gitai Z, Seyedsayamdost MR | Proceedings of the National Academy of Sciences of the United States of America | 26802120 | Proc Natl Acad Sci U S A | 2016 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/26802120 |
| Colonization, competition, and dispersal of pathogens in fluid flow networks. | Siryaporn A, Kim MK, Shen Y, Stone HA, Gitai Z | Current biology : CB | 25843031 | Curr Biol | 2015 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/25843031 |
| Caulobacter chromosome segregation is an ordered multistep process. | Shebelut CW, Guberman JM, van Teeffelen S, Yakhnina AA, Gitai Z | Proceedings of the National Academy of Sciences of the United States of America | 20660743 | Proc Natl Acad Sci U S A | 2010 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/20660743 |
| Dynamic polar sequestration of excess MurG may regulate enzymatic function. | Michaelis AM, Gitai Z | Journal of bacteriology | 20644141 | J Bacteriol | 2010 Sep | https://www.ncbi.nlm.nih.gov/pubmed/20644141 |
| New fluorescence microscopy methods for microbiology: sharper, faster, and quantitative. | Gitai Z | Current opinion in microbiology | 19356974 | Curr Opin Microbiol | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19356974 |
| Flow directs surface-attached bacteria to twitch upstream. | Shen Y, Siryaporn A, Lecuyer S, Gitai Z, Stone HA | Biophysical journal | 22828341 | Biophys J | 2012 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/22828341 |
| The small protein MbiA interacts with MreB and modulates cell shape in Caulobacter crescentus. | Yakhnina AA, Gitai Z | Molecular microbiology | 22804814 | Mol Microbiol | 2012 Sep | https://www.ncbi.nlm.nih.gov/pubmed/22804814 |
| General protein diffusion barriers create compartments within bacterial cells. | Schlimpert S, Klein EA, Briegel A, Hughes V, Kahnt J, Bolte K, Maier UG, Brun YV, Jensen GJ, Gitai Z, Thanbichler M | Cell | 23201141 | Cell | 2012 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/23201141 |
| Filament depolymerization can explain chromosome pulling during bacterial mitosis. | Banigan EJ, Gelbart MA, Gitai Z, Wingreen NS, Liu AJ | PLoS computational biology | 21966261 | PLoS Comput Biol | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21966261 |
| High-throughput screening of bacterial protein localization. | Werner JN, Gitai Z | Methods in enzymology | 20946849 | Methods Enzymol | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20946849 |
| The curved shape of Caulobacter crescentus enhances surface colonization in flow. | Persat A, Stone HA, Gitai Z | Nature communications | 24806788 | Nat Commun | 2014 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/24806788 |
| Bacterial evolution: rewiring modules to get in shape. | Persat A, Gitai Z | Current biology : CB | 24892912 | Curr Biol | 2014 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/24892912 |
| The putative Poc complex controls two distinct Pseudomonas aeruginosa polar motility mechanisms. | Cowles KN, Moser TS, Siryaporn A, Nyakudarika N, Dixon W, Turner JJ, Gitai Z | Molecular microbiology | 24102920 | Mol Microbiol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24102920 |
| BapE DNA endonuclease induces an apoptotic-like response to DNA damage in Caulobacter. | Bos J, Yakhnina AA, Gitai Z | Proceedings of the National Academy of Sciences of the United States of America | 23074244 | Proc Natl Acad Sci U S A | 2012 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/23074244 |
| Beyond the cytoskeleton: mesoscale assemblies and their function in spatial organization. | Wilson MZ, Gitai Z | Current opinion in microbiology | 23601587 | Curr Opin Microbiol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23601587 |
| Physiological role of stalk lengthening in Caulobacter crescentus. | Klein EA, Schlimpert S, Hughes V, Brun YV, Thanbichler M, Gitai Z | Communicative & integrative biology | 23986806 | Commun Integr Biol | 2013 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/23986806 |
| Draft Genome Sequence of Uropathogenic Escherichia coli Strain J96. | Klein EA, Gitai Z | Genome announcements | 23469357 | Genome Announc | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23469357 |
| The metabolic enzyme CTP synthase forms cytoskeletal filaments. | Ingerson-Mahar M, Briegel A, Werner JN, Jensen GJ, Gitai Z | Nature cell biology | 20639870 | Nat Cell Biol | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20639870 |
| A growing family: the expanding universe of the bacterial cytoskeleton. | Ingerson-Mahar M, Gitai Z | FEMS microbiology reviews | 22092065 | FEMS Microbiol Rev | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22092065 |
| Self-assembling enzymes and the origins of the cytoskeleton. | Barry RM, Gitai Z | Current opinion in microbiology | 22014508 | Curr Opin Microbiol | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22014508 |
| Serial monitoring of endogenous neuroblast migration by cellular MRI. | Granot D, Scheinost D, Markakis EA, Papademetris X, Shapiro EM | NeuroImage | 21571076 | Neuroimage | 2011 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/21571076 |
| Magnetic poly(lactide-co-glycolide) and cellulose particles for MRI-based cell tracking. | Nkansah MK, Thakral D, Shapiro EM | Magnetic resonance in medicine | 21404328 | Magn Reson Med | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21404328 |
| Biocompatible and pH-sensitive PLGA encapsulated MnO nanocrystals for molecular and cellular MRI. | Bennewitz MF, Lobo TL, Nkansah MK, Ulas G, Brudvig GW, Shapiro EM | ACS nano | 21495676 | ACS Nano | 2011 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/21495676 |
| The effect of cryoprotection on the use of PLGA encapsulated iron oxide nanoparticles for magnetic cell labeling. | Tang KS, Hashmi SM, Shapiro EM | Nanotechnology | 23459030 | Nanotechnology | 2013 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/23459030 |
| Intelligent and automatic in vivo detection and quantification of transplanted cells in MRI. | Afridi MJ, Ross A, Liu X, Bennewitz MF, Shuboni DD, Shapiro EM | Magnetic resonance in medicine | 28019017 | Magn Reson Med | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28019017 |
| On the use of micron-sized iron oxide particles (MPIOS) to label resting monocytes in bone marrow. | Tang KS, Hann B, Shapiro EM | Molecular imaging and biology | 20936363 | Mol Imaging Biol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/20936363 |
| Enhanced magnetic cell labeling efficiency using -NH2 coated MPIOs. | Tang KS, Shapiro EM | Magnetic resonance in medicine | 21446031 | Magn Reson Med | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21446031 |
| Poly(lactic-co-glycolic acid) encapsulated gadolinium oxide nanoparticles for MRI-based cell tracking. | Bennewitz MF, Williams SS, Nkansah MK, Shapiro EM | Journal of nanoscience and nanotechnology | 23862407 | J Nanosci Nanotechnol | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23862407 |
| Biodegradable, polymer encapsulated, metal oxide particles for MRI-based cell tracking. | Shapiro EM | Magnetic resonance in medicine | 24753150 | Magn Reson Med | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24753150 |
| Acquired resistance of EGFR-mutant lung adenocarcinomas to afatinib plus cetuximab is associated with activation of mTORC1. | Pirazzoli V, Nebhan C, Song X, Wurtz A, Walther Z, Cai G, Zhao Z, Jia P, de Stanchina E, Shapiro EM, Gale M, Yin R, Horn L, Carbone DP, Stephens PJ, Miller V, Gettinger S, Pao W, Politi K | Cell reports | 24813888 | Cell Rep | 2014 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/24813888 |
| In vivo serial MRI of age-dependent neural progenitor cell migration in the rat brain. | Shuboni-Mulligan DD, Chakravarty S, Mallett CL, Wolf AM, Dmitriev PM, Forton SM, Shapiro EM | NeuroImage | 31152841 | Neuroimage | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31152841 |
| Release activation of iron oxide nanoparticles: (REACTION) a novel environmentally sensitive MRI paradigm. | Granot D, Shapiro EM | Magnetic resonance in medicine | 21360745 | Magn Reson Med | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21360745 |
| Accumulation of micron sized iron oxide particles in endothelin-1 induced focal cortical ischemia in rats is independent of cell migration. | Granot D, Shapiro EM | Magnetic resonance in medicine | 23661604 | Magn Reson Med | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23661604 |
| On Automated Source Selection for Transfer Learning in Convolutional Neural Networks. | Afridi MJ, Ross A, Shapiro EM | Pattern recognition | 30774153 | Pattern Recognit | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30774153 |
| Clinically viable magnetic poly(lactide-co-glycolide) particles for MRI-based cell tracking. | Granot D, Nkansah MK, Bennewitz MF, Tang KS, Markakis EA, Shapiro EM | Magnetic resonance in medicine | 23568825 | Magn Reson Med | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/23568825 |
| Dual-modality, fluorescent, PLGA encapsulated bismuth nanoparticles for molecular and cellular fluorescence imaging and computed tomography. | Swy ER, Schwartz-Duval AS, Shuboni DD, Latourette MT, Mallet CL, Parys M, Cormode DP, Shapiro EM | Nanoscale | 25248645 | Nanoscale | 2014 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/25248645 |
| Specific chemotaxis of magnetically labeled mesenchymal stem cells: implications for MRI of glioma. | Bennewitz MF, Tang KS, Markakis EA, Shapiro EM | Molecular imaging and biology | 22418788 | Mol Imaging Biol | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22418788 |
| Fabrication of magnetic and fluorescent chitin and dibutyrylchitin sub-micron particles by oil-in-water emulsification. | Blanco-Fernandez B, Chakravarty S, Nkansah MK, Shapiro EM | Acta biomaterialia | 27592817 | Acta Biomater | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27592817 |
| Centromeric motion facilitates the mobility of interphase genomic regions in fission yeast. | Kim KD, Tanizawa H, Iwasaki O, Corcoran CJ, Capizzi JR, Hayden JE, Noma K | Journal of cell science | 23986481 | J Cell Sci | 2013 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/23986481 |
| Unravelling global genome organization by 3C-seq. | Tanizawa H, Noma K | Seminars in cell & developmental biology | 22120510 | Semin Cell Dev Biol | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22120510 |
| Centromeric localization of dispersed Pol III genes in fission yeast. | Iwasaki O, Tanaka A, Tanizawa H, Grewal SI, Noma K | Molecular biology of the cell | 19910488 | Mol Biol Cell | 2010 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/19910488 |
| The Yeast Genomes in Three Dimensions: Mechanisms and Functions. | Noma KI | Annual review of genetics | 28853923 | Annu Rev Genet | 2017 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/28853923 |
| Swi1Timeless Prevents Repeat Instability at Fission Yeast Telomeres. | Gadaleta MC, Das MM, Tanizawa H, Chang YT, Noma K, Nakamura TM, Noguchi E | PLoS genetics | 26990647 | PLoS Genet | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26990647 |
| Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation. | Tanizawa H, Iwasaki O, Tanaka A, Capizzi JR, Wickramasinghe P, Lee M, Fu Z, Noma K | Nucleic acids research | 21030438 | Nucleic Acids Res | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21030438 |
| An IF-FISH Approach for Covisualization of Gene Loci and Nuclear Architecture in Fission Yeast. | Kim KD, Iwasaki O, Noma K | Methods in enzymology | 27423862 | Methods Enzymol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27423862 |
| New vectors for epitope tagging and gene disruption in Schizosaccharomyces pombe. | Gadaleta MC, Iwasaki O, Noguchi C, Noma K, Noguchi E | BioTechniques | 24215641 | Biotechniques | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24215641 |
| Global genome organization mediated by RNA polymerase III-transcribed genes in fission yeast. | Iwasaki O, Noma K | Gene | 21195141 | Gene | 2012 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/21195141 |
| Interaction between TBP and Condensin Drives the Organization and Faithful Segregation of Mitotic Chromosomes. | Iwasaki O, Tanizawa H, Kim KD, Yokoyama Y, Corcoran CJ, Tanaka A, Skordalakes E, Showe LC, Noma K | Molecular cell | 26257282 | Mol Cell | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26257282 |
| Involvement of condensin-directed gene associations in the organization and regulation of chromosome territories during the cell cycle. | Iwasaki O, Corcoran CJ, Noma K | Nucleic acids research | 26704981 | Nucleic Acids Res | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/26704981 |
| Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast. | Kim KD, Tanizawa H, Iwasaki O, Noma K | Nature genetics | 27548313 | Nat Genet | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27548313 |
| Architectural alterations of the fission yeast genome during the cell cycle. | Tanizawa H, Kim KD, Iwasaki O, Noma KI | Nature structural & molecular biology | 28991264 | Nat Struct Mol Biol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28991264 |
| Epigenetic regulation of condensin-mediated genome organization during the cell cycle and upon DNA damage through histone H3 lysine 56 acetylation. | Tanaka A, Tanizawa H, Sriswasdi S, Iwasaki O, Chatterjee AG, Speicher DW, Levin HL, Noguchi E, Noma K | Molecular cell | 23084836 | Mol Cell | 2012 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/23084836 |
| Condensin-mediated chromosome organization in fission yeast. | Iwasaki O, Noma KI | Current genetics | 27061734 | Curr Genet | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27061734 |
| Self-folding polymeric containers for encapsulation and delivery of drugs. | Fernandes R, Gracias DH | Advanced drug delivery reviews | 22425612 | Adv Drug Deliv Rev | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/22425612 |
| Three-dimensional microwell arrays for cell culture. | Randall CL, Kalinin YV, Jamal M, Manohar T, Gracias DH | Lab on a chip | 21063585 | Lab Chip | 2011 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/21063585 |
| Self-folding micropatterned polymeric containers. | Azam A, Laflin KE, Jamal M, Fernandes R, Gracias DH | Biomedical microdevices | 20838901 | Biomed Microdevices | 2011 Feb | https://www.ncbi.nlm.nih.gov/pubmed/20838901 |
| Plastic deformation drives wrinkling, saddling, and wedging of annular bilayer nanostructures. | Cho JH, Datta D, Park SY, Shenoy VB, Gracias DH | Nano letters | 21090597 | Nano Lett | 2010 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/21090597 |
| Three dimensional nanofabrication using surface forces. | Cho JH, Azam A, Gracias DH | Langmuir : the ACS journal of surfaces and colloids | 20507147 | Langmuir | 2010 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/20507147 |
| Patternable nanowire sensors for electrochemical recording of dopamine. | Tyagi P, Postetter D, Saragnese DL, Randall CL, Mirski MA, Gracias DH | Analytical chemistry | 19904993 | Anal Chem | 2009 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/19904993 |
| Self-assembly of lithographically patterned nanoparticles. | Cho JH, Gracias DH | Nano letters | 19681638 | Nano Lett | 2009 Dec | https://www.ncbi.nlm.nih.gov/pubmed/19681638 |
| Three-dimensional chemical patterns for cellular self-organization. | Kalinin YV, Randhawa JS, Gracias DH | Angewandte Chemie (International ed. in English) | 21370335 | Angew Chem Int Ed Engl | 2011 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/21370335 |
| Silane surface modification for improved bioadhesion of esophageal stents. | Karakoy M, Gultepe E, Pandey S, Khashab MA, Gracias DH | Applied surface science | 25663731 | Appl Surf Sci | 2014 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/25663731 |
| Self-folding devices and materials for biomedical applications. | Randall CL, Gultepe E, Gracias DH | Trends in biotechnology | 21764161 | Trends Biotechnol | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21764161 |
| Voltage-gated ion transport through semiconducting conical nanopores formed by metal nanoparticle-assisted plasma etching. | James T, Kalinin YV, Chan CC, Randhawa JS, Gaevski M, Gracias DH | Nano letters | 22725714 | Nano Lett | 2012 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/22725714 |
| Microassembly based on hands free origami with bidirectional curvature. | Bassik N, Stern GM, Gracias DH | Applied physics letters | 19787072 | Appl Phys Lett | 2009 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/19787072 |
| Directed growth of fibroblasts into three dimensional micropatterned geometries via self-assembling scaffolds. | Jamal M, Bassik N, Cho JH, Randall CL, Gracias DH | Biomaterials | 20022106 | Biomaterials | 2010 Mar | https://www.ncbi.nlm.nih.gov/pubmed/20022106 |
| Biopsy with thermally-responsive untethered microtools. | Gultepe E, Randhawa JS, Kadam S, Yamanaka S, Selaru FM, Shin EJ, Kalloo AN, Gracias DH | Advanced materials (Deerfield Beach, Fla.) | 23047708 | Adv Mater | 2013 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/23047708 |
| 3D printed bionic ears. | Mannoor MS, Jiang Z, James T, Kong YL, Malatesta KA, Soboyejo WO, Verma N, Gracias DH, McAlpine MC | Nano letters | 23635097 | Nano Lett | 2013 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/23635097 |
| Self-folding thermo-magnetically responsive soft microgrippers. | Breger JC, Yoon C, Xiao R, Kwag HR, Wang MO, Fisher JP, Nguyen TD, Gracias DH | ACS applied materials & interfaces | 25594664 | ACS Appl Mater Interfaces | 2015 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/25594664 |
| Self-folding single cell grippers. | Malachowski K, Jamal M, Jin Q, Polat B, Morris CJ, Gracias DH | Nano letters | 24937214 | Nano Lett | 2014 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/24937214 |
| Stimuli-responsive theragrippers for chemomechanical controlled release. | Malachowski K, Breger J, Kwag HR, Wang MO, Fisher JP, Selaru FM, Gracias DH | Angewandte Chemie (International ed. in English) | 24634136 | Angew Chem Int Ed Engl | 2014 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/24634136 |
| Chemistry with spatial control using particles and streams(). | Kalinin YV, Murali A, Gracias DH | RSC advances | 23145348 | RSC Adv | 2012 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/23145348 |
| Bio-origami hydrogel scaffolds composed of photocrosslinked PEG bilayers. | Jamal M, Kadam SS, Xiao R, Jivan F, Onn TM, Fernandes R, Nguyen TD, Gracias DH | Advanced healthcare materials | 23386382 | Adv Healthc Mater | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23386382 |
| Biopsy using a magnetic capsule endoscope carrying, releasing, and retrieving untethered microgrippers. | Yim S, Gultepe E, Gracias DH, Sitti M | IEEE transactions on bio-medical engineering | 24108454 | IEEE Trans Biomed Eng | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24108454 |
| Three-dimensional fabrication at small size scales. | Leong TG, Zarafshar AM, Gracias DH | Small (Weinheim an der Bergstrasse, Germany) | 20349446 | Small | 2010 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/20349446 |
| Reversible actuation of microstructures by surface-chemical modification of thin-film bilayers. | Randhawa JS, Keung MD, Tyagi P, Gracias DH | Advanced materials (Deerfield Beach, Fla.) | 20217729 | Adv Mater | 2010 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/20217729 |
| Hierarchical self-assembly of complex polyhedral microcontainers. | Filipiak DJ, Azam A, Leong TG, Gracias DH | Journal of micromechanics and microengineering : structures, devices, and systems | 20161118 | J Micromech Microeng | 2009 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/20161118 |
| Curving nanostructures using extrinsic stress. | Cho JH, James T, Gracias DH | Advanced materials (Deerfield Beach, Fla.) | 20376856 | Adv Mater | 2010 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/20376856 |
| Enzymatically triggered actuation of miniaturized tools. | Bassik N, Brafman A, Zarafshar AM, Jamal M, Luvsanjav D, Selaru FM, Gracias DH | Journal of the American Chemical Society | 20849106 | J Am Chem Soc | 2010 Nov 24 | https://www.ncbi.nlm.nih.gov/pubmed/20849106 |
| Differentially photo-crosslinked polymers enable self-assembling microfluidics. | Jamal M, Zarafshar AM, Gracias DH | Nature communications | 22068594 | Nat Commun | 2011 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/22068594 |
| Enabling cargo-carrying bacteria via surface attachment and triggered release. | Fernandes R, Zuniga M, Sassine FR, Karakoy M, Gracias DH | Small (Weinheim an der Bergstrasse, Germany) | 21370460 | Small | 2011 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/21370460 |
| A zebrafish embryo culture system defines factors that promote vertebrate myogenesis across species. | Xu C, Tabebordbar M, Iovino S, Ciarlo C, Liu J, Castiglioni A, Price E, Liu M, Barton ER, Kahn CR, Wagers AJ, Zon LI | Cell | 24209627 | Cell | 2013 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/24209627 |
| The Hippo transducer YAP1 transforms activated satellite cells and is a potent effector of embryonal rhabdomyosarcoma formation. | Tremblay AM, Missiaglia E, Galli GG, Hettmer S, Urcia R, Carrara M, Judson RN, Thway K, Nadal G, Selfe JL, Murray G, Calogero RA, De Bari C, Zammit PS, Delorenzi M, Wagers AJ, Shipley J, Wackerhage H, Camargo FD | Cancer cell | 25087979 | Cancer Cell | 2014 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/25087979 |
| Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells. | Polo JM, Liu S, Figueroa ME, Kulalert W, Eminli S, Tan KY, Apostolou E, Stadtfeld M, Li Y, Shioda T, Natesan S, Wagers AJ, Melnick A, Evans T, Hochedlinger K | Nature biotechnology | 20644536 | Nat Biotechnol | 2010 Aug | https://www.ncbi.nlm.nih.gov/pubmed/20644536 |
| Systemic signals regulate ageing and rejuvenation of blood stem cell niches. | Mayack SR, Shadrach JL, Kim FS, Wagers AJ | Nature | 20110993 | Nature | 2010 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/20110993 |
| Rejuvenation of regeneration in the aging central nervous system. | Ruckh JM, Zhao JW, Shadrach JL, van Wijngaarden P, Rao TN, Wagers AJ, Franklin RJ | Cell stem cell | 22226359 | Cell Stem Cell | 2012 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/22226359 |
| Engineering Escherichia coli into a protein delivery system for mammalian cells. | Reeves AZ, Spears WE, Du J, Tan KY, Wagers AJ, Lesser CF | ACS synthetic biology | 25853840 | ACS Synth Biol | 2015 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/25853840 |
| Young, proliferative thymic epithelial cells engraft and function in aging thymuses. | Kim MJ, Miller CM, Shadrach JL, Wagers AJ, Serwold T | Journal of immunology (Baltimore, Md. : 1950) | 25870244 | J Immunol | 2015 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/25870244 |
| Vascular and neurogenic rejuvenation of the aging mouse brain by young systemic factors. | Katsimpardi L, Litterman NK, Schein PA, Miller CM, Loffredo FS, Wojtkiewicz GR, Chen JW, Lee RT, Wagers AJ, Rubin LL | Science (New York, N.Y.) | 24797482 | Science | 2014 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/24797482 |
| Growth differentiation factor 11 is a circulating factor that reverses age-related cardiac hypertrophy. | Loffredo FS, Steinhauser ML, Jay SM, Gannon J, Pancoast JR, Yalamanchi P, Sinha M, Dall'Osso C, Khong D, Shadrach JL, Miller CM, Singer BS, Stewart A, Psychogios N, Gerszten RE, Hartigan AJ, Kim MJ, Serwold T, Wagers AJ, Lee RT | Cell | 23663781 | Cell | 2013 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/23663781 |
| Mutations in Hedgehog pathway genes in fetal rhabdomyomas. | Hettmer S, Teot LA, van Hummelen P, MacConaill L, Bronson RT, Dall'Osso C, Mao J, McMahon AP, Gruber PJ, Grier HE, Rodriguez-Galindo C, Fletcher CD, Wagers AJ | The Journal of pathology | 23780909 | J Pathol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23780909 |
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| Liver-derived systemic factors drive β cell hyperplasia in insulin-resistant states. | El Ouaamari A, Kawamori D, Dirice E, Liew CW, Shadrach JL, Hu J, Katsuta H, Hollister-Lock J, Qian WJ, Wagers AJ, Kulkarni RN | Cell reports | 23375376 | Cell Rep | 2013 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/23375376 |
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| High-level Gpr56 expression is dispensable for the maintenance and function of hematopoietic stem and progenitor cells in mice. | Rao TN, Marks-Bluth J, Sullivan J, Gupta MK, Chandrakanthan V, Fitch SR, Ottersbach K, Jang YC, Piao X, Kulkarni RN, Serwold T, Pimanda JE, Wagers AJ | Stem cell research | 25840412 | Stem Cell Res | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25840412 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Porous silicon nanowires. | Qu Y, Zhou H, Duan X | Nanoscale | 21869999 | Nanoscale | 2011 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/21869999 |
| 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 |
| 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 |
| High-capacity silicon-air battery in alkaline solution. | Zhong X, Zhang H, Liu Y, Bai J, Liao L, Huang Y, Duan X | ChemSusChem | 22144348 | ChemSusChem | 2012 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/22144348 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| Fibroblasts influence muscle progenitor differentiation and alignment in contact independent and dependent manners in organized co-culture devices. | Rao N, Evans S, Stewart D, Spencer KH, Sheikh F, Hui EE, Christman KL | Biomedical microdevices | 22983793 | Biomed Microdevices | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/22983793 |
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| Modeling Rett syndrome with stem cells. | Walsh RM, Hochedlinger K | Cell | 21074040 | Cell | 2010 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/21074040 |
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| Stress Enables Reinforcement-Elicited Serotonergic Consolidation of Fear Memory. | Baratta MV, Kodandaramaiah SB, Monahan PE, Yao J, Weber MD, Lin PA, Gisabella B, Petrossian N, Amat J, Kim K, Yang A, Forest CR, Boyden ES, Goosens KA | Biological psychiatry | 26248536 | Biol Psychiatry | 2016 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/26248536 |
| Striatal origin of the pathologic beta oscillations in Parkinson's disease. | McCarthy MM, Moore-Kochlacs C, Gu X, Boyden ES, Han X, Kopell N | Proceedings of the National Academy of Sciences of the United States of America | 21697509 | Proc Natl Acad Sci U S A | 2011 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/21697509 |
| Multiwaveguide implantable probe for light delivery to sets of distributed brain targets. | Zorzos AN, Boyden ES, Fonstad CG | Optics letters | 21165114 | Opt Lett | 2010 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/21165114 |
| 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 |
| Entry of herpesviruses into mammalian cells. | Heldwein EE, Krummenacher C | Cellular and molecular life sciences : CMLS | 18351291 | Cell Mol Life Sci | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18351291 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| IRE1alpha kinase activation modes control alternate endoribonuclease outputs to determine divergent cell fates. | Han D, Lerner AG, Vande Walle L, Upton JP, Xu W, Hagen A, Backes BJ, Oakes SA, Papa FR | Cell | 19665977 | Cell | 2009 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/19665977 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Impaired Recall of Positional Memory following Chemogenetic Disruption of Place Field Stability. | Zhao R, Grunke SD, Keralapurath MM, Yetman MJ, Lam A, Lee TC, Sousounis K, Jiang Y, Swing DA, Tessarollo L, Ji D, Jankowsky JL | Cell reports | 27373150 | Cell Rep | 2016 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/27373150 |
| 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 |
| Genetic modulation of soluble Aβ rescues cognitive and synaptic impairment in a mouse model of Alzheimer's disease. | Fowler SW, Chiang AC, Savjani RR, Larson ME, Sherman MA, Schuler DR, Cirrito JR, Lesné SE, Jankowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24899710 | J Neurosci | 2014 Jun 4 | https://www.ncbi.nlm.nih.gov/pubmed/24899710 |
| 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 |
| Brain-wide distribution of reporter expression in five transgenic tetracycline-transactivator mouse lines. | Lillehaug S, Yetman MJ, Puchades MA, Checinska MM, Kleven H, Jankowsky JL, Bjaalie JG, Leergaard TB | Scientific data | 30806643 | Sci Data | 2019 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/30806643 |
| Transgenic APP expression during postnatal development causes persistent locomotor hyperactivity in the adult. | Rodgers SP, Born HA, Das P, Jankowsky JL | Molecular neurodegeneration | 22709352 | Mol Neurodegener | 2012 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/22709352 |
| Intracerebroventricular viral injection of the neonatal mouse brain for persistent and widespread neuronal transduction. | Kim JY, Grunke SD, Levites Y, Golde TE, Jankowsky JL | Journal of visualized experiments : JoVE | 25286085 | J Vis Exp | 2014 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/25286085 |
| 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 |
| 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 |
| 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 |
| 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 |
| Robust amyloid clearance in a mouse model of Alzheimer's disease provides novel insights into the mechanism of amyloid-beta immunotherapy. | Wang A, Das P, Switzer RC 3rd, Golde TE, Jankowsky JL | The Journal of neuroscience : the official journal of the Society for Neuroscience | 21411653 | J Neurosci | 2011 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/21411653 |
| Discrete Pools of Oligomeric Amyloid-β Track with Spatial Learning Deficits in a Mouse Model of Alzheimer Amyloidosis. | Chiang ACA, Fowler SW, Reddy R, Pletnikova O, Troncoso JC, Sherman MA, Lesne SE, Jankowsky JL | The American journal of pathology | 29248459 | Am J Pathol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29248459 |
| Female human iPSCs retain an inactive X chromosome. | Tchieu J, Kuoy E, Chin MH, Trinh H, Patterson M, Sherman SP, Aimiuwu O, Lindgren A, Hakimian S, Zack JA, Clark AT, Pyle AD, Lowry WE, Plath K | Cell stem cell | 20727844 | Cell Stem Cell | 2010 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/20727844 |
| The pluripotency factor-bound intron 1 of Xist is dispensable for X chromosome inactivation and reactivation in vitro and in vivo. | Minkovsky A, Barakat TS, Sellami N, Chin MH, Gunhanlar N, Gribnau J, Plath K | Cell reports | 23523354 | Cell Rep | 2013 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/23523354 |
| Mechanistic insights into reprogramming to induced pluripotency. | Ho R, Chronis C, Plath K | Journal of cellular physiology | 20945378 | J Cell Physiol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/20945378 |
| Mediator coordinates PIC assembly with recruitment of CHD1. | Lin JJ, Lehmann LW, Bonora G, Sridharan R, Vashisht AA, Tran N, Plath K, Wohlschlegel JA, Carey M | Genes & development | 21979373 | Genes Dev | 2011 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/21979373 |
| Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. | Chin MH, Mason MJ, Xie W, Volinia S, Singer M, Peterson C, Ambartsumyan G, Aimiuwu O, Richter L, Zhang J, Khvorostov I, Ott V, Grunstein M, Lavon N, Benvenisty N, Croce CM, Clark AT, Baxter T, Pyle AD, Teitell MA, Pelegrini M, Plath K, Lowry WE | Cell stem cell | 19570518 | Cell Stem Cell | 2009 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/19570518 |
| Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape. | Papp B, Plath K | Cell research | 21321600 | Cell Res | 2011 Mar | https://www.ncbi.nlm.nih.gov/pubmed/21321600 |
| Small RNAs loom large during reprogramming. | Sridharan R, Plath K | Cell stem cell | 21624799 | Cell Stem Cell | 2011 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/21624799 |
| A high-throughput screen of inactive X chromosome reactivation identifies the enhancement of DNA demethylation by 5-aza-2'-dC upon inhibition of ribonucleotide reductase. | Minkovsky A, Sahakyan A, Bonora G, Damoiseaux R, Dimitrova E, Rubbi L, Pellegrini M, Radu CG, Plath K | Epigenetics & chromatin | 26468331 | Epigenetics Chromatin | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26468331 |
| Pluripotency in 3D: genome organization in pluripotent cells. | Denholtz M, Plath K | Current opinion in cell biology | 23199754 | Curr Opin Cell Biol | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23199754 |
| Stage-specific regulation of reprogramming to induced pluripotent stem cells by Wnt signaling and T cell factor proteins. | Ho R, Papp B, Hoffman JA, Merrill BJ, Plath K | Cell reports | 23791530 | Cell Rep | 2013 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/23791530 |
| High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome. | Keegan A, Plath K, Damoiseaux R | Methods in molecular biology (Clifton, N.J.) | 29671264 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29671264 |
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| Neighborhood Socioeconomic Status and Distance From Home Address to Imaging Center Influence the Acuity of Brain MRI Findings. | Raghuvanshi I, Risk BB, Sadigh G, Allen JW, Fleischer CC | Journal of the American College of Radiology : JACR | 41076172 | J Am Coll Radiol | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41076172 |
| 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 |
| 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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| Comparison of Magnetic Resonance Spectra Acquired With Hybrid PET/MR and Standalone MR Scanners. | Macdonald CB, Bhattacharya A, Risk BB, Zuleger TM, Mandava S, Noeske R, Fleischer CC | Journal of magnetic resonance imaging : JMRI | 40758419 | J Magn Reson Imaging | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40758419 |
| 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 |
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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 |
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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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| Piezo1-mediated spontaneous calcium transients in satellite glia impact dorsal root ganglia development. | Brandt JP, Smith CJ | PLoS biology | 37747915 | PLoS Biol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37747915 |
| 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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| 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 |
| Functional Regeneration of the Sensory Root via Axonal Invasion. | Nichols EL, Smith CJ | Cell reports | 31914401 | Cell Rep | 2020 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/31914401 |
| 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 |
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| The embryonic zebrafish brain is seeded by a lymphatic-dependent population of mrc1(+) microglia precursors. | Green LA, O'Dea MR, Hoover CA, DeSantis DF, Smith CJ | Nature neuroscience | 35710983 | Nat Neurosci | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35710983 |
| An ultrastructural map of a spinal sensorimotor circuit reveals the potential of astroglia modulation. | Koh ZM, Arceo RA, Hammer J, Chau K, Light SEW, Dolojan A, Januszewski M, Svara F, Smith CJ | Cell reports | 41428485 | Cell Rep | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41428485 |
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| 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 |
| 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 |
| Differentiation of Enteric Nervous System Lineages from Human Pluripotent Stem Cells. | Majd H, Richter MN, Samuel RM, Kalantari A, Ramirez JT, Fattahi F | Journal of visualized experiments : JoVE | 38829111 | J Vis Exp | 2024 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/38829111 |
| 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 |
| Deriving Schwann cells from hPSCs enables disease modeling and drug discovery for diabetic peripheral neuropathy. | Majd H, Amin S, Ghazizadeh Z, Cesiulis A, Arroyo E, Lankford K, Majd A, Farahvashi S, Chemel AK, Okoye M, Scantlen MD, Tchieu J, Calder EL, Le Rouzic V, Shibata B, Arab A, Goodarzi H, Pasternak G, Kocsis JD, Chen S, Studer L, Fattahi F | Cell stem cell | 37146583 | Cell Stem Cell | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/37146583 |
| 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 |
| 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, Wen KW, Guyer RA, Hao MM, Stamp LA, Goldstein AM, Fattahi F | The EMBO journal | 40954253 | EMBO J | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40954253 |
| 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 |
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| 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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| Engrafted nitrergic neurons derived from hPSCs improve gut dysmotility in mice. | Majd H, Samuel RM, Cesiulis A, Ramirez JT, Kalantari A, Barber K, Farahvashi S, Ghazizadeh Z, Majd A, Chemel AK, Richter MN, Das S, Bendrick JL, Keefe MG, Wang J, Shiv RK, Bhat S, Khoroshkin M, Yu J, Nowakowski TJ, Wen KW, Goodarzi H, Thapar N, Kaltschmidt JA, McCann CJ, Fattahi F | Nature | 40562934 | Nature | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40562934 |
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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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| Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features. | Li D, Wang Q, Gong NN, Kurolap A, Feldman HB, Boy N, Brugger M, Grand K, McWalter K, Guillen Sacoto MJ, Wakeling E, Hurst J, March ME, Bhoj EJ, Nowaczyk MJM, Gonzaga-Jauregui C, Mathew M, Dava-Wala A, Siemon A, Bartholomew D, Huang Y, Lee H, Martinez-Agosto JA, Schwaibold EMC, Brunet T, Choukair D, Pais LS, White SM, Christodoulou J, Brown D, Lindstrom K, Grebe T, Tiosano D, Kayser MS, Tan TY, Deardorff MA, Song Y, Hakonarson H | Science advances | 33980485 | Sci Adv | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33980485 |
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| Energetic Demands Regulate Sleep-Wake Rhythm Circuit Development. | Poe AR, Zhu L, Tang SH, Valencia E, Kayser MS | bioRxiv : the preprint server for biology | 37786713 | bioRxiv | 2024 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/37786713 |
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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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| 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 |
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| 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 |
| Direct Thalamic Inputs to Hippocampal CA1 Transmit a Signal That Suppresses Ongoing Contextual Fear Memory Retrieval. | Ratigan HC, Krishnan S, Smith S, Sheffield MEJ | Research square | 37034716 | Res Sq | 2023 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/37034716 |
| Reward Expectation Reduces Representational Drift in the Hippocampus. | Krishnan S, Sheffield MEJ | bioRxiv : the preprint server for biology | 38187677 | bioRxiv | 2023 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/38187677 |
| A contextual fear conditioning paradigm in head-fixed mice exploring virtual reality. | Krishnan S, Dong C, Ratigan H, Morales-Rodriguez D, Cherian C, Sheffield M | bioRxiv : the preprint server for biology | 39651122 | bioRxiv | 2025 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/39651122 |
| A Preprocessing Toolbox for 2-Photon Subcellular Calcium Imaging. | Jiang A, Zhao C, Sheffield MEJ | eNeuro | 40360280 | eNeuro | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40360280 |
| Distinct catecholaminergic pathways projecting to hippocampal CA1 transmit contrasting signals during navigation in familiar and novel environments. | Heer CM, Sheffield MEJ | bioRxiv : the preprint server for biology | 38076843 | bioRxiv | 2024 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/38076843 |
| 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 |
| 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 |
| Formulation methods for peptide-modified lipid nanoparticles. | Miyasaki K, Han S, Carton O, Kandell RM, Gunn J, Kwon EJ | Journal of controlled release : official journal of the Controlled Release Society | 40645295 | J Control Release | 2025 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/40645295 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Impact of Conjugation Chemistry on the Pharmacokinetics of Peptide-Polymer Conjugates in a Model of Traumatic Brain Injury. | Wu JR, Canjels A, Miyauchi R, Kwon EJ | Bioconjugate chemistry | 40577388 | Bioconjug Chem | 2025 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/40577388 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Ultrasound-mediated blood-brain barrier opening increases cell-free DNA in a time-dependent manner. | Zhang DY, Gould A, Happ HC, Youngblood MW, Dmello C, Kang SJ, Canney M, Stupp R, Carvill GL, Sonabend AM | Neuro-oncology advances | 34993480 | Neurooncol Adv | 2021 Jan-Dec | https://www.ncbi.nlm.nih.gov/pubmed/34993480 |
| Poison exons in neurodevelopment and disease. | Carvill GL, Mefford HC | Current opinion in genetics & development | 32615329 | Curr Opin Genet Dev | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32615329 |
| 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 |
| Engineering rhodopsins' activation spectra using a FRET-based approach. | Beck C, Gong Y | Biophysical journal | 35331688 | Biophys J | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35331688 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| In-Cell Sensitivity-Enhanced NMR of Intact Viable Mammalian Cells. | Ghosh R, Xiao Y, Kragelj J, Frederick KK | Journal of the American Chemical Society | 34724614 | J Am Chem Soc | 2021 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/34724614 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins. | Kragelj J, Dumarieh R, Xiao Y, Frederick KK | Protein science : a publication of the Protein Society | 36930141 | Protein Sci | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36930141 |
| Stability of the polarization agent AsymPolPOK in intact and lysed mammalian cells. | Lagasca D, Ghosh R, Xiao Y, Frederick KK | Journal of magnetic resonance (San Diego, Calif. : 1997) | 40081142 | J Magn Reson | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40081142 |
| 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 |
| CELLULAR RESOLUTION IMAGING OF NEURONAL ACTIVITY ACROSS SPACE AND TIME IN THE MAMMALIAN BRAIN. | Clough M, Chen JL | Current opinion in biomedical engineering | 32104747 | Curr Opin Biomed Eng | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32104747 |
| Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds. | Clough M, Chen IA, Park SW, Ahrens AM, Stirman JN, Smith SL, Chen JL | Nature communications | 34789730 | Nat Commun | 2021 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/34789730 |
| Perirhinal cortex learns a predictive map of the task environment. | Lee DG, McLachlan CA, Nogueira R, Kwon O, Carey AE, House G, Lagani GD, LaMay D, Fusi S, Chen JL | Nature communications | 38956015 | Nat Commun | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38956015 |
| High-speed low-light in vivo two-photon voltage imaging of large neuronal populations. | Platisa J, Ye X, Ahrens AM, Liu C, Chen IA, Davison IG, Tian L, Pieribone VA, Chen JL | Nature methods | 36973547 | Nat Methods | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/36973547 |
| Context-Dependent Sensory Processing across Primary and Secondary Somatosensory Cortex. | Condylis C, Lowet E, Ni J, Bistrong K, Ouellette T, Josephs N, Chen JL | Neuron | 32164873 | Neuron | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/32164873 |
| 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 |
| Dense functional and molecular readout of a circuit hub in sensory cortex. | Condylis C, Ghanbari A, Manjrekar N, Bistrong K, Yao S, Yao Z, Nguyen TN, Zeng H, Tasic B, Chen JL | Science (New York, N.Y.) | 34990233 | Science | 2022 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/34990233 |
| 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 |
| 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 |
| 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 |
| 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 | 2025 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/39763840 |
| 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 |
| Synaptic vesicles transiently dock to refill release sites. | Kusick GF, Chin M, Raychaudhuri S, Lippmann K, Adula KP, Hujber EJ, Vu T, Davis MW, Jorgensen EM, Watanabe S | Nature neuroscience | 32989294 | Nat Neurosci | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32989294 |
| 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 |
| 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 |
| 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 |
| Defunctionalizing intracellular organelles such as mitochondria and peroxisomes with engineered phospholipase A/acyltransferases. | Watanabe S, Nihongaki Y, Itoh K, Uyama T, Toda S, Watanabe S, Inoue T | Nature communications | 35906209 | Nat Commun | 2022 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/35906209 |
| 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 |
| 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 |
| 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 |
| Synaptic Vesicle Recycling Through the Lens of Ultrafast Endocytosis. | Watanabe S | Annual review of neuroscience | 40670291 | Annu Rev Neurosci | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40670291 |
| Intersectin and endophilin condensates prime synaptic vesicles for release site replenishment. | Ogunmowo TH, Hoffmann C, Patel C, Pepper R, Wang H, Gowrisankaran S, Idel J, Ho A, Raychaudhuri S, Maher BJ, Cooper BH, Milosevic I, Milovanovic D, Watanabe S | Nature neuroscience | 40629141 | Nat Neurosci | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40629141 |
| Beyond Clathrin: Decoding the Mechanism of Ultrafast Endocytosis. | Imoto Y, Watanabe S | Physiology (Bethesda, Md.) | 40062769 | Physiology (Bethesda) | 2025 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/40062769 |
| SynapsEM: Computer-Assisted Synapse Morphometry. | Watanabe S, Davis MW, Kusick GF, Iwasa J, Jorgensen EM | Frontiers in synaptic neuroscience | 33390925 | Front Synaptic Neurosci | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/33390925 |
| Synaptotagmin 7 is targeted to the axonal plasma membrane through γ-secretase processing to promote synaptic vesicle docking in mouse hippocampal neurons. | Vevea JD, Kusick GF, Courtney KC, Chen E, Watanabe S, Chapman ER | eLife | 34543184 | Elife | 2021 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/34543184 |
| 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 |
| Intersectin and Endophilin condensates prime synaptic vesicles for release site replenishment. | Ogunmowo T, Hoffmann C, Pepper R, Wang H, Gowrisankaran S, Ho A, Raychaudhuri S, Cooper BH, Milosevic I, Milovanovic D, Watanabe S | bioRxiv : the preprint server for biology | 37662300 | bioRxiv | 2023 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/37662300 |
| 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 |
| Synaptotagmin 7 docks synaptic vesicles to support facilitation and Doc2α-triggered asynchronous release. | Wu Z, Kusick GF, Berns MMM, Raychaudhuri S, Itoh K, Walter AM, Chapman ER, Watanabe S | eLife | 38536730 | Elife | 2024 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/38536730 |
| 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 | Neuron | 41289997 | Neuron | 2026 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/41289997 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Neuropathic Pain-Like Responses in a Chronic CNS Injury Model Are Mediated by Corticospinal-Targeted Spinal Interneurons. | Guan X, Zhu Y, Zhong J, Hollis E | The Journal of neuroscience : the official journal of the Society for Neuroscience | 40550694 | J Neurosci | 2025 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/40550694 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Development and Validation of a Machine Learning-Derived Kinematic Deviation Index for the Evaluation of Forelimb in Rodents. | Torres-Espin A, Bernstein A, Soliman M, Jara JS, Moreno-López Y, Hollis E | AI in neuroscience | 41675258 | AI Neurosci | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/41675258 |
| 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 |
| Conditioning Electrical Nerve Stimulation Enhances Functional Rewiring in a Mouse Model of Nerve Transfer to Treat Chronic Spinal Cord Injury. | Jara JS, Soliman MA, Bernstein A, di Grazia P, Ferguson AR, Brown JM, Torres-Espín A, Hollis ER | Brain sciences | 40149773 | Brain Sci | 2025 Feb 27 | https://www.ncbi.nlm.nih.gov/pubmed/40149773 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | eNeuro | 40829942 | eNeuro | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40829942 |
| 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 |
| 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 |
| 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 |
| Subsecond dopamine fluctuations do not specify the vigor of ongoing actions. | Liu H, Melani R, Maltese M, Taniguchi J, Sankaramanchi A, Zeng R, Martin JR, Tritsch NX | Nature neuroscience | 41214177 | Nat Neurosci | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41214177 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Inorganic semiconductor biointerfaces. | Jiang Y, Tian B | Nature reviews. Materials | 31656635 | Nat Rev Mater | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31656635 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanowired Bioelectric Interfaces. | Tian B, Lieber CM | Chemical reviews | 30995019 | Chem Rev | 2019 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/30995019 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Precise multimodal optical control of neural ensemble activity. | Mardinly AR, Oldenburg IA, Pégard NC, Sridharan S, Lyall EH, Chesnov K, Brohawn SG, Waller L, Adesnik H | Nature neuroscience | 29713079 | Nat Neurosci | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29713079 |
| Inhibitory Circuits in Cortical Layer 5. | Naka A, Adesnik H | Frontiers in neural circuits | 27199675 | Front Neural Circuits | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27199675 |
| 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 |
| Synthesis of a comprehensive population code for contextual features in the awake sensory cortex. | Lyall EH, Mossing DP, Pluta SR, Chu YW, Dudai A, Adesnik H | eLife | 34723796 | Elife | 2021 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/34723796 |
| 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 |
| 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 |
| 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 |
| A direct translaminar inhibitory circuit tunes cortical output. | Pluta S, Naka A, Veit J, Telian G, Yao L, Hakim R, Taylor D, Adesnik H | Nature neuroscience | 26414615 | Nat Neurosci | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26414615 |
| 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 |
| 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 |
| 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 |
| 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 |
| MicroRNA-dependent genetic networks during neural development. | Abernathy DG, Yoo AS | Cell and tissue research | 24865244 | Cell Tissue Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24865244 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| LONGO: an R package for interactive gene length dependent analysis for neuronal identity. | McCoy MJ, Paul AJ, Victor MB, Richner M, Gabel HW, Gong H, Yoo AS, Ahn TH | Bioinformatics (Oxford, England) | 29950021 | Bioinformatics | 2018 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/29950021 |
| MicroRNAs: regulators of neuronal fate. | Sun AX, Crabtree GR, Yoo AS | Current opinion in cell biology | 23374323 | Curr Opin Cell Biol | 2013 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23374323 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Large-scale recording of astrocyte activity. | Nimmerjahn A, Bergles DE | Current opinion in neurobiology | 25665733 | Curr Opin Neurobiol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25665733 |
| 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 |
| Reorganization between preparatory and movement population responses in motor cortex. | Elsayed GF, Lara AH, Kaufman MT, Churchland MM, Cunningham JP | Nature communications | 27807345 | Nat Commun | 2016 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/27807345 |
| Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1. | Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM | PLoS computational biology | 27814353 | PLoS Comput Biol | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27814353 |
| Different population dynamics in the supplementary motor area and motor cortex during reaching. | Lara AH, Cunningham JP, Churchland MM | Nature communications | 30013188 | Nat Commun | 2018 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/30013188 |
| Motor Cortex Embeds Muscle-like Commands in an Untangled Population Response. | Russo AA, Bittner SR, Perkins SM, Seely JS, London BM, Lara AH, Miri A, Marshall NJ, Kohn A, Jessell TM, Abbott LF, Cunningham JP, Churchland MM | Neuron | 29398358 | Neuron | 2018 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/29398358 |
| Independent generation of sequence elements by motor cortex. | Zimnik AJ, Churchland MM | Nature neuroscience | 33619403 | Nat Neurosci | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33619403 |
| Neural Trajectories in the Supplementary Motor Area and Motor Cortex Exhibit Distinct Geometries, Compatible with Different Classes of Computation. | Russo AA, Khajeh R, Bittner SR, Perkins SM, Cunningham JP, Abbott LF, Churchland MM | Neuron | 32516573 | Neuron | 2020 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/32516573 |
| A Dynamical Basis Set for Generating Reaches. | Churchland MM, Cunningham JP | Cold Spring Harbor symposia on quantitative biology | 25851506 | Cold Spring Harb Symp Quant Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25851506 |
| Behaviorally Selective Engagement of Short-Latency Effector Pathways by Motor Cortex. | Miri A, Warriner CL, Seely JS, Elsayed GF, Cunningham JP, Churchland MM, Jessell TM | Neuron | 28735748 | Neuron | 2017 Aug 2 | https://www.ncbi.nlm.nih.gov/pubmed/28735748 |
| Identifying Interpretable Latent Factors with Sparse Component Analysis. | Zimnik AJ, Cora Ames K, An X, Driscoll L, Lara AH, Russo AA, Susoy V, Cunningham JP, Paninski L, Churchland MM, Glaser JI | bioRxiv : the preprint server for biology | 38370650 | bioRxiv | 2024 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/38370650 |
| The Largest Response Component in the Motor Cortex Reflects Movement Timing but Not Movement Type. | Kaufman MT, Seely JS, Sussillo D, Ryu SI, Shenoy KV, Churchland MM | eNeuro | 27761519 | eNeuro | 2016 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/27761519 |
| Cortical Control of Virtual Self-Motion Using Task-Specific Subspaces. | Schroeder KE, Perkins SM, Wang Q, Churchland MM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34716229 | J Neurosci | 2022 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/34716229 |
| Postural control of arm and fingers through integration of movement commands. | Albert ST, Hadjiosif AM, Jang J, Zimnik AJ, Soteropoulos DS, Baker SN, Churchland MM, Krakauer JW, Shadmehr R | eLife | 32043973 | Elife | 2020 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/32043973 |
| Perturbation of Macaque Supplementary Motor Area Produces Context-Independent Changes in the Probability of Movement Initiation. | Zimnik AJ, Lara AH, Churchland MM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30755488 | J Neurosci | 2019 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/30755488 |
| A neural network that finds a naturalistic solution for the production of muscle activity. | Sussillo D, Churchland MM, Kaufman MT, Shenoy KV | Nature neuroscience | 26075643 | Nat Neurosci | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26075643 |
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| Dual-Functional Lipid Coating for the Nanopillar-Based Capture of Circulating Tumor Cells with High Purity and Efficiency. | Lou HY, Zhao W, Hanson L, Zeng C, Cui Y, Cui B | Langmuir : the ACS journal of surfaces and colloids | 28059522 | Langmuir | 2017 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/28059522 |
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| Family Accommodation of Pediatric Irritability: Development and Psychometric Properties of the Family Accommodation Scale for Irritability. | Whiting C, Fling K, Meigs JM, Naim R, Haller SP, Henry LM, Silverman WK, Lebowitz ER, Brotman MA, Tseng WL | Behavior therapy | 41620240 | Behav Ther | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41620240 |
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| Ventral hippocampal parvalbumin interneurons gate the acute anxiolytic action of the serotonergic psychedelic DOI. | Tiwari P, Davoudian PA, Kapri D, Vuruputuri RM, Karaba LA, Sharma M, Zanni G, Balakrishnan A, Chaudhari PR, Pradhan A, Suryavanshi S, Bath KG, Ansorge MS, Fernandez-Ruiz A, Kwan AC, Vaidya VA | Neuron | 39321791 | Neuron | 2024 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/39321791 |
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| Using machine learning with passive wearable sensors to pilot the detection of eating disorder behaviors in everyday life. | Ralph-Nearman C, Sandoval-Araujo LE, Karem A, Cusack CE, Glatt S, Hooper MA, Rodriguez Pena C, Cohen D, Allen S, Cash ED, Welch K, Levinson CA | Psychological medicine | 37859600 | Psychol Med | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37859600 |
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| Preliminary Investigation of a Focused Regular Eating Intervention to Address Problematic Restriction in the Context of Evidence-Based Personalized Treatment. | Harris LM, Vanzhula IA, Hooper S, Levinson CA | The International journal of eating disorders | 41250820 | Int J Eat Disord | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41250820 |
| Differentiation between atypical anorexia nervosa and anorexia nervosa using machine learning. | Sandoval-Araujo LE, Cusack CE, Ralph-Nearman C, Glatt S, Han Y, Bryan J, Hooper MA, Karem A, Levinson CA | The International journal of eating disorders | 38352982 | Int J Eat Disord | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38352982 |
| Are recent decreases in adult obesity trends in the United States encouraging or alarming? | Peiper NC, Vanzhula IA, Levinson CA | Preventive medicine | 40334816 | Prev Med | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40334816 |
| The integration of oppression related variables into eating disorder research. | Kapadia A, Hooper SC, Crumby EK, Mekawi Y, Levinson CA | Body image | 41270497 | Body Image | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41270497 |
| Mild focal cooling selectively impacts computations in dendritic trees. | Matin MH, Xiao S, Jayant K | bioRxiv : the preprint server for biology | 39553978 | bioRxiv | 2024 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/39553978 |
| Touch-evoked traveling waves establish a translaminar spacetime code. | Gonzales DL, Khan HF, Keri HVS, Yadav S, Steward C, Muller LE, Pluta SR, Jayant K | Science advances | 39889002 | Sci Adv | 2025 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/39889002 |
| A Translaminar Spacetime Code Supports Touch-Evoked Traveling Waves. | Gonzales DL, Khan HF, Keri HVS, Yadav S, Steward C, Muller LE, Pluta SR, Jayant K | bioRxiv : the preprint server for biology | 38766232 | bioRxiv | 2024 May 9 | https://www.ncbi.nlm.nih.gov/pubmed/38766232 |
| Site-specific seeding of Lewy pathology induces distinct pre-motor cellular and dendritic vulnerabilities in the cortex. | Khan HF, Dutta S, Scott AN, Xiao S, Yadav S, Chen X, Aryal UK, Kinzer-Ursem TL, Rochet JC, Jayant K | Nature communications | 39737978 | Nat Commun | 2024 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/39737978 |
| GPU-accelerated, self-optimizing processing for 3D multiplexed iterative RNA-FISH experiments. | Kruithoff R, Spendlove MD, Sheppard SJ, Schweiger MC, Pessoa P, Abbasi M, Pressé S, Bartelle BB, Shepherd DP | bioRxiv : the preprint server for biology | 41279966 | bioRxiv | 2025 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/41279966 |
| Microglia express Tie2 in a longitudinal imaging study of acute neural injury in mice. | Brodsky J, Tashi Z, Christopher SK, Kruitoff R, Abbasi M, Cerna G, Gohsman SB, Mana MD, Bartelle BB | Molecular biology of the cell | 40668596 | Mol Biol Cell | 2025 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/40668596 |
| Subicular Plateaus Signal Reward Locations during Goal-Directed Behavior. | Bhatia A, Adel M, Grienberger C | bioRxiv : the preprint server for biology | 41756946 | bioRxiv | 2026 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/41756946 |
| Learning-dependent feedback by OLM interneurons shapes CA1 representations. | Campbell EP, Martin L, Magee JC, Grienberger C | bioRxiv : the preprint server for biology | 41509422 | bioRxiv | 2026 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/41509422 |
| The promise of cerebral organoids for neonatology. | Howard CE, Cheenath M, Crouch EE | Current opinion in pediatrics | 40013913 | Curr Opin Pediatr | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40013913 |
| Meningeal solitary fibrous tumor cell states phenocopy cerebral vascular development and homeostasis. | Mirchia K, Choudhury A, Joseph T, Birrueta JO, Phillips JJ, Bhaduri A, Crouch EE, Perry A, Raleigh DR | Neuro-oncology | 39207122 | Neuro Oncol | 2025 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/39207122 |
| The molecular landscape of vascular cells in the human brain. | Crouch EE | Nature reviews. Cardiology | 39304749 | Nat Rev Cardiol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39304749 |
| Gel-assisted mass spectrometry imaging enables sub-micrometer spatial lipidomics. | Chan YH, Pathmasiri KC, Pierre-Jacques D, Hibbard MC, Tao N, Fischer JL, Yang E, Cologna SM, Gao R | Nature communications | 38866734 | Nat Commun | 2024 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/38866734 |
| Gel-assisted mass spectrometry imaging. | Chan YH, Pathmasiri KC, Pierre-Jacques D, Cologna SM, Gao R | bioRxiv : the preprint server for biology | 37398444 | bioRxiv | 2023 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/37398444 |
| Super-resolved, three-dimensional spatial transcriptomics reveals cell-type and brain-region-specific modulation of key epitranscriptomic switches following adolescent alcohol exposure. | Tandukar J, Islam A, Malovic E, Afzal B, Zhang H, Pandey SC, Gao R | bioRxiv : the preprint server for biology | 41648353 | bioRxiv | 2026 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/41648353 |
| Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer's disease mouse model. | Orlowski A, Karippaparambil J, Paumier JM, Ghanta S, Pallares E, Chandran R, Edmison D, Tandukar J, Gao R, Gowrishankar S | bioRxiv : the preprint server for biology | 38617351 | bioRxiv | 2024 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/38617351 |
| Axonal organelle buildup from loss of AP-4 complex function causes exacerbation of amyloid plaque pathology and gliosis in Alzheimer's disease mouse model. | Orlowski A, Karippaparambil J, Paumier JM, Ghanta S, Pallares E, Chandran R, Edmison D, Tandukar J, Gao R, Gowrishankar S | eNeuro | 39632089 | eNeuro | 2024 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/39632089 |
| Behavioral control through the direct, focal silencing of neuronal activity. | Elleman AV, Milicic N, Williams DJ, Simko J, Liu CJ, Haynes AL, Ehrlich DE, Makinson CD, Du Bois J | Cell chemical biology | 38729162 | Cell Chem Biol | 2024 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/38729162 |
| Emerging roles of oligodendrocyte precursor cells in neural circuit development and remodeling. | Buchanan J, da Costa NM, Cheadle L | Trends in neurosciences | 37286422 | Trends Neurosci | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37286422 |
| A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. | Xavier AM, Lin Q, Kang CJ, Cheadle L | bioRxiv : the preprint server for biology | 38979325 | bioRxiv | 2024 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/38979325 |
| The Many Lives of an Oligodendrocyte Precursor Cell. | Buchanan J, Cheadle L | Annual review of neuroscience | 40233142 | Annu Rev Neurosci | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40233142 |
| Experience-dependent control of synaptic remodeling and structural plasticity by glia. | Vita DJ, Ferro A, Cheadle L | Current opinion in neurobiology | 40479809 | Curr Opin Neurobiol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40479809 |
| A single-cell transcriptomic atlas of sensory-dependent gene expression in developing mouse visual cortex. | Xavier AM, Lin Q, Kang CJ, Cheadle L | Development (Cambridge, England) | 40018816 | Development | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/40018816 |
| Fn14 is an activity-dependent, Bmal1-regulated cytokine receptor that induces rod-like microglia and restricts neuronal activity in vivo. | Ferro A, Vita DJ, Fallon T, Arshad A, Boyd L, Stanley T, Lin Q, Berisha A, Vrudhula U, Gomez AM, Sanchez-Martin I, Borniger JC, Cheadle L | Cell reports | 41615803 | Cell Rep | 2026 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/41615803 |
| The cytokine receptor Fn14 is a molecular brake on neuronal activity that mediates circadian function in vivo. | Ferro A, Arshad A, Boyd L, Stanley T, Berisha A, Vrudhula U, Gomez AM, Borniger JC, Cheadle L | bioRxiv : the preprint server for biology | 38617238 | bioRxiv | 2024 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/38617238 |
| Integrated high-confidence and high-throughput approaches for quantifying synapse engulfment by oligodendrocyte precursor cells. | Kahng JA, Xavier AM, Ferro A, Auguste YSS, Cheadle L | bioRxiv : the preprint server for biology | 37662250 | bioRxiv | 2023 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/37662250 |
| High-confidence and high-throughput quantification of synapse engulfment by oligodendrocyte precursor cells. | Kahng JA, Xavier AM, Ferro A, Tang SX, Auguste YSS, Cheadle L | Nature protocols | 39363108 | Nat Protoc | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39363108 |
| Disruption of Cholinergic Retinal Waves Alters Visual Cortex Development and Function. | Burbridge TJ, Ratliff JM, Dwivedi D, Vrudhula U, Alvarado-Huerta F, Sjulson L, Ibrahim LA, Cheadle L, Fishell G, Batista-Brito R | bioRxiv : the preprint server for biology | 38644996 | bioRxiv | 2024 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/38644996 |
| Maternal-fetal immune conflict contributes to male-specific impairments in a mouse model of neurodevelopmental disorders. | Sanchez-Martin I, Kukreja B, Henderson P, Lin Q, DiMartino D, Bagan V, Park J, Kalish BT, Cheadle L | bioRxiv : the preprint server for biology | 41676570 | bioRxiv | 2026 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/41676570 |
| Comparison of methods for characterizing skin pigment diversity in research cohorts. | Lipnick MS, Chen D, Law T, Moore K Jr, Lester JC, Monk EP, Hendrickson CM, Chou Y, Hughes C, Behnke E, Elmankabadi S, Ortiz L, Negussie F, Leeb G, Ehie O, Auchus I, Igaga EN, Bisegerwa R, Okunlola O, Bickler P, Feiner J, Shmuylovich L | The British journal of dermatology | 41073884 | Br J Dermatol | 2026 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/41073884 |
| Objective and Perceived Skin Color: Consequences for the Use of Skintone Scales. | Verkruysse W, Monk EP Jr, Jaffe MB | Anesthesia and analgesia | 39480708 | Anesth Analg | 2025 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/39480708 |
| Comparison of methods for characterizing skin pigment diversity in research cohorts. | Lipnick MS, Chen D, Law T, Moore K Jr, Lester JC, Monk EP, Hendrickson CM, Chou Y, Hughes C, Behnke E, Elmankabadi S, Ortiz L, Negussie F, Leeb G, Ehie O, Auchus I, Igaga EN, Bisegerwa R, Okunlola O, Bickler P, Feiner J, Shmuylovich L | medRxiv : the preprint server for health sciences | 40061342 | medRxiv | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/40061342 |
| Open Access Dataset and Common Data Model for Pulse Oximeter Performance Data. | Fong N, Lipnick MS, Behnke E, Chou Y, Elmankabadi S, Ortiz L, Almond CS, Auchus I, Burnett GW, Bisegerwa R, Conrad DR, Hendrickson CM, Hooli S, Kopotic R, Leeb G, Martin D, McCollum ED, Monk EP, Moore KL Jr, Shmuylovich L, Scott JB, Wong AI, Zhou T, Pirracchio R, Bickler PE, Feiner J, Law TJ | Scientific data | 40180919 | Sci Data | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/40180919 |
| Pulse oximeter performance and skin pigment: comparison of 34 oximeters using current and emerging regulatory frameworks. | Hughes C, Chen D, Law T, Bickler P, Feiner J, Shmuylovich L, Behnke E, Ortiz L, Leeb G, Auchus I, Negussie F, Bisegerwa R, Zamora RV, Igaga E, Moore K Jr, Okunlola O, Monk E, Fernandez JL, Ehie O, Wilks B, Oyefeso K, Schornack D, Sendagire C, Lipnick MS | medRxiv : the preprint server for health sciences | 40832401 | medRxiv | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/40832401 |
| The performance of 11 fingertip pulse oximeters during hypoxemia in healthy human participants with varied, quantified skin pigment. | Leeb G, Auchus I, Law T, Bickler P, Feiner J, Hashi S, Monk E, Igaga E, Bernstein M, Chou YC, Hughes C, Schornack D, Lester J, Moore K Jr, Okunlola O, Fernandez J, Shmuylovich L, Lipnick M | EBioMedicine | 38458110 | EBioMedicine | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38458110 |
| Open Access Data Repository and Common Data Model for Pulse Oximeter Performance Data. | Fong N, Lipnick MS, Behnke E, Chou Y, Elmankabadi S, Ortiz L, Almond CS, Auchus I, Burnett GW, Bisegerwa R, Conrad DR, Hendrickson CM, Hooli S, Kopotic R, Leeb G, Martin D, McCollum ED, Monk EP, Moore KL Jr, Shmuylovich L, Scott JB, Wong AI, Zhou T, Pirracchio R, Bickler PE, Feiner J, Law T | medRxiv : the preprint server for health sciences | 39252896 | medRxiv | 2024 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/39252896 |
| xIV-LDDMM Toolkit: A Suite of Image-Varifold Based Technologies for Representing and Mapping 3D Imaging and Spatial-omics Data Simultaneously Across Scales. | Stouffer KM, Chen X, Zeng H, Charlier B, Younes L, Trouvé A, Miller MI | bioRxiv : the preprint server for biology | 39574713 | bioRxiv | 2025 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/39574713 |
| Histone variant H2BE controls activity-dependent gene expression and homeostatic scaling. | Feierman ER, Paranjapye A, Sangree AK, Ahmad R, Maroni MJ, Qiu Q, Choi K, Fuccillo M, Wu H, Korb E | Cell reports | 41422507 | Cell Rep | 2026 Jan 27 | https://www.ncbi.nlm.nih.gov/pubmed/41422507 |
| Loss of DOT1L disrupts neuronal transcription and leads to a neurodevelopmental disorder. | Maroni MJ, Barton M, Lynch K, Deshwar AR, Campbell PD, Millard J, Lee R, Cohen A, Ahmad R, Paranjapye A, Faundes V, Repetto GM, McKenna C, Shillington AL, Phornphutkul C, Hove HB, Mancini GMS, Schot R, Barakat TS, Richmond CM, Lauzon J, Ibrahim AIE, Nava C, Héron D, van Aalst MMA, Atemin S, Sleptsova M, Aleksandrova I, Todorova A, Watkins DL, Kozenko MA, Natera-de Benito D, Ortez C, Estevez-Arias B, Lecoquierre F, Cassinari K, Guerrot AM, Levy J, Latypova X, Verloes A, Innes AM, Yang XR, Banka S, Vill K, Jacob M, Kruer M, Skidmore P, Galaz-Montoya CI, Bakhtiari S, Mester JL, Granato M, Armache KJ, Costain G, Korb E | Brain : a journal of neurology | 40494548 | Brain | 2026 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/40494548 |
| Material hardship and use of social safety net programs among LGBT adults and their families. | Henderson ER, Hotchkiss M, Lin CA, Blosnich JR | Analyses of social issues and public policy : ASAP | 40734955 | Anal Soc Issues Public Policy | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40734955 |
| Poor Mental Health Days and Depression by Farming Occupation and Sociodemographic Factors: BRFSS 2019 Data from 13 States. | Ward JM, Blosnich JR | Journal of agromedicine | 41195547 | J Agromedicine | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41195547 |
| Interpersonal and self-directed violence among sexual and gender minority populations: Moving research from prevalence to prevention. | Blosnich JR | Current epidemiology reports | 36845319 | Curr Epidemiol Rep | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36845319 |
| Concept Analysis: Challenge Coins as a Caring Support Tool to Prevent Farmer Suicide. | Ward JM, Blosnich JR, Dean-Witt C | Journal of agromedicine | 39440398 | J Agromedicine | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39440398 |
| Re-evaluating National Suicide Prevention Month: Strategic Timing and Enhanced Impact. | Ward JM, Yang A, Shi Y, Haydinger A, Blosnich JR | Critical public health | 40741523 | Crit Public Health | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40741523 |
| Mortality among sexual and gender minority populations: A systematic review. | Zachry CE, O'Brien RP, Clark KA, Ding ML, Blosnich JR | PloS one | 39899557 | PLoS One | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/39899557 |
| Differences in Beliefs About Suicide by Occupation in a Representative Sample of Adults in the United States, General Social Survey 2002-2021. | Blosnich JR, Haydinger AM, Rhoades H, De Luca SM | Archives of suicide research : official journal of the International Academy for Suicide Research | 36916390 | Arch Suicide Res | 2024 Apr-Jun | https://www.ncbi.nlm.nih.gov/pubmed/36916390 |
| Adverse Childhood Experiences Among Lesbian, Gay, Bisexual, and Queer Veterans. | Hahn HA, Blosnich JR | American journal of preventive medicine | 37037327 | Am J Prev Med | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37037327 |
| Seasonal and Sociodemographic Factors Associated With Farmer Suicide: National Violent Death Reporting System 2014-2021. | Ward JM, Blosnich JR | Rural mental health | 40741097 | Rural Ment Health | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40741097 |
| "Stop, Think, and Appreciate": A Qualitative Exploration of a Challenge Coin Suicide Prevention Intervention among Farmers. | Ward JM, Perkins M, Blosnich JR | Community mental health journal | 40833660 | Community Ment Health J | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40833660 |
| Exploring Bankruptcy Attorneys' Experiences With Clients Exhibiting Suicidality: Challenges and Recommendations for Suicide Prevention. | Blosnich JR, Ward JM, Perkins M, Ding M, De Luca S | Behavioral sciences & the law | 41431169 | Behav Sci Law | 2026 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/41431169 |
| Structured experience shapes strategy learning and neural dynamics in the medial entorhinal cortex. | Bowler JC, Azhar D, Jensen C, Lee H, Heys JG | Research square | 40502753 | Res Sq | 2025 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/40502753 |
| Structured experience shapes strategy learning and neural dynamics in the medial entorhinal cortex. | Bowler JC, Azhar D, Jensen CM, Lee HW, Heys JG | bioRxiv : the preprint server for biology | 40463160 | bioRxiv | 2025 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/40463160 |
| Medial entorhinal cortex plays a specialized role in learning of flexible, context-dependent interval timing behavior. | Bigus ER, Lee HW, Shi J, Heys JG | Research square | 37131646 | Res Sq | 2023 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/37131646 |
| Medial entorhinal cortex mediates learning of context-dependent interval timing behavior. | Bigus ER, Lee HW, Bowler JC, Shi J, Heys JG | Nature neuroscience | 38877306 | Nat Neurosci | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38877306 |
| Hippocampal time cell dynamics evolve with learning to reflect cognitive demands. | Bigus ER, Bowler JC, Azhar D, Zukowsky D, Heys JG | bioRxiv : the preprint server for biology | 40475495 | bioRxiv | 2025 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/40475495 |
| Dynamic assemblies of parvalbumin interneurons in brain oscillations. | Huang YC, Chen HC, Lin YT, Lin ST, Zheng Q, Abdelfattah AS, Lavis LD, Schreiter ER, Lin BJ, Chen TW | Neuron | 38955183 | Neuron | 2024 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/38955183 |
| Neurophotonic tools for microscopic measurements and manipulation: status report. | Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y | Neurophotonics | 35493335 | Neurophotonics | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/35493335 |
| A novel rhodopsin-based voltage indicator for simultaneous two-photon optical recording with GCaMP in vivo. | Villette V, Yang S, Valenti R, Macklin JJ, Bradley J, Mathieu B, Lombardini A, Podgorski K, Dieudonné S, Schreiter ER, Abdelfattah AS | bioRxiv : the preprint server for biology | 39605646 | bioRxiv | 2024 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/39605646 |
| Sensitivity optimization of a rhodopsin-based fluorescent voltage indicator. | Abdelfattah AS, Zheng J, Singh A, Huang YC, Reep D, Tsegaye G, Tsang A, Arthur BJ, Rehorova M, Olson CVL, Shuai Y, Zhang L, Fu TM, Milkie DE, Moya MV, Weber TD, Lemire AL, Baker CA, Falco N, Zheng Q, Grimm JB, Yip MC, Walpita D, Chase M, Campagnola L, Murphy GJ, Wong AM, Forest CR, Mertz J, Economo MN, Turner GC, Koyama M, Lin BJ, Betzig E, Novak O, Lavis LD, Svoboda K, Korff W, Chen TW, Schreiter ER, Hasseman JP, Kolb I | Neuron | 37015225 | Neuron | 2023 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/37015225 |
| Gene Clusters Reveal Fundamental Principles of Genome Folding and Transcriptional Regulation. | Buckley A, Vetralla C, Canzio D | Annual review of cell and developmental biology | 41034155 | Annu Rev Cell Dev Biol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41034155 |
| Tuning cohesin trajectories enables differential readout of the Pcdhα cluster across neurons. | Kiefer L, Gaudin S, Rajkumar SM, Servito GIF, Langen J, Mui MH, Nawsheen S, Canzio D | Science (New York, N.Y.) | 39052779 | Science | 2024 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/39052779 |
| Dynamical Modeling of Behaviorally Relevant Spatiotemporal Patterns in Neural Imaging Data. | Hosseini M, Shanechi MM | ArXiv | 41040797 | ArXiv | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/41040797 |
| Dynamical flexible inference of nonlinear latent factors and structures in neural population activity. | Abbaspourazad H, Erturk E, Pesaran B, Shanechi MM | Nature biomedical engineering | 38082181 | Nat Biomed Eng | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38082181 |
| Modeling multiscale causal interactions between spiking and field potential signals during behavior. | Wang C, Pesaran B, Shanechi MM | Journal of neural engineering | 35073530 | J Neural Eng | 2022 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/35073530 |
| Multimodal subspace identification for modeling discrete-continuous spiking and field potential population activity. | Ahmadipour P, Sani OG, Pesaran B, Shanechi MM | Journal of neural engineering | 38016450 | J Neural Eng | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/38016450 |
| Dynamical Modeling of Behaviorally Relevant Spatiotemporal Patterns in Neural Imaging Data. | Hosseini M, Shanechi MM | Proceedings of machine learning research | 41321375 | Proc Mach Learn Res | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/41321375 |
| Spectral Learning of Shared Dynamics Between Generalized-Linear Processes. | Oganesian LL, Sani OG, Shanechi MM | Advances in neural information processing systems | 41306626 | Adv Neural Inf Process Syst | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41306626 |
| Modeling and dissociation of intrinsic and input-driven neural population dynamics underlying behavior. | Vahidi P, Sani OG, Shanechi MM | Proceedings of the National Academy of Sciences of the United States of America | 38335258 | Proc Natl Acad Sci U S A | 2024 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/38335258 |
| Dissociative and prioritized modeling of behaviorally relevant neural dynamics using recurrent neural networks. | Sani OG, Pesaran B, Shanechi MM | Nature neuroscience | 39242944 | Nat Neurosci | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39242944 |
| BRAID: Input-driven nonlinear dynamical modeling of neural-behavioral data. | Vahidi P, Sani OG, Shanechi MM | ArXiv | 41040807 | ArXiv | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/41040807 |
| Probabilistic Geometric Principal Component Analysis with application to neural data. | Hsieh HL, Shanechi MM | ArXiv | 41040801 | ArXiv | 2025 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/41040801 |
| Challenges and opportunities of acquiring cortical recordings for chronic adaptive deep brain stimulation. | Herron J, Kullmann A, Denison T, Goodman WK, Gunduz A, Neumann WJ, Provenza NR, Shanechi MM, Sheth SA, Starr PA, Widge AS | Nature biomedical engineering | 39730913 | Nat Biomed Eng | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39730913 |
| Unsupervised learning of stationary and switching dynamical system models from Poisson observations. | Song CY, Shanechi MM | Journal of neural engineering | 38083862 | J Neural Eng | 2023 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/38083862 |
| Early Life Stress induces brain-wide electrical network predisposition to migraine. | Johnson M, Eberle M, Hultman I, Zhang X, Filali Y, Hing B, Matkovich M, Jimenez A, Mitchell S, Adegboyo A, Velamuri R, Miller J, Chan KS, Srivastava S, Hultman R | bioRxiv : the preprint server for biology | 40462923 | bioRxiv | 2025 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/40462923 |
| Mechanistic intersections between migraine and major depressive disorder. | Johnson M, Filali Y, Adegboyo A, Eberle M, Townsend A, Hussien Y, Marcinkiewcz C, Hultman R | The journal of headache and pain | 40634879 | J Headache Pain | 2025 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/40634879 |
| An Automated Squint Method for Time-syncing Behavior and Brain Dynamics in Mouse Pain Studies. | McCutcheon N, Johnson MS, Rea B, Ghumman M, Sowers L, Hultman R | Journal of visualized experiments : JoVE | 39555788 | J Vis Exp | 2024 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/39555788 |
| Single Cell Transcriptome of Stress Vulnerability Network in mouse Prefrontal Cortex. | Hing B, Mitchell SB, Eberle M, Filali Y, Hultman I, Matkovich M, Kasturirangan M, Wyche W, Jimenez A, Velamuri R, Johnson M, Srivastava S, Hultman R | bioRxiv : the preprint server for biology | 37662266 | bioRxiv | 2023 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/37662266 |
| Transcriptomic Evaluation of a Stress Vulnerability Network Using Single-Cell RNA Sequencing in Mouse Prefrontal Cortex. | Hing B, Mitchell SB, Filali Y, Eberle M, Hultman I, Matkovich M, Kasturirangan M, Johnson M, Wyche W, Jimenez A, Velamuri R, Ghumman M, Wickramasinghe H, Christian O, Srivastava S, Hultman R | Biological psychiatry | 38866174 | Biol Psychiatry | 2024 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/38866174 |
| 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 |
| Acetylcholine demixes heterogeneous dopamine signals for learning and moving. | Jang HJ, McMahon Ward R, Golden CEM, Constantinople CM | bioRxiv : the preprint server for biology | 38746300 | bioRxiv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/38746300 |
| 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 |
| Estrogenic control of reward prediction errors and reinforcement learning. | Golden CEM, Martin AC, Kaur D, Mah A, Levy DH, Yamaguchi T, Lasek AW, Lin D, Aoki C, Constantinople CM | bioRxiv : the preprint server for biology | 38105956 | bioRxiv | 2024 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/38105956 |
| The orbitofrontal cortex updates beliefs for state inference. | Schiereck SS, Pérez-Rivera DT, Mah A, DeMaegd ML, Hocker D, Ward RM, Savin C, Constantinople CM | bioRxiv : the preprint server for biology | 39554155 | bioRxiv | 2025 Aug 13 | 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 |
| Estrogen modulates reward prediction errors and reinforcement learning. | Golden CEM, Martin AC, Kaur D, Mah A, Levy DH, Yamaguchi T, Lasek AW, Lin D, Aoki C, Constantinople CM | Nature neuroscience | 41219504 | Nat Neurosci | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41219504 |
| The orbitofrontal cortex updates beliefs for state inference. | Schiereck SS, Pérez-Rivera DT, Mah A, DeMaegd ML, Hocker D, Ward RM, Savin C, Constantinople CM | Neuron | 41253149 | Neuron | 2026 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/41253149 |
| 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 |
| 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 |
| 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 |
| Context rescales a social action code in a hormone-sensitive network. | Guthman EM, Iravedra-Garcia JM, Sirrs L, Le A, Falkner AL | bioRxiv : the preprint server for biology | 41040254 | bioRxiv | 2025 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/41040254 |
| A bifunctional optical reporter for tracking estrogen response dynamics in neurons. | Cara AL, Guthman EM, Mishra A, Hall AL, Yokoyama S, Sandoval NP, Gregg I, Aghi K, Soma KK, Correa SM, Falkner AL, van Veen JE | bioRxiv : the preprint server for biology | 41427375 | bioRxiv | 2025 Dec 14 | https://www.ncbi.nlm.nih.gov/pubmed/41427375 |
| Two-color Multifiber Photometry Recordings of the Social Behavior Network in Mice. | Guthman EM, Iravedra-García JM, Cherepanova P, Yokoyama S, Lockwood SE, Oline SN, Falkner AL | Journal of visualized experiments : JoVE | 41941465 | J Vis Exp | 2026 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/41941465 |
| 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 |
| An automated two-choice social operant task for probing moment-to-moment changes in social satiety. | Mack NR, Minakuchi T, Igarza K, Wonnenberg P, Oline SN, Falkner AL | bioRxiv : the preprint server for biology | 40791340 | bioRxiv | 2025 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/40791340 |
| 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 |
| 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 |
| 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 |
| Eye-specific differences in active zone addition during synaptic competition in the developing visual system. | Zhang C, Vatan T, Speer CM | bioRxiv : the preprint server for biology | 39484601 | bioRxiv | 2025 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/39484601 |
| Eye-specific differences in active zone addition during synaptic competition in the developing visual system. | Zhang C, Vatan T, Speer CM | eLife | 41212074 | Elife | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41212074 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| What's the Weight? Estimating Controlled Outcome Differences in Complex Surveys for Health Disparities Research. | Salerno S, Roberts EK, Needham BL, McCormick TH, Li F, Mukherjee B, Shi X | Statistics in medicine | 41055541 | Stat Med | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/41055541 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Parietal cortex is causally required for state-dependent decisions. | Bandi AC, McCann JP, Carpenter RM, Lower MJ, Long JN, Runyan CA | Cell reports | 41389207 | Cell Rep | 2025 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/41389207 |
| 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 |
| Parietal cortex is causally required for state-dependent decisions. | Bandi AC, McCann JP, Carpenter RM, Lower MJ, Long JN, Runyan CA | bioRxiv : the preprint server for biology | 38826351 | bioRxiv | 2025 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/38826351 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 Crunchometer: A Low-Cost, Open-Source Acoustic Analysis of Feeding Microstructure. | Gil-Lievana E, Arroyo B, Pérez-Ortega J, Lopez A, Rodriguez Blanco LA, Diaz X, Hernandez G, Coss A, Alway E, Reicher N, Lemus EH, Kaelberer M, Bohórquez DV, Gutierrez R | bioRxiv : the preprint server for biology | 40766613 | bioRxiv | 2025 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/40766613 |
| 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 |
| 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 |
| 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 |
| 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 |
| A gut sense for a microbial pattern regulates feeding. | Liu WW, Reicher N, Alway E, Rupprecht LE, Weng P, Schaefgen C, Klein ME, Villalobos JA, Puerto-Hernandez C, Kiesling Altún YG, Carbajal A, Aguayo-Guerrero JA, Coss A, Sahasrabudhe A, Anikeeva P, de Araujo A, Bali A, de Lartigue G, Gil-Lievana E, Gutierrez R, Miao EA, Rawls JF, Kaelberer MM, Bohórquez DV | Nature | 40702192 | Nature | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40702192 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
| Comparative characterization of human accelerated regions in neurons. | Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y | Nature | 40011774 | Nature | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40011774 |
| ANTIPODE Provides a Global View of Cell Type Homology and Transcriptomic Divergence in the Developing Mammalian Brain. | Schmitz MT, Ding JW, Nolbrant S, McMullen R, Kim CN, Pavlovic BJ, Nowakowski TJ, Bakken TE, Ye CJ, Pollen AA | bioRxiv : the preprint server for biology | 41278807 | bioRxiv | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/41278807 |
| 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 |
| Dissecting Gene Regulatory Networks Governing Human Cortical Cell Fate. | Ding JW, Kim CN, Ostrowski MS, Abeykoon Y, Pavlovic BJ, Wallace JL, Nowakowski TJ, Pollen AA | bioRxiv : the preprint server for biology | 41040362 | bioRxiv | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/41040362 |
| 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 |
| Interrogating the Regulatory Function of HAQERs during Human Cortical Development. | Abeykoon Y, Dzikowski N, Luo Y, Sinniah E, Weaver S, Pavlovic BJ, Wallace JL, Mangan RJ, Lowe CB, Pollen AA | bioRxiv : the preprint server for biology | 41377512 | bioRxiv | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41377512 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 two-color imaging with a dual-channel miniscope 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 | Science advances | 40601747 | Sci Adv | 2025 Jul 4 | https://www.ncbi.nlm.nih.gov/pubmed/40601747 |
| Interneuron theta phase locking controls seizure susceptibility. | Wick ZC, Philipsberg PA, Kohler C, Lamsifer SI, Katanov E, Adam CD, Gordon KE, Feng Y, Vetere LM, Donnelly GC, Humphrey C, Cai DJ, Shuman T | bioRxiv : the preprint server for biology | 40964369 | bioRxiv | 2025 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/40964369 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Prime Editing of Mouse Primary Neurons. | Robertson CD, Richardson RR, Steyert M, Martin CA, Flynn C, Poulopoulos A | Methods in molecular biology (Clifton, N.J.) | 40220094 | Methods Mol Biol | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40220094 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Network neuroscience (Cambridge, Mass.) | 39735492 | Netw Neurosci | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/39735492 |
| 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 |
| 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 |
| 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 |
| Topological data analysis reveals rigid brain-state dynamics during self-viewing in trait rumination. | Geniesse C, Jahanikia S, Xie H, Sonalkar NS, Williams LM, Saggar M | bioRxiv : the preprint server for biology | 41497618 | bioRxiv | 2025 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/41497618 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Hormones and behavior | 40627990 | Horm Behav | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40627990 |
| 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 |
| 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 |
| 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 |
| Accumbal calcium-permeable AMPA receptors orchestrate neuronal ensembles underlying social attachment. | El-Kalliny MM, Kushner JK, Sheeran WM, Neilly OE, Winther KE, Brusman LE, Kelberman MA, Hoeffer CA, Donaldson ZR | Nature communications | 41501009 | Nat Commun | 2026 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/41501009 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Behavioral state and stimulus strength regulate the role of somatostatin interneurons in stabilizing network activity. | Cammarata CM, Pei Y, Hu T, Shields BC, Lim SSX, Hawley T, Li JY, St Amand D, Brunel N, Tadross MR, Glickfeld LL | Cell reports | 40638386 | Cell Rep | 2025 Jul 22 | https://www.ncbi.nlm.nih.gov/pubmed/40638386 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 AC, 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 AK, Boesch C, Kühl HS, Dennis MY, Marques-Bonet T, Arandjelovic M, Andrés AM | Science (New York, N.Y.) | 41296989 | Science | 2025 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/41296989 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cortical overgrowth in a preclinical forebrain organoid model of CNTNAP2-associated autism spectrum disorder. | de Jong JO, Llapashtica C, Genestine M, Strauss K, Provenzano F, Sun Y, Zhu H, Cortese GP, Brundu F, Brigatti KW, Corneo B, Migliori B, Tomer R, Kushner SA, Kellendonk C, Javitch JA, Xu B, Markx S | Nature communications | 34471112 | Nat Commun | 2021 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/34471112 |
| Focused ultrasound-mediated brain genome editing. | Leong K, Lao YH, Ji R, Zhou J, Snow K, Kwon N, Saville E, He S, Chauhan S, Chi CW, Datta M, Zhang H, Quek CH, Cai S, Li M, Gaitan Y, Bechtel L, Wu SY, Lutz C, Tomer R, Murray S, Chavez A, Konofagou E | Research square | 36712096 | Res Sq | 2023 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/36712096 |
| Focused ultrasound-mediated brain genome editing. | Lao YH, Ji R, Zhou JK, Snow KJ, Kwon N, Saville E, He S, Chauhan S, Chi CW, Datta MS, Zhang H, Quek CH, Cai SS, Li M, Gaitan Y, Bechtel L, Wu SY, Lutz CM, Tomer R, Murray SA, Chavez A, Konofagou EE, Leong KW | Proceedings of the National Academy of Sciences of the United States of America | 37579143 | Proc Natl Acad Sci U S A | 2023 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/37579143 |
| Capillary connections between sensory circumventricular organs and adjacent parenchyma enable local volume transmission. | Yao Y, Chen Y, Tomer R, Silver R | Journal of neuroendocrinology | 39764696 | J Neuroendocrinol | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/39764696 |
| Whole-brain mapping reveals the divergent impact of ketamine on the dopamine system. | Datta MS, Chen Y, Chauhan S, Zhang J, De La Cruz ED, Gong C, Tomer R | Cell reports | 38052211 | Cell Rep | 2023 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/38052211 |
| Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution. | Chakraborty T, Driscoll MK, Jeffery E, Murphy MM, Roudot P, Chang BJ, Vora S, Wong WM, Nielson CD, Zhang H, Zhemkov V, Hiremath C, De La Cruz ED, Yi Y, Bezprozvanny I, Zhao H, Tomer R, Heintzmann R, Meeks JP, Marciano DK, Morrison SJ, Danuser G, Dean KM, Fiolka R | Nature methods | 31673159 | Nat Methods | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31673159 |
| An in vitro model of neuronal ensembles. | Rabadan MA, De La Cruz ED, Rao SB, Chen Y, Gong C, Crabtree G, Xu B, Markx S, Gogos JA, Yuste R, Tomer R | Nature communications | 35680927 | Nat Commun | 2022 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/35680927 |
| Whole-brain mapping reveals the divergent impact of ketamine on the dopamine system. | Datta MS, Chen Y, Chauhan S, Zhang J, De La Cruz ED, Gong C, Tomer R | bioRxiv : the preprint server for biology | 37090584 | bioRxiv | 2023 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/37090584 |
| Scalable projected Light Sheet Microscopy for high-resolution imaging of living and cleared samples. | Chen Y, Chauhan S, Gong C, Dayton H, Xu C, De La Cruz ED, Datta MS, Leong KW, Dietrich LEP, Tomer R | bioRxiv : the preprint server for biology | 37333196 | bioRxiv | 2023 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/37333196 |
| Multi-immersion Oblique Plane Microscope (miOPM): A reconfigurable platform for high-resolution Light-Sheet Fluorescence Microscopy. | Chen B, Millett-Sikking A, Gałecki S, Daetwyler S, Jiou J, Monistrol J, Shen Q, Zhou F, Lin HY, Jenkins E, Stein MC, Marlar-Pavey M, Sturm G, Li AL, Tang Q, Feng B, Diaz U, Chen Y, Shalizi A, Gillich A, Friedman JR, Tomer R, Chang BJ, Marshall WF, Shahmoradian S, Dean KM, Fiolka R | bioRxiv : the preprint server for biology | 41279040 | bioRxiv | 2025 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/41279040 |
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| A miniaturized multi-clamp CMOS amplifier for intracellular neural recording. | Shekar S, Jayant K, Rabadan MA, Tomer R, Yuste R, Shepard KL | Nature electronics | 31850397 | Nat Electron | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31850397 |
| 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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| Cell 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 | bioRxiv : the preprint server for biology | 37645902 | bioRxiv | 2023 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/37645902 |
| A Microfluidic Dual-Aptamer Sandwich Assay for Rapid and Cost-Effective Detection of Recombinant Proteins. | Wen K, Chen Y, Meng X, Botros S, Dai W, Stojanovic MN, Tomer R, Lin Q | Microchemical journal : devoted to the application of microtechniques in all branches of science | 36992861 | Microchem J | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36992861 |
| Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy. | Gong C, Affatato P, Fay M, Guttikonda SR, O'Connor NJ, Noble E, Heal M, Haydock B, Mapa R, De La Cruz ED, Kowalko JE, Tosches MA, Gerfen CR, Hen R, Makinson CD, Hibshoosh H, Glaser J, Tomer R | bioRxiv : the preprint server for biology | 41278967 | bioRxiv | 2025 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/41278967 |
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| 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 |
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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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Microglial pattern recognition via IL-33 promotes synaptic refinement in developing corticothalamic circuits in mice. | Han RT, Vainchtein ID, Schlachetzki JCM, Cho FS, Dorman LC, Ahn E, Kim DK, Barron JJ, Nakao-Inoue H, Molofsky AB, Glass CK, Paz JT, Molofsky AV | The Journal of experimental medicine | 36520518 | J Exp Med | 2023 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/36520518 |
| 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 |
| Variation among intact tissue samples reveals the core transcriptional features of human CNS cell classes. | Kelley KW, Nakao-Inoue H, Molofsky AV, Oldham MC | Nature neuroscience | 30154505 | Nat Neurosci | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30154505 |
| 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 |
| Circuit and molecular architecture of a ventral hippocampal network. | Gergues MM, Han KJ, Choi HS, Brown B, Clausing KJ, Turner VS, Vainchtein ID, Molofsky AV, Kheirbek MA | Nature neuroscience | 32929245 | Nat Neurosci | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32929245 |
| Type-I-interferon-responsive microglia shape cortical development and behavior. | Escoubas CC, Dorman LC, Nguyen PT, Lagares-Linares C, Nakajo H, Anderson SR, Barron JJ, Wade SD, Cuevas B, Vainchtein ID, Silva NJ, Guajardo R, Xiao Y, Lidsky PV, Wang EY, Rivera BM, Taloma SE, Kim DK, Kaminskaya E, Nakao-Inoue H, Schwer B, Arnold TD, Molofsky AB, Condello C, Andino R, Nowakowski TJ, Molofsky AV | Cell | 38490196 | Cell | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38490196 |
| 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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| Nonhuman Primate Optogenetics: Recent Advances and Future Directions. | Galvan A, Stauffer WR, Acker L, El-Shamayleh Y, Inoue KI, Ohayon S, Schmid MC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 29118219 | J Neurosci | 2017 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/29118219 |
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| Dopamine prediction error responses update demand. | Rothenhoefer KM, Stauffer WR | Proceedings of the National Academy of Sciences of the United States of America | 29233946 | Proc Natl Acad Sci U S A | 2017 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/29233946 |
| Transcriptional and anatomical diversity of medium spiny neurons in the primate striatum. | He J, Kleyman M, Chen J, Alikaya A, Rothenhoefer KM, Ozturk BE, Wirthlin M, Bostan AC, Fish K, Byrne LC, Pfenning AR, Stauffer WR | Current biology : CB | 34727523 | Curr Biol | 2021 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/34727523 |
| Anterior cingulate learns reward distribution. | Hong T, Stauffer WR | Nature neuroscience | 38351324 | Nat Neurosci | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38351324 |
| Local Genome Topology Can Exhibit an Incompletely Rewired 3D-Folding State during Somatic Cell Reprogramming. | Beagan JA, Gilgenast TG, Kim J, Plona Z, Norton HK, Hu G, Hsu SC, Shields EJ, Lyu X, Apostolou E, Hochedlinger K, Corces VG, Dekker J, Phillips-Cremins JE | Cell stem cell | 27152443 | Cell Stem Cell | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/27152443 |
| 3DeFDR: statistical methods for identifying cell type-specific looping interactions in 5C and Hi-C data. | Fernandez LR, Gilgenast TG, Phillips-Cremins JE | Genome biology | 32859248 | Genome Biol | 2020 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/32859248 |
| CRISPR/Cas9 genome editing throws descriptive 3-D genome folding studies for a loop. | Beagan JA, Phillips-Cremins JE | Wiley interdisciplinary reviews. Systems biology and medicine | 27265842 | Wiley Interdiscip Rev Syst Biol Med | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27265842 |
| On the existence and functionality of topologically associating domains. | Beagan JA, Phillips-Cremins JE | Nature genetics | 31925403 | Nat Genet | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31925403 |
| Chromatin structure dynamics during the mitosis-to-G1 phase transition. | Zhang H, Emerson DJ, Gilgenast TG, Titus KR, Lan Y, Huang P, Zhang D, Wang H, Keller CA, Giardine B, Hardison RC, Phillips-Cremins JE, Blobel GA | Nature | 31776509 | Nature | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31776509 |
| LADL: light-activated dynamic looping for endogenous gene expression control. | Kim JH, Rege M, Valeri J, Dunagin MC, Metzger A, Titus KR, Gilgenast TG, Gong W, Beagan JA, Raj A, Phillips-Cremins JE | Nature methods | 31235883 | Nat Methods | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31235883 |
| Detecting hierarchical genome folding with network modularity. | Norton HK, Emerson DJ, Huang H, Kim J, Titus KR, Gu S, Bassett DS, Phillips-Cremins JE | Nature methods | 29334377 | Nat Methods | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29334377 |
| Disease-Associated Short Tandem Repeats Co-localize with Chromatin Domain Boundaries. | Sun JH, Zhou L, Emerson DJ, Phyo SA, Titus KR, Gong W, Gilgenast TG, Beagan JA, Davidson BL, Tassone F, Phillips-Cremins JE | Cell | 30173918 | Cell | 2018 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/30173918 |
| Dynamic Looping Interactions: Setting the 3D Stage for the Macrophage. | Rege M, Phillips-Cremins JE | Molecular cell | 28938095 | Mol Cell | 2017 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/28938095 |
| YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment. | Beagan JA, Duong MT, Titus KR, Zhou L, Cao Z, Ma J, Lachanski CV, Gillis DR, Phillips-Cremins JE | Genome research | 28536180 | Genome Res | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28536180 |
| Three-dimensional genome restructuring across timescales of activity-induced neuronal gene expression. | Beagan JA, Pastuzyn ED, Fernandez LR, Guo MH, Feng K, Titus KR, Chandrashekar H, Shepherd JD, Phillips-Cremins JE | Nature neuroscience | 32451484 | Nat Neurosci | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32451484 |
| 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 |
| Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data. | Gilgenast TG, Phillips-Cremins JE | Cell systems | 30904376 | Cell Syst | 2019 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/30904376 |
| A subset of topologically associating domains fold into mesoscale core-periphery networks. | Huang H, Chen ST, Titus KR, Emerson DJ, Bassett DS, Phillips-Cremins JE | Scientific reports | 31266973 | Sci Rep | 2019 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/31266973 |
| Tonic activity in lateral habenula neurons acts as a neutral valence brake on reward-seeking behavior. | Post RJ, Bulkin DA, Ebitz RB, Lee V, Han K, Warden MR | Current biology : CB | 36049479 | Curr Biol | 2022 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/36049479 |
| 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 |
| Infralimbic parvalbumin neural activity facilitates cued threat avoidance. | Ho YY, Yang Q, Boddu P, Bulkin DA, Warden MR | eLife | 40168058 | Elife | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40168058 |
| 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 |
| Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain. | Wang T, Wu C, Ouzounov DG, Gu W, Xia F, Kim M, Yang X, Warden MR, Xu C | eLife | 31999253 | Elife | 2020 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/31999253 |
| Hebbian Learning in a Random Network Captures Selectivity Properties of the Prefrontal Cortex. | Lindsay GW, Rigotti M, Warden MR, Miller EK, Fusi S | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28986463 | J Neurosci | 2017 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/28986463 |
| Working memory control dynamics follow principles of spatial computing. | Lundqvist M, Brincat SL, Rose J, Warden MR, Buschman TJ, Miller EK, Herman P | Nature communications | 36918567 | Nat Commun | 2023 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/36918567 |
| Prefrontal cortical regulation of brainwide circuit dynamics and reward-related behavior. | Ferenczi EA, Zalocusky KA, Liston C, Grosenick L, Warden MR, Amatya D, Katovich K, Mehta H, Patenaude B, Ramakrishnan C, Kalanithi P, Etkin A, Knutson B, Glover GH, Deisseroth K | Science (New York, N.Y.) | 26722001 | Science | 2016 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/26722001 |
| Serotonin neurons in mating female mice are activated by male ejaculation. | Troconis EL, Seo C, Guru A, Warden MR | bioRxiv : the preprint server for biology | 37645786 | bioRxiv | 2023 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/37645786 |
| Depression: the search for separable behaviors and circuits. | Post RJ, Warden MR | Current opinion in neurobiology | 29529482 | Curr Opin Neurobiol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29529482 |
| 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 |
| Infralimbic parvalbumin neural activity facilitates cued threat avoidance. | Ho YY, Yang Q, Boddu P, Bulkin DA, Warden MR | bioRxiv : the preprint server for biology | 37645876 | bioRxiv | 2024 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/37645876 |
| Serotonin neurons in mating female mice are activated by male ejaculation. | Troconis EL, Seo C, Guru A, Warden MR | Current biology : CB | 37865094 | Curr Biol | 2023 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/37865094 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Biosensors Show the Pharmacokinetics of S-Ketamine in the Endoplasmic Reticulum. | Bera K, Kamajaya A, Shivange AV, Muthusamy AK, Nichols AL, Borden PM, Grant S, Jeon J, Lin E, Bishara I, Chin TM, Cohen BN, Kim CH, Unger EK, Tian L, Marvin JS, Looger LL, Lester HA | Frontiers in cellular neuroscience | 31798415 | Front Cell Neurosci | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31798415 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification. | Nicetto D, Donahue G, Jain T, Peng T, Sidoli S, Sheng L, Montavon T, Becker JS, Grindheim JM, Blahnik K, Garcia BA, Tan K, Bonasio R, Jenuwein T, Zaret KS | Science (New York, N.Y.) | 30606806 | Science | 2019 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/30606806 |
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| 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 |
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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 |
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| 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 |
| Hypnotic treatment improves sleep architecture and EEG disruptions and rescues memory deficits in a mouse model of fragile X syndrome. | Martinez JD, Wilson LG, Brancaleone WP, Peterson KG, Popke DS, Garzon VC, Perez Tremble RE, Donnelly MJ, Mendez Ortega SL, Torres D, Shaver JJ, Jiang S, Yang Z, Aton SJ | Cell reports | 38787724 | Cell Rep | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38787724 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 Dec | 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cervical Cancer Screening Rates and Associated Sociodemographic and Behavioral Factors among People Experiencing Homelessness in Indiana. | Rodriguez NM, Case X, Balian L, Ziolkowski R, Smith K, Tipton J | Research square | 41646352 | Res Sq | 2026 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/41646352 |
| Before the wave: Exploring early perspectives on COVID-19 self-testing among African Americans in Eastern North Carolina. | Ritchwood TD, Burton K, Wynn M | PloS one | 40901842 | PLoS One | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40901842 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | Health services research | 41204802 | Health Serv Res | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41204802 |
| 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 |
| 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 |
| 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 |
| Fair regression for health care spending. | Zink A, Rose S | Biometrics | 31860120 | Biometrics | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31860120 |
| 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 |
| 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 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/40321285 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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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 Hematopoiesis Is Associated With Higher Risk of Stroke. | Bhattacharya R, Zekavat SM, Haessler J, Fornage M, Raffield L, Uddin MM, Bick AG, Niroula A, Yu B, Gibson C, Griffin G, Morrison AC, Psaty BM, Longstreth WT, Bis JC, Rich SS, Rotter JI, Tracy RP, Correa A, Seshadri S, Johnson A, Collins JM, Hayden KM, Madsen TE, Ballantyne CM, Jaiswal S, Ebert BL, Kooperberg C, Manson JE, Whitsel EA, NHLBI Trans-Omics for Precision Medicine Program, Natarajan P, Reiner AP | Stroke | 34743536 | Stroke | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34743536 |
| Association of clonal hematopoiesis with chronic obstructive pulmonary disease. | Miller PG, Qiao D, Rojas-Quintero J, Honigberg MC, Sperling AS, Gibson CJ, Bick AG, Niroula A, McConkey ME, Sandoval B, Miller BC, Shi W, Viswanathan K, Leventhal M, Werner L, Moll M, Cade BE, Barr RG, Correa A, Cupples LA, Gharib SA, Jain D, Gogarten SM, Lange LA, London SJ, Manichaikul A, O'Connor GT, Oelsner EC, Redline S, Rich SS, Rotter JI, Ramachandran V, Yu B, Sholl L, Neuberg D, Jaiswal S, Levy BD, Owen CA, Natarajan P, Silverman EK, van Galen P, Tesfaigzi Y, Cho MH, Ebert BL, COPDGene Study Investigators, National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine Consortium | Blood | 34855941 | Blood | 2022 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/34855941 |
| 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 |
| The genetic determinants of recurrent somatic mutations in 43,693 blood genomes. | Weinstock JS, Laurie CA, Broome JG, Taylor KD, Guo X, Shuldiner AR, O'Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJF, Fornage M, Redline S, Cade BE, Gilliland FD, Chen Z, Gauderman WJ, Kumar R, Grammer L, Schleimer RP, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Weiss ST, Lasky-Su J, DeMeo DL, Palmer ND, Freedman BI, Bowden DW, Cho MH, Vasan RS, Johnson AD, Yanek LR, Becker LC, Kardia S, He J, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Manichaikul AW, Konkle BA, Johnsen JM, Wheeler MM, Custer BS, Duggirala R, Curran JE, Blangero J, Gui H, Xiao S, Williams LK, Meyers DA, Li X, Ortega V, McGarvey S, Gu CC, Chen YI, Lee WJ, Shoemaker MB, Darbar D, Roden D, Albert C, Kooperberg C, Desai P, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Mathias R, Natarajan P, Jaiswal S, Reiner AP, Bick AG, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium | Science advances | 37126548 | Sci Adv | 2023 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/37126548 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| Nasal Epithelial Extracellular Vesicles Correlate with Type 2 Inflammation during Aspirin-induced Respiratory Reactions. | Bunn KE, Bressman ZJ, Nation GK, Wu P, Amin T, Lehman C, Lin A, Gray CJ, Laidlaw TM, Cahill KN, Pua HH | American journal of respiratory cell and molecular biology | 40085481 | Am J Respir Cell Mol Biol | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40085481 |
| RNY1 partitions into extracellular vesicles and ribonucleoprotein particles during airway inflammation to regulate macrophage programming. | Saffold CE, Richardson AC, Pua HH | bioRxiv : the preprint server for biology | 41427290 | bioRxiv | 2025 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/41427290 |
| RNA regulation in immunity. | Pua H, Ansel KM | Immunological reviews | 34816450 | Immunol Rev | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34816450 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| High-throughput bioprinted 3D cultures for probing host-pathogen interactions in bioinspired microenvironments. | Graf J, Moore D, Grimes CL, Fromen CA, Kloxin AM | RSC applied polymers | 41602571 | RSC Appl Polym | 2026 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/41602571 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Macrophage variance: investigating how macrophage origin influences responses to soluble and physical cues with immortalized vs. primary cells in 2D and 3D culture. | Graf J, Bomb K, Trautmann-Rodriguez M, Jarai BM, Gill N, Kloxin AM, Fromen CA | Frontiers in biomaterials science | 40740983 | Front Biomater Sci | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40740983 |
| 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 |
| 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 |
| 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 |
| 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 |
| Integrative analysis of single-cell transcriptomics and genetic associations identify cell states associated with vascular disease. | Pepin ME, Schwartzman WE, Fang S, Vellarikkal SK, Atri DS, Reddy A, Xu Q, Hamel AR, Billaud M, Segrè AV, Gupta RM | Atherosclerosis | 40120433 | Atherosclerosis | 2025 Apr | https://www.ncbi.nlm.nih.gov/pubmed/40120433 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Decoding Vascular Cell Diversity: Single-Cell Approaches to Mechanisms of Vascular Disease. | Schwartzman WE, Jiang J, Rao JS, Schnitzler G, Maurya M, Widdup L, Pepin ME, Kang H, Zheng C, Gupta RM | Circulation research | 41481684 | Circ Res | 2026 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/41481684 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/39345504 |
| 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 |
| 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 multimodal genomic profiles from DNA sequence at single-cell resolution. | Hingerl JC, Martens LD, Karollus A, Manz T, Buenrostro JD, Theis FJ, Gagneur J | Nature methods | 41125796 | Nat Methods | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41125796 |
| 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 |
| Understanding Human Oncogene Function and Cooperativity in Myeloid Malignancy Using iPSCs. | Sarchi M, Doulatov S | Experimental hematology | 39674361 | Exp Hematol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39674361 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Developmental regulation of endothelial-to-hematopoietic transition from induced pluripotent stem cells. | Wellington R, Cheng X, Dutta S, Campbell CA, Trapnell C, Espin-Palazon R, Hadland B, Doulatov S | Stem cell reports | 40972587 | Stem Cell Reports | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/40972587 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease. | Gao W, Hu P, Wick B, Qiu Q, Zhang H, Li Y, Kang X, Bedi K, Haeussler M, Sasaki K, Margulies K, Wu H | Genome biology | 41937210 | Genome Biol | 2026 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/41937210 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Machine Learning in Medicine. | Deo RC | Circulation | 26572668 | Circulation | 2015 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/26572668 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Long-lived IgE plasma cells persist in secondary lymphoid tissues using a navitoclax-sensitive survival program. | Ding Z, Dowling MR, Wade-Vallance AK, Dvorscek AR, Pitt C, Mulder J, O'Donnell K, McKenzie C, Karaviotis AB, Scrofani J, Perdijk O, Hill DL, Quast I, Tarlinton DM, Allen CDC, Robinson MJ | Immunity | 41192430 | Immunity | 2025 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/41192430 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Towards predictive virtual embryos with genomics and AI. | Cao N, Lu Y, Qiu X | Nature methods | 41888299 | Nat Methods | 2026 Mar 26 | https://www.ncbi.nlm.nih.gov/pubmed/41888299 |
| Spatiotemporal profiling reveals the impact of caloric restriction in the aging mammalian brain. | Zhang Z, Epstein A, Schaefer C, Abdulraouf A, Jiang W, Zhou W, Cao J | Cell reports | 40833855 | Cell Rep | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/40833855 |
| Spatiotemporal profiling reveals the impact of caloric restriction on mammalian brain aging. | Zhang Z, Epstein A, Schaefer C, Abdulraouf A, Jiang W, Zhou W, Cao J | bioRxiv : the preprint server for biology | 40654944 | bioRxiv | 2025 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/40654944 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| The Genomics of Aging at the Single-Cell Scale. | Zhou W, Cao J | Annual review of genomics and human genetics | 40279573 | Annu Rev Genomics Hum Genet | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40279573 |
| EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing. | Liao A, Zhang Z, Sziraki A, Abdulraouf A, Xu Z, Lu Z, Zhou W, Cao J | bioRxiv : the preprint server for biology | 40654882 | bioRxiv | 2025 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/40654882 |
| 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 |
| 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 |
| RNA reinforces condensate nucleation on chromatin to amplify oncogenic transcription. | Budinich KA, Yao X, Gong C, Song L, Wang X, Lee MC, Mathias KM, Li Q, Tang S, Liu Y, Nguyen SC, Joyce EF, Li Y, Li H, Wan L | bioRxiv : the preprint server for biology | 40766627 | bioRxiv | 2025 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/40766627 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The eukaryotic replisome intrinsically generates asymmetric daughter chromatin fibers. | Eckhardt BV, Richter HJ, Rondeel I, Renduchintala K, Mattiroli F, Ramani V | bioRxiv : the preprint server for biology | 41000940 | bioRxiv | 2025 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/41000940 |
| Defective RNA processing and ELOA-mediated transcriptional elongation in reversible cellular senescence suggest aging by transcription. | Parast S, Wang S, Iwanaszko M, He Y, Olgun DG, Gold S, Zeidner JM, Aoi Y, Howard BC, Thakur WR, Ramani V, Shilatifard A | Molecular cell | 41418754 | Mol Cell | 2025 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/41418754 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| HMGB1 deforms nucleosomal DNA to generate a dynamic chromatin environment counteracting the effects of linker histone. | Saunders HS, Chio US, Moore CM, Ramani V, Cheng Y, Narlikar GJ | Science advances | 40815652 | Sci Adv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40815652 |
| 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 |
| 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 |
| 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 |
| ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes. | Moore C, Wong E, Kaur U, Chio US, Zhou Z, Ostrowski M, Wu K, Irkliyenko I, Wang S, Ramani V, Narlikar GJ | Science (New York, N.Y.) | 41037607 | Science | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41037607 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 recombinases for large DNA insertions. | Lampe GD, Sternberg SH | Nature biotechnology | 36424492 | Nat Biotechnol | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36424492 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Programmable gene insertion in human cells with a laboratory-evolved CRISPR-associated transposase. | Witte IP, Lampe GD, Eitzinger S, Miller SM, Berríos KN, McElroy AN, King RT, Stringham OG, Gelsinger DR, Vo PLH, Chen AT, Tolar J, Osborn MJ, Sternberg SH, Liu DR | Science (New York, N.Y.) | 40373119 | Science | 2025 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/40373119 |
| Precise virulence inactivation using a CRISPR-associated transposase for combating Enterobacteriaceae gut pathogens. | Ronda C, Perdue T, Schwanz L, Rivera Gelsinger D, Brockmann L, Kaufman A, Huang Y, Sternberg SH, Wang HH | Nature biomedical engineering | 40681864 | Nat Biomed Eng | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40681864 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39572737 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox. | Schertzer MD, Stirn A, Isaev K, Pereira L, Park SH, Das A, Réal A, Jeffery ED, Harbison C, Wessels HH, Sheynkman GM, Sanjana NE, Knowles DA | Nature communications | 40730819 | Nat Commun | 2025 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/40730819 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity. | Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi MA, Ellerby LM, Zhang F, Levin JZ, Meshorer E | Genome biology | 33663567 | Genome Biol | 2021 Mar 4 | https://www.ncbi.nlm.nih.gov/pubmed/33663567 |
| 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 |
| 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 |
| RETRACTED: 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Conserved enhancers control 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 | Nature communications | 37852970 | Nat Commun | 2023 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/37852970 |
| 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 |
| 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 |
| 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 |
| Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. | Jindal GA, Lim F, Tellez K, Song BP, Bantle AT, Farley EK | STAR protocols | 38963758 | STAR Protoc | 2024 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/38963758 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| Improving reproducibility of differentially expressed genes in single-cell transcriptomic studies of neurodegenerative diseases through meta-analysis. | Nakatsuka N, Adler D, Jiang L, Hartman A, Cheng E, Klann E, Satija R | Nature communications | 40796563 | Nat Commun | 2025 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/40796563 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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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 |
| 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 |
| 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 |
| DIO3 coordinates photoreceptor development timing and fate stability in human retinal organoids. | McNerney C, Santiago CP, Eldred KC, Glass I, Reh TA, Hernandez A, Blackshaw S, Lord ND, Johnston RJ Jr | Genes & development | 41102017 | Genes Dev | 2026 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/41102017 |
| Versican controlled by Lmx1b regulates hyaluronate density and hydration for semicircular canal morphogenesis. | Mori Y, Smith S, Wang J, Eliora N, Heikes KL, Munjal A | Development (Cambridge, England) | 39651757 | Development | 2025 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/39651757 |
| A self-limiting mechanotransduction feedback loop ensures robust organ formation. | Mori Y, Robin P, Briggs AB, Levic DS, Wang J, Heikes KL, Bagnat M, Hannezo E, Munjal A | bioRxiv : the preprint server for biology | 41040377 | bioRxiv | 2025 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/41040377 |
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| 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 |
| 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 |
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| AI-driven universal lower-limb exoskeleton system for community ambulation. | Lee D, Lee S, Young AJ | Science advances | 39693442 | Sci Adv | 2024 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/39693442 |
| 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 |
| 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 |
| 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 |
| Human-in-the-Loop Optimization of Hip Exoskeleton Assistance During Stair Climbing. | Park D, An J, Lee D, Kang I, Young AJ | IEEE transactions on bio-medical engineering | 40031367 | IEEE Trans Biomed Eng | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40031367 |
| Online Adaptation Framework Enables Personalization of Exoskeleton Assistance During Locomotion in Patients Affected by Stroke. | Kang I, Molinaro DD, Park D, Lee D, Kunapuli P, Herrin KR, Young AJ | IEEE transactions on robotics : a publication of the IEEE Robotics and Automation Society | 40958952 | IEEE Trans Robot | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40958952 |
| Machine Learning Enables Rapid Detection of Slips Using a Robotic Hip Exoskeleton. | Peterson RR, Leestma JK, Kang I, Young AJ | IEEE transactions on medical robotics and bionics | 40837732 | IEEE Trans Med Robot Bionics | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40837732 |
| 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 |
| 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 |
| 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 |
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| Induction of menstruation in mice reveals the regulation of menstrual shedding. | Çevrim Ç, Hilgert NJ, Kaage AM, Russell AJC, Goldstein AE, Ang CJ, Gable JLR, Bagamery LE, Breznik A, Di Bella DJ, Talay M, Peng J, O'Neill KE, Chen F, Eddy SR, McKinley KL | bioRxiv : the preprint server for biology | 41332577 | bioRxiv | 2025 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/41332577 |
| A Biosynthetic Thumb Prosthesis. | Bansal S, Lai GV, Belingheri M, Kashay AQ, Kim J, Tomkinson A, Herman S, Bollavaram K, Zukotynski BK, Jain NS, Azari KK, Wessel LE, Clites TR | bioRxiv : the preprint server for biology | 40501995 | bioRxiv | 2025 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/40501995 |
| A biosynthetic thumb prosthesis. | Bansal S, Lai GV, Belingheri M, Kashay AQ, Kim J, Tomkinson A, Herman S, Bollavaram K, Zukotynski BK, Thomas S, Jain NS, Azari KK, Wessel LE, Clites TR | npj biomedical innovations | 40620413 | NPJ Biomed Innov | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40620413 |
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| A single cluster of RNA Polymerase II molecules is stably associated with active genes. | Mukherjee A, Kapoor M, Shankta K, Fallacaro S, Carter RD, Hayward-Lara G, Ratchasanmuang P, Haloush YI, Mir M | Nature communications | 41862494 | Nat Commun | 2026 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/41862494 |
| 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 |
| 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 |
| A single cluster of RNA Polymerase II molecules is stably associated with active genes. | Mukherjee A, Kapoor M, Shankta K, Fallacaro S, Carter RD, Hayward-Lara G, Ratchasanmuang P, Haloush YI, Mir M | bioRxiv : the preprint server for biology | 39990393 | bioRxiv | 2025 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/39990393 |
| Quantifying Transcription Factor Enrichment at Target Loci in Live Embryos. | Fallacaro S, Mukherjee A, Gamauf E, Mir M | Methods in molecular biology (Clifton, N.J.) | 40418447 | Methods Mol Biol | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40418447 |
| Transcription factor hubs exhibit gene-specific properties that tune expression. | Fallacaro S, Mukherjee A, Turner MA, Garcia HG, Mir M | bioRxiv : the preprint server for biology | 40291650 | bioRxiv | 2025 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/40291650 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Compliance and Satisfaction With a Protocol for Identifying Novel Targets to Support Postpartum Opioid Use Disorder Recovery: Prospective Cohort Study. | Allen AM, Linde-Krieger LB, Deschenes J, Mallahan S, Harris A, Felix M, Chalke A, Anderson A, Sharma P, King KM, Grant MT, Baurley J, Rankin L, Tecot S | JMIR formative research | 41264808 | JMIR Form Res | 2025 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/41264808 |
| 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 |
| Childhood and Prenatal Stressors Shape Breastfeeding Behavior in Individuals with Opioid Use Disorder: A Prospective Investigation of Stress Effects. | Linde-Krieger LB, Ryan CJ, Rankin L, Tecot S, Allen AM | Breastfeeding medicine : the official journal of the Academy of Breastfeeding Medicine | 40938739 | Breastfeed Med | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40938739 |
| Infant caregiving, relational factors, mood, and pain in perinatal opioid use disorder: A prospective cohort with ecological momentary assessment. | Allen AM, Linde-Krieger LB, Baurley J, Deschenes J, Mallahan S, Anderson A, Tecot S, Rankin L | Addictive behaviors | 41690258 | Addict Behav | 2026 Jun | https://www.ncbi.nlm.nih.gov/pubmed/41690258 |
| 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 |
| Changes in cellular composition shape the inductive properties of Hensen's Node. | Kanno TY, Rothstein M, Simoes-Costa M | Nature communications | 40841542 | Nat Commun | 2025 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/40841542 |
| Spatial patterning of the epigenome during vertebrate gastrulation. | Azambuja AP, Rothstein M, Kanno TY, Simoes-Costa M | Nature communications | 41397979 | Nat Commun | 2025 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/41397979 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Activity of forkhead box P2-positive neurons is associated with tadpole begging behaviour. | Ludington SC, McKinney JE, Butler JM, Goolsby BC, Callan AA, Gaines-Richardson M, O'Connell LA | Biology letters | 39317327 | Biol Lett | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39317327 |
| 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 | eLife | 40742751 | Elife | 2025 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/40742751 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Microbiota-derived bile acids antagonize the host androgen receptor and drive anti-tumor immunity. | Jin WB, Xiao L, Jeong M, Han SJ, Zhang W, Yano H, Shi H, Arifuzzaman M, Lyu M, Wang D, Tang YA, Qiao S, JRI IBD Live Cell Bank Consortium, Yang X, Yang HS, Fu J, Sonnenberg GF, Collins N, Artis D, Guo CJ | Cell | 40239649 | Cell | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/40239649 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Automated 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 | Human brain mapping | 41074651 | Hum Brain Mapp | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/41074651 |
| Unsupervised semi-automated MRI segmentation detects 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 DP, Hunt D, Seifert AC, Bodien YG, Hoffman JM, Mac Donald CL, Dams-O'Connor K, Edlow BL | Frontiers in neurology | 41170325 | Front Neurol | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/41170325 |
| Probabilistic mapping and automated segmentation of human brainstem white matter bundles. | Olchanyi MD, Schreier DR, Li J, Maffei C, Sorby-Adams A, Kinney HC, Healy BC, Freeman HJ, Shless J, Destrieux C, Tregidgo H, Iglesias JE, Brown EN, Edlow BL | Proceedings of the National Academy of Sciences of the United States of America | 41650217 | Proc Natl Acad Sci U S A | 2026 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/41650217 |
| Emotional Processing After Severe Traumatic Brain Injury: Insights from Functional MRI and Pupillometry. | Kazazian K, Zhang SO, de Jeu J, Lawrence PK, Sanders WR, Meydan A, Bremner F, Mallas EJ, Bodien YG, Dams-O'Connor K, Edlow BL, Li LM | medRxiv : the preprint server for health sciences | 40832426 | medRxiv | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40832426 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Covert consciousness. | Young MJ, Edlow BL, Bodien YG | NeuroRehabilitation | 38217619 | NeuroRehabilitation | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38217619 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Visualizing effective connectivity in the human brain. | Atalay AS, Fecchio M, Edlow BL | Brain stimulation | 40550389 | Brain Stimul | 2025 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/40550389 |
| Behavioral Fluctuation in Disorders of Consciousness: A Retrospective Analysis. | Barra A, Bodien YG, Tan CO, Martens G, Malone C, Giacino JT | Archives of physical medicine and rehabilitation | 40139629 | Arch Phys Med Rehabil | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40139629 |
| 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 |
| 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 |
| 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 |
| 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 |
| Subcortical Hubs of Brain Networks Sustaining Human Consciousness. | Cambareri MK, Horn A, Lewis LD, Li J, Edlow BL | Human brain mapping | 41074653 | Hum Brain Mapp | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/41074653 |
| Preservation of anticorrelated brain networks predicts recovery after traumatic brain injury. | Snider SB, Shi H, Bodien YG, Howard C, Sun X, Golby AJ, Zimmerman KA, Bertolini G, Magnoni S, Dunet V, Oddo M, Graham NSN, Mallas EJ, Moro F, Mukherjee P, Temkin NR, Jain S, Sharp DJ, Edlow BL, Fox MD | Proceedings of the National Academy of Sciences of the United States of America | 41428880 | Proc Natl Acad Sci U S A | 2025 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/41428880 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Multimodal Biomarkers of Consciousness in Acute 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 | Journal of neurotrauma | 41182259 | J Neurotrauma | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41182259 |
| Structural injuries are associated with better emotional wellbeing after traumatic brain injury. | Snider SB, Shi H, Maffei C, Gilmore N, Freeman HJ, Atalay AS, Li J, Yeager JA, Kumar RG, Yew B, Conley EM, Velazquez AL, Kirschenbaum J, Selmanovic E, Carrington H, Bodien YG, Hoffman JM, Donald CM, Edlow BL, Dams-O'Connor K | medRxiv : the preprint server for health sciences | 40778143 | medRxiv | 2025 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/40778143 |
| JOSA: Joint surface-based registration and atlas construction of brain geometry and function. | Li J, Tuckute G, Fedorenko E, Edlow BL, Dalca AV, Fischl B | Medical image analysis | 39173411 | Med Image Anal | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39173411 |
| 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 |
| 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 | Nature communications | 40691170 | Nat Commun | 2025 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/40691170 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Cognitive Performance is Associated With 1-Year Participation and Life Satisfaction Outcomes: A Traumatic Brain Injury Model Systems Study. | Gilmore N, Bergquist TF, Bogner J, Corrigan JD, Dams-O'Connor K, Dreer LE, Healy BC, Juengst SB, Kumar RG, O'Neil-Pirozzi TM, Wagner AK, Giacino JT, Edlow BL, Bodien YG | The Journal of head trauma rehabilitation | 39330921 | J Head Trauma Rehabil | 2025 May-Jun 01 | https://www.ncbi.nlm.nih.gov/pubmed/39330921 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Functional fractionation of large-scale brain networks in the human subcortex. | Li J, Atalay AS, Olchanyi M, Cambareri MK, Ghosh SS, Horn A, Lewis L, Brown EN, Fischl B, Kinney HC, Edlow BL | bioRxiv : the preprint server for biology | 41509362 | bioRxiv | 2025 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/41509362 |
| High Resolution Postmortem MRI Discovers Developing Structural Connectivity in the Human Ascending Arousal Network. | Licandro R, Olchanyi M, Ferraz da Silva LF, van der Kouwe A, Jaimes C, Ngo NX, Kelley W, Folkerth R, Haynes RL, Edlow BL, Kinney HC, Zöllei L | Human brain mapping | 41319039 | Hum Brain Mapp | 2025 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/41319039 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| GWAS of Active Music Engagement Frequency in the Canadian Longitudinal Study on Aging. | Henechowicz T, Wolford B, Nitin R, Mekki Y, Scartozzi A, Coleman P, Tio E, Schlicht G, Nayak S, Thaut M, Felsky D, Gordon R | Research square | 41646368 | Res Sq | 2026 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/41646368 |
| 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 |
| 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 |
| 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 |
| 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 |
| Large-scale collaboration in ENIGMA-EEG: A perspective on the meta-analytic approach to link neurological and psychiatric liability genes to electrophysiological brain activity. | Smit DJA, Andreassen OA, Boomsma DI, Burwell SJ, Chorlian DB, de Geus EJC, Elvsåshagen T, Gordon RL, Harper J, Hegerl U, Hensch T, Iacono WG, Jawinski P, Jönsson EG, Luykx JJ, Magne CL, Malone SM, Medland SE, Meyers JL, Moberget T, Porjesz B, Sander C, Sisodiya SM, Thompson PM, van Beijsterveldt CEM, van Dellen E, Via M, Wright MJ | Brain and behavior | 34291596 | Brain Behav | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34291596 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Structural Basis for Methine Excision by a Heme Oxygenase-like Enzyme. | Simke WC, Walker ME, Calderone LA, Putz AT, Patteson JB, Vitro CN, Zizola CF, Redinbo MR, Pandelia ME, Grove TL, Li B | ACS central science | 39220707 | ACS Cent Sci | 2024 Aug 28 | https://www.ncbi.nlm.nih.gov/pubmed/39220707 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| "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 |
| 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 |
| Parallel CRISPR screens reveal pathways controlling the cell surface levels of the attractant receptor FPR1. | Akdoğan E, Lundgren SM, Kamber RA, Bassik MC, Collins SR | Communications biology | 41882347 | Commun Biol | 2026 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/41882347 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation. | Tower CA, Manske G, Ferrell EL, Anbarci DN, Jorgensen K, Ma B, Aboelenain M, Ranjan R, Chakraborty S, Moritz L, Das A, Boiani M, Black BE, Chavez S, Marsh EE, Shikanov A, Schindler K, Chen X, Hammoud SS | bioRxiv : the preprint server for biology | 40766472 | bioRxiv | 2025 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/40766472 |
| 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 |
| 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 |
| 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 |
| Maternal CENP-C restores centromere symmetry in mammalian zygotes to ensure proper chromosome segregation. | Tower CA, Manske G, Ferrell EL, Anbarci DN, Jorgensen K, Ma B, Aboelenain M, Ranjan R, Chakraborty S, Moritz L, Das A, Boiani M, Black BE, Chavez S, Marsh EE, Shikanov A, Schindler K, Chen X, Hammoud SS | Developmental cell | 40997799 | Dev Cell | 2026 Jan 14 | https://www.ncbi.nlm.nih.gov/pubmed/40997799 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| ZCWPW1 organizes telomeric architecture to drive meiotic chromosome movements. | Xie W, Gowder M, Bazzano D, Shami AN, Pandey A, Frasca M, Paniker L, de Almeida LP, Bharati BK, Liang J, Tóth A, DeSantis M, Nandakumar J, Nudler E, Mosalaganti S, Pezza R, Cole F, Hammoud SS | bioRxiv : the preprint server for biology | 41676639 | bioRxiv | 2026 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/41676639 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Computational methods for birth-death processes. | Crawford FW, Ho LST, Suchard MA | Wiley interdisciplinary reviews | 29942419 | Wiley Interdiscip Rev Comput Stat | 2018 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/29942419 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Engineered antimicrobial-derived peptides to manipulate mixed microbial systems. | Trivedi VD, Van Deventer JA, Nair NU | bioRxiv : the preprint server for biology | 41256581 | bioRxiv | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/41256581 |
| Pharmacophore-driven antibody discovery on the yeast surface. | Huang M, Williams SJ, Trivedi VD, Nair NU, Van Deventer JA | bioRxiv : the preprint server for biology | 41279963 | bioRxiv | 2025 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/41279963 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity. | Porokhin V, Amin SA, Nicks TB, Gopinarayanan VE, Nair NU, Hassoun S | Metabolic engineering communications | 33850714 | Metab Eng Commun | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33850714 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Macrophage Sensors for Early Cancer Detection. | Kwong GA | Clinical chemistry | 32040571 | Clin Chem | 2020 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/32040571 |
| 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 |
| 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 |
| Sensitizing solid tumors to CAR-mediated cytotoxicity by lipid nanoparticle delivery of synthetic antigens. | Gamboa L, Zamat AH, Thiveaud CA, Lee HJ, Kulaksizoglu E, Zha Z, Campbell NS, Chan CS, Fábrega S, Oliver SA, Su FY, Phuengkham H, Vanover D, Peck HE, Sivakumar A, Dahotre SN, Harris AM, Santangelo PJ, Kwong GA | Nature cancer | 40379831 | Nat Cancer | 2025 Jun | https://www.ncbi.nlm.nih.gov/pubmed/40379831 |
| 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 |
| Protease-Activated Plasmonic Nanosensors for Predictive Ultrasound-Guided Photoacoustic Imaging of Tumor Responses to Adoptive T Cell Therapy. | Kim M, Song S, Zamat A, Pelkowski PS, Subramanian S, Cadena M, Fabrega S, Brienen M, Kim J, Kwong GA, Emelianov SY | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 41391042 | Adv Sci (Weinh) | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41391042 |
| 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 |
| 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 |
| Synthetic immunity by remote control. | Gamboa L, Zamat AH, Kwong GA | Theranostics | 32206114 | Theranostics | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32206114 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Biologically Derived Neoproteoglycans for Profiling Protein-Glycosaminoglycan Interactions. | Porell RN, Follmar JL, Purcell SC, Timm B, Laubach LK, Kozirovskiy D, Thacker BE, Glass CA, Gordts PLSM, Godula K | ACS chemical biology | 35574759 | ACS Chem Biol | 2022 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/35574759 |
| Cell surface photoengineering enables modeling of glycocalyx shedding dynamics. | Purcell SC, Zhang MH, Honigfort DJ, Ng HJC, Michalak AL, Godula K | Chemical science | 35756522 | Chem Sci | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35756522 |
| Following sugar patterns in search of galectin function. | Godula K | Proceedings of the National Academy of Sciences of the United States of America | 29496962 | Proc Natl Acad Sci U S A | 2018 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/29496962 |
| DNA Aptamer-Guided Glycomimetics for Developmental Stage-Specific Glycocalyx Engineering to Control Stem Cell Differentiation. | Purcell SC, Naticchia MR, Follmar JL, Marroquin N, Ng HJC, Godula K | Journal of the American Chemical Society | 40626724 | J Am Chem Soc | 2025 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/40626724 |
| Glycomaterials for probing host-pathogen interactions and the immune response. | Huang ML, Fisher CJ, Godula K | Experimental biology and medicine (Maywood, N.J.) | 27190259 | Exp Biol Med (Maywood) | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27190259 |
| Synthetic glycoscapes: addressing the structural and functional complexity of the glycocalyx. | Purcell SC, Godula K | Interface focus | 30842878 | Interface Focus | 2019 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/30842878 |
| 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 |
| Silencing glycosaminoglycan functions in mouse embryonic stem cells with small molecule antagonists. | Chatterjee S, Stephenson TN, Michalak AL, Godula K, Huang ML | Methods in enzymology | 31606078 | Methods Enzymol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31606078 |
| Efficient Synthesis of Heparinoid Bioconjugates for Tailoring FGF2 Activity at the Stem Cell-Matrix Interface. | Trieger GW, Verespy S 3rd, Gordts PLSM, Godula K | Bioconjugate chemistry | 30668905 | Bioconjug Chem | 2019 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/30668905 |
| Glycocalyx Scaffolding to Control Cell Surface Glycan Displays. | Huang ML, Tota EM, Verespy S 3rd, Godula K | Current protocols in chemical biology | 29927116 | Curr Protoc Chem Biol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29927116 |
| Heparin-fibronectin interactions in the development of extracellular matrix insolubility. | Raitman I, Huang ML, Williams SA, Friedman B, Godula K, Schwarzbauer JE | Matrix biology : journal of the International Society for Matrix Biology | 29223498 | Matrix Biol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29223498 |
| Stem Cell Microarrays for Assessing Growth Factor Signaling in Engineered Glycan Microenvironments. | Michalak AL, Trieger GW, Trieger KA, Godula K | Advanced healthcare materials | 34541824 | Adv Healthc Mater | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34541824 |
| Mucin-mimetic glycan arrays integrating machine learning for analyzing receptor pattern recognition by influenza A viruses. | Lucas TM, Gupta C, Altman MO, Sanchez E, Naticchia MR, Gagneux P, Singharoy A, Godula K | Chem | 34993358 | Chem | 2021 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/34993358 |
| LDL-Bound PCSK9 Has a Slower Clearance Kinetic and Higher Use for HSPGs Than Free-PCSK9-Brief Report. | Pacheco-Velázquez SC, Oleaga C, Ramms B, Hay J, Mueller PA, López-Aguilar E, Miles J, Porell RN, Cheng C, Godula K, Tavori H, Gordts PLSM, Fazio S, Pamir N | Arteriosclerosis, thrombosis, and vascular biology | 40605748 | Arterioscler Thromb Vasc Biol | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40605748 |
| Synthetic Mucus Nanobarriers for Identification of Glycan-Dependent Primary Influenza A Infection Inhibitors. | Cohen M, Senaati HP, Fisher CJ, Huang ML, Gagneux P, Godula K | ACS central science | 27800553 | ACS Cent Sci | 2016 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/27800553 |
| 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 |
| Engineering of spectator glycocalyx structures to evaluate molecular interactions at crowded cellular boundaries. | Honigfort DJ, Zhang MH, Verespy S, Godula K | Faraday discussions | 31313786 | Faraday Discuss | 2019 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/31313786 |
| 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 |
| Glycocalyx crowding with mucin mimetics strengthens binding of soluble and virus-associated lectins to host cell glycan receptors. | Honigfort DJ, Altman MO, Gagneux P, Godula K | Proceedings of the National Academy of Sciences of the United States of America | 34583992 | Proc Natl Acad Sci U S A | 2021 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/34583992 |
| Glycocalyx scaffolding with synthetic nanoscale glycomaterials. | Huang ML, Purcell SC, Verespy S III, Wang Y, Godula K | Biomaterials science | 28616946 | Biomater Sci | 2017 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/28616946 |
| 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 |
| Glycocalyx Remodeling with Glycopolymer-Based Proteoglycan Mimetics. | Huang ML, Smith RA, Trieger GW, Godula K | Methods in molecular biology (Clifton, N.J.) | 26537476 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26537476 |
| Spatially controlled glycocalyx engineering for growth factor patterning in embryoid bodies. | Naticchia MR, Laubach LK, Honigfort DJ, Purcell SC, Godula K | Biomaterials science | 33409513 | Biomater Sci | 2021 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/33409513 |
| SARS-CoV-2 Infection Depends on Cellular Heparan Sulfate and ACE2. | Clausen TM, Sandoval DR, Spliid CB, Pihl J, Perrett HR, Painter CD, Narayanan A, Majowicz SA, Kwong EM, McVicar RN, Thacker BE, Glass CA, Yang Z, Torres JL, Golden GJ, Bartels PL, Porell RN, Garretson AF, Laubach L, Feldman J, Yin X, Pu Y, Hauser BM, Caradonna TM, Kellman BP, Martino C, Gordts PLSM, Chanda SK, Schmidt AG, Godula K, Leibel SL, Jose J, Corbett KD, Ward AB, Carlin AF, Esko JD | Cell | 32970989 | Cell | 2020 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/32970989 |
| Glycocalyx engineering with heparan sulfate mimetics attenuates Wnt activity during adipogenesis to promote glucose uptake and metabolism. | Trieger GW, Pessentheiner AR, Purcell SC, Green CR, DeForest N, Willert K, Majithia AR, Metallo CM, Godula K, Gordts PLSM | The Journal of biological chemistry | 36931394 | J Biol Chem | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36931394 |
| A Practical Guide for CRISPR-Cas9-Induced Mutations in Axolotls. | Sousounis K, Courtemanche K, Whited JL | Methods in molecular biology (Clifton, N.J.) | 36272086 | Methods Mol Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36272086 |
| Complement Receptor C5aR1 Plays an Evolutionarily Conserved Role in Successful Cardiac Regeneration. | Natarajan N, Abbas Y, Bryant DM, Gonzalez-Rosa JM, Sharpe M, Uygur A, Cocco-Delgado LH, Ho NN, Gerard NP, Gerard CJ, MacRae CA, Burns CE, Burns CG, Whited JL, Lee RT | Circulation | 29348261 | Circulation | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29348261 |
| Repeated removal of developing limb buds permanently reduces appendage size in the highly-regenerative axolotl. | Bryant DM, Sousounis K, Farkas JE, Bryant S, Thao N, Guzikowski AR, Monaghan JR, Levin M, Whited JL | Developmental biology | 28235582 | Dev Biol | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28235582 |
| Common themes in tetrapod appendage regeneration: a cellular perspective. | Miller BM, Johnson K, Whited JL | EvoDevo | 31236203 | Evodevo | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31236203 |
| Bioelectrical controls of morphogenesis: from ancient mechanisms of cell coordination to biomedical opportunities. | Whited JL, Levin M | Current opinion in genetics & development | 31442749 | Curr Opin Genet Dev | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31442749 |
| von Willebrand factor D and EGF domains is an evolutionarily conserved and required feature of blastemas capable of multitissue appendage regeneration. | Leigh ND, Sessa S, Dragalzew AC, Payzin-Dogru D, Sousa JF, Aggouras AN, Johnson K, Dunlap GS, Haas BJ, Levin M, Schneider I, Whited JL | Evolution & development | 32163674 | Evol Dev | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32163674 |
| Eya2 promotes cell cycle progression by regulating DNA damage response during vertebrate limb regeneration. | Sousounis K, Bryant DM, Martinez Fernandez J, Eddy SS, Tsai SL, Gundberg GC, Han J, Courtemanche K, Levin M, Whited JL | eLife | 32142407 | Elife | 2020 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/32142407 |
| Parallels between wound healing, epimorphic regeneration and solid tumors. | Wong AY, Whited JL | Development (Cambridge, England) | 31898582 | Development | 2020 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/31898582 |
| Discussing limb development and regeneration in Barcelona: The future is at hand. | Rosello-Diez A, Whited JL | Developmental dynamics : an official publication of the American Association of Anatomists | 31587395 | Dev Dyn | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31587395 |
| A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. | Bryant DM, Johnson K, DiTommaso T, Tickle T, Couger MB, Payzin-Dogru D, Lee TJ, Leigh ND, Kuo TH, Davis FG, Bateman J, Bryant S, Guzikowski AR, Tsai SL, Coyne S, Ye WW, Freeman RM Jr, Peshkin L, Tabin CJ, Regev A, Haas BJ, Whited JL | Cell reports | 28099853 | Cell Rep | 2017 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/28099853 |
| Identification of regenerative roadblocks via repeat deployment of limb regeneration in axolotls. | Bryant DM, Sousounis K, Payzin-Dogru D, Bryant S, Sandoval AGW, Martinez Fernandez J, Mariano R, Oshiro R, Wong AY, Leigh ND, Johnson K, Whited JL | NPJ Regenerative medicine | 29302364 | NPJ Regen Med | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29302364 |
| Adrenergic signaling coordinates distant and local responses to amputation in axolotl. | Payzin-Dogru D, Froitzheim T, Blair SJ, Jena SG, Singer H, Paoli JC, Kim RT, Kriukov E, Wilson SE, Hou R, Savage AM, Cat V, Cammarata LV, Wu SYC, Bothe V, Erdogan B, Hossain S, Lopez N, Losner J, Velazquez Matos J, Min S, Böhm S, Striker AE, Dooling KE, Freedman AH, Groves B, Tajer B, Kalu G, Wynn E, Wong AYL, Fröbisch N, Baranov P, Plikus MV, Buenrostro JD, Haas BJ, Chiu IM, Sackton TB, Whited JL | Cell | 41138727 | Cell | 2025 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/41138727 |
| Transcriptomic landscape of the blastema niche in regenerating adult axolotl limbs at single-cell resolution. | Leigh ND, Dunlap GS, Johnson K, Mariano R, Oshiro R, Wong AY, Bryant DM, Miller BM, Ratner A, Chen A, Ye WW, Haas BJ, Whited JL | Nature communications | 30514844 | Nat Commun | 2018 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/30514844 |
| Adrenergic signaling coordinates distant and local responses to amputation in axolotl. | Payzin-Dogru D, Froitzheim T, Blair SJ, Jena SG, Singer H, Paoli JC, Kim RT, Kriukov E, Wilson SE, Hou R, Savage AM, Cat V, Cammarata LV, Wu SYC, Bothe V, Erdogan B, Hossain S, Lopez N, Losner J, Matos JV, Min S, Böhm S, Striker AE, Dooling KE, Freedman AH, Groves B, Tajer B, Kalu G, Wynn E, Wong AYL, Fröbisch N, Baranov P, Plikus MV, Buenrostro JD, Haas BJ, Chiu IM, Sackton TB, Whited JL | bioRxiv : the preprint server for biology | 40777403 | bioRxiv | 2025 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/40777403 |
| Systemic cell cycle activation is induced following complex tissue injury in axolotl. | Johnson K, Bateman J, DiTommaso T, Wong AY, Whited JL | Developmental biology | 29111100 | Dev Biol | 2018 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/29111100 |
| Advances in Decoding Axolotl Limb Regeneration. | Haas BJ, Whited JL | Trends in genetics : TIG | 28648452 | Trends Genet | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28648452 |
| Motor cortical inactivation impairs corrective submovements in mice performing a hold-still center-out reach task. | Bollu T, Whitehead SC, Prasad N, Walker J, Shyamkumar N, Subramaniam R, Kardon B, Cohen I, Goldberg JH | Journal of neurophysiology | 39081209 | J Neurophysiol | 2024 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/39081209 |
| Cortex-dependent corrections as the tongue reaches for and misses targets. | Bollu T, Ito BS, Whitehead SC, Kardon B, Redd J, Liu MH, Goldberg JH | Nature | 34012117 | Nature | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34012117 |
| Automated home cage training of mice in a hold-still center-out reach task. | Bollu T, Whitehead SC, Prasad N, Walker J, Shyamkumar N, Subramaniam R, Kardon B, Cohen I, Goldberg JH | Journal of neurophysiology | 30540551 | J Neurophysiol | 2019 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/30540551 |
| 2018 PLOS Genetics Research Prize: Bundling, stabilizing, organizing-The orchestration of acentriolar spindle assembly by microtubule motor proteins. | Barsh GS, Bhalla N, Cole F, Copenhaver GP, Lacefield S, Libuda DE | PLoS genetics | 30212501 | PLoS Genet | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30212501 |
| RB localizes to DNA double-strand breaks and promotes DNA end resection and homologous recombination through the recruitment of BRG1. | Vélez-Cruz R, Manickavinayaham S, Biswas AK, Clary RW, Premkumar T, Cole F, Johnson DG | Genes & development | 27940962 | Genes Dev | 2016 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/27940962 |
| Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase. | Patel L, Kang R, Rosenberg SC, Qiu Y, Raviram R, Chee S, Hu R, Ren B, Cole F, Corbett KD | Nature structural & molecular biology | 30778236 | Nat Struct Mol Biol | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30778236 |
| MutSgamma promotes meiotic recombination and homolog pairing in mouse spermatocytes. | Frasca M, Paniker L, Kang R, Chakraborty P, Pandey A, LoPresti J, Cole F | Genetics | 40404295 | Genetics | 2025 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/40404295 |
| Genetic dissection of crossover mutants defines discrete intermediates in mouse meiosis. | Premkumar T, Paniker L, Kang R, Biot M, Humphrey E, Destain H, Ferranti I, Okulate I, Nguyen H, Kilaru V, Frasca M, Chakraborty P, Cole F | Molecular cell | 37595556 | Mol Cell | 2023 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/37595556 |
| SCAI promotes DNA double-strand break repair in distinct chromosomal contexts. | Hansen RK, Mund A, Poulsen SL, Sandoval M, Klement K, Tsouroula K, Tollenaere MA, Räschle M, Soria R, Offermanns S, Worzfeld T, Grosse R, Brandt DT, Rozell B, Mann M, Cole F, Soutoglou E, Goodarzi AA, Daniel JA, Mailand N, Bekker-Jensen S | Nature cell biology | 27820601 | Nat Cell Biol | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27820601 |
| X marks the spot: PRDM9 rescues hybrid sterility by finding hidden treasure in the genome. | Zelazowski MJ, Cole F | Nature structural & molecular biology | 27045445 | Nat Struct Mol Biol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27045445 |
| Special issue on "recent advances in meiosis from DNA replication to chromosome segregation". | Cole F, Borde V | Chromosoma | 31616989 | Chromosoma | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31616989 |
| Age-Dependent Alterations in Meiotic Recombination Cause Chromosome Segregation Errors in Spermatocytes. | Zelazowski MJ, Sandoval M, Paniker L, Hamilton HM, Han J, Gribbell MA, Kang R, Cole F | Cell | 28942922 | Cell | 2017 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/28942922 |
| Analysis of DNA polymerase ν function in meiotic recombination, immunoglobulin class-switching, and DNA damage tolerance. | Takata KI, Reh S, Yousefzadeh MJ, Zelazowski MJ, Bhetawal S, Trono D, Lowery MG, Sandoval M, Takata Y, Lu Y, Lin K, Shen J, Kusewitt DF, McBride KM, Cole F, Wood RD | PLoS genetics | 28570559 | PLoS Genet | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28570559 |
| 53BP1 ablation rescues genomic instability in mice expressing 'RING-less' BRCA1. | Li M, Cole F, Patel DS, Misenko SM, Her J, Malhowski A, Alhamza A, Zheng H, Baer R, Ludwig T, Jasin M, Nussenzweig A, Serrano L, Bunting SF | EMBO reports | 27670884 | EMBO Rep | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27670884 |
| Missing the Mark: PRDM9-Dependent Methylation Is Required for Meiotic DSB Targeting. | Kang R, Zelazowski MJ, Cole F | Molecular cell | 29499130 | Mol Cell | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29499130 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Poverty, Deprivation, and Mortality Risk Among Women With HIV in the United States. | Edmonds A, Breskin A, Cole SR, Westreich D, Ramirez C, Cocohoba J, Wingood G, Cohen MH, Golub ET, Kassaye SG, Metsch LR, Sharma A, Konkle-Parker D, Wilson TE, Adimora AA | Epidemiology (Cambridge, Mass.) | 34347686 | Epidemiology | 2021 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/34347686 |
| 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 |
| 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 |
| 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 |
| Baseline Characteristics Explain Differences in Effectiveness of Randomization to Daily Oral TDF/FTC PrEP Between Transgender Women and Cisgender Men Who Have Sex With Men in the iPrEx Trial. | Mehrotra ML, Westreich D, McMahan VM, Glymour MM, Geng E, Grant RM, Glidden DV | Journal of acquired immune deficiency syndromes (1999) | 31192894 | J Acquir Immune Defic Syndr | 2019 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/31192894 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The effect of antiretroviral therapy on all-cause mortality, generalized to persons diagnosed with HIV in the USA, 2009-11. | Lesko CR, Cole SR, Hall HI, Westreich D, Miller WC, Eron JJ, Li J, Mugavero MJ, CNICS Investigators | International journal of epidemiology | 26772869 | Int J Epidemiol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26772869 |
| 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 |
| Reduction in diarrhoeal rates through interventions that prevent unnecessary antibiotic exposure early in life in an observational birth cohort. | Rogawski ET, Meshnick SR, Becker-Dreps S, Adair LS, Sandler RS, Sarkar R, Kattula D, Ward HD, Kang G, Westreich DJ | Journal of epidemiology and community health | 26621194 | J Epidemiol Community Health | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26621194 |
| 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 |
| 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 |
| The Authors Respond. | Breskin A, Cole SR, Hudgens MG | Epidemiology (Cambridge, Mass.) | 30052540 | Epidemiology | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30052540 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Associations of semaglutide with incidence and recurrence of alcohol use disorder in real-world population. | Wang W, Volkow ND, Berger NA, Davis PB, Kaelber DC, Xu R | Nature communications | 38806481 | Nat Commun | 2024 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/38806481 |
| Association of GLP-1 Receptor Agonists and Hepatocellular Carcinoma Incidence and Hepatic Decompensation in Patients With Type 2 Diabetes. | Wang L, Berger NA, Kaelber DC, Xu R | Gastroenterology | 38692395 | Gastroenterology | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38692395 |
| GLP-1R agonist medications for addiction treatment. | Volkow ND, Xu R | Addiction (Abingdon, England) | 39049203 | Addiction | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39049203 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 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 |
| Effects of Alzheimer's Disease-Related Proteins on the Chirality of Brain Endothelial Cells. | Zhang H, Fan J, Zhao Z, Wang C, Wan LQ | Cellular and molecular bioengineering | 34109002 | Cell Mol Bioeng | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34109002 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 27180907 | Cell | 2016 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/27180907 |
| No detectable alloreactive transcriptional responses under standard sample preparation conditions during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. | McGinnis CS, Siegel DA, Xie G, Hartoularos G, Stone M, Ye CJ, Gartner ZJ, Roan NR, Lee SA | BMC biology | 33472616 | BMC Biol | 2021 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/33472616 |
| 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 |
| 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 |
| 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 |
| Non-autonomous cell proliferation in the mammary gland and cancer. | Weber RJ, Desai TA, Gartner ZJ | Current opinion in cell biology | 28314237 | Curr Opin Cell Biol | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28314237 |
| DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors. | McGinnis CS, Murrow LM, Gartner ZJ | Cell systems | 30954475 | Cell Syst | 2019 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/30954475 |
| 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 |
| Programmed synthesis of three-dimensional tissues. | Todhunter ME, Jee NY, Hughes AJ, Coyle MC, Cerchiari A, Farlow J, Garbe JC, LaBarge MA, Desai TA, Gartner ZJ | Nature methods | 26322836 | Nat Methods | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26322836 |
| Opportunities for organoids as new models of aging. | Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ | The Journal of cell biology | 29263081 | J Cell Biol | 2018 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/29263081 |
| Organoid models for mammary gland dynamics and breast cancer. | Srivastava V, Huycke TR, Phong KT, Gartner ZJ | Current opinion in cell biology | 32535255 | Curr Opin Cell Biol | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32535255 |
| 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 |
| Single-cell mechanogenetics using monovalent magnetoplasmonic nanoparticles. | Kim JW, Seo D, Lee JU, Southard KM, Lim Y, Kim D, Gartner ZJ, Jun YW, Cheon J | Nature protocols | 28817122 | Nat Protoc | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28817122 |
| 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 |
| Fabrication of 3-D Reconstituted Organoid Arrays by DNA-Programmed Assembly of Cells (DPAC). | Todhunter ME, Weber RJ, Farlow J, Jee NY, Cerchiari AE, Gartner ZJ | Current protocols in chemical biology | 27622567 | Curr Protoc Chem Biol | 2016 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/27622567 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Roadmap for the multiscale coupling of biochemical and mechanical signals during development. | Lenne PF, Munro E, Heemskerk I, Warmflash A, Bocanegra-Moreno L, Kishi K, Kicheva A, Long Y, Fruleux A, Boudaoud A, Saunders TE, Caldarelli P, Michaut A, Gros J, Maroudas-Sacks Y, Keren K, Hannezo E, Gartner ZJ, Stormo B, Gladfelter A, Rodrigues A, Shyer A, Minc N, Maître JL, Di Talia S, Khamaisi B, Sprinzak D, Tlili S | Physical biology | 33276350 | Phys Biol | 2021 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/33276350 |
| Single cell enhancer activity distinguishes GABAergic and cholinergic lineages in embryonic mouse basal ganglia. | Su-Feher L, Rubin AN, Silberberg SN, Catta-Preta R, Lim KJ, Ypsilanti AR, Zdilar I, McGinnis CS, McKinsey GL, Rubino TE Jr, Hawrylycz MJ, Thompson C, Gartner ZJ, Puelles L, Zeng H, Rubenstein JLR, Nord AS | Proceedings of the National Academy of Sciences of the United States of America | 35377797 | Proc Natl Acad Sci U S A | 2022 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/35377797 |
| 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 |
| Multicolor Fluorescence Detection for Droplet Microfluidics Using Optical Fibers. | Cole RH, Gartner ZJ, Abate AR | Journal of visualized experiments : JoVE | 27214249 | J Vis Exp | 2016 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/27214249 |
| 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 |
| Phosphorylated EGFR Dimers Are Not Sufficient to Activate Ras. | Liang SI, van Lengerich B, Eichel K, Cha M, Patterson DM, Yoon TY, von Zastrow M, Jura N, Gartner ZJ | Cell reports | 29514089 | Cell Rep | 2018 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/29514089 |
| Engineered Tissue Folding by Mechanical Compaction of the Mesenchyme. | Hughes AJ, Miyazaki H, Coyle MC, Zhang J, Laurie MT, Chu D, Vavrušová Z, Schneider RA, Klein OD, Gartner ZJ | Developmental cell | 29290586 | Dev Cell | 2018 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/29290586 |
| 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 |
| 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 |
| 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 |
| 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 |
| Getting the measure of living biomaterials. | Gartner Z, Hughes A | Nature | 31358937 | Nature | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31358937 |
| 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 |
| The roles of outlet density and norms in alcohol use disorder. | Ahern J, Balzer L, Galea S | Drug and alcohol dependence | 25858787 | Drug Alcohol Depend | 2015 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/25858787 |
| Optimizing matching and analysis combinations for estimating causal effects. | Colson KE, Rudolph KE, Zimmerman SC, Goin DE, Stuart EA, Laan Mv, Ahern J | Scientific reports | 26980444 | Sci Rep | 2016 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/26980444 |
| Predictors of firearm violence in urban communities: A machine-learning approach. | Goin DE, Rudolph KE, Ahern J | Health & place | 29549755 | Health Place | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29549755 |
| Experimental Implementation of Underactuated Potential Energy Shaping on a Powered Ankle-Foot Orthosis. | Lv G, Zhu H, Elery T, Li L, Gregg RD | IEEE International Conference on Robotics and Automation : ICRA : [proceedings]. IEEE International Conference on Robotics and Automation | 27390625 | IEEE Int Conf Robot Autom | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27390625 |
| Hybrid Nonlinear Disturbance Observer Design for Underactuated Bipedal Robots. | Mohammadi A, Fakoorian S, Horn JC, Simon D, Gregg RD | Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control | 30778276 | Proc IEEE Conf Decis Control | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30778276 |
| A Phase Variable Approach to Volitional Control of Powered Knee-Ankle Prostheses. | Rezazadeh S, Quintero D, Divekar N, Gregg RD | Proceedings of the ... IEEE/RSJ International Conference on Intelligent Robots and Systems. IEEE/RSJ International Conference on Intelligent Robots and Systems | 30746286 | Rep U S | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30746286 |
| Intuitive Clinician Control Interface for a Powered Knee-Ankle Prosthesis: A Case Study. | Quintero D, Reznick E, Lambert DJ, Rezazadeh S, Gray L, Gregg RD | IEEE journal of translational engineering in health and medicine | 30546971 | IEEE J Transl Eng Health Med | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30546971 |
| Removing Phase Variables from Biped Robot Parametric Gaits. | Mohammadi A, Horn J, Gregg RD | Control Technology and Applications. Control Technology and Applications | 30198027 | Control Technol Appl | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30198027 |
| Orthotic Body-Weight Support Through Underactuated Potential Energy Shaping with Contact Constraints. | Lv G, Gregg RD | Proceedings of the ... IEEE Conference on Decision & Control. IEEE Conference on Decision & Control | 26900254 | Proc IEEE Conf Decis Control | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26900254 |
| A Perturbation Mechanism for Investigations of Phase Variables in Human Locomotion. | Villarreal DJ, Quintero D, Gregg RD | ... IEEE International Conference on Robotics and Biomimetics. IEEE International Conference on Robotics and Biomimetics | 27158684 | IEEE ROBIO | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27158684 |
| Continuous-Phase Control of a Powered Knee-Ankle Prosthesis: Amputee Experiments Across Speeds and Inclines. | Quintero D, Villarreal DJ, Lambert DJ, Kapp S, Gregg RD | IEEE transactions on robotics : a publication of the IEEE Robotics and Automation Society | 30008623 | IEEE Trans Robot | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30008623 |
| Unified Phase Variables of Relative Degree Two for Human Locomotion. | Villarreal DJ, Gregg RD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 28261013 | Annu Int Conf IEEE Eng Med Biol Soc | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28261013 |
| A Perturbation Mechanism for Investigations of Phase-Dependent Behavior in Human Locomotion. | Villarreal DJ, Quintero D, Gregg RD | IEEE access : practical innovations, open solutions | 27570719 | IEEE Access | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27570719 |
| Preliminary Experiments with a Unified Controller for a Powered Knee-Ankle Prosthetic Leg Across Walking Speeds. | Quintero D, Villarreal DJ, Gregg RD | Proceedings of the ... IEEE/RSJ International Conference on Intelligent Robots and Systems. IEEE/RSJ International Conference on Intelligent Robots and Systems | 28392969 | Rep U S | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28392969 |
| Prosthetic Leg Control in the Nullspace of Human Interaction. | Gregg RD, Martin AE | Proceedings of the ... American Control Conference. American Control Conference | 27746585 | Proc Am Control Conf | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27746585 |
| Virtual Constraint Control of a Powered Prosthetic Leg: From Simulation to Experiments with Transfemoral Amputees. | Gregg RD, Lenzi T, Hargrove LJ, Sensinger JW | IEEE transactions on robotics : a publication of the IEEE Robotics and Automation Society | 25558185 | IEEE Trans Robot | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25558185 |
| Design Principles for Compact, Backdrivable Actuation in Partial-Assist Powered Knee Orthoses. | Zhu H, Nesler C, Divekar N, Peddinti V, Gregg RD | IEEE/ASME transactions on mechatronics : a joint publication of the IEEE Industrial Electronics Society and the ASME Dynamic Systems and Control Division | 34916771 | IEEE ASME Trans Mechatron | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34916771 |
| Design and Validation of a Torque Dense, Highly Backdrivable Powered Knee-Ankle Orthosis. | Zhu H, Doan J, Stence C, Lv G, Elery T, Gregg R | IEEE International Conference on Robotics and Automation : ICRA : [proceedings]. IEEE International Conference on Robotics and Automation | 29057142 | IEEE Int Conf Robot Autom | 2017 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/29057142 |
| Unifying the Gait Cycle in the Control of a Powered Prosthetic Leg. | Quintero D, Martin AE, Gregg RD | IEEE ... International Conference on Rehabilitation Robotics : [proceedings] | 26913092 | IEEE Int Conf Rehabil Robot | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26913092 |
| Characterizing and modeling the joint-level variability in human walking. | Martin AE, Villarreal DJ, Gregg RD | Journal of biomechanics | 27594679 | J Biomech | 2016 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/27594679 |
| A Haptic Feedback System for Phase-Based Sensory Restoration in Above-Knee Prosthetic Leg Users. | Plauche A, Villarreal D, Gregg RD | IEEE transactions on haptics | 27323375 | IEEE Trans Haptics | 2016 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/27323375 |
| A Unified Parameterization of Human Gait Across Ambulation Modes. | Embry KR, Villarreal DJ, Gregg RD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 28261005 | Annu Int Conf IEEE Eng Med Biol Soc | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28261005 |
| Real-Time Continuous Gait Phase and Speed Estimation from a Single Sensor. | Quintero D, Lambert DJ, Villarreal DJ, Gregg RD | Control Technology and Applications. Control Technology and Applications | 30148285 | Control Technol Appl | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30148285 |
| Passivity-Based Control with a Generalized Energy Storage Function for Robust Walking of Biped Robots. | Yeatman MR, Lv G, Gregg RD | Proceedings of the ... American Control Conference. American Control Conference | 30220783 | Proc Am Control Conf | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30220783 |
| Automatic Tuning of Virtual Constraint-Based Control Algorithms for Powered Knee-Ankle Prostheses. | Kumar S, Mohammadi A, Gans N, Gregg RD | Control Technology and Applications. Control Technology and Applications | 30175324 | Control Technol Appl | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30175324 |
| A Robust Parameterization of Human Gait Patterns Across Phase-Shifting Perturbations. | Villarreal DJ, Poonawala HA, Gregg RD | IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society | 27187967 | IEEE Trans Neural Syst Rehabil Eng | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27187967 |
| Decentralized Feedback Controllers for Exponential Stabilization of Hybrid Periodic Orbits: Application to Robotic Walking. | Hamed KA, Gregg RD | Proceedings of the ... American Control Conference. American Control Conference | 27990059 | Proc Am Control Conf | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27990059 |
| Design and Benchtop Validation of a Powered Knee-Ankle Prosthesis with High-Torque, Low-Impedance Actuators. | Elery T, Rezazadeh S, Nesler C, Doan J, Zhu H, Gregg RD | IEEE International Conference on Robotics and Automation : ICRA : [proceedings]. IEEE International Conference on Robotics and Automation | 30598854 | IEEE Int Conf Robot Autom | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/30598854 |
| HUMAN-INSPIRED ALGEBRAIC CURVES FOR WEARABLE ROBOT CONTROL. | Mohammadi A, Gregg RD | Proceedings of the ASME Dynamic Systems and Control Conference. ASME Dynamic Systems and Control Conference | 30906619 | Proc ASME Dyn Syst Control Conf | 2018 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30906619 |
| On the Design and Control of Highly Backdrivable Lower-Limb Exoskeletons: A Discussion of Past and Ongoing Work. | Lv G, Zhu H, Gregg RD | IEEE control systems | 30598586 | IEEE Control Syst | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30598586 |
| Robust Optimal Design of Energy Efficient Series Elastic Actuators: Application to a Powered Prosthetic Ankle. | Bolivar E, Rezazadeh S, Summers T, Gregg RD | IEEE ... International Conference on Rehabilitation Robotics : [proceedings] | 31374719 | IEEE Int Conf Rehabil Robot | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31374719 |
| Extremum Seeking Control for Model-Free Auto-Tuning of Powered Prosthetic Legs. | Kumar S, Mohammadi A, Quintero D, Rezazadeh S, Gans N, Gregg RD | IEEE transactions on control systems technology : a publication of the IEEE Control Systems Society | 33041615 | IEEE Trans Control Syst Technol | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33041615 |
| Effect of Mucosal Cytokine Administration on Selective Expansion of Vaginal Dendritic Cells to Support Nanoparticle Transport. | Ramanathan R, Park J, Hughes SM, Lykins WR, Bennett HR, Hladik F, Woodrow KA | American journal of reproductive immunology (New York, N.Y. : 1989) | 26118309 | Am J Reprod Immunol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26118309 |
| 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 |
| Rational design of charged peptides that self-assemble into robust nanofibers as immune-functional scaffolds. | Zhang H, Park J, Jiang Y, Woodrow KA | Acta biomaterialia | 28365480 | Acta Biomater | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28365480 |
| Oral mucosal vaccination using integrated fiber microneedles. | Creighton RL, Faber KA, Tobos CI, Doan MA, Guo T, Woodrow KA | Journal of controlled release : official journal of the Controlled Release Society | 38295993 | J Control Release | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38295993 |
| Role of heterogeneous cell population on modulation of dendritic cell phenotype and activation of CD8 T cells for use in cell-based immunotherapies. | Frizzell H, Park J, Comandante Lou N, Woodrow KA | Cellular immunology | 27793335 | Cell Immunol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27793335 |
| 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 |
| Engineering immunity in the mucosal niche against sexually transmitted infections. | Ramanathan R, Woodrow K | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 26153141 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2016 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/26153141 |
| 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 |
| 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 |
| 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 |
| Protein-loaded emulsion electrospun fibers optimized for bioactivity retention and pH-controlled release for peroral delivery of biologic therapeutics. | Frizzell H, Ohlsen TJ, Woodrow KA | International journal of pharmaceutics | 28941831 | Int J Pharm | 2017 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/28941831 |
| Biophysical characterization of small molecule antiviral-loaded nanolipogels for HIV-1 chemoprophylaxis and topical mucosal application. | Ramanathan R, Jiang Y, Read B, Golan-Paz S, Woodrow KA | Acta biomaterialia | 26947382 | Acta Biomater | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26947382 |
| 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 |
| A new era in cytomegalovirus vaccinology: considerations for rational design of next-generation vaccines to prevent congenital cytomegalovirus infection. | Nelson CS, Herold BC, Permar SR | NPJ vaccines | 30275984 | NPJ Vaccines | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30275984 |
| 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 |
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| An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation. | Khavnekar S, Wan W | bioRxiv : the preprint server for biology | 39416009 | bioRxiv | 2024 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/39416009 |
| Mobilizing phospholipids on tumor plasma membrane implicates phosphatidylserine externalization blockade for cancer immunotherapy. | Wang W, Wu S, Cen Z, Zhang Y, Chen Y, Huang Y, Cillo AR, Prokopec JS, Quarato G, Vignali DAA, Stewart-Ornstein J, Li S, Lu B, Gong YN | Cell reports | 36323258 | Cell Rep | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36323258 |
| Sensing plasma membrane pore formation induces chemokine production in survivors of regulated necrosis. | Wang W, Prokopec JS, Zhang Y, Sukhoplyasova M, Shinglot H, Wang MT, Linkermann A, Stewart-Ornstein J, Gong YN | Developmental cell | 35016014 | Dev Cell | 2022 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/35016014 |
| LANCE: a Label-Free Live Apoptotic and Necrotic Cell Explorer Using Convolutional Neural Network Image Analysis. | Hartnett EB, Zhou M, Gong YN, Chen YC | Analytical chemistry | 36251981 | Anal Chem | 2022 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/36251981 |
| Thymidine rescues ATR kinase inhibitor-induced deoxyuridine contamination in genomic DNA, cell death, and interferon-α/β expression. | Sugitani N, Vendetti FP, Cipriano AJ, Pandya P, Deppas JJ, Moiseeva TN, Schamus-Haynes S, Wang Y, Palmer D, Osmanbeyoglu HU, Bostwick A, Snyder NW, Gong YN, Aird KM, Delgoffe GM, Beumer JH, Bakkenist CJ | Cell reports | 36130512 | Cell Rep | 2022 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/36130512 |
| MLKL ubiquitylation: more than a makeover. | Wang W, Gong YN | Cell death and differentiation | 35022572 | Cell Death Differ | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/35022572 |
| Mycobacterium tuberculosis, Mycobacterium kansasii and Rhodococcus equi induce macrophage necroptosis in the presence of a caspase inhibitor acting on a non-canonical target(s). | Hu R, Li P, Han J, Huang J, Huang G, Jiang X, Pfau D, Li G, Gong YN, Nathan CF, Zhang L | bioRxiv : the preprint server for biology | 40950000 | bioRxiv | 2025 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/40950000 |
| Gasdermin C cleavage by Cathepsin S modulates Rab7 vesicles in intestinal epithelial cells to amplify anti-helminth immunity. | Pandey SP, Yang D, Hedden L, Laughlin CR, Wang W, Soto AS, Winner H, Medina Sanchez L, Campana EE, Engl C, Zeng Y, Rana M, Van Der Kraak L, Bender MJ, Prokopec J, Ferrick JM, Meng X, Fong E, Sun M, Mullett SJ, MacDonald M, Gelhaus SL, Watkins SC, Meisel M, von Moltke J, Xu S, Gong YN, Hinterleitner R | Immunity | 40701157 | Immunity | 2025 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/40701157 |
| Plasma membrane repair empowers the necrotic survivors as innate immune modulators. | Xu S, Yang TJ, Xu S, Gong YN | Seminars in cell & developmental biology | 37648621 | Semin Cell Dev Biol | 2024 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/37648621 |
| D-MAINS: A Deep-Learning Model for the Label-Free Detection of Mitosis, Apoptosis, Interphase, Necrosis, and Senescence in Cancer Cells. | He S, Sillah M, Cole AR, Uboveja A, Aird KM, Chen YC, Gong YN | Cells | 38920634 | Cells | 2024 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/38920634 |
| Two parallel lineage-committed progenitors contribute to the developing brain. | Dundes CE, Jokhai RT, Ahsan H, Kang RS, Salomon-Shulman REA, Rajan A, Kim YS, Stanton LJ, Xu C, Do S, McDonald BD, López JMA, Urrutia HA, Greenfeld H, Wong A, Qu Y, Petkovic AS, Miao Y, Garcia KC, Monje M, Wagner DE, Bronner ME, Lowe CJ, Loh KM | bioRxiv : the preprint server for biology | 40631129 | bioRxiv | 2025 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/40631129 |
| Structural Basis for Allostery in PLP-dependent Enzymes. | Tran JU, Brown BL | Frontiers in molecular biosciences | 35547395 | Front Mol Biosci | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35547395 |
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| The yeast ALA synthase C-terminus positively controls enzyme structure and function. | Tran JU, Brown BL | Protein science : a publication of the Protein Society | 36807942 | Protein Sci | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36807942 |
| Elucidating the Role of Human ALAS2 C-terminal Mutations Resulting in Loss of Function and Disease. | Taylor JL, Ayres-Galhardo PH, Brown BL | Biochemistry | 38888931 | Biochemistry | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38888931 |
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| A massively parallel reporter assay library to screen short synthetic promoters in mammalian cells. | Zahm AM, Owens WS, Himes SR, Fallon BS, Rondem KE, Gormick AN, Bloom JS, Kosuri S, Chan H, English JG | Nature communications | 39609378 | Nat Commun | 2024 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/39609378 |
| Functionalizing tandem mass tags for streamlining click-based quantitative chemoproteomics. | Burton NR, Backus KM | Communications chemistry | 38600184 | Commun Chem | 2024 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/38600184 |
| Prioritizing disease-associated missense variants with chemoproteomic-detected amino acids. | Palafox MF, Boatner L, Wilde BR, Christofk H, Backus KM, Arboleda VA | American journal of human genetics | 40412387 | Am J Hum Genet | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40412387 |
| Chemoproteomics Identifies State-Dependent and Proteoform-Selective Caspase-2 Inhibitors. | Castellón JO, Ofori S, Burton NR, Julio AR, Turmon AC, Armenta E, Sandoval C, Boatner LM, Takayoshi EE, Faragalla M, Taylor C, Zhou AL, Tran K, Shek J, Yan T, Desai HS, Fregoso OI, Damoiseaux R, Backus KM | Journal of the American Chemical Society | 38787738 | J Am Chem Soc | 2024 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/38787738 |
| An activation-based high throughput screen identifies caspase-10 inhibitors. | Castellón JO, Yuen C, Han B, Andrews KH, Ofori S, Julio AR, Boatner LM, Palafox MF, Perumal N, Damoiseaux R, Backus KM | RSC chemical biology | 40013156 | RSC Chem Biol | 2025 Apr 2 | https://www.ncbi.nlm.nih.gov/pubmed/40013156 |
| Proximity-labeling chemoproteomics defines the subcellular cysteinome and inflammation-responsive mitochondrial redoxome. | Yan T, Julio AR, Villanueva M, Jones AE, Ball AB, Boatner LM, Turmon AC, Nguyễn KB, Yen SL, Desai HS, Divakaruni AS, Backus KM | Cell chemical biology | 37419112 | Cell Chem Biol | 2023 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/37419112 |
| Defining STING-sterol interactions with chemoproteomics. | Ford I, Villanueva M, Lee MS, Zhou QD, Yuen C, Damoiseaux R, Bensinger SJ, Backus KM | RSC chemical biology | 40747213 | RSC Chem Biol | 2025 Aug 27 | https://www.ncbi.nlm.nih.gov/pubmed/40747213 |
| Delineating cysteine-reactive compound modulation of cellular proteostasis processes. | Julio AR, Shikwana F, Truong C, Burton NR, Dominguez ER 3rd, Turmon AC, Cao J, Backus KM | Nature chemical biology | 39448844 | Nat Chem Biol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/39448844 |
| Cholesterol binding to VCAM-1 promotes vascular inflammation. | Kennelly JP, Xiao X, Gao Y, Kim S, Hong SG, Villanueva M, Ferrari A, Vanharanta L, Nguyen A, Nagari RT, Burton NR, Tol MJ, Becker AP, Lee MJ, Ikonen E, Backus KM, Mack JJ, Tontonoz P | bioRxiv : the preprint server for biology | 39345495 | bioRxiv | 2024 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/39345495 |
| Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome. | Becker AP, Biletch E, Kennelly JP, Julio AR, Villaneuva M, Nagari RT, Turner DW, Burton NR, Fukuta T, Cui L, Xiao X, Hong SG, Mack JJ, Tontonoz P, Backus KM | bioRxiv : the preprint server for biology | 39229057 | bioRxiv | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39229057 |
| Solid-Phase Compatible Silane-Based Cleavable Linker Enables Custom Isobaric Quantitative Chemoproteomics. | Burton NR, Polasky DA, Shikwana F, Ofori S, Yan T, Geiszler DJ, Veiga Leprevost FD, Nesvizhskii AI, Backus KM | Journal of the American Chemical Society | 37738129 | J Am Chem Soc | 2023 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/37738129 |
| Photosensitizer proximity labeling captures the lipid and protein interactomes. | Becker AP, Biletch E, Kennelly JP, Hong SG, Julio AR, Villanueva M, Nagari RT, Turner DW, Burton NR, Fukuta T, Cui L, Xiao X, Vellani Z, Nguyen A, Mack JJ, Tontonoz P, Backus KM | Nature chemical biology | 41652064 | Nat Chem Biol | 2026 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/41652064 |
| Multimodal charting of molecular and functional cell states via in situ electro-sequencing. | Li Q, Lin Z, Liu R, Tang X, Huang J, He Y, Sui X, Tian W, Shen H, Zhou H, Sheng H, Shi H, Xiao L, Wang X, Liu J | Cell | 37080201 | Cell | 2023 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/37080201 |
| Integrative in situ mapping of single-cell transcriptional states and tissue histopathology in a mouse model of Alzheimer's disease. | Zeng H, Huang J, Zhou H, Meilandt WJ, Dejanovic B, Zhou Y, Bohlen CJ, Lee SH, Ren J, Liu A, Tang Z, Sheng H, Liu J, Sheng M, Wang X | Nature neuroscience | 36732642 | Nat Neurosci | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36732642 |
| Spatially resolved in situ profiling of mRNA life cycle at transcriptome scale in intact cells and tissues using STARmap PLUS, RIBOmap and TEMPOmap. | Ren J, Zeng H, Huang J, Tian J, Wu M, Shi H, Sui X, Wang CK, Zhou H, Tang Z, Luo S, Wang X | Nature protocols | 41028562 | Nat Protoc | 2026 Apr | https://www.ncbi.nlm.nih.gov/pubmed/41028562 |
| Diversity of ribosomes at the level of rRNA variation associated with human health and disease. | Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M | Cell genomics | 39111318 | Cell Genom | 2024 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/39111318 |
| Spatial omics advances for in situ RNA biology. | Ren J, Luo S, Shi H, Wang X | Molecular cell | 39270643 | Mol Cell | 2024 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/39270643 |
| Search and match across spatial omics samples at single-cell resolution. | Tang Z, Luo S, Zeng H, Huang J, Sui X, Wu M, Wang X | Nature methods | 39294367 | Nat Methods | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39294367 |
| Graph-based autoencoder integrates spatial transcriptomics with chromatin images and identifies joint biomarkers for Alzheimer's disease. | Zhang X, Wang X, Shivashankar GV, Uhler C | Nature communications | 36463283 | Nat Commun | 2022 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/36463283 |
| Spatiotemporally resolved transcriptomics reveals the subcellular RNA kinetic landscape. | Ren J, Zhou H, Zeng H, Wang CK, Huang J, Qiu X, Sui X, Li Q, Wu X, Lin Z, Lo JA, Maher K, He Y, Tang X, Lam J, Chen H, Li B, Fisher DE, Liu J, Wang X | Nature methods | 37038000 | Nat Methods | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37038000 |
| 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 | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39313647 |
| ClusterMap for multi-scale clustering analysis of spatial gene expression. | He Y, Tang X, Huang J, Ren J, Zhou H, Chen K, Liu A, Shi H, Lin Z, Li Q, Aditham A, Ounadjela J, Grody EI, Shu J, Liu J, Wang X | Nature communications | 34625546 | Nat Commun | 2021 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/34625546 |
| Branched chemically modified poly(A) tails enhance the translation capacity of mRNA. | Chen H, Liu D, Guo J, Aditham A, Zhou Y, Tian J, Luo S, Ren J, Hsu A, Huang J, Kostas F, Wu M, Liu DR, Wang X | Nature biotechnology | 38519719 | Nat Biotechnol | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38519719 |
| Spatially resolved translational dysregulation in Grin2a+/- mouse model of schizophrenia. | Wu M, Huang J, Aryal S, Farsi Z, Chen H, Zhou Y, Luo S, Wang WX, Bonanno K, Yin M, Picard I, Dejanovic B, Keshishian H, Carr SA, Sheng M, Wang X | bioRxiv : the preprint server for biology | 41509319 | bioRxiv | 2025 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/41509319 |
| Structure and biochemistry-guided engineering of an all-RNA system for DNA insertion with R2 retrotransposons. | Edmonds KK, Wilkinson ME, Strebinger D, Chen H, Lash B, Schaefer CC, Zhu S, Liu D, Zilberzwige-Tal S, Ladha A, Walsh ML, Frangieh CJ, Vaz Reay NA, Macrae RK, Wang X, Zhang F | Nature communications | 40603868 | Nat Commun | 2025 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/40603868 |
| 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 |
| Spatially resolved single-cell translatomics at molecular resolution. | Zeng H, Huang J, Ren J, Wang CK, Tang Z, Zhou H, Zhou Y, Shi H, Aditham A, Sui X, Chen H, Lo JA, Wang X | Science (New York, N.Y.) | 37384709 | Science | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37384709 |
| Spatial atlas of the mouse central nervous system at molecular resolution. | Shi H, He Y, Zhou Y, Huang J, Maher K, Wang B, Tang Z, Luo S, Tan P, Wu M, Lin Z, Ren J, Thapa Y, Tang X, Chan KY, Deverman BE, Shen H, Liu A, Liu J, Wang X | Nature | 37758947 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37758947 |
| Diversity of ribosomes at the level of rRNA variation associated with human health and disease. | Rothschild D, Susanto TT, Sui X, Spence JP, Rangan R, Genuth NR, Sinnott-Armstrong N, Wang X, Pritchard JK, Barna M | bioRxiv : the preprint server for biology | 36778251 | bioRxiv | 2024 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/36778251 |
| Targeting Tmem63b and Piezo2 in C-fiber low-threshold mechanoreceptors: Limitation of Vglut3-IRES-Cre. | Orlin DJ, Muñoz A, Berryman S, Semidey D, Murthy SE | Biophysical journal | 41176617 | Biophys J | 2025 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/41176617 |
| TMEM63A, associated with hypomyelinating leukodystrophies, is an evolutionarily conserved regulator of myelination. | Halford J, Senatore AJ, Berryman S, Muñoz A, Semidey D, Doan RA, Coombs AM, Noimany B, Emberley K, Emery B, Monk KR, Murthy SE | Proceedings of the National Academy of Sciences of the United States of America | 40694323 | Proc Natl Acad Sci U S A | 2025 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/40694323 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| TRF1 and TRF2 form distinct shelterin subcomplexes at telomeres. | Janovič T, Perez GI, Boelting G, Schmidt JC | Cell reports | 40849907 | Cell Rep | 2025 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/40849907 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Protocol for fast antibiotic resistance-based gene editing of mammalian cells with CRISPR-Cas9. | Adarska P, Fox E, Heyza J, Barnaba C, Schmidt J, Bottanelli F | STAR protocols | 40768339 | STAR Protoc | 2025 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/40768339 |
| A dynamic RNA hub facilitates activation induced cytidine deaminase recruitment to the immunoglobulin heavy chain locus. | Mikhova M, Kapanka M, Han L, Schmidt JC, Yu K | bioRxiv : the preprint server for biology | 41648117 | bioRxiv | 2026 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/41648117 |
| Ku limits aberrant mRNA splicing promoted by intronic antisense Alu elements. | Pascarella G, Mikhova M, Parkhi G, Godfrey J, Heyza J, Janovič T, Olive A, Carninci P, Schmidt JC, Meek K | bioRxiv : the preprint server for biology | 41332606 | bioRxiv | 2025 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/41332606 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Sensitive detection of structural dynamics using a statistical framework for comparative crystallography. | Hekstra DR, Wang HK, Klureza MA, Greisman JB, Dalton KM | Science advances | 41337576 | Sci Adv | 2025 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/41337576 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| AlphaFold as a prior: experimental structure determination conditioned on a pretrained neural network. | Fadini A, Li M, McCoy AJ, Banjara S, Okumura H, Napier E, Fontana P, Khan AR, Jovine L, Terwilliger TC, Read RJ, Hekstra DR, AlQuraishi M | Nature methods | 41922571 | Nat Methods | 2026 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/41922571 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Decoding the MYC locus reveals a druggable ultraconserved RNA element. | Shi P, Yang F, Fnu T, Huang W, Aparicio AO, Kalicki CH, Trehan A, Murphy MR, Rotlevi ER, Xing L, Reilly MP, Que J, Wu X | bioRxiv : the preprint server for biology | 41659676 | bioRxiv | 2026 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/41659676 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function. | Narducci DN, Hansen AS | Molecular cell | 39708803 | Mol Cell | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39708803 |
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| 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 |
| 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 |
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| 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 |
| Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation. | Do C, Jiang G, Cova G, Katsifis CC, Narducci DN, Sakellaropoulos T, Vidal R, Lhoumaud P, Tsirigos A, Regis FFD, Kakabadze N, Nora EP, Noyes M, Hansen AS, Skok JA | Cell genomics | 40118069 | Cell Genom | 2025 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/40118069 |
| 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 |
| Distance matters: How protein regulators facilitate enhancer-promoter interactions and transcription. | Nagano M, Hansen AS | Cell genomics | 40081334 | Cell Genom | 2025 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/40081334 |
| 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 |
| Genome structure mapping with high-resolution 3D genomics and deep learning. | Hong CKY, Feng F, Ramanathan V, Liu J, Hansen AS | bioRxiv : the preprint server for biology | 40654659 | bioRxiv | 2025 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/40654659 |
| 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 |
| 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 |
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| Construction of complex and diverse DNA sequences using DNA three-way junctions. | Robinson NE, Zhang W, Ghosh R, Gerber B, Zhang H, Sanfiorenzo C, Wang S, Di Carlo D, Wang K | Nature | 41565816 | Nature | 2026 Mar | https://www.ncbi.nlm.nih.gov/pubmed/41565816 |
| 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 |
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| 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 |
| 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 |
| Global Analysis of Aggregation Determinants in Small Protein Domains. | Martell CM, Gebis KK, Van HM, Gutierrez YM, Jung MD, Savas JN, Rocklin GJ | bioRxiv : the preprint server for biology | 41292870 | bioRxiv | 2025 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/41292870 |
| 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 |
| 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 |
| 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 |
| Non-native entanglement protein misfolding observed in all-atom simulations and supported by experimental structural ensembles. | Vu QV, Sitarik I, Jiang Y, Xia Y, Sharma P, Yadav D, Song H, Li MS, Fried SD, O'Brien EP | Science advances | 40779622 | Sci Adv | 2025 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/40779622 |
| Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy. | Dallon E, Moran HM, Chidambaran SR, Kian A, Huang BYH, Fried SD, DiRuggiero J | mSphere | 40920071 | mSphere | 2025 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/40920071 |
| Investigation of the global translational response to oxidative stress in the model archaeon Haloferax volcanii reveals untranslated small RNAs with ribosome occupancy. | Dallon E, Moran HM, Chidambaran SR, Kian A, Huang BYH, Fried SD, DiRuggiero J | bioRxiv : the preprint server for biology | 40672279 | bioRxiv | 2025 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/40672279 |
| Chaperone Dependency during Primary Protein Biogenesis Does Not Correlate with Chaperone Dependency during in vitro Refolding. | Yadav D, Demiralp İI, Fakler M, Fried SD | bioRxiv : the preprint server for biology | 40611891 | bioRxiv | 2025 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/40611891 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Proteins with cognition-associated structural changes in a rat model of aging exhibit reduced refolding capacity. | Tarbox HE, Branch A, Fried SD | Science advances | 40644533 | Sci Adv | 2025 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/40644533 |
| Phosphoglycerate Kinase Can Adopt a Topologically Misfolded Form that is More Stable than its Native State. | Xia Y, Amann B, Gillilan RE, Sharma P, Sen S, Fleming KG, Fried SD | bioRxiv : the preprint server for biology | 40667093 | bioRxiv | 2025 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/40667093 |
| Prebiotically Plausible Peptides can Self-assemble into β-rich Nanostructures. | Makarov M, Kryštůfek R, Friček M, Manriquez-Sandoval E, Dutta S, Kormaník JM, Kalvoda T, Verner V, Bednárová L, Charnavets T, Lebl M, Brown SM, Hadravová R, Konvalinka J, Singharoy A, Fried SD, Hlouchová K | bioRxiv : the preprint server for biology | 41292710 | bioRxiv | 2025 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/41292710 |
| 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 |
| 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 |
| Protein surface chemistry encodes an adaptive tolerance to desiccation. | Romero-Pérez PS, Moran HM, Cordone DP Jr, Horani A, Truong A, Manriquez-Sandoval E, Ramirez JF, Martinez A, Gollub E, Hunter K, Kolamunna KC, Lotthammer JM, Emenecker RJ, Liu H, Iwasa JH, Boothby TC, Holehouse AS, Fried SD, Sukenik S | Cell systems | 41043424 | Cell Syst | 2025 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/41043424 |
| Phase separation of PGL-3 driven by structured domains that oligomerize and interact with terminal RGG motifs. | Kuroiwa R, Sharma P, Putnam A, Fried SD, Seydoux G | bioRxiv : the preprint server for biology | 40666952 | bioRxiv | 2025 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/40666952 |
| 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 |
| An intrinsically disordered region of Ubp10 regulates its binding and activity on ubiquitinated histone substrates. | Faustino AM, Nune M, Merino-Urteaga R, Manriquez-Sandoval E, Poyton M, Ha T, Wolberger C, Fried SD | Protein science : a publication of the Protein Society | 40716115 | Protein Sci | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40716115 |
| Phase separation of PGL-3 driven by structured domains that oligomerize and interact with RGG motifs. | Kuroiwa R, Sharma P, Putnam AA, Fried SD, Seydoux G | EMBO reports | 41862773 | EMBO Rep | 2026 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/41862773 |
| 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 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 |
| Cryo-EM structures of plant Augmin reveal coiled-coil assembly, antiparallel dimerization, and NEDD1 binding. | Ashaduzzaman M, Taheri A, Lee YJ, Tang Y, Mittal S, Guo F, Morcos F, Fried SD, Liu B, Al-Bassam J | Nature communications | 41387433 | Nat Commun | 2025 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/41387433 |
| Protein misfolding involving entanglements providesa structural explanation for the origin of stretched-exponential refolding kinetics. | Jiang Y, Xia Y, Sitarik I, Sharma P, Song H, Fried SD, O'Brien EP | Science advances | 40085700 | Sci Adv | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/40085700 |
| 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 |
| 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 |
| 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 |
| Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states. | Southard KM, Ardy RC, Tang A, O'Sullivan DD, Metzner E, Guruvayurappan K, Norman TM | Nature genetics | 40770575 | Nat Genet | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/40770575 |
| 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 |
| Large-scale mapping of environmental-genetic interactions illustrates the dynamic nature of cell-cycle and DNA repair regulation. | Herken BW, Wong GT, Mäkiniemi A, Lundberg E, Norman TM, Gilbert LA | Molecular cell | 41720076 | Mol Cell | 2026 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/41720076 |
| 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 |
| Scaling perturbations: beyond genome-scale CRISPR screens. | Tang A, Ardy RC, Mendes RE, Norman TM | bioRxiv : the preprint server for biology | 41648157 | bioRxiv | 2026 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/41648157 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 | Nature communications | 40764481 | Nat Commun | 2025 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/40764481 |
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| 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 |
| 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 |
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| An experimental census of retrons for DNA production and genome editing. | Khan AG, Rojas-Montero M, González-Delgado A, Lopez SC, Fang RF, Shipman SL | bioRxiv : the preprint server for biology | 38328236 | bioRxiv | 2024 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/38328236 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Activity-based CRISPR scanning uncovers allostery in DNA methylation maintenance machinery. | Ngan KC, Hoenig SM, Kwok HS, Lue NZ, Gosavi PM, Tanner DA, Garcia EM, Lee C, Liau BB | eLife | 36762644 | Elife | 2023 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/36762644 |
| 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 |
| Oxidation of retromer complex controls mitochondrial translation. | Zhang J, Ali MY, Chong HB, Tien PC, Woods J, Noble C, Vornbäumen T, Ordulu Z, Possemato AP, Harry S, Fonticella JM, Fellah L, Harrison D, Ge M, Khandelwal N, Huang Y, Chauvin M, Bischof AT, Hambelton GM, Gohar MF, Zhang S, Choi M, Bouberhan S, Oliva E, Mino-Kenudson M, Pavlova NN, Lawrence M, Gainor JF, Beausoleil SA, Bardeesy N, Mostoslavsky R, Pépin D, Ott CJ, Liau B, Bar-Peled L | Nature | 40140582 | Nature | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40140582 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Shifting redox reaction equilibria on demand using an orthogonal redox cofactor. | Aspacio D, Zhang Y, Cui Y, Luu E, King E, Black WB, Perea S, Zhu Q, Wu Y, Luo R, Siegel JB, Li H | Nature chemical biology | 39138383 | Nat Chem Biol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39138383 |
| Engineering Escherichia coli Pyruvate Metabolism to Generate Noncanonical Reducing Power. | Aspacio D, Luu E, Worakaensai S, Cui Y, Maxel S, King E, Hagerty R, Chu A, Minn D, Siegel JB, Li H | ACS catalysis | 40734716 | ACS Catal | 2024 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/40734716 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38108560 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39532536 | J Neurosci | 2025 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/39532536 |
| 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 |
| Yeast de novo proteins integrate into cellular systems using ancient protein targeting and degradation pathways. | Houghton CJ, Coelho NC, Chiang A, Wacholder A, Hedayati S, Guyer A, Wankiiri-Hale M, Raza H, Lord ND, Parikh SB, Ozbaki-Yagan N, Iannotta J, Berger A, Wohlever ML, Carvunis AR, O'Donnell AF | bioRxiv : the preprint server for biology | 39257767 | bioRxiv | 2025 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/39257767 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 | The EMBO journal | 41484366 | EMBO J | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41484366 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| ORF3a is a key driver of maternal SARS-CoV-2 infection-associated placental dysfunction. | Mysorekar I, Kumar D, McColl E, Karvas R, Jones B, Tran L, Diveley E, Jash S, Sharma S, Kelly J, Theunissen T | Research square | 40630515 | Res Sq | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40630515 |
| Trophoblast ferroptosis restricts SARS-CoV-2 spread in the placenta. | McColl ER, Kumar D, Jones BR, Marks N, Diveley E, Karvas R, Theunissen TW, Kelly JC, Mysorekar IU | bioRxiv : the preprint server for biology | 41659473 | bioRxiv | 2026 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/41659473 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Active site diversification of a non-canonical amino acid decarboxylase by merging substrate multiplexed screening with computationally guided recombination. | McDonald AD, Ellis JM, Steger-Wilson L, Campbell ME, Buller AR | Protein science : a publication of the Protein Society | 41123281 | Protein Sci | 2025 Nov | https://www.ncbi.nlm.nih.gov/pubmed/41123281 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Chemoenzymatic Cascade Synthesis of Metal-Chelating α-Amino Acids. | Young SH, Andon JS, Lim J, Franke MC, Weix DJ, Wang T, Buller AR | ChemCatChem | 40761323 | ChemCatChem | 2025 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/40761323 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Highly Sensitive Detection of Tyrosine and Neurotransmitters by Stereoselective Biosynthesis and Photochemically Induced Dynamic Nuclear Polarization. | Shapla UM, Smith JL, Halder A, Thompson L, Buller AR, Cavagnero S | Journal of the American Chemical Society | 41190608 | J Am Chem Soc | 2025 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/41190608 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 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 |
| 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 |
| Sequential CRISPR screening reveals partial NatB inhibition as a strategy to mitigate alpha-synuclein levels in human neurons. | Santhosh Kumar S, Naseri NN, Pather SR, Hallacli E, Ndayisaba A, Buenaventura C, Acosta K, Roof J, Fazelinia H, Spruce LA, Luk K, Khurana V, Rhoades E, Shalem O | Science advances | 38335281 | Sci Adv | 2024 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/38335281 |
| 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 |
| 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 |
| 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 |
| GCN1 couples GCN2 to ribosomal state to initiate amino acid response pathway signaling. | Zhou C, Zhang M, Murray J, Paulo J, Gygi S, Shao S, Whitman M, Keller T | Science (New York, N.Y.) | 41037622 | Science | 2025 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/41037622 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Epigenetic priming promotes tyrosine kinase inhibitor resistance and oncogene amplification. | Starble RM, Sun EG, Gbyli R, Radda J, Lu J, Jensen TB, Sun N, Khudaverdyan N, Zhao T, Hu B, Melnick MA, Zhao S, Roper N, Wang GG, Tackett AJ, Wang Y, Song J, Politi K, Wang S, Xiao AZ | Nature structural & molecular biology | 41131337 | Nat Struct Mol Biol | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/41131337 |
| Sequencing-free whole-genome spatial transcriptomics at single-molecule resolution. | Cheng Y, Dang S, Zhang Y, Chen Y, Yu R, Liu M, Jin S, Han A, Katz S, Wang S | Cell | 41038164 | Cell | 2025 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/41038164 |
| 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, Jo S, Qiao SN, Lee DE, Hong JY, Xiong Y, Jin J, Wang S, Jiang YH | Nature communications | 40610428 | Nat Commun | 2025 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/40610428 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. | Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Rajaei M, Li FY, Townsend JP, Muzumdar MD, Wang S | Nature genetics | 40825871 | Nat Genet | 2025 Dec | https://www.ncbi.nlm.nih.gov/pubmed/40825871 |
| 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 |
| 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 |
| 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 |
| 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 |
| Image-based 3D genomics through chromatin tracing. | Yang T, Wang S | Nature reviews. Methods primers | 40756061 | Nat Rev Methods Primers | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/40756061 |
| 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 |
| 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 |
| 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 |
| TransDiscovery: Discovering Biotransformation from Human Microbiota by Integrating Metagenomic and Metabolomic Data. | Yan D, Cao L, Zhou M, Mohimani H | Metabolites | 35208194 | Metabolites | 2022 Jan 26 | https://www.ncbi.nlm.nih.gov/pubmed/35208194 |
| 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 |
| 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 |
| Large scale sequence alignment via efficient inference in generative models. | Mongia M, Shen C, Davoodi AG, Marçais G, Mohimani H | Scientific reports | 37142645 | Sci Rep | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/37142645 |
| 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 |
| microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. | Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, 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, Pessotti RC, 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, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La 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 | Nature microbiology | 38316926 | Nat Microbiol | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38316926 |
| The undiscovered natural product potential of Actinomycetes. | Caraballo-Rodríguez AM, Cumsille A, Magyari S, Taboada-Alquerque M, Behsaz B, Leão TF, Broders K, El Abiead Y, Clement JA, Charron-Lamoureux V, Zuffa S, Nothias LF, Hu M, Leone C, Kakhkhorov SA, Cámara B, Mohimani H, Dorrestein PC | The Journal of antibiotics | 41331045 | J Antibiot (Tokyo) | 2026 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41331045 |
| 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 |
| Repository scale classification and decomposition of tandem mass spectral data. | Mongia M, Mohimani H | Scientific reports | 33859284 | Sci Rep | 2021 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/33859284 |
| Chemical interplay and complementary adaptative strategies toggle bacterial antagonism and co-existence. | Molina-Santiago C, Vela-Corcía D, Petras D, Díaz-Martínez L, Pérez-Lorente AI, Sopeña-Torres S, Pearson J, Caraballo-Rodríguez AM, Dorrestein PC, de Vicente A, Romero D | Cell reports | 34320359 | Cell Rep | 2021 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/34320359 |
| 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 |
| Seq2Saccharide: Discovering Oligosaccharides and Aminoglycosides Natural Products by Integrating Computational Mass Spectrometry and Genome Mining. | Yan D, Behsaz B, Li Y, Wang X, Skala L, Liu S, Lew HW, Guler M, Jayaprakash H, Zhou M, Cao L, Tripathi A, Clement JA, Mahmud T, Kersten RD, Mohimani H | Journal of the American Chemical Society | 40964993 | J Am Chem Soc | 2025 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/40964993 |
| 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 |
| EnHiC: learning fine-resolution Hi-C contact maps using a generative adversarial framework. | Hu Y, Ma W | Bioinformatics (Oxford, England) | 34252966 | Bioinformatics | 2021 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/34252966 |
| Discovering type I cis-AT polyketides through computational mass spectrometry and genome mining with Seq2PKS. | Yan D, Zhou M, Adduri A, Zhuang Y, Guler M, Liu S, Shin H, Kovach T, Oh G, Liu X, Deng Y, Wang X, Cao L, Sherman DH, Schultz PJ, Kersten RD, Clement JA, Tripathi A, Behsaz B, Mohimani H | Nature communications | 38918378 | Nat Commun | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38918378 |
| MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. | Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H | Cell systems | 31629686 | Cell Syst | 2019 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/31629686 |
| 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 |
| HypoRiPPAtlas as an Atlas of hypothetical natural products for mass spectrometry database search. | Lee YY, Guler M, Chigumba DN, Wang S, Mittal N, Miller C, Krummenacher B, Liu H, Cao L, Kannan A, Narayan K, Slocum ST, Roth BL, Gurevich A, Behsaz B, Kersten RD, Mohimani H | Nature communications | 37452020 | Nat Commun | 2023 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/37452020 |
| Structural basis for membrane insertion by the human ER membrane protein complex. | Pleiner T, Tomaleri GP, Januszyk K, Inglis AJ, Hazu M, Voorhees RM | Science (New York, N.Y.) | 32439656 | Science | 2020 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/32439656 |
| 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 |
| 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 |
| A selectivity filter in the ER membrane protein complex limits protein misinsertion at the ER. | Pleiner T, Hazu M, Pinton Tomaleri G, Nguyen VN, Januszyk K, Voorhees RM | The Journal of cell biology | 37199759 | J Cell Biol | 2023 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/37199759 |
| A nanobody-based strategy for rapid and scalable purification of human protein complexes. | Stevens TA, Tomaleri GP, Hazu M, Wei S, Nguyen VN, DeKalb C, Voorhees RM, Pleiner T | Nature protocols | 37974029 | Nat Protoc | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37974029 |
| 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 |
| WNK1 is an assembly factor for the human ER membrane protein complex. | Pleiner T, Hazu M, Tomaleri GP, Januszyk K, Oania RS, Sweredoski MJ, Moradian A, Guna A, Voorhees RM | Molecular cell | 33964204 | Mol Cell | 2021 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/33964204 |
| 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 |
| 3D ATAC-PALM: super-resolution imaging of the accessible genome. | Xie L, Dong P, Chen X, Hsieh TS, Banala S, De Marzio M, English BP, Qi Y, Jung SK, Kieffer-Kwon KR, Legant WR, Hansen AS, Schulmann A, Casellas R, Zhang B, Betzig E, Lavis LD, Chang HY, Tjian R, Liu Z | Nature methods | 32203384 | Nat Methods | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32203384 |
| A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms. | Fu TM, Liu G, Milkie DE, Ruan X, Görlitz F, Shi Y, Ferro V, Divekar NS, Wang W, York HM, Kilic V, Mueller M, Liang Y, Daugird TA, Gacha-Garay MJ, Larkin KA, Adikes RC, Harrison N, Shirazinejad C, Williams S, Nourse JL, Sheu SH, Gao L, Li T, Mondal C, Achour K, Hercule W, Stabley D, Emmerich K, Dong P, Drubin D, Liu ZJ, Clapham D, Mumm JS, Koyama M, Killilea A, Bravo-Cordero JJ, Keene CD, Luo L, Kirchhausen T, Pathak MM, Arumugam S, Nunez JK, Gao R, Matus DQ, Martin BL, Swinburne IA, Betzig E, Legant WR, Upadhyayula S | bioRxiv : the preprint server for biology | 40661351 | bioRxiv | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40661351 |
| 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 |
| 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 |
| 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 |
| 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 |
| A series of spontaneously blinking dyes for super-resolution microscopy. | Holland KL, Plutkis SE, Daugird TA, Sau A, Grimm JB, English BP, Zheng Q, Dave S, Rahman F, Xie L, Dong P, Tkachuk AN, Brown TA, Singer RH, Liu Z, Galbraith CG, Musser SM, Legant WR, Lavis LD | bioRxiv : the preprint server for biology | 38766149 | bioRxiv | 2024 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/38766149 |
| 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 |
| 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 |
| 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 |
| Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. | Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR | bioRxiv : the preprint server for biology | 39211261 | bioRxiv | 2024 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/39211261 |
| Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy. | Rahman F, Augoustides V, Tyler E, Daugird TA, Arthur C, Legant WR | Nature communications | 40593784 | Nat Commun | 2025 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/40593784 |
| Measurement of cellular traction forces during confined migration. | Hockenberry MA, Ulmer AJ, Rapp JL, Truscott HH, Leibfarth FA, Bear JE, Legant WR | Proceedings of the National Academy of Sciences of the United States of America | 41289376 | Proc Natl Acad Sci U S A | 2025 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/41289376 |
| 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 |
| 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 |
| Cell dynamics revealed by microscopy advances. | Hockenberry MA, Daugird TA, Legant WR | Current opinion in cell biology | 39159598 | Curr Opin Cell Biol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39159598 |
| 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 |
| Multi-kingdom ecological drivers of microbiota assembly in preterm infants. | Rao C, Coyte KZ, Bainter W, Geha RS, Martin CR, Rakoff-Nahoum S | Nature | 33627867 | Nature | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33627867 |
| The gut microbiome. | Kuziel GA, Rakoff-Nahoum S | Current biology : CB | 35349808 | Curr Biol | 2022 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/35349808 |
| Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. | Park SY, Rao C, Coyte KZ, Kuziel GA, Zhang Y, Huang W, Franzosa EA, Weng JK, Huttenhower C, Rakoff-Nahoum S | Cell | 35120663 | Cell | 2022 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/35120663 |
| Ecological rules for the assembly of microbiome communities. | Coyte KZ, Rao C, Rakoff-Nahoum S, Foster KR | PLoS biology | 33606675 | PLoS Biol | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33606675 |
| 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 |
| A glycan atlas of the mammalian intestine through ontogeny and inflammation. | Siegel SJ, Pomerantz D, Heimburg-Molinaro J, Danish Mahmood S, Korzenik JR, Cummings RD, Rakoff-Nahoum S | bioRxiv : the preprint server for biology | 40661523 | bioRxiv | 2025 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/40661523 |
| Innate immune Galectin-7 specifically targets microbes that decorate themselves in blood group-like antigens. | Wu SC, Kamili NA, Dias-Baruffi M, Josephson CD, Rathgeber MF, Yeung MY, Lane WJ, Wang J, Jan HM, Rakoff-Nahoum S, Cummings RD, Stowell SR, Arthur CM | iScience | 35754739 | iScience | 2022 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/35754739 |
| 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 |
| Galectin-4 Antimicrobial Activity Primarily Occurs Through its C-Terminal Domain. | Jan HM, Wu SC, Stowell CJ, Vallecillo-Zúniga ML, Paul A, Patel KR, Muthusamy S, Lin HY, Ayona D, Jajosky RP, Varadkar SP, Nakahara H, Chan R, Bhave D, Lane WJ, Yeung MY, Hollenhorst MA, Rakoff-Nahoum S, Cummings RD, Arthur CM, Stowell SR | Molecular & cellular proteomics : MCP | 38490531 | Mol Cell Proteomics | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38490531 |
| Functional diversification of dietary plant small molecules by the gut microbiome. | Kuziel GA, Lozano GL, Simian C, Li L, Manion J, Stephen-Victor E, Chatila T, Dong M, Weng JK, Rakoff-Nahoum S | Cell | 40056901 | Cell | 2025 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/40056901 |
| Veni, vidi, vici: the success of wtf meiotic drivers in fission yeast. | López Hernández JF, Zanders SE | Yeast (Chichester, England) | 29322557 | Yeast | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29322557 |
| Gene conversion generates evolutionary novelty that fuels genetic conflicts. | Daugherty MD, Zanders SE | Current opinion in genetics & development | 31466040 | Curr Opin Genet Dev | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31466040 |
| Molecular Mechanisms and Evolutionary Consequences of Spore Killers in Ascomycetes. | Zanders S, Johannesson H | Microbiology and molecular biology reviews : MMBR | 34756084 | Microbiol Mol Biol Rev | 2021 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/34756084 |
| Landscape of essential growth and fluconazole-resistance genes in the human fungal pathogen Cryptococcus neoformans. | Billmyre RB, Craig CJ, Lyon JW, Reichardt C, Kuhn AM, Eickbush MT, Zanders SE | PLoS biology | 40402997 | PLoS Biol | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40402997 |
| Functional constraints of wtf killer meiotic drivers. | Nidamangala Srinivasa A, Campbell S, Venkatesan S, Nuckolls NL, Lange JJ, Halfmann R, Zanders SE | PLoS genetics | 39965018 | PLoS Genet | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39965018 |
| wtf genes are prolific dual poison-antidote meiotic drivers. | Nuckolls NL, Bravo Núñez MA, Eickbush MT, Young JM, Lange JJ, Yu JS, Smith GR, Jaspersen SL, Malik HS, Zanders SE | eLife | 28631612 | Elife | 2017 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/28631612 |
| Genome-wide quantification of contributions to sexual fitness identifies genes required for spore viability and health in fission yeast. | Billmyre RB, Eickbush MT, Craig CJ, Lange JJ, Wood C, Helston RM, Zanders SE | PLoS genetics | 36301993 | PLoS Genet | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36301993 |
| Meiotic drive. | Srinivasa AN, Zanders SE | Current biology : CB | 32516606 | Curr Biol | 2020 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/32516606 |
| Dramatically diverse Schizosaccharomyces pombe wtf meiotic drivers all display high gamete-killing efficiency. | Bravo Núñez MA, Sabbarini IM, Eickbush MT, Liang Y, Lange JJ, Kent AM, Zanders SE | PLoS genetics | 32032353 | PLoS Genet | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32032353 |
| S. pombe wtf drivers use dual transcriptional regulation and selective protein exclusion from spores to cause meiotic drive. | Nuckolls NL, Nidamangala Srinivasa A, Mok AC, Helston RM, Bravo Núñez MA, Lange JJ, Gallagher TJ, Seidel CW, Zanders SE | PLoS genetics | 36477651 | PLoS Genet | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36477651 |
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| A suppressor of a wtf poison-antidote meiotic driver acts via mimicry of the driver's antidote. | Bravo Núñez MA, Lange JJ, Zanders SE | PLoS genetics | 30475921 | PLoS Genet | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30475921 |
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| Diverse mating phenotypes impact the spread of wtf meiotic drivers in Schizosaccharomyces pombe. | López Hernández JF, Helston RM, Lange JJ, Billmyre RB, Schaffner SH, Eickbush MT, McCroskey S, Zanders SE | eLife | 34895466 | Elife | 2021 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/34895466 |
| The wtf meiotic driver gene family has unexpectedly persisted for over 100 million years. | De Carvalho M, Jia GS, Nidamangala Srinivasa A, Billmyre RB, Xu YH, Lange JJ, Sabbarini IM, Du LL, Zanders SE | eLife | 36227631 | Elife | 2022 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/36227631 |
| 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 |
| What can we learn from selfish loci that break Mendel's law? | Zanders SE | PLoS biology | 35853012 | PLoS Biol | 2022 Jul | https://www.ncbi.nlm.nih.gov/pubmed/35853012 |
| Modeling the evolution of Schizosaccharomyces pombe populations with multiple killer meiotic drivers. | López Hernández JF, Rubinstein BY, Unckless RL, Zanders SE | G3 (Bethesda, Md.) | 38938172 | G3 (Bethesda) | 2024 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/38938172 |
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| Atypical meiosis can be adaptive in outcrossed Schizosaccharomyces pombe due to wtf meiotic drivers. | Bravo Núñez MA, Sabbarini IM, Eide LE, Unckless RL, Zanders SE | eLife | 32790622 | Elife | 2020 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/32790622 |
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| Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. | Rajpurkar AR, Mateo LJ, Murphy SE, Boettiger AN | Nature communications | 34103507 | Nat Commun | 2021 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/34103507 |
| mSWI/SNF promotes Polycomb repression both directly and through genome-wide redistribution. | Weber CM, Hafner A, Kirkland JG, Braun SMG, Stanton BZ, Boettiger AN, Crabtree GR | Nature structural & molecular biology | 34117481 | Nat Struct Mol Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34117481 |
| Visualizing DNA folding and RNA in embryos at single-cell resolution. | Mateo LJ, Murphy SE, Hafner A, Cinquini IS, Walker CA, Boettiger AN | Nature | 30886393 | Nature | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30886393 |
| Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. | Mateo LJ, Sinnott-Armstrong N, Boettiger AN | Nature protocols | 33619390 | Nat Protoc | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33619390 |
| How subtle changes in 3D structure can create large changes in transcription. | Xiao JY, Hafner A, Boettiger AN | eLife | 34240703 | Elife | 2021 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/34240703 |
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| Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus. | Chen LF, Long HK, Park M, Swigut T, Boettiger AN, Wysocka J | Molecular cell | 36996812 | Mol Cell | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/36996812 |
| The Future Application of Organ-on-a-Chip Technologies as Proving Grounds for MicroBioRobots. | Fuller HC, Wei TY, Behrens MR, Ruder WC | Micromachines | 33092054 | Micromachines (Basel) | 2020 Oct 20 | https://www.ncbi.nlm.nih.gov/pubmed/33092054 |
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| Open-source, 3D-printed Peristaltic Pumps for Small Volume Point-of-Care Liquid Handling. | Behrens MR, Fuller HC, Swist ER, Wu J, Islam MM, Long Z, Ruder WC, Steward R Jr | Scientific reports | 32005961 | Sci Rep | 2020 Jan 31 | https://www.ncbi.nlm.nih.gov/pubmed/32005961 |
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| The Warburg Effect is the result of faster ATP production by glycolysis than respiration. | Kukurugya MA, Rosset S, Titov DV | Proceedings of the National Academy of Sciences of the United States of America | 39514306 | Proc Natl Acad Sci U S A | 2024 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/39514306 |
| Distinct mitochondrial defects trigger the integrated stress response depending on the metabolic state of the cell. | Mick E, Titov DV, Skinner OS, Sharma R, Jourdain AA, Mootha VK | eLife | 32463360 | Elife | 2020 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/32463360 |
| Genetically encoded tool for manipulation of ΔΨm identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction. | Choe M, Titov DV | bioRxiv : the preprint server for biology | 38234735 | bioRxiv | 2023 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/38234735 |
| SRS microscopy identifies inhibition of vitellogenesis as a mediator of lifespan extension by caloric restriction in C. elegans. | Yang B, Manifold B, Han W, DeSousa C, Zhu W, Streets A, Titov DV | bioRxiv : the preprint server for biology | 40034647 | bioRxiv | 2025 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/40034647 |
| Physical bioenergetics: Energy fluxes, budgets, and constraints in cells. | Yang X, Heinemann M, Howard J, Huber G, Iyer-Biswas S, Le Treut G, Lynch M, Montooth KL, Needleman DJ, Pigolotti S, Rodenfels J, Ronceray P, Shankar S, Tavassoly I, Thutupalli S, Titov DV, Wang J, Foster PJ | Proceedings of the National Academy of Sciences of the United States of America | 34140336 | Proc Natl Acad Sci U S A | 2021 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/34140336 |
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| Listeria monocytogenes requires cellular respiration for NAD(+) regeneration and pathogenesis. | Rivera-Lugo R, Deng D, Anaya-Sanchez A, Tejedor-Sanz S, Tang E, Reyes Ruiz VM, Smith HB, Titov DV, Sauer JD, Skaar EP, Ajo-Franklin CM, Portnoy DA, Light SH | eLife | 35380108 | Elife | 2022 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/35380108 |
| A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X. | Jowhar Z, Xu A, Venkataramanan S, Dossena F, Hoye ML, Silver DL, Floor SN, Calviello L | Molecular systems biology | 38273160 | Mol Syst Biol | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38273160 |
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| 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 |
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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 |
| 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 |
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| Pathogenic DDX3X Mutations Impair RNA Metabolism and Neurogenesis during Fetal Cortical Development. | Lennox AL, Hoye ML, Jiang R, Johnson-Kerner BL, Suit LA, Venkataramanan S, Sheehan CJ, Alsina FC, Fregeau B, Aldinger KA, Moey C, Lobach I, Afenjar A, Babovic-Vuksanovic D, Bézieau S, Blackburn PR, Bunt J, Burglen L, Campeau PM, Charles P, Chung BHY, Cogné B, Curry C, D'Agostino MD, Di Donato N, Faivre L, Héron D, Innes AM, Isidor B, Keren B, Kimball A, Klee EW, Kuentz P, Küry S, Martin-Coignard D, Mirzaa G, Mignot C, Miyake N, Matsumoto N, Fujita A, Nava C, Nizon M, Rodriguez D, Blok LS, Thauvin-Robinet C, Thevenon J, Vincent M, Ziegler A, Dobyns W, Richards LJ, Barkovich AJ, Floor SN, Silver DL, Sherr EH | Neuron | 32135084 | Neuron | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/32135084 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Coding functions of "noncoding" RNAs. | Wei LH, Guo JU | Science (New York, N.Y.) | 32139529 | Science | 2020 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/32139529 |
| C9orf72 arginine-rich dipeptide repeats inhibit UPF1-mediated RNA decay via translational repression. | Sun Y, Eshov A, Zhou J, Isiktas AU, Guo JU | Nature communications | 32620797 | Nat Commun | 2020 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/32620797 |
| 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 |
| Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. | Lee PJ, Sun Y, Soares AR, Fai C, Picciotto MR, Guo JU | Molecular cell | 39317199 | Mol Cell | 2024 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/39317199 |
| Aberrant splicing exonizes C9orf72 repeat expansion in ALS/FTD. | Yang S, Wijegunawardana D, Sheth U, Veire AM, Salgado JMS, Arab T, Agrawal M, Zhou J, Pereira JD, Gendron TF, Guo JU | Nature neuroscience | 40790269 | Nat Neurosci | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40790269 |
| 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 |
| Regulation of nonsense-mediated mRNA decay in neural development and disease. | Lee PJ, Yang S, Sun Y, Guo JU | Journal of molecular cell biology | 33783512 | J Mol Cell Biol | 2021 Aug 4 | https://www.ncbi.nlm.nih.gov/pubmed/33783512 |
| 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 |
| 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 |
| Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions. | Lee PJ, Soares AR, Sun Y, Fai C, Picciotto MR, Guo JU | bioRxiv : the preprint server for biology | 38405936 | bioRxiv | 2024 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/38405936 |
| 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 |
| 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 |
| Steroid Hormone Entry into the Brain Requires a Membrane Transporter in Drosophila. | Okamoto N, Yamanaka N | Current biology : CB | 31928869 | Curr Biol | 2020 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/31928869 |
| 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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| Functional characterization of eicosanoid signaling in Drosophila development. | Fujinaga D, Nolan C, Yamanaka N | PLoS genetics | 40344083 | PLoS Genet | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40344083 |
| Steroid hormone-dependent glial-neuronal interaction promotes brain development during Drosophila metamorphosis. | Imura E, Okamoto N, Yamanaka N | bioRxiv : the preprint server for biology | 41509261 | bioRxiv | 2025 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/41509261 |
| Steroid hormone signaling: What we can learn from insect models. | Okamoto N, Fujinaga D, Yamanaka N | Vitamins and hormones | 37717997 | Vitam Horm | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37717997 |
| 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 |
| Understanding, inhibiting, and engineering membrane transporters with high-throughput mutational screens. | Miller ST, Macdonald CB, Raman S | Cell chemical biology | 40168989 | Cell Chem Biol | 2025 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/40168989 |
| 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 |
| 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 |
| 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 |
| A parameterized two-domain thermodynamic model explains diverse mutational effects on protein allostery. | Liu Z, Gillis TG, Raman S, Cui Q | eLife | 38836839 | Elife | 2024 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/38836839 |
| Computation-guided redesign of promoter specificity of a bacterial RNA polymerase. | Liu X, Meger AT, Gillis T, O'Mara Schwartz J, Sah B, Landick R, Raman S | bioRxiv : the preprint server for biology | 40667222 | bioRxiv | 2025 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/40667222 |
| 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 |
| Functional plasticity and evolutionary adaptation of allosteric regulation. | Leander M, Yuan Y, Meger A, Cui Q, Raman S | Proceedings of the National Academy of Sciences of the United States of America | 32999067 | Proc Natl Acad Sci U S A | 2020 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/32999067 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| Carboranes without Cage Carbons: closo-Dodecaborate Mimics of Neutral closo-Carboranes. | Ready AD, Tej Raviprolu V, Kerr TA, Treacy JW, Matsumoto ML, Hammer PE, Sletten EM, Houk KN, Spokoyny AM | Journal of the American Chemical Society | 40643954 | J Am Chem Soc | 2025 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/40643954 |
| 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 |
| 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 |
| 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 |
| 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 |
| Achieving Olympicene Functionalization Three Ways. | Hartung KM, Sletten EM | The Journal of organic chemistry | 39698889 | J Org Chem | 2025 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/39698889 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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-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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Optical Patterning of Two-Dimensional Materials. | Kollipara PS, Li J, Zheng Y | Research (Washington, D.C.) | 32043085 | Research (Wash D C) | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32043085 |
| 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 |
| 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 |
| 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 |
| 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 |
| Opto-thermophoretic fiber tweezers. | Kotnala A, Zheng Y | Nanophotonics (Berlin, Germany) | 34290953 | Nanophotonics | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34290953 |
| 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 |
| 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 |
| Opto-Thermophoretic Manipulation and Construction of Colloidal Superstructures in Photocurable Hydrogels. | Peng X, Li J, Lin L, Liu Y, Zheng Y | ACS applied nano materials | 31106296 | ACS Appl Nano Mater | 2018 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/31106296 |
| 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 |
| 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 |
| 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 |
| A mixture-density-based tandem optimization network for on-demand inverse design of thin-film high reflectors. | Unni R, Yao K, Han X, Zhou M, Zheng Y | Nanophotonics (Berlin, Germany) | 36425324 | Nanophotonics | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36425324 |
| 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 |
| 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 |
| 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 |
| 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 |
| Programmable Multimodal Optothermal Manipulation of Synthetic Particles and Biological Cells. | Ding H, Chen Z, Kollipara PS, Liu Y, Kim Y, Huang S, Zheng Y | ACS nano | 35816157 | ACS Nano | 2022 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/35816157 |
| 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 |
| 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 |
| 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-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 |
| Light-driven C-H activation mediated by 2D transition metal dichalcogenides. | Li J, Zhang D, Guo Z, Jiang X, Larson JM, Zhu H, Zhang T, Gu Y, Blankenship B, Chen M, Wu Z, Huang S, Kostecki R, Minor AM, Grigoropoulos CP, Akinwande D, Terrones M, Redwing JM, Li H, Zheng Y | Research square | 38260621 | Res Sq | 2024 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/38260621 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Opto-Thermocapillary Nanomotors on Solid Substrates. | Li J, Kollipara PS, Liu Y, Yao K, Liu Y, Zheng Y | ACS nano | 35594375 | ACS Nano | 2022 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/35594375 |
| Investigating water/oil interfaces with opto-thermophoresis. | Kim Y, Ding H, Zheng Y | Nature communications | 35768421 | Nat Commun | 2022 Jun 29 | https://www.ncbi.nlm.nih.gov/pubmed/35768421 |
| The shape of pleomorphic virions determines resistance to cell-entry pressure. | Li T, Li Z, Deans EE, Mittler E, Liu M, Chandran K, Ivanovic T | Nature microbiology | 33737748 | Nat Microbiol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33737748 |
| Hemagglutinin Stability Determines Influenza A Virus Susceptibility to a Broad-Spectrum Fusion Inhibitor Arbidol. | Li Z, Li T, Liu M, Ivanovic T | ACS infectious diseases | 35819162 | ACS Infect Dis | 2022 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/35819162 |
| Influenza A virus rapidly adapts particle shape to environmental pressures. | Partlow EA, Jaeggi-Wong A, Planitzer SD, Berg N, Li Z, Ivanovic T | Nature microbiology | 39929974 | Nat Microbiol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39929974 |
| Using Gjd3-CreEGFP mice to examine atrioventricular node morphology and composition. | Bhattacharyya S, Duan J, Wang L, Li B, Bhakta M, Fernandez-Perez A, Hon GC, Munshi NV | Scientific reports | 30765799 | Sci Rep | 2019 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/30765799 |
| Rational Reprogramming of Cellular States by Combinatorial Perturbation. | Duan J, Li B, Bhakta M, Xie S, Zhou P, Munshi NV, Hon GC | Cell reports | 31216470 | Cell Rep | 2019 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/31216470 |
| Identification of functionally distinct fibro-inflammatory and adipogenic stromal subpopulations in visceral adipose tissue of adult mice. | Hepler C, Shan B, Zhang Q, Henry GH, Shao M, Vishvanath L, Ghaben AL, Mobley AB, Strand D, Hon GC, Gupta RK | eLife | 30265241 | Elife | 2018 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/30265241 |
| Computational identification of clonal cells in single-cell CRISPR screens. | Wang Y, Xie S, Armendariz D, Hon GC | BMC genomics | 35168568 | BMC Genomics | 2022 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/35168568 |
| Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules. | Xie S, Armendariz D, Zhou P, Duan J, Hon GC | Cell reports | 31775028 | Cell Rep | 2019 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/31775028 |
| A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. | Henry GH, Malewska A, Joseph DB, Malladi VS, Lee J, Torrealba J, Mauck RJ, Gahan JC, Raj GV, Roehrborn CG, Hon GC, MacConmara MP, Reese JC, Hutchinson RC, Vezina CM, Strand DW | Cell reports | 30566875 | Cell Rep | 2018 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/30566875 |
| Experimental and Computational Approaches for Single-Cell Enhancer Perturbation Assay. | Xie S, Hon GC | Methods in molecular biology (Clifton, N.J.) | 30758829 | Methods Mol Biol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30758829 |
| CHD-associated enhancers shape human cardiomyocyte lineage commitment. | Armendariz DA, Goetsch SC, Sundarrajan A, Sivakumar S, Wang Y, Xie S, Munshi NV, Hon GC | eLife | 37096669 | Elife | 2023 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/37096669 |
| Dynamic states of cervical epithelia during pregnancy and epithelial barrier disruption. | Cooley A, Madhukaran S, Stroebele E, Colon Caraballo M, Wang L, Akgul Y, Hon GC, Mahendroo M | iScience | 36718364 | iScience | 2023 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/36718364 |
| A single factor elicits multilineage reprogramming of astrocytes in the adult mouse striatum. | Zhang Y, Li B, Cananzi S, Han C, Wang LL, Zou Y, Fu YX, Hon GC, Zhang CL | Proceedings of the National Academy of Sciences of the United States of America | 35254903 | Proc Natl Acad Sci U S A | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/35254903 |
| Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes. | Wang Y, Armendariz D, Wang L, Zhao H, Xie S, Hon GC | bioRxiv : the preprint server for biology | 38045327 | bioRxiv | 2023 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/38045327 |
| Benchmarking and optimizing Perturb-seq in differentiating human pluripotent stem cells. | Sivakumar S, Wang Y, Goetsch SC, Pandit V, Wang L, Zhao H, Sundarrajan A, Armendariz D, Takeuchi C, Nzima M, Chen WC, Dederich AE, El Hayek L, Gao T, Ghazawi R, Gogate A, Kaur K, Kim HB, McCoy MK, Niederstrasser H, Oura S, Pinzon-Arteaga CA, Sanghvi M, Schmitz DA, Yu L, Zhang Y, Zhou Q, Kraus WL, Xu L, Wu J, Posner BA, Chahrour MH, Hon GC, Munshi NV | bioRxiv : the preprint server for biology | 39896670 | bioRxiv | 2025 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/39896670 |
| Accurate Classification of Cardiomyopathy Diagnosis by Chromatin Accessibility. | Bhattacharyya S, Duan J, Vela RJ, Bhakta M, Bajona P, Mammen PPA, Hon GC, Munshi NV | Circulation | 36095061 | Circulation | 2022 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/36095061 |
| Breaking enhancers to gain insights into developmental defects. | Armendariz DA, Sundarrajan A, Hon GC | eLife | 37497775 | Elife | 2023 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/37497775 |
| FBA: feature barcoding analysis for single cell RNA-Seq. | Duan J, Hon GC | Bioinformatics (Oxford, England) | 33999185 | Bioinformatics | 2021 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/33999185 |
| Single-Cell Genomics: Catalyst for Cell Fate Engineering. | Li B, Hon GC | Frontiers in bioengineering and biotechnology | 34733831 | Front Bioeng Biotechnol | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34733831 |
| SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples. | Zhang Z, Luo D, Zhong X, Choi JH, Ma Y, Wang S, Mahrt E, Guo W, Stawiski EW, Modrusan Z, Seshagiri S, Kapur P, Hon GC, Brugarolas J, Wang T | Genes | 31336988 | Genes (Basel) | 2019 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/31336988 |
| Frequent sgRNA-barcode recombination in single-cell perturbation assays. | Xie S, Cooley A, Armendariz D, Zhou P, Hon GC | PloS one | 29874289 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29874289 |
| Rapid local adaptation linked with phenotypic plasticity. | Sun SJ, Catherall AM, Pascoal S, Jarrett BJM, Miller SE, Sheehan MJ, Kilner RM | Evolution letters | 32774883 | Evol Lett | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32774883 |
| Dynamic neurogenomic responses to social interactions and dominance outcomes in female paper wasps. | Uy FMK, Jernigan CM, Zaba NC, Mehrotra E, Miller SE, Sheehan MJ | PLoS genetics | 34478434 | PLoS Genet | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34478434 |
| The promises and challenges of archiving insect behavior and natural history in a changing world. | Sheehan MJ, Miller SE | Current opinion in insect science | 33857642 | Curr Opin Insect Sci | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33857642 |
| Sex differences in deleterious genetic variants in a haplodiploid social insect. | Miller SE, Sheehan MJ | Molecular ecology | 37350360 | Mol Ecol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37350360 |
| Evidence for a selective link between cooperation and individual recognition. | Tumulty JP, Miller SE, Van Belleghem SM, Weller HI, Jernigan CM, Vincent S, Staudenraus RJ, Legan AW, Polnaszek TJ, Uy FMK, Walton A, Sheehan MJ | Current biology : CB | 38065097 | Curr Biol | 2023 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/38065097 |
| Fine-Scale Population Structure but Limited Genetic Differentiation in a Cooperatively Breeding Paper Wasp. | Bluher SE, Miller SE, Sheehan MJ | Genome biology and evolution | 32271866 | Genome Biol Evol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32271866 |
| Evolutionary dynamics of recent selection on cognitive abilities. | Miller SE, Legan AW, Henshaw MT, Ostevik KL, Samuk K, Uy FMK, Sheehan MJ | Proceedings of the National Academy of Sciences of the United States of America | 31980529 | Proc Natl Acad Sci U S A | 2020 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/31980529 |
| Hormonal modulation of reproduction in Polistes fuscatus social wasps: Dual functions in both ovary development and sexual receptivity. | Walton A, Tumulty JP, Toth AL, Sheehan MJ | Journal of insect physiology | 31705844 | J Insect Physiol | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31705844 |
| Age and social experience induced plasticity across brain regions of the paper wasp Polistes fuscatus. | Jernigan CM, Zaba NC, Sheehan MJ | Biology letters | 33849349 | Biol Lett | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33849349 |
| WASPnest: a worldwide assessment of social Polistine nesting behavior. | Miller SE, Bluher SE, Bell E, Cini A, Silva RCD, de Souza AR, Gandia KM, Jandt J, Loope K, Prato A, Pruitt JN, Rankin D, Rankin E, Southon RJ, Uy FMK, Weiner S, Wright CM, Downing H, Gadagkar R, Cristina Lorenzi M, Rusina L, Sumner S, Tibbetts EA, Toth A, Sheehan MJ | Ecology | 29999519 | Ecology | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29999519 |
| Evolutionarily stable investments in recognition systems explain patterns of discrimination failure and success. | Sheehan MJ, Reeve HK | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 32420853 | Philos Trans R Soc Lond B Biol Sci | 2020 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/32420853 |
| Coevolution of cognitive abilities and identity signals in individual recognition systems. | Miller SE, Sheehan MJ, Reeve HK | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 32420843 | Philos Trans R Soc Lond B Biol Sci | 2020 Jul 6 | https://www.ncbi.nlm.nih.gov/pubmed/32420843 |
| Color is necessary for face discrimination in the Northern paper wasp, Polistes fuscatus. | Jernigan CM, Stafstrom JA, Zaba NC, Vogt CC, Sheehan MJ | Animal cognition | 36245014 | Anim Cogn | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36245014 |
| Expansion and Accelerated Evolution of 9-Exon Odorant Receptors in Polistes Paper Wasps. | Legan AW, Jernigan CM, Miller SE, Fuchs MF, Sheehan MJ | Molecular biology and evolution | 34151983 | Mol Biol Evol | 2021 Aug 23 | https://www.ncbi.nlm.nih.gov/pubmed/34151983 |
| Animal Behavior: Socially Distanced Wasps Learn About Rivals. | Sheehan MJ, Goldberg J | Current biology : CB | 32750347 | Curr Biol | 2020 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/32750347 |
| Distinct evolutionary trajectories of V1R clades across mouse species. | Miller CH, Campbell P, Sheehan MJ | BMC evolutionary biology | 32770934 | BMC Evol Biol | 2020 Aug 8 | https://www.ncbi.nlm.nih.gov/pubmed/32770934 |
| Strong, but incomplete, mate choice discrimination between two closely related species of paper wasp. | Miller SE, Legan AW, Flores ZA, Ng HY, Sheehan MJ | Biological journal of the Linnean Society. Linnean Society of London | 30853716 | Biol J Linn Soc Lond | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30853716 |
| Highly Contiguous Genome Assemblies of the Guinea Paper Wasp (Polistes exclamans) and Mischocyttarus mexicanus. | Miller SE, Legan AW, Uy FMK, Sheehan MJ | Genome biology and evolution | 35880292 | Genome Biol Evol | 2022 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/35880292 |
| Postural analysis reveals persistent changes in paper wasp foundress behavioral state after conspecific challenge. | Legan AW, Vogt CC, Sheehan MJ | Ecology and evolution | 37664514 | Ecol Evol | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37664514 |
| Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins. | Franklin MW, Nepomnyachyi S, Feehan R, Ben-Tal N, Kolodny R, Slusky JS | eLife | 30489257 | Elife | 2018 Nov 29 | https://www.ncbi.nlm.nih.gov/pubmed/30489257 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Evolutionary engineering a larger porin using a loop-to-hairpin mechanism. | Dhar R, Bowman AM, Hatungimana B, Slusky JS | bioRxiv : the preprint server for biology | 37398247 | bioRxiv | 2023 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/37398247 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Detergent headgroups control TolC folding in vitro. | Ikujuni AP, Budiardjo SJ, Dhar R, Slusky JSG | Biophysical journal | 36772796 | Biophys J | 2023 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/36772796 |
| 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 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Single-cell chemoproteomics identifies metastatic activity signatures in breast cancer. | Smitha Pillai K, Laxton O, Li G, Lin J, Karginova O, Nanda R, Olopade OI, Tay S, Moellering RE | Science advances | 39441940 | Sci Adv | 2024 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/39441940 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
| 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 |
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| 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 |
| Linker histone regulates the myeloid versus lymphoid bifurcation of multipotent hematopoietic stem and progenitors. | Karatepe K, Mafra de Faria B, Zhang J, Chen X, Pinto H, Fyodorov D, Sefik E, Willcockson MA, Flavell RA, Skoultchi AI, Guo S | Proceedings of the National Academy of Sciences of the United States of America | 41118213 | Proc Natl Acad Sci U S A | 2025 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/41118213 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Increasing proteomics throughput. | Slavov N | Nature biotechnology | 33767394 | Nat Biotechnol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33767394 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Proteome asymmetry in mouse and human embryos before fate specification. | Iwamoto-Stohl LK, Petelski AA, Meglicki M, Fu A, Khan S, Specht H, Huffman G, Derks J, Jorgensen V, Weatherbee BAT, Weberling A, Gantner CW, Mandelbaum RS, Paulson RJ, Lam L, Ahmady A, Vasquez ES, Slavov N, Zernicka-Goetz M | bioRxiv : the preprint server for biology | 39253500 | bioRxiv | 2024 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/39253500 |
| Fertilization triggers early proteomic symmetry breaking in mammalian embryos. | Iwamoto-Stohl LK, Petelski AA, Quan B, Meglicki M, Fu A, Nakagawa S, McMahon B, Wang TY, Khan S, Specht H, Huffman G, Derks J, Junyent S, Weatherbee BAT, Weberling A, Gantner CW, Mandelbaum RS, Paulson RJ, Lam L, Chou TF, Slavov N, Zernicka-Goetz M | Cell | 41344326 | Cell | 2025 Dec 24 | https://www.ncbi.nlm.nih.gov/pubmed/41344326 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. | Kennedy DR, Lemière J, Amine AA, Martin EW, Tan C, Simental E, Braxton J, Maxwell RA, Al-Sady B | bioRxiv : the preprint server for biology | 39554105 | bioRxiv | 2025 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/39554105 |
| Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading. | Kennedy DR, Lemière J, Amine AAA, Martin EW, Tan C, Simental E, Braxton J, Maxwell RA, Al-Sady B | Nucleic acids research | 41385327 | Nucleic Acids Res | 2025 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/41385327 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Sparse Bayesian Group Factor Model for Feature Interactions in Multiple Count Tables Data. | Zhang S, Shen Y, Chen IA, Lee J | Journal of the American Statistical Association | 40678201 | J Am Stat Assoc | 2025 | https://www.ncbi.nlm.nih.gov/pubmed/40678201 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| A genome-to-proteome map reveals how natural variants drive proteome diversity and shape fitness. | Jakobson CM, Hartl J, Trébulle P, Mülleder M, Jarosz DF, Ralser M | Science (New York, N.Y.) | 41066569 | Science | 2025 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/41066569 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation. | Aguilar-Rodriguez J, Vila JCC, Chen SA, Razo-Mejia M, Ghosh OM, Jarosz DF, Fraser HB, Petrov DA | bioRxiv : the preprint server for biology | 39553990 | bioRxiv | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/39553990 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Stress-driven emergence of heritable non-genetic drug resistance. | Xie JL, Yin S, Yang TS, Chandrasekher K, Hanson L, Kim SH, Esqueda L, Hogan CA, Banaei N, Round JL, Ost KS, Berman J, Jarosz DF | Research square | 41356366 | Res Sq | 2025 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/41356366 |
| Protein structure shapes natural genetic variation and de novo adaptation. | Jakobson CM, Van Elgort A, Aguilar-Rodríguez J, Jarosz DF | bioRxiv : the preprint server for biology | 41509306 | bioRxiv | 2025 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/41509306 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| Beyond the Triplet Code: Context Cues Transform Translation. | Brar GA | Cell | 27984720 | Cell | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27984720 |
| 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 |
| 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 |
| 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 |
| 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 |
| Increasing the uptake of carbon dioxide. | Franklin E, Jonikas M | eLife | 33270556 | Elife | 2020 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/33270556 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| SCML2 promotes heterochromatin organization in late spermatogenesis. | Maezawa S, Hasegawa K, Alavattam KG, Funakoshi M, Sato T, Barski A, Namekawa SH | Journal of cell science | 30097555 | J Cell Sci | 2018 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/30097555 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| 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 |
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| 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 |
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| 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 |
| 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 |
| 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 |
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| 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| TrueSpot: a robust automated tool for quantifying signal puncta in fluorescent imaging. | Hospelhorn BG, Kesler BK, Jashnsaz H, Neuert G | Genome biology | 41024246 | Genome Biol | 2025 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/41024246 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Transcriptional stochasticity reveals multiple mechanisms of long non-coding RNA regulation at the Xist-Tsix locus. | Kesler BK, Adams J, Neuert G | Nature communications | 40328749 | Nat Commun | 2025 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/40328749 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
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| miR-155 promotes T follicular helper cell accumulation during chronic, low-grade inflammation. | Hu R, Kagele DA, Huffaker TB, Runtsch MC, Alexander M, Liu J, Bake E, Su W, Williams MA, Rao DS, Möller T, Garden GA, Round JL, O'Connell RM | Immunity | 25367574 | Immunity | 2014 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/25367574 |
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| Rab27-Dependent Exosome Production Inhibits Chronic Inflammation and Enables Acute Responses to Inflammatory Stimuli. | Alexander M, Ramstead AG, Bauer KM, Lee SH, Runtsch MC, Wallace J, Huffaker TB, Larsen DK, Tolmachova T, Seabra MC, Round JL, Ward DM, O'Connell RM | Journal of immunology (Baltimore, Md. : 1950) | 28978688 | J Immunol | 2017 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/28978688 |
| Colitis reduces active social engagement in mice and is ameliorated by supplementation with human microbiota members. | Brown DG, Murphy M, Cadeddu R, Bell R, Weis A, Chiaro T, Klag K, Morgan J, Coon H, Stephens WZ, Bortolato M, Round JL | Nature communications | 38553486 | Nat Commun | 2024 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/38553486 |
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| Genome-Wide CRISPR-Cas9 Screen Identifies MicroRNAs That Regulate Myeloid Leukemia Cell Growth. | Wallace J, Hu R, Mosbruger TL, Dahlem TJ, Stephens WZ, Rao DS, Round JL, O'Connell RM | PloS one | 27081855 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27081855 |
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| Expansion of Bacteriophages Is Linked to Aggravated Intestinal Inflammation and Colitis. | Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, Porter N, Martens E, O'Connell R, Jacob V, Scherl E, Crawford C, Stephens WZ, Casjens SR, Longman RS, Round JL | Cell host & microbe | 30763538 | Cell Host Microbe | 2019 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/30763538 |
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| Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. | Watters KE, Abbott TR, Lucks JB | Nucleic acids research | 26350218 | Nucleic Acids Res | 2016 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/26350218 |
| Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq). | Watters KE, Lucks JB | Methods in molecular biology (Clifton, N.J.) | 27665597 | Methods Mol Biol | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27665597 |
| Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. | Yu AM, Gasper PM, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA, Lucks JB | Molecular cell | 33453165 | Mol Cell | 2021 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/33453165 |
| DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. | Xue AY, Yu AM, Lucks JB, Bagheri N | Bioinformatics (Oxford, England) | 31389563 | Bioinformatics | 2019 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/31389563 |
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| Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). | Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB | Methods (San Diego, Calif.) | 27064082 | Methods | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/27064082 |
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| A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. | Strobel EJ, Cheng L, Berman KE, Carlson PD, Lucks JB | Nature chemical biology | 31636437 | Nat Chem Biol | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31636437 |
| Computational design of three-dimensional RNA structure and function. | Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R | Nature nanotechnology | 31427748 | Nat Nanotechnol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31427748 |
| Choosing the right pharmacotherapeutic strategy for HIV maintenance in patients with alcohol addiction. | Kodidela S, Kumar S | Expert opinion on pharmacotherapy | 30724618 | Expert Opin Pharmacother | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30724618 |
| Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. | Strobel EJ, Watters KE, Nedialkov Y, Artsimovitch I, Lucks JB | Nucleic acids research | 28398514 | Nucleic Acids Res | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28398514 |
| Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer. | Meyer S, Carlson PD, Lucks JB | Biochemistry | 29172455 | Biochemistry | 2017 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/29172455 |
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| The B. subtilis Accessory Helicase PcrA Facilitates DNA Replication through Transcription Units. | Merrikh CN, Brewer BJ, Merrikh H | PLoS genetics | 26070154 | PLoS Genet | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26070154 |
| An underlying mechanism for the increased mutagenesis of lagging-strand genes in Bacillus subtilis. | Million-Weaver S, Samadpour AN, Moreno-Habel DA, Nugent P, Brittnacher MJ, Weiss E, Hayden HS, Miller SI, Liachko I, Merrikh H | Proceedings of the National Academy of Sciences of the United States of America | 25713353 | Proc Natl Acad Sci U S A | 2015 Mar 10 | https://www.ncbi.nlm.nih.gov/pubmed/25713353 |
| Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis. | Lang KS, Hall AN, Merrikh CN, Ragheb M, Tabakh H, Pollock AJ, Woodward JJ, Dreifus JE, Merrikh H | Cell | 28802046 | Cell | 2017 Aug 10 | https://www.ncbi.nlm.nih.gov/pubmed/28802046 |
| Replication Restart after Replication-Transcription Conflicts Requires RecA in Bacillus subtilis. | Million-Weaver S, Samadpour AN, Merrikh H | Journal of bacteriology | 25939832 | J Bacteriol | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25939832 |
| The Accelerated Evolution of Lagging Strand Genes Is Independent of Sequence Context. | Merrikh CN, Weiss E, Merrikh H | Genome biology and evolution | 28039230 | Genome Biol Evol | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/28039230 |
| Spatial and Temporal Control of Evolution through Replication-Transcription Conflicts. | Merrikh H | Trends in microbiology | 28216294 | Trends Microbiol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28216294 |
| The bacterial replisome has factory-like localization. | Mangiameli SM, Cass JA, Merrikh H, Wiggins PA | Current genetics | 29632994 | Curr Genet | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/29632994 |
| The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria. | Lang KS, Merrikh H | Annual review of microbiology | 29856930 | Annu Rev Microbiol | 2018 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/29856930 |
| Inhibiting the Evolution of Antibiotic Resistance. | Ragheb MN, Thomason MK, Hsu C, Nugent P, Gage J, Samadpour AN, Kariisa A, Merrikh CN, Miller SI, Sherman DR, Merrikh H | Molecular cell | 30449724 | Mol Cell | 2019 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/30449724 |
| Gene inversion potentiates bacterial evolvability and virulence. | Merrikh CN, Merrikh H | Nature communications | 30405125 | Nat Commun | 2018 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/30405125 |
| Crystal structure of a membrane-bound O-acyltransferase. | Ma D, Wang Z, Merrikh CN, Lang KS, Lu P, Li X, Merrikh H, Rao Z, Xu W | Nature | 30283133 | Nature | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30283133 |
| Topological stress is responsible for the detrimental outcomes of head-on replication-transcription conflicts. | Lang KS, Merrikh H | Cell reports | 33657379 | Cell Rep | 2021 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/33657379 |
| DNA gyrase activity regulates DnaA-dependent replication initiation in Bacillus subtilis. | Samadpour AN, Merrikh H | Molecular microbiology | 29396913 | Mol Microbiol | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29396913 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Structural and functional studies of membrane remodeling machines. | Kalia R, Talledge N, Frost A | Methods in cell biology | 25997348 | Methods Cell Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25997348 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut. | Lim B, Zimmermann M, Barry NA, Goodman AL | Cell | 28431252 | Cell | 2017 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/28431252 |
| Gut microbiota. Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation. | Cullen TW, Schofield WB, Barry NA, Putnam EE, Rundell EA, Trent MS, Degnan PH, Booth CJ, Yu H, Goodman AL | Science (New York, N.Y.) | 25574022 | Science | 2015 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/25574022 |
| A type VI secretion-related pathway in Bacteroidetes mediates interbacterial antagonism. | Russell AB, Wexler AG, Harding BN, Whitney JC, Bohn AJ, Goo YA, Tran BQ, Barry NA, Zheng H, Peterson SB, Chou S, Gonen T, Goodlett DR, Goodman AL, Mougous JD | Cell host & microbe | 25070807 | Cell Host Microbe | 2014 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/25070807 |
| Separating host and microbiome contributions to drug pharmacokinetics and toxicity. | Zimmermann M, Zimmermann-Kogadeeva M, Wegmann R, Goodman AL | Science (New York, N.Y.) | 30733391 | Science | 2019 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/30733391 |
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| Mechanisms of Toll-like Receptor 4 Endocytosis Reveal a Common Immune-Evasion Strategy Used by Pathogenic and Commensal Bacteria. | Tan Y, Zanoni I, Cullen TW, Goodman AL, Kagan JC | Immunity | 26546281 | Immunity | 2015 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/26546281 |
| 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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| The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. | Schofield WB, Zimmermann-Kogadeeva M, Zimmermann M, Barry NA, Goodman AL | Cell host & microbe | 30008292 | Cell Host Microbe | 2018 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/30008292 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| High-throughput Flow Cytometry Assay to Investigate TDP43 Splicing Function. | Schmidt HB, Rohatgi R | Bio-protocol | 33659560 | Bio Protoc | 2020 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/33659560 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Manganese transporter genetics and sex modify the association between environmental manganese exposure and neurobehavioral outcomes in children. | Broberg K, Taj T, Guazzetti S, Peli M, Cagna G, Pineda D, Placidi D, Wright RO, Smith DR, Lucchini RG, Wahlberg K | Environment international | 31233999 | Environ Int | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31233999 |
| Modeling the health effects of time-varying complex environmental mixtures: Mean field variational Bayes for lagged kernel machine regression. | Liu SH, Bobb JF, Claus Henn B, Schnaas L, Tellez-Rojo MM, Gennings C, Arora M, Wright RO, Coull BA, Wand MP | Environmetrics | 30686915 | Environmetrics | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30686915 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Multitarget neurostimulation of the deep brain: clinical opportunities, challenges, and emerging technologies. | Del Sesto MJ, Negoita S, Bruzzone Giraldez M, LaJoie Z, Akhter Sathi K, Wong JK, Widge AS, Okun MS, Khalifa A | Journal of neural engineering | 40967240 | J Neural Eng | 2025 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/40967240 |
| A Method for Minimally-Invasive Injection of Wireless Microdevices into Brain Tissue. | Acebal C, Kainth G, Villanueva H, Hajjar A, Fuhrer V, Wanczuk P, Lim AS, Srinivasan S, Otto KJ, Khalifa A | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 40039251 | Annu Int Conf IEEE Eng Med Biol Soc | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/40039251 |
| Monitoring Gene Expression in Retina with synthetic serum markers. | Lu J, Lee S, Wang M, Zheng K, Oh SH, Lee J, Soh S, Cao Y, Bao X, Huang Y, Nouraein S, Wu Z, Szablowski JO, Chen R | bioRxiv : the preprint server for biology | 41648130 | bioRxiv | 2026 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/41648130 |
| Erasable serum markers. | Nouraein S, Li H, Lee S, Saenz VA, Raisley EK, Watanabe S, Costa VD, Szablowski JO | Proceedings of the National Academy of Sciences of the United States of America | 41329742 | Proc Natl Acad Sci U S A | 2025 Dec 9 | https://www.ncbi.nlm.nih.gov/pubmed/41329742 |
| Orthogonalized human protease control of secreted signals. | Aldrete CA, Call CC, Sant'Anna LE, Vlahos AE, Pei J, Cong Q, Gao XJ | Nature chemical biology | 39814991 | Nat Chem Biol | 2025 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39814991 |
| Machine-guided dual-objective protein engineering for deimmunization and therapeutic functions. | Wolfsberg E, Paul JS, Tycko J, Chen B, Bassik MC, Bintu L, Alizadeh AA, Gao XJ | Cell systems | 40466641 | Cell Syst | 2025 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/40466641 |
| Sequence-Independent RNA Sensing in Living Mammalian Cells. | Kolber NS, Kaseniit KE, Lanz TV, Robinson WH, Gao XJ | bioRxiv : the preprint server for biology | 41000785 | bioRxiv | 2025 Sep 18 | https://www.ncbi.nlm.nih.gov/pubmed/41000785 |
| Post-transcriptional modular synthetic receptors. | Zhang X, Mille-Fragoso LS, Kaseniit KE, Lee AP, Zhang M, Call CC, Hu Y, Xie Y, Gao XJ | Nature chemical biology | 40155716 | Nat Chem Biol | 2025 Aug | https://www.ncbi.nlm.nih.gov/pubmed/40155716 |
| Efficient generation of epitope-targeted de novo antibodies with Germinal. | Mille-Fragoso LS, Wang JN, Driscoll CL, Dai H, Widatalla T, Zhang X, Hie BL, Gao XJ | bioRxiv : the preprint server for biology | 41040335 | bioRxiv | 2025 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/41040335 |
| Digitally Diagnosing Multiple Developmental Delays Using Crowdsourcing Fused With Machine Learning: Protocol for a Human-in-the-Loop Machine Learning Study. | Jaiswal A, Kruiper R, Rasool A, Nandkeolyar A, Wall DP, Washington P | JMIR research protocols | 38329783 | JMIR Res Protoc | 2024 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/38329783 |
| Challenges in the Differential Classification of Individual Diagnoses from Co-Occurring Autism and ADHD Using Survey Data. | Jaiswal A, Wall DP, Washington P | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 40256615 | IEEE EMBS Int Conf Biomed Health Inform | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/40256615 |
| Audio-Based Emotion Recognition Using Self-Supervised Learning on an Engineered Feature Space. | Nimitsurachat P, Washington P | AI (Basel, Switzerland) | 38715564 | AI (Basel) | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38715564 |
| A Perspective on Crowdsourcing and Human-in-the-Loop Workflows in Precision Health. | Washington P | Journal of medical Internet research | 38602750 | J Med Internet Res | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38602750 |
| Compact subsets of autism screening items predict clinical diagnoses with a machine learning analysis of the QCHAT-10. | Sollis LJ, Wall DP, Washington PY | Scientific reports | 41203747 | Sci Rep | 2025 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/41203747 |
| Immune-compatible designs of semiconducting polymers for bioelectronics with suppressed foreign-body response. | Li N, Kang S, Liu Z, Wai S, Cheng Z, Dai Y, Solanki A, Li S, Li Y, Strzalka J, White MJV, Kim YH, Tian B, Hubbell JA, Wang S | Nature materials | 40247019 | Nat Mater | 2026 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40247019 |
| Achieving tissue-level softness on stretchable electronics through a generalizable soft interlayer design. | Li Y, Li N, Liu W, Prominski A, Kang S, Dai Y, Liu Y, Hu H, Wai S, Dai S, Cheng Z, Su Q, Cheng P, Wei C, Jin L, Hubbell JA, Tian B, Wang S | Nature communications | 37495580 | Nat Commun | 2023 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/37495580 |
| Soft mechanical sensors for wearable and implantable applications. | Papani R, Li Y, Wang S | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 38723798 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2024 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/38723798 |
| Bioadhesive polymer semiconductors and transistors for intimate biointerfaces. | Li N, Li Y, Cheng Z, Liu Y, Dai Y, Kang S, Li S, Shan N, Wai S, Ziaja A, Wang Y, Strzalka J, Liu W, Zhang C, Gu X, Hubbell JA, Tian B, Wang S | Science (New York, N.Y.) | 37561870 | Science | 2023 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/37561870 |
| Zwitterionic hydrogel designs for conducting polymers enable bioelectronics with suppressed foreign body responses. | Wai S, Kang S, Li N, Dai Y, Lavoie T, Strzalka J, Sutyak S, Weires M, Fu T, Wang J, Stevens KC, Li R, Hubbell JA, Tirrell MV, Wang S | bioRxiv : the preprint server for biology | 41279826 | bioRxiv | 2025 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/41279826 |
| Soft hydrogel semiconductors with augmented biointeractive functions. | Dai Y, Wai S, Li P, Shan N, Cao Z, Li Y, Wang Y, Liu Y, Liu W, Tang K, Liu Y, Hua M, Li S, Li N, Chatterji S, Fry HC, Lee S, Zhang C, Weires M, Sutyak S, Shi J, Zhu C, Xu J, Gu X, Tian B, Wang S | Science (New York, N.Y.) | 39446940 | Science | 2024 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/39446940 |
| E-Cannula reveals anatomical diversity in sharp-wave ripples as a driver for the recruitment of distinct hippocampal assemblies. | Liu X, Terada S, Ramezani M, Kim JH, Lu Y, Grosmark A, Losonczy A, Kuzum D | Cell reports | 36198271 | Cell Rep | 2022 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/36198271 |
| 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 |
| Modeling of Conduction Mechanism in Filament-free Multi-layer Bulk RRAM. | Zhou Y, Kumar A, Park J, Zhang Y, Zhou Y, Kim S, Cubukcu E, Kuzum D | IEEE transactions on electron devices | 41059383 | IEEE Trans Electron Devices | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/41059383 |
| Decoding of cortex-wide brain activity from local recordings of neural potentials. | Liu X, Ren C, Huang Z, Wilson M, Kim JH, Lu Y, Ramezani M, Komiyama T, Kuzum D | Journal of neural engineering | 34706356 | J Neural Eng | 2021 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/34706356 |
| Evaluation of Durability of Transparent Graphene Electrodes Fabricated on Different Flexible Substrates for Chronic In Vivo Experiments. | Ding D, Lu Y, Zhao R, Liu X, De-Eknamkul C, Ren C, Mehrsa A, Komiyama T, Kuzum D | IEEE transactions on bio-medical engineering | 32191878 | IEEE Trans Biomed Eng | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32191878 |
| Energy-efficient Mott activation neuron for full-hardware implementation of neural networks. | Oh S, Shi Y, Del Valle J, Salev P, Lu Y, Huang Z, Kalcheim Y, Schuller IK, Kuzum D | Nature nanotechnology | 33737724 | Nat Nanotechnol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33737724 |
| 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 |
| Trionic All-optical Biological Voltage Sensing via Quantum Statistics. | Ren Y, De-Eknamkul C, Sun F, Ramezani M, Gonzalez G, Huang W, Schwab JH, Wilson M, Engler AJ, Kuzum D, Cubukcu E | Nature photonics | 40822555 | Nat Photonics | 2025 May | https://www.ncbi.nlm.nih.gov/pubmed/40822555 |
| Atomically thin bioelectronics. | Kireev D, Kutagulla S, Hong J, Wilson MN, Ramezani M, Kuzum D, Ahn JH, Akinwande D | Nature reviews. Materials | 41058940 | Nat Rev Mater | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/41058940 |
| Innovating beyond electrophysiology through multimodal neural interfaces. | Ramezani M, Ren Y, Cubukcu E, Kuzum D | Nature reviews electrical engineering | 40552318 | Nat Rev Electr Eng | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/40552318 |
| Multimodal monitoring of human cortical organoids implanted in mice reveal functional connection with visual cortex. | Wilson MN, Thunemann M, Liu X, Lu Y, Puppo F, Adams JW, Kim JH, Ramezani M, Pizzo DP, Djurovic S, Andreassen OA, Mansour AA, Gage FH, Muotri AR, Devor A, Kuzum D | Nature communications | 36572698 | Nat Commun | 2022 Dec 26 | https://www.ncbi.nlm.nih.gov/pubmed/36572698 |
| A Neuromorphic Brain Interface based on RRAM Crossbar Arrays for High Throughput Real-time Spike Sorting. | Shi Y, Ananthakrishnan A, Oh S, Liu X, Hota G, Cauwenberghs G, Kuzum D | IEEE transactions on electron devices | 37168652 | IEEE Trans Electron Devices | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37168652 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Microscale Physiological Events on the Human Cortical Surface. | Paulk AC, Yang JC, Cleary DR, Soper DJ, Halgren M, O'Donnell AR, Lee SH, Ganji M, Ro YG, Oh H, Hossain L, Lee J, Tchoe Y, Rogers N, Kiliç K, Ryu SB, Lee SW, Hermiz J, Gilja V, Ulbert I, Fabó D, Thesen T, Doyle WK, Devinsky O, Madsen JR, Schomer DL, Eskandar EN, Lee JW, Maus D, Devor A, Fried SI, Jones PS, Nahed BV, Ben-Haim S, Bick SK, Richardson RM, Raslan AM, Siler DA, Cahill DP, Williams ZM, Cosgrove GR, Dayeh SA, Cash SS | Cerebral cortex (New York, N.Y. : 1991) | 33749727 | Cereb Cortex | 2021 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/33749727 |
| 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 |
| Electrochemical and electrophysiological considerations for clinical high channel count neural interfaces. | Vatsyayan R, Lee J, Bourhis AM, Tchoe Y, Cleary DR, Tonsfeldt KJ, Lee K, Montgomery-Walsh R, Paulk AC, U HS, Cash SS, Dayeh SA | MRS bulletin | 37476355 | MRS Bull | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/37476355 |
| 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 |
| 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 |
| The conformal, high-density SpineWrap microelectrode array for focal stimulation and selective muscle recruitment. | Russman SM, Montgomery-Walsh R, Vatsyayan R, Sang U H, Diaz-Aguilar LD, Chang EY, Tang Q, Lee K, Yaksh TL, Ben-Haim S, Ciacci J, Dayeh SA | Advanced functional materials | 40787278 | Adv Funct Mater | 2025 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/40787278 |
| The Brain Electroencephalogram Microdisplay for Precision Neurosurgery. | 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 | bioRxiv : the preprint server for biology | 37503216 | bioRxiv | 2023 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/37503216 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| A Scalable Fishbone Nanowire Array (FINE) for 3D Quasi-Intracellular Recording in Intact Brains. | Tchoe Y, Lee J, Tonsfeldt KJ, Wu T, Cleary DR, U HS, Liu R, Bouvier G, Vatsyayan R, Bourhis AM, Lee SH, Halgren E, Galton I, Scanziani M, Dayeh SA | Advanced materials (Deerfield Beach, Fla.) | 40697101 | Adv Mater | 2025 Oct | https://www.ncbi.nlm.nih.gov/pubmed/40697101 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Basics of Expansion Microscopy. | Klimas A, Gallagher B, Zhao Y | Current protocols in cytometry | 31763769 | Curr Protoc Cytom | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31763769 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanoscale imaging of clinical specimens using conventional and rapid-expansion pathology. | Bucur O, Fu F, Calderon M, Mylvaganam GH, Ly NL, Day J, Watkin S, Walker BD, Boyden ES, Zhao Y | Nature protocols | 32238952 | Nat Protoc | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32238952 |
| 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 |
| 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 |
| 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 |
| 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 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 |
| 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 |
| 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 |
| 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 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 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Two-dimensional metal organic frameworks for biomedical applications. | Arun Kumar S, Balasubramaniam B, Bhunia S, Jaiswal MK, Verma K, Prateek, Khademhosseini A, Gupta RK, Gaharwar AK | Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology | 33137846 | Wiley Interdiscip Rev Nanomed Nanobiotechnol | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33137846 |
| 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 |
| Correction: 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) | 40815125 | Chem Commun (Camb) | 2025 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/40815125 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Shear-Thinning and Thermo-Reversible Nanoengineered Inks for 3D Bioprinting. | Wilson SA, Cross LM, Peak CW, Gaharwar AK | ACS applied materials & interfaces | 29214803 | ACS Appl Mater Interfaces | 2017 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/29214803 |
| 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 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| Nanoengineered Shape-Memory Hemostat. | Hargett SE, Lokhande GK, Duran J, Hirani Z, Jang LK, Foster S, Deo KA, George S, Javed M, Ware TH, Maitland DJ, Gaharwar AK | Small science | 40213067 | Small Sci | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/40213067 |
