NIH Director's Transformative Research Award
NIH Director's Transformative Research Award
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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 |
|---|---|---|---|---|---|---|
| The T Cell Antigen Receptor α Transmembrane Domain Coordinates Triggering through Regulation of Bilayer Immersion and CD3 Subunit Associations. | Brazin KN, Mallis RJ, Boeszoermenyi A, Feng Y, Yoshizawa A, Reche PA, Kaur P, Bi K, Hussey RE, Duke-Cohan JS, Song L, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Immunity | 30389415 | Immunity | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30389415 |
| NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology. | Mallis RJ, Brazin KN, Duke-Cohan JS, Hwang W, Wang JH, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Journal of biomolecular NMR | 30815789 | J Biomol NMR | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30815789 |
| αβ T Cell Receptor Mechanosensing Forces out Serial Engagement. | Feng Y, Reinherz EL, Lang MJ | Trends in immunology | 30060805 | Trends Immunol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30060805 |
| TCR-pMHC encounter differentially regulates transcriptomes of tissue-resident CD8 T cells. | Yoshizawa A, Bi K, Keskin DB, Zhang G, Reinhold B, Reinherz EL | European journal of immunology | 28872670 | Eur J Immunol | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28872670 |
| Brain cell somatic gene recombination and its phylogenetic foundations. | Kaeser G, Chun J | The Journal of biological chemistry | 32699111 | J Biol Chem | 2020 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/32699111 |
| Reply to: APP gene copy number changes reflect exogenous contamination. | Lee MH, Liu CS, Zhu Y, Kaeser GE, Rivera R, Romanow WJ, Kihara Y, Chun J | Nature | 32814882 | Nature | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32814882 |
| Mosaic Somatic Gene Recombination as a Potentially Unifying Hypothesis for Alzheimer's Disease. | Kaeser GE, Chun J | Frontiers in genetics | 32457796 | Front Genet | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32457796 |
| The Gene Conundrum in Alzheimer's Disease. | Chun J | Cerebrum : the Dana forum on brain science | 32206173 | Cerebrum | 2019 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/32206173 |
| Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract. | Sidhwani P, Leerberg DM, Boezio GLM, Capasso TL, Yang H, Chi NC, Roman BL, Stainier DYR, Yelon D | Development (Cambridge, England) | 32439760 | Development | 2020 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/32439760 |
| Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence. | Sahai-Hernandez P, Pouget C, Eyal S, Svoboda O, Chacon J, Grimm L, Gjøen T, Traver D | eLife | 37695317 | Elife | 2023 Sep 11 | https://www.ncbi.nlm.nih.gov/pubmed/37695317 |
| The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. | Boos F, Chen J, Brunet A | Cold Spring Harbor protocols | 37100468 | Cold Spring Harb Protoc | 2024 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/37100468 |
| Tutorial: practical considerations for tissue clearing and imaging. | Weiss KR, Voigt FF, Shepherd DP, Huisken J | Nature protocols | 34021294 | Nat Protoc | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34021294 |
| Drivers of vessel progenitor fate define intermediate mesoderm dimensions by inhibiting kidney progenitor specification. | Perens EA, Yelon D | Developmental biology | 39307382 | Dev Biol | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39307382 |
| Deep learning modeling of rare noncoding genetic variants in human motor neurons defines CCDC146 as a therapeutic target for ALS. | Zhang S, Moll T, Rubin-Sigler J, Tu S, Li S, Yuan E, Liu M, Butt A, Harvey C, Gornall S, Alhalthli E, Shaw A, Souza CDS, Ferraiuolo L, Hornstein E, Shelkovnikova T, van Dijk CH, Timpanaro IS, Kenna KP, Zeng J, Tsao PS, Shaw PJ, Ichida JK, Cooper-Knock J, Snyder MP | medRxiv : the preprint server for health sciences | 38633814 | medRxiv | 2024 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/38633814 |
| SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS. | Linares GR, Li Y, Chang WH, Rubin-Sigler J, Mendonca S, Hong S, Eoh Y, Guo W, Huang YH, Chang J, Tu S, Dorjsuren N, Santana M, Hung ST, Yu J, Perez J, Chickering M, Cheng TY, Huang CC, Lee SJ, Deng HJ, Bach KT, Gray K, Subramanyam V, Rosenfeld J, Alworth SV, Goodarzi H, Ichida JK | Cell stem cell | 36736291 | Cell Stem Cell | 2023 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/36736291 |
| CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology. | Ortega JA, Sasselli IR, Boccitto M, Fleming AC, Fortuna TR, Li Y, Sato K, Clemons TD, Mckenna ED, Nguyen TP, Anderson EN, Asin J, Ichida JK, Pandey UB, Wolin SL, Stupp SI, Kiskinis E | Science advances | 37948524 | Sci Adv | 2023 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/37948524 |
| Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. | Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP | bioRxiv : the preprint server for biology | 38798507 | bioRxiv | 2024 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/38798507 |
| PIKFYVE inhibition mitigates disease in models of diverse forms of ALS. | Hung ST, Linares GR, Chang WH, Eoh Y, Krishnan G, Mendonca S, Hong S, Shi Y, Santana M, Kueth C, Macklin-Isquierdo S, Perry S, Duhaime S, Maios C, Chang J, Perez J, Couto A, Lai J, Li Y, Alworth SV, Hendricks E, Wang Y, Zlokovic BV, Dickman DK, Parker JA, Zarnescu DC, Gao FB, Ichida JK | Cell | 36754049 | Cell | 2023 Feb 16 | https://www.ncbi.nlm.nih.gov/pubmed/36754049 |
| Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods. | Du J, Boss J, Han P, Beesley LJ, Kleinsasser M, Goutman SA, Batterman S, Feldman EL, Mukherjee B | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 36644406 | J Comput Graph Stat | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36644406 |
| Role of the Exposome in Neurodegenerative Disease: Recent Insights and Future Directions. | Sakowski SA, Koubek EJ, Chen KS, Goutman SA, Feldman EL | Annals of neurology | 38411261 | Ann Neurol | 2024 Apr | https://www.ncbi.nlm.nih.gov/pubmed/38411261 |
| Priorities and Recommendations to Make ALS a Livable Disease Emanating from the 2024 National Academies of Sciences, Engineering, and Medicine Report Living with ALS. | Howard IM, Babu S, Carter C, Sakowski SA, Kurent JE, Cudkowicz ME, Feldman EL | Annals of neurology | 39390661 | Ann Neurol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39390661 |
| Residential exposure associations with ALS risk, survival, and phenotype: a Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 38557405 | Amyotroph Lateral Scler Frontotemporal Degener | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38557405 |
| Peripheral Immune Profiles Predict ALS Progression in an Age- and Sex-Dependent Manner. | Murdock BJ, Zhao B, Pawlowski KD, Famie JP, Piecuch CE, Webber-Davis IF, Teener SJ, Feldman EL, Zhao L, Goutman SA | Neurology(R) neuroimmunology & neuroinflammation | 38626361 | Neurol Neuroimmunol Neuroinflamm | 2024 May | https://www.ncbi.nlm.nih.gov/pubmed/38626361 |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | medRxiv : the preprint server for health sciences | 38585910 | medRxiv | 2024 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/38585910 |
| Nanoplastics and Neurodegeneration in ALS. | Eisen A, Pioro EP, Goutman SA, Kiernan MC | Brain sciences | 38790450 | Brain Sci | 2024 May 7 | https://www.ncbi.nlm.nih.gov/pubmed/38790450 |
| Multiple metal exposures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou JF, Koubek EJ, Teener S, Zhou L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | Journal of neurology, neurosurgery, and psychiatry | 39107037 | J Neurol Neurosurg Psychiatry | 2025 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/39107037 |
| Amyotrophic lateral sclerosis. | Feldman EL, Goutman SA, Petri S, Mazzini L, Savelieff MG, Shaw PJ, Sobue G | Lancet (London, England) | 36116464 | Lancet | 2022 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/36116464 |
| Stem cell therapy for central nervous system disorders: Metabolic interactions between transplanted cells and local microenvironments. | Sakowski SA, Chen KS | Neurobiology of disease | 35988874 | Neurobiol Dis | 2022 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/35988874 |
| The amyotrophic lateral sclerosis exposome: recent advances and future directions. | Goutman SA, Savelieff MG, Jang DG, Hur J, Feldman EL | Nature reviews. Neurology | 37709948 | Nat Rev Neurol | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37709948 |
| miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis. | Hur J, Paez-Colasante X, Figueroa-Romero C, Lo TW, Barmada SJ, Paulsen MT, Ljungman M, Alakwaa FM, Savelieff MG, Goutman SA, Feldman EL | Human molecular genetics | 36219176 | Hum Mol Genet | 2023 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/36219176 |
| Cumulative Genetic Score and C9orf72 Repeat Status Independently Contribute to Amyotrophic Lateral Sclerosis Risk in 2 Case-Control Studies. | Dou J, Bakulski K, Guo K, Hur J, Zhao L, Saez-Atienzar S, Stark A, Chia R, García-Redondo A, Rojas-Garcia R, Vázquez Costa JF, Fernandez Santiago R, Bandres-Ciga S, Gómez-Garre P, Periñán MT, Mir P, Pérez-Tur J, Cardona F, Menendez-Gonzalez M, Riancho J, Borrego-Hernández D, Galán-Dávila L, Infante Ceberio J, Pastor P, Paradas C, Dols-Icardo O, Traynor BJ, Feldman EL, Goutman SA, Spanish Neurological Consortium | Neurology. Genetics | 37293291 | Neurol Genet | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37293291 |
| Longitudinal Metabolomics in Amyotrophic Lateral Sclerosis Implicates Impaired Lipid Metabolism. | Guo K, Savelieff MG, Jang DG, Teener SJ, Zhao L, Hur J, Goutman SA, Feldman EL | Annals of neurology | 39976286 | Ann Neurol | 2025 Jul | https://www.ncbi.nlm.nih.gov/pubmed/39976286 |
| Environmental risk scores of persistent organic pollutants associate with higher ALS risk and shorter survival in a new Michigan case/control cohort. | Goutman SA, Boss J, Jang DG, Mukherjee B, Richardson RJ, Batterman S, Feldman EL | Journal of neurology, neurosurgery, and psychiatry | 37758454 | J Neurol Neurosurg Psychiatry | 2024 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/37758454 |
| Metal mixtures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou J, Koubek EJ, Teener S, Zhao L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | medRxiv : the preprint server for health sciences | 38464233 | medRxiv | 2024 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/38464233 |
| Awareness and care practices for rare neurologic diseases among senior neurologists: A global survey. | Jang DG, Federico A, Savelieff MG, Grisold W, Mancuso M, Molnar MJ, Feldman EL, Reynolds EL, World Federation of Neurology Subspecialist Group on Rare Neurologic Diseases | Journal of the neurological sciences | 39855013 | J Neurol Sci | 2025 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/39855013 |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | Journal of neurology | 39249108 | J Neurol | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/39249108 |
| Life Course Exposure to Cyanobacteria and Amyotrophic Lateral Sclerosis Survival. | Batterman SA, Islam MK, Jang DG, Feldman EL, Goutman SA | International journal of environmental research and public health | 40427878 | Int J Environ Res Public Health | 2025 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/40427878 |
| Emerging insights into the complex genetics and pathophysiology of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334234 | Lancet Neurol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35334234 |
| Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis. | Guo K, Figueroa-Romero C, Noureldein MH, Murdock BJ, Savelieff MG, Hur J, Goutman SA, Feldman EL | Brain : a journal of neurology | 37721161 | Brain | 2024 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/37721161 |
| Recent advances in the diagnosis and prognosis of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334233 | Lancet Neurol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35334233 |
| Occupational history associates with ALS survival and onset segment. | Goutman SA, Boss J, Godwin C, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 36193557 | Amyotroph Lateral Scler Frontotemporal Degener | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36193557 |
| Body mass index associates with amyotrophic lateral sclerosis survival and metabolomic profiles. | Goutman SA, Boss J, Iyer G, Habra H, Savelieff MG, Karnovsky A, Mukherjee B, Feldman EL | Muscle & nerve | 36321729 | Muscle Nerve | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36321729 |
| Avocational exposure associations with ALS risk, survival, and phenotype: A Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Journal of the neurological sciences | 38278093 | J Neurol Sci | 2024 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/38278093 |
| Epigenetic age acceleration is associated with occupational exposures, sex, and survival in amyotrophic lateral sclerosis. | Zhao Y, Li X, Wang K, Iyer G, Sakowski SA, Zhao L, Teener S, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Feldman EL, Sartor MA, Goutman SA | EBioMedicine | 39369616 | EBioMedicine | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39369616 |
| Impact of the Adverse Social Exposome on Survival in Individuals With Amyotrophic Lateral Sclerosis. | Jang DG, Kind AJ, Patterson A, Pedde M, Powell WR, Feldman EL, Goutman SA | Neurology | 39879575 | Neurology | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39879575 |
| Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. | Xiong X, James BT, Boix CA, Park YP, Galani K, Victor MB, Sun N, Hou L, Ho LL, Mantero J, Scannail AN, Dileep V, Dong W, Mathys H, Bennett DA, Tsai LH, Kellis M | Cell | 37774680 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774680 |
| Local translation in primary afferents and its contribution to pain. | Gale JR, Gedeon JY, Donnelly CJ, Gold MS | Pain | 35438669 | Pain | 2022 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/35438669 |
| Assays to measure small molecule Hsp70 agonist activity in vitro and in vivo. | Shapiro O, Woods C, Gleixner AM, Sannino S, Ngo M, McDaniels MD, Wipf P, Hukriede NA, Donnelly CJ, Brodsky JL | Analytical biochemistry | 39522672 | Anal Biochem | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39522672 |
| Integrated multimodal cell atlas of Alzheimer's disease. | Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES | Nature neuroscience | 39402379 | Nat Neurosci | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39402379 |
| Power of inclusion: Enhancing polygenic prediction with admixed individuals. | Tanigawa Y, Kellis M | American journal of human genetics | 37890495 | Am J Hum Genet | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37890495 |
| Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology. | Mathys H, Peng Z, Boix CA, Victor MB, Leary N, Babu S, Abdelhady G, Jiang X, Ng AP, Ghafari K, Kunisky AK, Mantero J, Galani K, Lohia VN, Fortier GE, Lotfi Y, Ivey J, Brown HP, Patel PR, Chakraborty N, Beaudway JI, Imhoff EJ, Keeler CF, McChesney MM, Patel HH, Patel SP, Thai MT, Bennett DA, Kellis M, Tsai LH | Cell | 37774677 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774677 |
| Multifaceted impact of specialized neuropeptide-intensive neurons on the selective vulnerability in Alzheimer's disease. | Li M, Flack N, Larsen PA | bioRxiv : the preprint server for biology | 38014130 | bioRxiv | 2024 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/38014130 |
| Multifaceted Role of Specialized Neuropeptide-Intensive Neurons on the Selective Vulnerability to Alzheimer's Disease in the Human Brain. | Li M, Flack N, Larsen PA | Biomolecules | 39766225 | Biomolecules | 2024 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/39766225 |
| Opposing roles of p38α-mediated phosphorylation and PRMT1-mediated arginine methylation in driving TDP-43 proteinopathy. | Aikio M, Odeh HM, Wobst HJ, Lee BL, Chan Ú, Mauna JC, Mack KL, Class B, Ollerhead TA, Ford AF, Barbieri EM, Cupo RR, Drake LE, Smalley JL, Lin YT, Lam S, Thomas R, Castello N, Baral A, Beyer JN, Najar MA, Dunlop J, Gitler AD, Javaherian A, Kaye JA, Burslem GM, Brown DG, Donnelly CJ, Finkbeiner S, Moss SJ, Brandon NJ, Shorter J | Cell reports | 39817908 | Cell Rep | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39817908 |
| Human microglial state dynamics in Alzheimer's disease progression. | Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Cell | 37774678 | Cell | 2023 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/37774678 |
| Hypometric genetics: Improved power in genetic discovery by incorporating quality control flags. | Tanigawa Y, Kellis M | American journal of human genetics | 39442521 | Am J Hum Genet | 2024 Nov 7 | https://www.ncbi.nlm.nih.gov/pubmed/39442521 |
| Single-cell multiregion dissection of Alzheimer's disease. | Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M | Nature | 39048816 | Nature | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/39048816 |
| A polygenic score method boosted by non-additive models. | Ohta R, Tanigawa Y, Suzuki Y, Kellis M, Morishita S | Nature communications | 38811555 | Nat Commun | 2024 May 29 | https://www.ncbi.nlm.nih.gov/pubmed/38811555 |
| Integrating single-cell RNA-seq datasets with substantial batch effects. | Hrovatin K, Moinfar AA, Zappia L, Lapuerta AT, Lengerich B, Kellis M, Theis FJ | bioRxiv : the preprint server for biology | 37961672 | bioRxiv | 2024 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/37961672 |
| Disrupting pathologic phase transitions in neurodegeneration. | Hurtle BT, Xie L, Donnelly CJ | The Journal of clinical investigation | 37395272 | J Clin Invest | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/37395272 |
| Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. | Sun N, Akay LA, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Nature neuroscience | 37264161 | Nat Neurosci | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37264161 |
| CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function. | Xie L, Merjane J, Bergmann CA, Xu J, Hurtle B, Donnelly CJ | bioRxiv : the preprint server for biology | 39026766 | bioRxiv | 2024 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/39026766 |
| Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD. | Pineda SS, Lee H, Ulloa-Navas MJ, Linville RM, Garcia FJ, Galani K, Engelberg-Cook E, Castanedes MC, Fitzwalter BE, Pregent LJ, Gardashli ME, DeTure M, Vera-Garcia DV, Hucke ATS, Oskarsson BE, Murray ME, Dickson DW, Heiman M, Belzil VV, Kellis M | Cell | 38521060 | Cell | 2024 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/38521060 |
| Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease. | Linna-Kuosmanen S, Schmauch E, Galani K, Ojanen J, Boix CA, Örd T, Toropainen A, Singha PK, Moreau PR, Harju K, Blazeski A, Segerstolpe Å, Lahtinen V, Hou L, Kang K, Meibalan E, Agudelo LZ, Kokki H, Halonen J, Jalkanen J, Gunn J, MacRae CA, Hollmén M, Hartikainen JEK, Kaikkonen MU, García-Cardeña G, Tavi P, Kiviniemi T, Kellis M | Cell reports. Medicine | 38776872 | Cell Rep Med | 2024 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/38776872 |
| The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. | Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A | Frontiers in cell and developmental biology | 37123399 | Front Cell Dev Biol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37123399 |
| Condensation of LINE-1 is critical for retrotransposition. | Sil S, Keegan S, Ettefa F, Denes LT, Boeke JD, Holt LJ | eLife | 37114770 | Elife | 2023 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/37114770 |
| Oligodendroglial macroautophagy is essential for myelin sheath turnover to prevent neurodegeneration and death. | Aber ER, Griffey CJ, Davies T, Li AM, Yang YJ, Croce KR, Goldman JE, Grutzendler J, Canman JC, Yamamoto A | Cell reports | 36261002 | Cell Rep | 2022 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/36261002 |
| mRNA condensation fluidizes the cytoplasm. | Xie Y, Liu T, Gresham D, Holt LJ | bioRxiv : the preprint server for biology | 37398029 | bioRxiv | 2023 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37398029 |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | Proceedings of the National Academy of Sciences of the United States of America | 39854229 | Proc Natl Acad Sci U S A | 2025 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/39854229 |
| Adult-onset deactivation of autophagy leads to loss of synapse homeostasis and cognitive impairment, with implications for alzheimer disease. | Grosso Jasutkar H, Wasserlein EM, Ishola A, Litt N, Staniszewski A, Arancio O, Yamamoto A | Autophagy | 38949671 | Autophagy | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/38949671 |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | bioRxiv : the preprint server for biology | 38585850 | bioRxiv | 2024 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/38585850 |
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| NOVA2-mediated RNA regulation is required for axonal pathfinding during development. | Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB | eLife | 27223325 | Elife | 2016 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/27223325 |
| Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. | Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG | Nature genetics | 31133750 | Nat Genet | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31133750 |
| Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease. | Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB | Nature communications | 37407548 | Nat Commun | 2023 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/37407548 |
| An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. | Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 25186741 | J Neurosci | 2014 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/25186741 |
| Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse. | Zhang Y, Sloan SA, Clarke LE, Caneda C, Plaza CA, Blumenthal PD, Vogel H, Steinberg GK, Edwards MS, Li G, Duncan JA 3rd, Cheshier SH, Shuer LM, Chang EF, Grant GA, Gephart MG, Barres BA | Neuron | 26687838 | Neuron | 2016 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/26687838 |
| Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. | Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR | Cell reports | 29091775 | Cell Rep | 2017 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/29091775 |
| Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. | Dong X, Chen K, Cuevas-Diaz Duran R, You Y, Sloan SA, Zhang Y, Zong S, Cao Q, Barres BA, Wu JQ | PLoS genetics | 26683846 | PLoS Genet | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26683846 |
| Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. | Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA, Paşca SP | Neuron | 28817799 | Neuron | 2017 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/28817799 |
| A survey of human brain transcriptome diversity at the single cell level. | Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR | Proceedings of the National Academy of Sciences of the United States of America | 26060301 | Proc Natl Acad Sci U S A | 2015 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/26060301 |
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| Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation. | Greene MJ, Kim JS, Seung HS, EyeWirers | Cell reports | 26904938 | Cell Rep | 2016 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/26904938 |
| Design and Evaluation of Interactive Proofreading Tools for Connectomics. | Haehn D, Knowles-Barley S, Roberts M, Beyer J, Kasthuri N, Lichtman JW, Pfister H | IEEE transactions on visualization and computer graphics | 26356960 | IEEE Trans Vis Comput Graph | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26356960 |
| Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. | Joesch M, Mankus D, Yamagata M, Shahbazi A, Schalek R, Suissa-Peleg A, Meister M, Lichtman JW, Scheirer WJ, Sanes JR | eLife | 27383271 | Elife | 2016 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/27383271 |
| Saturated Reconstruction of a Volume of Neocortex. | Kasthuri N, Hayworth KJ, Berger DR, Schalek RL, Conchello JA, Knowles-Barley S, Lee D, Vázquez-Reina A, Kaynig V, Jones TR, Roberts M, Morgan JL, Tapia JC, Seung HS, Roncal WG, Vogelstein JT, Burns R, Sussman DL, Priebe CE, Pfister H, Lichtman JW | Cell | 26232230 | Cell | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26232230 |
| Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits. | Hayworth KJ, Morgan JL, Schalek R, Berger DR, Hildebrand DG, Lichtman JW | Frontiers in neural circuits | 25018701 | Front Neural Circuits | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25018701 |
| Multispectral tracing in densely labeled mouse brain with nTracer. | Roossien DH, Sadis BV, Yan Y, Webb JM, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Li Y, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D | Bioinformatics (Oxford, England) | 30715234 | Bioinformatics | 2019 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/30715234 |
| Large-scale automatic reconstruction of neuronal processes from electron microscopy images. | Kaynig V, Vazquez-Reina A, Knowles-Barley S, Roberts M, Jones TR, Kasthuri N, Miller E, Lichtman J, Pfister H | Medical image analysis | 25791436 | Med Image Anal | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25791436 |
| The big data challenges of connectomics. | Lichtman JW, Pfister H, Shavit N | Nature neuroscience | 25349911 | Nat Neurosci | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25349911 |
| Digital tissue and what it may reveal about the brain. | Morgan JL, Lichtman JW | BMC biology | 29084528 | BMC Biol | 2017 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/29084528 |
| Clarifying Tissue Clearing. | Richardson DS, Lichtman JW | Cell | 26186186 | Cell | 2015 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/26186186 |
| NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity. | Al-Awami AK, Beyer J, Strobelt H, Kasthuri N, Lichtman JW, Pfister H, Hadwiger M | IEEE transactions on visualization and computer graphics | 26356951 | IEEE Trans Vis Comput Graph | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26356951 |
| Neural Circuit Inference from Function to Structure. | Real E, Asari H, Gollisch T, Meister M | Current biology : CB | 28065610 | Curr Biol | 2017 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/28065610 |
| Neuronal cell types and connectivity: lessons from the retina. | Seung HS, Sümbül U | Neuron | 25233310 | Neuron | 2014 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/25233310 |
| Developmental Rewiring between Cerebellar Climbing Fibers and Purkinje Cells Begins with Positive Feedback Synapse Addition. | Wilson AM, Schalek R, Suissa-Peleg A, Jones TR, Knowles-Barley S, Pfister H, Lichtman JW | Cell reports | 31775050 | Cell Rep | 2019 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/31775050 |
| Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator. | Vishwanathan A, Daie K, Ramirez AD, Lichtman JW, Aksay ERF, Seung HS | Current biology : CB | 28712570 | Curr Biol | 2017 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/28712570 |
| Digital Museum of Retinal Ganglion Cells with Dense Anatomy and Physiology. | Bae JA, Mu S, Kim JS, Turner NL, Tartavull I, Kemnitz N, Jordan CS, Norton AD, Silversmith WM, Prentki R, Sorek M, David C, Jones DL, Bland D, Sterling ALR, Park J, Briggman KL, Seung HS, Eyewirers | Cell | 29775596 | Cell | 2018 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/29775596 |
| Why not connectomics? | Morgan JL, Lichtman JW | Nature methods | 23722208 | Nat Methods | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23722208 |
| Space-time wiring specificity supports direction selectivity in the retina. | Kim JS, Greene MJ, Zlateski A, Lee K, Richardson M, Turaga SC, Purcaro M, Balkam M, Robinson A, Behabadi BF, Campos M, Denk W, Seung HS, EyeWirers | Nature | 24805243 | Nature | 2014 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/24805243 |
| An Individual Interneuron Participates in Many Kinds of Inhibition and Innervates Much of the Mouse Visual Thalamus. | Morgan JL, Lichtman JW | Neuron | 32142646 | Neuron | 2020 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/32142646 |
| Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish. | Wanner AA, Vishwanathan A | Frontiers in neural circuits | 30410437 | Front Neural Circuits | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30410437 |
| Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. | Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR | Cell | 22608085 | Cell | 2012 Jun 22 | https://www.ncbi.nlm.nih.gov/pubmed/22608085 |
| Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. | Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME | PLoS genetics | 22737091 | PLoS Genet | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22737091 |
| An optimized algorithm for detecting and annotating regional differential methylation. | Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE | BMC bioinformatics | 23735126 | BMC Bioinformatics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23735126 |
| Two methods for full-length RNA sequencing for low quantities of cells and single cells. | Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM | Proceedings of the National Academy of Sciences of the United States of America | 23267071 | Proc Natl Acad Sci U S A | 2013 Jan 8 | https://www.ncbi.nlm.nih.gov/pubmed/23267071 |
| Autism-Like Behavior and Epigenetic Changes Associated with Autism as Consequences of In Utero Exposure to Environmental Pollutants in a Mouse Model. | Hill DS, Cabrera R, Wallis Schultz D, Zhu H, Lu W, Finnell RH, Wlodarczyk BJ | Behavioural neurology | 26586927 | Behav Neurol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26586927 |
| Rfx2 is required for spermatogenesis in the mouse. | Shawlot W, Vazquez-Chantada M, Wallingford JB, Finnell RH | Genesis (New York, N.Y. : 2000) | 26248850 | Genesis | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26248850 |
| Autoantibodies against homocysteinylated protein in a mouse model of folate deficiency-induced neural tube defects. | Denny KJ, Kelly CF, Kumar V, Witham KL, Cabrera RM, Finnell RH, Taylor SM, Jeanes A, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 26900104 | Birth Defects Res A Clin Mol Teratol | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26900104 |
| New Techniques for the Study of Neural Tube Defects. | Lei Y, Finnell RH | Advanced techniques in biology & medicine | 27066597 | Adv Tech Biol Med | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27066597 |
| Extensive sequencing of seven human genomes to characterize benchmark reference materials. | Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M | Scientific data | 27271295 | Sci Data | 2016 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/27271295 |
| The Impact of Heterogeneity on Single-Cell Sequencing. | Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE | Frontiers in genetics | 30881372 | Front Genet | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30881372 |
| N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection. | Gokhale NS, McIntyre ABR, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vazquez C, Willer J, Ilkayeva OR, Law BA, Holley CL, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM | Cell host & microbe | 27773535 | Cell Host Microbe | 2016 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/27773535 |
| Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). | Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE | Journal of biomolecular techniques : JBT | 28337070 | J Biomol Tech | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28337070 |
| A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. | Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY | Science advances | 33536218 | Sci Adv | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33536218 |
| Characterization of the public transit air microbiome and resistome reveals geographical specificity. | Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH | Microbiome | 34039416 | Microbiome | 2021 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/34039416 |
| Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. | Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE | iScience | 33376973 | iScience | 2020 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/33376973 |
| Rare LRP6 variants identified in spina bifida patients. | Lei Y, Fathe K, McCartney D, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | Human mutation | 25546815 | Hum Mutat | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25546815 |
| An integrative computational approach for prioritization of genomic variants. | Dubchak I, Balasubramanian S, Wang S, Cem M, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC | PloS one | 25506935 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25506935 |
| Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. | Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL | Cancer discovery | 28193779 | Cancer Discov | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28193779 |
| Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity. | Goldman SL, Hassan C, Khunte M, Soldatenko A, Jong Y, Afshinnekoo E, Mason CE | Frontiers in genetics | 30881380 | Front Genet | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30881380 |
| Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. | Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE | Nature biotechnology | 34504351 | Nat Biotechnol | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34504351 |
| The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. | MetaSUB International Consortium | Microbiome | 27255532 | Microbiome | 2016 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/27255532 |
| Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain. | Nandi S, Chandramohan D, Fioriti L, Melnick AM, Hébert JM, Mason CE, Rajasethupathy P, Kandel ER | Proceedings of the National Academy of Sciences of the United States of America | 27791114 | Proc Natl Acad Sci U S A | 2016 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/27791114 |
| The Power of Engaging Citizen Scientists for Scientific Progress. | Garbarino J, Mason CE | Journal of microbiology & biology education | 27047581 | J Microbiol Biol Educ | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27047581 |
| Genetic and epigenetic heterogeneity and the impact on cancer relapse. | Hassan C, Afshinnekoo E, Li S, Wu S, Mason CE | Experimental hematology | 28705639 | Exp Hematol | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28705639 |
| Folate-dependent methylation of septins governs ciliogenesis during neural tube closure. | Toriyama M, Toriyama M, Wallingford JB, Finnell RH | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 28432198 | FASEB J | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28432198 |
| Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance. | Afshinnekoo E, Chou C, Alexander N, Ahsanuddin S, Schuetz AN, Mason CE | Journal of biomolecular techniques : JBT | 28337072 | J Biomol Tech | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28337072 |
| The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. | Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG | Nucleic acids research | 23203872 | Nucleic Acids Res | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23203872 |
| Neural tube defects, folate, and immune modulation. | Denny KJ, Jeanes A, Fathe K, Finnell RH, Taylor SM, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 24078477 | Birth Defects Res A Clin Mol Teratol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24078477 |
| Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. | Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D | Genome biology | 24020486 | Genome Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24020486 |
| Genomic approaches to the assessment of human spina bifida risk. | Ross ME, Mason CE, Finnell RH | Birth defects research | 27883265 | Birth Defects Res | 2017 Jan 30 | https://www.ncbi.nlm.nih.gov/pubmed/27883265 |
| Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. | Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE | Nature communications | 26836631 | Nat Commun | 2016 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/26836631 |
| The pivotal regulatory landscape of RNA modifications. | Li S, Mason CE | Annual review of genomics and human genetics | 24898039 | Annu Rev Genomics Hum Genet | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24898039 |
| Enabling large-scale next-generation sequence assembly with Blacklight. | Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD | Concurrency and computation : practice & experience | 25294974 | Concurr Comput | 2014 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/25294974 |
| Haplotype diversity and sequence heterogeneity of human telomeres. | Grigorev K, Foox J, Bezdan D, Butler D, Luxton JJ, Reed J, McKenna MJ, Taylor L, George KA, Meydan C, Bailey SM, Mason CE | Genome research | 34162698 | Genome Res | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34162698 |
| Identification of novel CELSR1 mutations in spina bifida. | Lei Y, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | PloS one | 24632739 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24632739 |
| Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. | Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR | Nature methods | 26121403 | Nat Methods | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26121403 |
| The impact of read length on quantification of differentially expressed genes and splice junction detection. | Chhangawala S, Rudy G, Mason CE, Rosenfeld JA | Genome biology | 26100517 | Genome Biol | 2015 Jun 23 | https://www.ncbi.nlm.nih.gov/pubmed/26100517 |
| Characterizing multi-omic data in systems biology. | Mason CE, Porter SG, Smith TM | Advances in experimental medicine and biology | 24292960 | Adv Exp Med Biol | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24292960 |
| Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. | Gertz ML, Chin CR, Tomoiaga D, MacKay M, Chang C, Butler D, Afshinnekoo E, Bezdan D, Schmidt MA, Mozsary C, Melnick A, Garrett-Bakelman F, Crucian B, Lee SMC, Zwart SR, Smith SM, Meydan C, Mason CE | Cell reports | 33242408 | Cell Rep | 2020 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/33242408 |
| CIC missense variants contribute to susceptibility for spina bifida. | Han X, Cao X, Aguiar-Pulido V, Yang W, Karki M, Ramirez PAP, Cabrera RM, Lin YL, Wlodarczyk BJ, Shaw GM, Ross ME, Zhang C, Finnell RH, Lei Y | Human mutation | 36054333 | Hum Mutat | 2022 Dec | https://www.ncbi.nlm.nih.gov/pubmed/36054333 |
| The continuing challenge of understanding, preventing, and treating neural tube defects. | Wallingford JB, Niswander LA, Shaw GM, Finnell RH | Science (New York, N.Y.) | 23449594 | Science | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23449594 |
| The birth of the Epitranscriptome: deciphering the function of RNA modifications. | Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE | Genome biology | 23113984 | Genome Biol | 2012 Oct 31 | https://www.ncbi.nlm.nih.gov/pubmed/23113984 |
| Analysis of archived residual newborn screening blood spots after whole genome amplification. | Cantarel BL, Lei Y, Weaver D, Zhu H, Farrell A, Benstead-Hume G, Reese J, Finnell RH | BMC genomics | 26268606 | BMC Genomics | 2015 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/26268606 |
| Fuz mutant mice reveal shared mechanisms between ciliopathies and FGF-related syndromes. | Tabler JM, Barrell WB, Szabo-Rogers HL, Healy C, Yeung Y, Perdiguero EG, Schulz C, Yannakoudakis BZ, Mesbahi A, Wlodarczyk B, Geissmann F, Finnell RH, Wallingford JB, Liu KJ | Developmental cell | 23806618 | Dev Cell | 2013 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/23806618 |
| Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. | Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF | Orphanet journal of rare diseases | 27179618 | Orphanet J Rare Dis | 2016 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/27179618 |
| Assessment of pharmacogenomic agreement. | Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B | F1000Research | 27408686 | F1000Res | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27408686 |
| Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. | Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM | Journal of visualized experiments : JoVE | 25742437 | J Vis Exp | 2015 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/25742437 |
| Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. | Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL | Cancer cell | 25873173 | Cancer Cell | 2015 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/25873173 |
| High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. | Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE | The Journal of comparative neurology | 26132897 | J Comp Neurol | 2016 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/26132897 |
| Dynamic evolution of clonal epialleles revealed by methclone. | Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE | Genome biology | 25260792 | Genome Biol | 2014 Sep 27 | https://www.ncbi.nlm.nih.gov/pubmed/25260792 |
| Detecting and correcting systematic variation in large-scale RNA sequencing data. | Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE | Nature biotechnology | 25150837 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150837 |
| Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). | Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE | Nucleic acids research | 25392405 | Nucleic Acids Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25392405 |
| Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. | Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG | Journal of medical primatology | 24810475 | J Med Primatol | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/24810475 |
| Translating current biomedical therapies for long duration, deep space missions. | Iosim S, MacKay M, Westover C, Mason CE | Precision clinical medicine | 31886035 | Precis Clin Med | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31886035 |
| Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments. | Westover C, Rahmatulloev S, Danko D, Afshin EE, O'Hara NB, Ounit R, Bezdan D, Mason CE | Genes | 36672826 | Genes (Basel) | 2022 Dec 28 | https://www.ncbi.nlm.nih.gov/pubmed/36672826 |
| Clinical Genomics: Challenges and Opportunities. | Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S | Critical reviews in eukaryotic gene expression | 27480773 | Crit Rev Eukaryot Gene Expr | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27480773 |
| Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. | Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE | Nature medicine | 27322744 | Nat Med | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27322744 |
| Antiepileptic drugs and pregnancy outcomes. | Wlodarczyk BJ, Palacios AM, George TM, Finnell RH | American journal of medical genetics. Part A | 22711424 | Am J Med Genet A | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22711424 |
| A GCH1 haplotype and risk of neural tube defects in the National Birth Defects Prevention Study. | Lupo PJ, Chapa C, Nousome D, Duhon C, Canfield MA, Shaw GM, Finnell RH, Zhu H, National Birth Defects Prevention Study | Molecular genetics and metabolism | 23059057 | Mol Genet Metab | 2012 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23059057 |
| methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. | Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE | Genome biology | 23034086 | Genome Biol | 2012 Oct 3 | https://www.ncbi.nlm.nih.gov/pubmed/23034086 |
| Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. | Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE | Nature biotechnology | 25150835 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150835 |
| A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. | SEQC/MAQC-III Consortium | Nature biotechnology | 25150838 | Nat Biotechnol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25150838 |
| Mutations in planar cell polarity gene SCRIB are associated with spina bifida. | Lei Y, Zhu H, Duhon C, Yang W, Ross ME, Shaw GM, Finnell RH | PloS one | 23922697 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23922697 |
| Epigenetic therapy in a new era of medicine: creating and integrating molecular profiles of patients. | Afshinnekoo E, Mason CE | Annals of translational medicine | 27942527 | Ann Transl Med | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27942527 |
| Nanopore sequencing in microgravity. | McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE | NPJ microgravity | 28725742 | NPJ Microgravity | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28725742 |
| Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. | Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE | Journal of biomolecular techniques : JBT | 28344519 | J Biomol Tech | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28344519 |
| Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. | Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Abdel Aleem A, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y, El-Bashir H, Musser JM, Al-Kaabi A, Shaw GM, Khurana E, Suhre K, Mason CE, Elemento O, Finnell RH, Ross ME | Proceedings of the National Academy of Sciences of the United States of America | 34916285 | Proc Natl Acad Sci U S A | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34916285 |
| Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research. | Bøifot KO, Gohli J, Skogan G, Dybwad M | Environmental microbiome | 33902714 | Environ Microbiome | 2020 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/33902714 |
| Genome-wide investigation identifies a rare copy-number variant burden associated with human spina bifida. | Wolujewicz P, Aguiar-Pulido V, AbdelAleem A, Nair V, Thareja G, Suhre K, Shaw GM, Finnell RH, Elemento O, Ross ME | Genetics in medicine : official journal of the American College of Medical Genetics | 33686259 | Genet Med | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33686259 |
| Genetic and epigenetic heterogeneity in acute myeloid leukemia. | Li S, Mason CE, Melnick A | Current opinion in genetics & development | 27162099 | Curr Opin Genet Dev | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27162099 |
| The Microbe Directory: An annotated, searchable inventory of microbes' characteristics. | Shaaban H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE | Gates open research | 29630066 | Gates Open Res | 2018 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/29630066 |
| Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. | Ricarte-Filho JC, Li S, Garcia-Rendueles ME, Montero-Conde C, Voza F, Knauf JA, Heguy A, Viale A, Bogdanova T, Thomas GA, Mason CE, Fagin JA | The Journal of clinical investigation | 24135138 | J Clin Invest | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24135138 |
| DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. | Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, Li Y, Ahn J, Abdel-Wahab O, Shih A, Lu C, Ward PS, Tsai JJ, Hricik T, Tosello V, Tallman JE, Zhao X, Daniels D, Dai Q, Ciminio L, Aifantis I, He C, Fuks F, Tallman MS, Ferrando A, Nimer S, Paietta E, Thompson CB, Licht JD, Mason CE, Godley LA, Melnick A, Figueroa ME, Levine RL | Cell reports | 25482556 | Cell Rep | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25482556 |
| Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. | McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE | Nature communications | 30718479 | Nat Commun | 2019 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/30718479 |
| Adventures in neurobioengineering. | Jasanoff A | ACS chemical neuroscience | 22896800 | ACS Chem Neurosci | 2012 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/22896800 |
| Metalloprotein-based MRI probes. | Matsumoto Y, Jasanoff A | FEBS letters | 23376346 | FEBS Lett | 2013 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/23376346 |
| Molecular fMRI of Serotonin Transport. | Hai A, Cai LX, Lee T, Lelyveld VS, Jasanoff A | Neuron | 27773583 | Neuron | 2016 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/27773583 |
| Magneto-fluorescent core-shell supernanoparticles. | Chen O, Riedemann L, Etoc F, Herrmann H, Coppey M, Barch M, Farrar CT, Zhao J, Bruns OT, Wei H, Guo P, Cui J, Jensen R, Chen Y, Harris DK, Cordero JM, Wang Z, Jasanoff A, Fukumura D, Reimer R, Dahan M, Jain RK, Bawendi MG | Nature communications | 25298155 | Nat Commun | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25298155 |
| Wireless resonant circuits for the minimally invasive sensing of biophysical processes in magnetic resonance imaging. | Hai A, Spanoudaki VC, Bartelle BB, Jasanoff A | Nature biomedical engineering | 30932065 | Nat Biomed Eng | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30932065 |
| Molecular imaging with engineered physiology. | Desai M, Slusarczyk AL, Chapin A, Barch M, Jasanoff A | Nature communications | 27910951 | Nat Commun | 2016 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/27910951 |
| Magnetic nanosensors optimized for rapid and reversible self-assembly. | Rodriguez E, Lelyveld VS, Atanasijevic T, Okada S, Jasanoff A | Chemical communications (Cambridge, England) | 24566735 | Chem Commun (Camb) | 2014 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/24566735 |
| Screen-based analysis of magnetic nanoparticle libraries formed using peptidic iron oxide ligands. | Barch M, Okada S, Bartelle BB, Jasanoff A | Journal of the American Chemical Society | 25158100 | J Am Chem Soc | 2014 Sep 10 | https://www.ncbi.nlm.nih.gov/pubmed/25158100 |
| Engineering intracellular biomineralization and biosensing by a magnetic protein. | Matsumoto Y, Chen R, Anikeeva P, Jasanoff A | Nature communications | 26522873 | Nat Commun | 2015 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/26522873 |
| Molecular-level functional magnetic resonance imaging of dopaminergic signaling. | Lee T, Cai LX, Lelyveld VS, Hai A, Jasanoff A | Science (New York, N.Y.) | 24786083 | Science | 2014 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/24786083 |
| Magnetic Detection of Neural Activity by Nanocoil Transducers. | Bok I, Phillips J, Zhu T, Lu J, Detienne E, Lima EA, Weiss BP, Jasanoff A, Hai A | Nano letters | 39319575 | Nano Lett | 2024 Oct 23 | https://www.ncbi.nlm.nih.gov/pubmed/39319575 |
| Combining Wireless Neural Recording and Video Capture for the Analysis of Natural Gait. | Foster JD, Freifeld O, Nuyujukian P, Ryu SI, Black MJ, Shenoy KV | International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering | 26019730 | Int IEEE EMBS Conf Neural Eng | 2011 Apr-May | https://www.ncbi.nlm.nih.gov/pubmed/26019730 |
| 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 |
| Leveraging historical knowledge of neural dynamics to rescue decoder performance as neural channels are lost: "Decoder hysteresis". | Kao JC, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736448 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26736448 |
| A High-Performance Neural Prosthesis Incorporating Discrete State Selection With Hidden Markov Models. | Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | IEEE transactions on bio-medical engineering | 27337709 | IEEE Trans Biomed Eng | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27337709 |
| Inferring single-trial neural population dynamics using sequential auto-encoders. | Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D | Nature methods | 30224673 | Nat Methods | 2018 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30224673 |
| 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 |
| ERAASR: an algorithm for removing electrical stimulation artifacts from multielectrode array recordings. | O'Shea DJ, Shenoy KV | Journal of neural engineering | 29265009 | J Neural Eng | 2018 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29265009 |
| Augmenting intracortical brain-machine interface with neurally driven error detectors. | Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Journal of neural engineering | 29130452 | J Neural Eng | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29130452 |
| A freely-moving monkey treadmill model. | Foster JD, Nuyujukian P, Freifeld O, Gao H, Walker R, I Ryu S, H Meng T, Murmann B, J Black M, Shenoy KV | Journal of neural engineering | 24995476 | J Neural Eng | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24995476 |
| Spiking Neural Network Decoder for Brain-Machine Interfaces. | Dethier J, Gilja V, Nuyujukian P, Elassaad SA, Shenoy KV, Boahen K | International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering | 24352611 | Int IEEE EMBS Conf Neural Eng | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/24352611 |
| Performance sustaining intracortical neural prostheses. | Nuyujukian P, Kao JC, Fan JM, Stavisky SD, Ryu SI, Shenoy KV | Journal of neural engineering | 25307561 | J Neural Eng | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25307561 |
| Studying brain organization via spontaneous fMRI signal. | Power JD, Schlaggar BL, Petersen SE | Neuron | 25459408 | Neuron | 2014 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/25459408 |
| Discovering Precise Temporal Patterns in Large-Scale Neural Recordings through Robust and Interpretable Time Warping. | Williams AH, Poole B, Maheswaranathan N, Dhawale AK, Fisher T, Wilson CD, Brann DH, Trautmann EM, Ryu S, Shusterman R, Rinberg D, Ölveczky BP, Shenoy KV, Ganguli S | Neuron | 31786013 | Neuron | 2020 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/31786013 |
| Speech-related dorsal motor cortex activity does not interfere with iBCI cursor control. | Stavisky SD, Willett FR, Avansino DT, Hochberg LR, Shenoy KV, Henderson JM | Journal of neural engineering | 32023225 | J Neural Eng | 2020 Feb 5 | https://www.ncbi.nlm.nih.gov/pubmed/32023225 |
| Neural Population Dynamics Underlying Motor Learning Transfer. | Vyas S, Even-Chen N, Stavisky SD, Ryu SI, Nuyujukian P, Shenoy KV | Neuron | 29456026 | Neuron | 2018 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/29456026 |
| Structure and variability of delay activity in premotor cortex. | Even-Chen N, Sheffer B, Vyas S, Ryu SI, Shenoy KV | PLoS computational biology | 30794541 | PLoS Comput Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30794541 |
| Leveraging neural dynamics to extend functional lifetime of brain-machine interfaces. | Kao JC, Ryu SI, Shenoy KV | Scientific reports | 28784984 | Sci Rep | 2017 Aug 7 | https://www.ncbi.nlm.nih.gov/pubmed/28784984 |
| Design and validation of a real-time spiking-neural-network decoder for brain-machine interfaces. | Dethier J, Nuyujukian P, Ryu SI, Shenoy KV, Boahen K | Journal of neural engineering | 23574919 | J Neural Eng | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23574919 |
| Selective modulation of cortical state during spatial attention. | Engel TA, Steinmetz NA, Gieselmann MA, Thiele A, Moore T, Boahen K | Science (New York, N.Y.) | 27934763 | Science | 2016 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/27934763 |
| Simultaneous motor preparation and execution in a last-moment reach correction task. | Ames KC, Ryu SI, Shenoy KV | Nature communications | 31221968 | Nat Commun | 2019 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/31221968 |
| Self-recalibrating classifiers for intracortical brain-computer interfaces. | Bishop W, Chestek CC, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Yu BM | Journal of neural engineering | 24503597 | J Neural Eng | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24503597 |
| Hybrid decoding of both spikes and low-frequency local field potentials for brain-machine interfaces. | Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 25570632 | Annu Int Conf IEEE Eng Med Biol Soc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25570632 |
| Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis. | Williams AH, Kim TH, Wang F, Vyas S, Ryu SI, Shenoy KV, Schnitzer M, Kolda TG, Ganguli S | Neuron | 29887338 | Neuron | 2018 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/29887338 |
| Structure in Neural Activity during Observed and Executed Movements Is Shared at the Neural Population Level, Not in Single Neurons. | Jiang X, Saggar H, Ryu SI, Shenoy KV, Kao JC | Cell reports | 32783934 | Cell Rep | 2020 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/32783934 |
| High-fidelity musculoskeletal modeling reveals that motor planning variability contributes to the speed-accuracy tradeoff. | Al Borno M, Vyas S, Shenoy KV, Delp SL | eLife | 33325369 | Elife | 2020 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/33325369 |
| Trial-by-Trial Motor Cortical Correlates of a Rapidly Adapting Visuomotor Internal Model. | Stavisky SD, Kao JC, Ryu SI, Shenoy KV | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28087767 | J Neurosci | 2017 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/28087767 |
| Motor Cortical Visuomotor Feedback Activity Is Initially Isolated from Downstream Targets in Output-Null Neural State Space Dimensions. | Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Neuron | 28625485 | Neuron | 2017 Jul 5 | https://www.ncbi.nlm.nih.gov/pubmed/28625485 |
| Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements. | Stavisky SD, Kao JC, Nuyujukian P, Pandarinath C, Blabe C, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV | Scientific reports | 30397281 | Sci Rep | 2018 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/30397281 |
| Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. | Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV | Nature communications | 26220660 | Nat Commun | 2015 Jul 29 | https://www.ncbi.nlm.nih.gov/pubmed/26220660 |
| A low-power band of neuronal spiking activity dominated by local single units improves the performance of brain-machine interfaces. | Nason SR, Vaskov AK, Willsey MS, Welle EJ, An H, Vu PP, Bullard AJ, Nu CS, Kao JC, Shenoy KV, Jang T, Kim HS, Blaauw D, Patil PG, Chestek CA | Nature biomedical engineering | 32719512 | Nat Biomed Eng | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32719512 |
| Auto-deleting brain machine interface: Error detection using spiking neural activity in the motor cortex. | Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736203 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26736203 |
| Intention estimation in brain-machine interfaces. | Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV | Journal of neural engineering | 24654266 | J Neural Eng | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24654266 |
| A high-performance keyboard neural prosthesis enabled by task optimization. | Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV | IEEE transactions on bio-medical engineering | 25203982 | IEEE Trans Biomed Eng | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25203982 |
| A Brain-Machine Interface Operating with a Real-Time Spiking Neural Network Control Algorithm. | Dethier J, Nuyujukian P, Eliasmith C, Stewart T, Elassaad SA, Shenoy KV, Boahen K | Advances in neural information processing systems | 25309106 | Adv Neural Inf Process Syst | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/25309106 |
| A recurrent neural network for closed-loop intracortical brain-machine interface decoders. | Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu S, Shenoy K | Journal of neural engineering | 22427488 | J Neural Eng | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22427488 |
| Combining decoder design and neural adaptation in brain-machine interfaces. | Shenoy KV, Carmena JM | Neuron | 25459407 | Neuron | 2014 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/25459407 |
| A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes. | Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | Journal of neural engineering | 25946198 | J Neural Eng | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25946198 |
| Accurate Estimation of Neural Population Dynamics without Spike Sorting. | Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O'Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV | Neuron | 31171448 | Neuron | 2019 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/31171448 |
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| BLIMP1 Induces Transient Metastatic Heterogeneity in Pancreatic Cancer. | Chiou SH, Risca VI, Wang GX, Yang D, Grüner BM, Kathiria AS, Ma RK, Vaka D, Chu P, Kozak M, Castellini L, Graves EE, Kim GE, Mourrain P, Koong AC, Giaccia AJ, Winslow MM | Cancer discovery | 28790031 | Cancer Discov | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28790031 |
| Structural and molecular interrogation of intact biological systems. | Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K | Nature | 23575631 | Nature | 2013 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/23575631 |
| Permanent genetic access to transiently active neurons via TRAP: targeted recombination in active populations. | Guenthner CJ, Miyamichi K, Yang HH, Heller HC, Luo L | Neuron | 23764283 | Neuron | 2013 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/23764283 |
| Circuit dynamics of adaptive and maladaptive behaviour. | Deisseroth K | Nature | 24429629 | Nature | 2014 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/24429629 |
| Circuit Architecture of VTA Dopamine Neurons Revealed by Systematic Input-Output Mapping. | Beier KT, Steinberg EE, DeLoach KE, Xie S, Miyamichi K, Schwarz L, Gao XJ, Kremer EJ, Malenka RC, Luo L | Cell | 26232228 | Cell | 2015 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/26232228 |
| Diversity of transgenic mouse models for selective targeting of midbrain dopamine neurons. | Lammel S, Steinberg EE, Földy C, Wall NR, Beier K, Luo L, Malenka RC | Neuron | 25611513 | Neuron | 2015 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/25611513 |
| 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 |
| Mitochondria, Metabolism, and Redox Mechanisms in Psychiatric Disorders. | Kim Y, Vadodaria KC, Lenkei Z, Kato T, Gage FH, Marchetto MC, Santos R | Antioxidants & redox signaling | 30585734 | Antioxid Redox Signal | 2019 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/30585734 |
| Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. | van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C | Frontiers in molecular neuroscience | 30147644 | Front Mol Neurosci | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30147644 |
| An in vitro model of lissencephaly: expanding the role of DCX during neurogenesis. | Shahsavani M, Pronk RJ, Falk R, Lam M, Moslem M, Linker SB, Salma J, Day K, Schuster J, Anderlid BM, Dahl N, Gage FH, Falk A | Molecular psychiatry | 28924182 | Mol Psychiatry | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28924182 |
| Insights into the role of somatic mosaicism in the brain. | Paquola ACM, Erwin JA, Gage FH | Current opinion in systems biology | 29226270 | Curr Opin Syst Biol | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29226270 |
| Mobile DNA elements in the generation of diversity and complexity in the brain. | Erwin JA, Marchetto MC, Gage FH | Nature reviews. Neuroscience | 25005482 | Nat Rev Neurosci | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25005482 |
| Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. | Niemsiri V, Rosenthal SB, Nievergelt CM, Maihofer AX, Marchetto MC, Santos R, Shekhtman T, Alliey-Rodriguez N, Anand A, Balaraman Y, Berrettini WH, Bertram H, Burdick KE, Calabrese JR, Calkin CV, Conroy C, Coryell WH, DeModena A, Eyler LT, Feeder S, Fisher C, Frazier N, Frye MA, Gao K, Garnham J, Gershon ES, Goes FS, Goto T, Harrington GJ, Jakobsen P, Kamali M, Kelly M, Leckband SG, Lohoff FW, McCarthy MJ, McInnis MG, Craig D, Millett CE, Mondimore F, Morken G, Nurnberger JI, Donovan CO, Øedegaard KJ, Ryan K, Schinagle M, Shilling PD, Slaney C, Stapp EK, Stautland A, Tarwater B, Zandi PP, Alda M, Fisch KM, Gage FH, Kelsoe JR | Molecular psychiatry | 36991131 | Mol Psychiatry | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/36991131 |
| Nuclear RNA-seq of single neurons reveals molecular signatures of activation. | Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJE, Parylak SL, Paquola ACM, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH | Nature communications | 27090946 | Nat Commun | 2016 Apr 19 | https://www.ncbi.nlm.nih.gov/pubmed/27090946 |
| 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 |
| Transcriptional and epigenetic mechanisms of cellular reprogramming to induced pluripotency. | van den Hurk M, Kenis G, Bardy C, van den Hove DL, Gage FH, Steinbusch HW, Rutten BP | Epigenomics | 27419933 | Epigenomics | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27419933 |
| Mosaic copy number variation in human neurons. | McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH | Science (New York, N.Y.) | 24179226 | Science | 2013 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/24179226 |
| Environment-driven somatic mosaicism in brain disorders. | Bedrosian TA, Linker S, Gage FH | Genome medicine | 27215330 | Genome Med | 2016 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/27215330 |
| Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. | Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS | Nature protocols | 26890679 | Nat Protoc | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26890679 |
| Prediction of response to drug therapy in psychiatric disorders. | Stern S, Linker S, Vadodaria KC, Marchetto MC, Gage FH | Open biology | 29794033 | Open Biol | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29794033 |
| The role of adult hippocampal neurogenesis in brain health and disease. | Toda T, Parylak SL, Linker SB, Gage FH | Molecular psychiatry | 29679070 | Mol Psychiatry | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29679070 |
| A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons. | Jaeger BN, Linker SB, Parylak SL, Barron JJ, Gallina IS, Saavedra CD, Fitzpatrick C, Lim CK, Schafer ST, Lacar B, Jessberger S, Gage FH | Nature communications | 30082781 | Nat Commun | 2018 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/30082781 |
| Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. | Schafer ST, Paquola ACM, Stern S, Gosselin D, Ku M, Pena M, Kuret TJM, Liyanage M, Mansour AA, Jaeger BN, Marchetto MC, Glass CK, Mertens J, Gage FH | Nature neuroscience | 30617258 | Nat Neurosci | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30617258 |
| Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. | Bardy C, van den Hurk M, Kakaradov B, Erwin JA, Jaeger BN, Hernandez RV, Eames T, Paucar AA, Gorris M, Marchand C, Jappelli R, Barron J, Bryant AK, Kellogg M, Lasken RS, Rutten BP, Steinbusch HW, Yeo GW, Gage FH | Molecular psychiatry | 27698428 | Mol Psychiatry | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27698428 |
| Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. | Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE | Nature | 27487209 | Nature | 2016 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/27487209 |
| Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro. | Bardy C, van den Hurk M, Eames T, Marchand C, Hernandez RV, Kellogg M, Gorris M, Galet B, Palomares V, Brown J, Bang AG, Mertens J, Böhnke L, Boyer L, Simon S, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 25870293 | Proc Natl Acad Sci U S A | 2015 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/25870293 |
| Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. | Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R | Stem cell reports | 26610635 | Stem Cell Reports | 2015 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/26610635 |
| Molecular Mechanisms of Bipolar Disorder: Progress Made and Future Challenges. | Kim Y, Santos R, Gage FH, Marchetto MC | Frontiers in cellular neuroscience | 28261061 | Front Cell Neurosci | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28261061 |
| Early life experience drives structural variation of neural genomes in mice. | Bedrosian TA, Quayle C, Novaresi N, Gage FH | Science (New York, N.Y.) | 29567711 | Science | 2018 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/29567711 |
| Examining non-LTR retrotransposons in the context of the evolving primate brain. | Linker SB, Marchetto MC, Narvaiza I, Denli AM, Gage FH | BMC biology | 28800766 | BMC Biol | 2017 Aug 11 | https://www.ncbi.nlm.nih.gov/pubmed/28800766 |
| Increasing the resolution of the adult neurogenesis picture. | Lacar B, Parylak SL, Vadodaria KC, Sarkar A, Gage FH | F1000prime reports | 24592320 | F1000Prime Rep | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24592320 |
| Differential L1 regulation in pluripotent stem cells of humans and apes. | Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH | Nature | 24153179 | Nature | 2013 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/24153179 |
| L1-associated genomic regions are deleted in somatic cells of the healthy human brain. | Erwin JA, Paquola AC, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FI, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH | Nature neuroscience | 27618310 | Nat Neurosci | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/27618310 |
| In vivo imaging of dendritic pruning in dentate granule cells. | Gonçalves JT, Bloyd CW, Shtrahman M, Johnston ST, Schafer ST, Parylak SL, Tran T, Chang T, Gage FH | Nature neuroscience | 27135217 | Nat Neurosci | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27135217 |
| Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium. | Stern S, Santos R, Marchetto MC, Mendes APD, Rouleau GA, Biesmans S, Wang QW, Yao J, Charnay P, Bang AG, Alda M, Gage FH | Molecular psychiatry | 28242870 | Mol Psychiatry | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28242870 |
| Altered Neuronal Support and Inflammatory Response in Bipolar Disorder Patient-Derived Astrocytes. | Vadodaria KC, Mendes APD, Mei A, Racha V, Erikson G, Shokhirev MN, Oefner R, Heard KJ, McCarthy MJ, Eyler L, Kelsoe JR, Santos R, Marchetto MC, Gage FH | Stem cell reports | 33667413 | Stem Cell Reports | 2021 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/33667413 |
| Species-specific maturation profiles of human, chimpanzee and bonobo neural cells. | Marchetto MC, Hrvoj-Mihic B, Kerman BE, Yu DX, Vadodaria KC, Linker SB, Narvaiza I, Santos R, Denli AM, Mendes AP, Oefner R, Cook J, McHenry L, Grasmick JM, Heard K, Fredlender C, Randolph-Moore L, Kshirsagar R, Xenitopoulos R, Chou G, Hah N, Muotri AR, Padmanabhan K, Semendeferi K, Gage FH | eLife | 30730291 | Elife | 2019 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/30730291 |
| Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. | Prescott SL, Srinivasan R, Marchetto MC, Grishina I, Narvaiza I, Selleri L, Gage FH, Swigut T, Wysocka J | Cell | 26365491 | Cell | 2015 Sep 24 | https://www.ncbi.nlm.nih.gov/pubmed/26365491 |
| Conserved expression of transposon-derived non-coding transcripts in primate stem cells. | Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G | BMC genomics | 28245871 | BMC Genomics | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28245871 |
| Paradox of pattern separation and adult neurogenesis: A dual role for new neurons balancing memory resolution and robustness. | Johnston ST, Shtrahman M, Parylak S, Gonçalves JT, Gage FH | Neurobiology of learning and memory | 26549627 | Neurobiol Learn Mem | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26549627 |
| To eat, or not to eat, that is the question: Neural stem cells escape phagocytosis in autism with macrocephaly. | Schafer ST, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 33883269 | Proc Natl Acad Sci U S A | 2021 May 11 | https://www.ncbi.nlm.nih.gov/pubmed/33883269 |
| RNA-sequencing from single nuclei. | Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, Lasken RS | Proceedings of the National Academy of Sciences of the United States of America | 24248345 | Proc Natl Acad Sci U S A | 2013 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/24248345 |
| Adult Hippocampal Neurogenesis: A Coming-of-Age Story. | Kuhn HG, Toda T, Gage FH | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30381404 | J Neurosci | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30381404 |
| Induction of human neuronal cells by defined transcription factors. | Pang ZP, Yang N, Vierbuchen T, Ostermeier A, Fuentes DR, Yang TQ, Citri A, Sebastiano V, Marro S, Südhof TC, Wernig M | Nature | 21617644 | Nature | 2011 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/21617644 |
| Conditional deletion of L1CAM in human neurons impairs both axonal and dendritic arborization and action potential generation. | Patzke C, Acuna C, Giam LR, Wernig M, Südhof TC | The Journal of experimental medicine | 27001749 | J Exp Med | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27001749 |
| FoxO3 regulates neuronal reprogramming of cells from postnatal and aging mice. | Ahlenius H, Chanda S, Webb AE, Yousif I, Karmazin J, Prusiner SB, Brunet A, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 27402759 | Proc Natl Acad Sci U S A | 2016 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/27402759 |
| Transdifferentiation of human adult peripheral blood T cells into neurons. | Tanabe K, Ang CE, Chanda S, Olmos VH, Haag D, Levinson DF, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 29866841 | Proc Natl Acad Sci U S A | 2018 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/29866841 |
| Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation. | Chanda S, Marro S, Wernig M, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 24046374 | Proc Natl Acad Sci U S A | 2013 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/24046374 |
| Pathogenic mechanism of an autism-associated neuroligin mutation involves altered AMPA-receptor trafficking. | Chanda S, Aoto J, Lee SJ, Wernig M, Südhof TC | Molecular psychiatry | 25778475 | Mol Psychiatry | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25778475 |
| Comprehensive qPCR profiling of gene expression in single neuronal cells. | Citri A, Pang ZP, Südhof TC, Wernig M, Malenka RC | Nature protocols | 22193304 | Nat Protoc | 2011 Dec 22 | https://www.ncbi.nlm.nih.gov/pubmed/22193304 |
| Cellular reprogramming: recent advances in modeling neurological diseases. | Ming GL, Brüstle O, Muotri A, Studer L, Wernig M, Christian KM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22072658 | J Neurosci | 2011 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/22072658 |
| Induction of synapse formation by de novo neurotransmitter synthesis. | Burlingham SR, Wong NF, Peterkin L, Lubow L, Dos Santos Passos C, Benner O, Ghebrial M, Cast TP, Xu-Friedman MA, Südhof TC, Chanda S | Nature communications | 35650274 | Nat Commun | 2022 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/35650274 |
| Towards an Understanding of Synapse Formation. | Südhof TC | Neuron | 30359597 | Neuron | 2018 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/30359597 |
| Cerebellins are differentially expressed in selective subsets of neurons throughout the brain. | Seigneur E, Südhof TC | The Journal of comparative neurology | 28714144 | J Comp Neurol | 2017 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/28714144 |
| Generation of pure GABAergic neurons by transcription factor programming. | Yang N, Chanda S, Marro S, Ng YH, Janas JA, Haag D, Ang CE, Tang Y, Flores Q, Mall M, Wapinski O, Li M, Ahlenius H, Rubenstein JL, Chang HY, Buylla AA, Südhof TC, Wernig M | Nature methods | 28504679 | Nat Methods | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28504679 |
| Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates. | Mall M, Kareta MS, Chanda S, Ahlenius H, Perotti N, Zhou B, Grieder SD, Ge X, Drake S, Euong Ang C, Walker BM, Vierbuchen T, Fuentes DR, Brennecke P, Nitta KR, Jolma A, Steinmetz LM, Taipale J, Südhof TC, Wernig M | Nature | 28379941 | Nature | 2017 Apr 13 | https://www.ncbi.nlm.nih.gov/pubmed/28379941 |
| Acute reduction in oxygen tension enhances the induction of neurons from human fibroblasts. | Davila J, Chanda S, Ang CE, Südhof TC, Wernig M | Journal of neuroscience methods | 23562599 | J Neurosci Methods | 2013 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/23562599 |
| Generation of oligodendroglial cells by direct lineage conversion. | Yang N, Zuchero JB, Ahlenius H, Marro S, Ng YH, Vierbuchen T, Hawkins JS, Geissler R, Barres BA, Wernig M | Nature biotechnology | 23584610 | Nat Biotechnol | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23584610 |
| Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. | Lujan E, Chanda S, Ahlenius H, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 22308465 | Proc Natl Acad Sci U S A | 2012 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/22308465 |
| The many roads to Rome: induction of neural precursor cells from fibroblasts. | Lujan E, Wernig M | Current opinion in genetics & development | 22868177 | Curr Opin Genet Dev | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22868177 |
| Molecular roadblocks for cellular reprogramming. | Vierbuchen T, Wernig M | Molecular cell | 23020854 | Mol Cell | 2012 Sep 28 | https://www.ncbi.nlm.nih.gov/pubmed/23020854 |
| Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons. | Marro SG, Chanda S, Yang N, Janas JA, Valperga G, Trotter J, Zhou B, Merrill S, Yousif I, Shelby H, Vogel H, Kalani MYS, Südhof TC, Wernig M | Neuron | 31257103 | Neuron | 2019 Aug 21 | https://www.ncbi.nlm.nih.gov/pubmed/31257103 |
| Induced neuronal reprogramming. | Ang CE, Wernig M | The Journal of comparative neurology | 24771471 | J Comp Neurol | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/24771471 |
| FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis. | Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A | Cell reports | 23891001 | Cell Rep | 2013 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/23891001 |
| Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1. | Pak C, Danko T, Zhang Y, Aoto J, Anderson G, Maxeiner S, Yi F, Wernig M, Südhof TC | Cell stem cell | 26279266 | Cell Stem Cell | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26279266 |
| In Vivo Reprogramming for Brain and Spinal Cord Repair. | Chen G, Wernig M, Berninger B, Nakafuku M, Parmar M, Zhang CL | eNeuro | 26730402 | eNeuro | 2015 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/26730402 |
| Multiple signaling pathways are essential for synapse formation induced by synaptic adhesion molecules. | Jiang X, Sando R, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 33431662 | Proc Natl Acad Sci U S A | 2021 Jan 19 | https://www.ncbi.nlm.nih.gov/pubmed/33431662 |
| SPARCL1 Promotes Excitatory But Not Inhibitory Synapse Formation and Function Independent of Neurexins and Neuroligins. | Gan KJ, Südhof TC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 32973045 | J Neurosci | 2020 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/32973045 |
| Deletion of Neuroligins from Astrocytes Does Not Detectably Alter Synapse Numbers or Astrocyte Cytoarchitecture by Maturity. | Golf SR, Trotter JH, Wang J, Nakahara G, Han X, Wernig M, Südhof TC | bioRxiv : the preprint server for biology | 37090508 | bioRxiv | 2025 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/37090508 |
| Analyses of the autism-associated neuroligin-3 R451C mutation in human neurons reveal a gain-of-function synaptic mechanism. | Wang L, Mirabella VR, Dai R, Su X, Xu R, Jadali A, Bernabucci M, Singh I, Chen Y, Tian J, Jiang P, Kwan KY, Pak C, Liu C, Comoletti D, Hart RP, Chen C, Südhof TC, Pang ZP | Molecular psychiatry | 36280753 | Mol Psychiatry | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36280753 |
| Efficient generation of functional neurons from mouse embryonic stem cells via neurogenin-2 expression. | Liu Y, Wang J, Südhof TC, Wernig M | Nature protocols | 37596357 | Nat Protoc | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37596357 |
| Astrocytic Neuroligin-3 influences gene expression and social behavior, but is dispensable for synapse number. | Qin L, Liu Z, Guo S, Han Y, Wang X, Ren W, Chen J, Zhen H, Nie C, Xing KK, Chen T, Südhof TC, Sun Y, Zhang B | Molecular psychiatry | 39003414 | Mol Psychiatry | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39003414 |
| Rapid single-step induction of functional neurons from human pluripotent stem cells. | Zhang Y, Pak C, Han Y, Ahlenius H, Zhang Z, Chanda S, Marro S, Patzke C, Acuna C, Covy J, Xu W, Yang N, Danko T, Chen L, Wernig M, Südhof TC | Neuron | 23764284 | Neuron | 2013 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/23764284 |
| Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. | Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M | Cell stem cell | 21962918 | Cell Stem Cell | 2011 Oct 4 | https://www.ncbi.nlm.nih.gov/pubmed/21962918 |
| Direct lineage conversions: unnatural but useful? | Vierbuchen T, Wernig M | Nature biotechnology | 21997635 | Nat Biotechnol | 2011 Oct | https://www.ncbi.nlm.nih.gov/pubmed/21997635 |
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| Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons. | Yi F, Danko T, Botelho SC, Patzke C, Pak C, Wernig M, Südhof TC | Science (New York, N.Y.) | 26966193 | Science | 2016 May 6 | https://www.ncbi.nlm.nih.gov/pubmed/26966193 |
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| Reduced GABA neuron density in auditory cerebral cortex of subjects with major depressive disorder. | Smiley JF, Hackett TA, Bleiwas C, Petkova E, Stankov A, Mann JJ, Rosoklija G, Dwork AJ | Journal of chemical neuroanatomy | 26686292 | J Chem Neuroanat | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26686292 |
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| Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. | Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS | Frontiers in endocrinology | 38577257 | Front Endocrinol (Lausanne) | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/38577257 |
| The G-Protein-Coupled Estrogen Receptor Selective Agonist G-1 Attenuates Cell Viability and Migration in High-Grade Serous Ovarian Cancer Cell Lines. | Hanafi D, Onyenwoke RU, Kimbro KS | International journal of molecular sciences | 38928205 | Int J Mol Sci | 2024 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/38928205 |
| Applying a Gene Reversal Rate Computational Methodology to Identify Drugs for a Rare Cancer: Inflammatory Breast Cancer. | Ji X, Williams KP, Zheng W | Cancer informatics | 37846218 | Cancer Inform | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37846218 |
| Geospatial Associations between Female Breast Cancer Mortality Rates and Environmental Socioeconomic Indicators for North Carolina. | Burwell A, Kimbro S, Mulrooney T | International journal of environmental research and public health | 37510605 | Int J Environ Res Public Health | 2023 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/37510605 |
| Identification of Novel GANT61 Analogs with Activity in Hedgehog Functional Assays and GLI1-Dependent Cancer Cells. | Abu Rabe D, Chdid L, Lamson DR, Laudeman CP, Tarpley M, Elsayed N, Smith GR, Zheng W, Dixon MS, Williams KP | Molecules (Basel, Switzerland) | 38999049 | Molecules | 2024 Jun 28 | https://www.ncbi.nlm.nih.gov/pubmed/38999049 |
| Identification of small molecule antagonists of sonic hedgehog/heparin binding with activity in hedgehog functional assays. | Lamson DR, Tarpley M, Addo K, Ji X, Abu Rabe D, Ehe B, Hughes M, Smith GR, Daye LR, Musso DL, Zheng W, Williams KP | Biochimica et biophysica acta. General subjects | 39151833 | Biochim Biophys Acta Gen Subj | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39151833 |
| Interventions Across the Translational Research Spectrum: Addressing Disparities Among Racial and Ethnic Minoritized Youth with Type 1 Diabetes. | Ellis DA, Naar S | Endocrinology and metabolism clinics of North America | 37865475 | Endocrinol Metab Clin North Am | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37865475 |
| Study protocol for transforming health equity research in integrated primary care: Antiracism as a disruptive innovation. | Naar S, Pettus C, Anderson N, Pooler-Burgess M, Ralston P, Flynn H, Combs T, Baquet C, Schatschneider C, Luke D | PloS one | 38935743 | PLoS One | 2024 | https://www.ncbi.nlm.nih.gov/pubmed/38935743 |
| Usefulness of Elevated Troponin to Predict Death in Patients With COVID-19 and Myocardial Injury. | Majure DT, Gruberg L, Saba SG, Kvasnovsky C, Hirsch JS, Jauhar R, Northwell Health COVID-19 Research Consortium | The American journal of cardiology | 33058800 | Am J Cardiol | 2021 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/33058800 |
| Let Sleeping Patients Lie, avoiding unnecessary overnight vitals monitoring using a clinically based deep-learning model. | Tóth V, Meytlis M, Barnaby DP, Bock KR, Oppenheim MI, Al-Abed Y, McGinn T, Davidson KW, Becker LB, Hirsch JS, Zanos TP | NPJ digital medicine | 33299116 | NPJ Digit Med | 2020 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/33299116 |
| Effectiveness of SARS-CoV-2 Decontamination and Containment in a COVID-19 ICU. | Brune Z, Kuschner CE, Mootz J, Davidson KW, Pena RCF, Ghanem MH, Fischer A, Gitman M, Teperman L, Mason C, Becker LB | International journal of environmental research and public health | 33802332 | Int J Environ Res Public Health | 2021 Mar 3 | https://www.ncbi.nlm.nih.gov/pubmed/33802332 |
| Racial and ethnic minority patient participation in N-of-1 trials: perspectives of healthcare providers and patients. | Marrast L, Conigliaro J, Chan C, Kim EJ, Duer-Hefele J, Diefenbach MA, Davidson KW | Personalized medicine | 34047197 | Per Med | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34047197 |
| Examination of patient characteristics and hydroxychloroquine use based on the US Food and Drug Administration's recommendation: a cross-sectional analysis in New York. | Kim EJ, Coppa K, Hirsch JS, Abrahams S, Johnson J, Lesser M, Davidson KW, Conigliaro J, Northwell Health COVID-19 Research Consortium, Northwell Health COVID-19 Research Consortium | BMJ open | 33558355 | BMJ Open | 2021 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/33558355 |
| Experimental Designs to Optimize Treatments for Individuals: Personalized N-of-1 Trials. | Davidson KW, Silverstein M, Cheung K, Paluch RA, Epstein LH | JAMA pediatrics | 33587109 | JAMA Pediatr | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33587109 |
| Sex-Based Differences in COVID-19 Outcomes. | Tejpal A, Gianos E, Cerise J, Hirsch JS, Rosen S, Kohn N, Lesser M, Weinberg C, Majure D, Satapathy SK, Bernstein D, Barish MA, Spyropoulos AC, Brown RM | Journal of women's health (2002) | 33885345 | J Womens Health (Larchmt) | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33885345 |
| Clinical Usefulness of Bright White Light Therapy for Depressive Symptoms in Cancer Survivors: Results from a Series of Personalized (N-of-1) Trials. | Kronish IM, Cheung YK, Julian J, Parsons F, Lee J, Yoon S, Valdimarsdottir H, Green P, Suls J, Hershman DL, Davidson KW | Healthcare (Basel, Switzerland) | 31905890 | Healthcare (Basel) | 2019 Dec 30 | https://www.ncbi.nlm.nih.gov/pubmed/31905890 |
| Intubated COVID-19 predictive (ICOP) score for early mortality after intubation in patients with COVID-19. | Nishikimi M, Rasul R, Sison CP, Jafari D, Shoaib M, Shinozaki K, Li T, Hayashida K, Rolston DM, Hirsch JS, Becker LB, Northwell Health COVID-19 Research Consortium | Scientific reports | 34702896 | Sci Rep | 2021 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/34702896 |
| Impact of Timing of Tocilizumab Use in Hospitalized Patients With SARS-CoV-2 Infection. | Singh AK, Oks M, Husk G, Dechario SP, Mina B, Singh K, Kirschenbaum L, Carpati CM, Mahmoud O, Gabra NI, Ishikawa O, Altschultz E, Shah V, Mahajan A, Gautam A, Birnbaum B, Antonacci AC, Raoof S | Respiratory care | 34548407 | Respir Care | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34548407 |
| Barriers to and Facilitators for Acceptance of Comprehensive Clinical Decision Support System-Driven Care Maps for Patients With Thoracic Trauma: Interview Study Among Health Care Providers and Nurses. | Jones EK, Banks A, Melton GB, Porta CM, Tignanelli CJ | JMIR human factors | 35293873 | JMIR Hum Factors | 2022 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/35293873 |
| A Series of Remote Melatonin Supplement Interventions for Poor Sleep: Protocol for a Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Perrin A, Rodillas J, Miller D, Arader L, Chandereng T, Cheung YK, Shechter A, Davidson KW | JMIR research protocols | 37535419 | JMIR Res Protoc | 2023 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/37535419 |
| Introducing Data Sciences to N-of-1 Designs, Statistics, Use-Cases, the Future, and the Moniker 'N-of-1' Trial. | Davidson KW, Cheung YK, Friel CP, Suls J | Harvard data science review | 38009132 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38009132 |
| Why Do I Get Side Effects? Personalized (N-of-1) Trials for Statin Intolerance and the Nocebo Effect. | Howard JP, Wood FA, Francis DP | Harvard data science review | 38344133 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38344133 |
| Single case designs for early phase behavioral translational research in health psychology. | Epstein LH, Bickel WK, Czajkowski SM, Paluch RA, Moeyaert M, Davidson KW | Health psychology : official journal of the Division of Health Psychology, American Psychological Association | 34370494 | Health Psychol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34370494 |
| Association of race/ethnicity with mortality in patients hospitalized with COVID-19. | Richardson S, Martinez J, Hirsch JS, Cerise J, Lesser M, Roswell RO, Davidson KW, Northwell Health COVID-19 Research Consortium | PloS one | 35925973 | PLoS One | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35925973 |
| Now is the time to assess the effects of open science practiceswith randomized control trials. | Suls J, Rothman AJ, Davidson KW | The American psychologist | 34807632 | Am Psychol | 2022 Apr | https://www.ncbi.nlm.nih.gov/pubmed/34807632 |
| Selected psychological comorbidities in coronary heart disease: Challenges and grand opportunities. | Davidson KW, Alcántara C, Miller GE | The American psychologist | 30394780 | Am Psychol | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30394780 |
| A look at the increasing demographic representation within behavioral medicine. | Yoon S, Falzon L, Anderson NB, Davidson KW | Journal of behavioral medicine | 30825089 | J Behav Med | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30825089 |
| Are Nomothetic or Ideographic Approaches Superior in Predicting Daily Exercise Behaviors? | Cheung YK, Hsueh PS, Qian M, Yoon S, Meli L, Diaz KM, Schwartz JE, Kronish IM, Davidson KW | Methods of information in medicine | 29582914 | Methods Inf Med | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29582914 |
| Envisioning a future for precision health psychology: innovative applied statistical approaches to N-of-1 studies. | Davidson KW, Cheung YK | Health psychology review | 28651455 | Health Psychol Rev | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28651455 |
| Risk factors and outcomes for acute-on-chronic liver failure in COVID-19: a large multi-center observational cohort study. | Satapathy SK, Roth NC, Kvasnovsky C, Hirsch JS, Trindade AJ, Molmenti E, Barish M, Hirschwerk D, Da BL, Bernstein D, Northwell Health COVID-19 Research Consortium | Hepatology international | 33826042 | Hepatol Int | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33826042 |
| Prevalence and Predictors of Venous Thromboembolism or Mortality in Hospitalized COVID-19 Patients. | Cohen SL, Gianos E, Barish MA, Chatterjee S, Kohn N, Lesser M, Giannis D, Coppa K, Hirsch JS, McGinn TG, Goldin ME, Spyropoulos AC, Northwell Health COVID-19 Research Consortium | Thrombosis and haemostasis | 33472255 | Thromb Haemost | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/33472255 |
| A Machine Learning Prediction Model of Respiratory Failure Within 48 Hours of Patient Admission for COVID-19: Model Development and Validation. | Bolourani S, Brenner M, Wang P, McGinn T, Hirsch JS, Barnaby D, Zanos TP, Northwell COVID-19 Research Consortium | Journal of medical Internet research | 33476281 | J Med Internet Res | 2021 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/33476281 |
| Increasing the Precision of Hypertension Treatment Through Personalized Trials: a Pilot Study. | Kronish IM, Cheung YK, Shimbo D, Julian J, Gallagher B, Parsons F, Davidson KW | Journal of general internal medicine | 30859504 | J Gen Intern Med | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30859504 |
| Patients and primary care providers identify opportunities for personalized (N-of-1) trials in the mobile health era. | Kronish IM, Alcántara C, Duer-Hefele J, St Onge T, Davidson KW, Carter EJ, Medina V, Cohn E, Moise N | Journal of clinical epidemiology | 28648833 | J Clin Epidemiol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28648833 |
| Characteristics, Cardiac Involvement, and Outcomes of Multisystem Inflammatory Syndrome of Childhood Associated with severe acute respiratory syndrome coronavirus 2 Infection. | Capone CA, Subramony A, Sweberg T, Schneider J, Shah S, Rubin L, Schleien C, Northwell Health COVID-19 Research Consortium, Epstein S, Johnson JC, Kessel A, Misra N, Mitchell E, Palumbo N, Rajan S, Rocker J, Williamson K, Davidson KW | The Journal of pediatrics | 32553873 | J Pediatr | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32553873 |
| An early experience on the effect of solid organ transplant status on hospitalized COVID-19 patients. | Nair V, Jandovitz N, Hirsch JS, Abate M, Satapathy SK, Roth N, Miyara SJ, Guevara S, Kressel AM, Xiang A, Wu G, Butensky SD, Lin D, Williams S, Bhaskaran MC, Majure DT, Grodstein E, Lau L, Nair G, Fahmy AE, Winnick A, Breslin N, Berlinrut I, Molmenti C, Becker LB, Malhotra P, Gautam-Goyal P, Lima B, Maybaum S, Shah SK, Takegawa R, Hayashida K, Shinozaki K, Teperman LW, Molmenti EP, Northwell Health COVID-19 Research Consortium | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 33443778 | Am J Transplant | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33443778 |
| A Series of Virtual Interventions for Chronic Lower Back Pain: A Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Kaplan M, Tashnim Z, Miller D, Ahn H, Falzon L, Dominello AJ, Foroughi C, Chandereng T, Cheung K, Davidson K | Harvard data science review | 37609556 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37609556 |
| Protocol for randomized personalized trial for stress management compared to standard of care. | Goodwin AM, Miller D, D'Angelo S, Perrin A, Wiener R, Greene B, Romain AN, Arader L, Chandereng T, Kuen Cheung Y, Davidson KW, Butler M | Frontiers in psychology | 37794909 | Front Psychol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37794909 |
| Accommodating Serial Correlation and Sequential Design Elements in Personalized Studies and Aggregated Personalized Studies. | Schork NJ | Harvard data science review | 37032736 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/37032736 |
| The Family of Single-Case Experimental Designs. | Epstein LH, Dallery J | Harvard data science review | 36926648 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36926648 |
| Personalized Data Science and Personalized (N-of-1) Trials: Promising Paradigms for Individualized Health Care. | Duan N, Norman D, Schmid C, Sim I, Kravitz RL | Harvard data science review | 38009133 | Harv Data Sci Rev | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/38009133 |
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| Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. | Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S | Nature | 32908310 | Nature | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32908310 |
| Conversion of adult endothelium to immunocompetent haematopoietic stem cells. | Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S | Nature | 28514438 | Nature | 2017 May 25 | https://www.ncbi.nlm.nih.gov/pubmed/28514438 |
| Sox17 drives functional engraftment of endothelium converted from non-vascular cells. | Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S | Nature communications | 28091527 | Nat Commun | 2017 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/28091527 |
| Endothelial jagged-2 sustains hematopoietic stem and progenitor reconstitution after myelosuppression. | Guo P, Poulos MG, Palikuqi B, Badwe CR, Lis R, Kunar B, Ding BS, Rabbany SY, Shido K, Butler JM, Rafii S | The Journal of clinical investigation | 29058691 | J Clin Invest | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/29058691 |
| Transplantation of Endothelial Cells to Mitigate Acute and Chronic Radiation Injury to Vital Organs. | Rafii S, Ginsberg M, Scandura J, Butler JM, Ding BS | Radiation research | 27459700 | Radiat Res | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27459700 |
| Morphological characterization of Etv2 vascular explants using fractal analysis and atomic force microscopy. | Adelson RP, Palikuqi B, Weiss Z, Checco A, Schreiner R, Rafii S, Rabbany SY | Microvascular research | 34146583 | Microvasc Res | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34146583 |
| Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice. | Barcia Durán JG, Lu T, Houghton S, Geng F, Schreiner R, Xiang J, Rafii S, Redmond D, Lis R | Communications biology | 33767339 | Commun Biol | 2021 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/33767339 |
| Angiocrine functions of organ-specific endothelial cells. | Rafii S, Butler JM, Ding BS | Nature | 26791722 | Nature | 2016 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/26791722 |
| Platelet-derived SDF-1 primes the pulmonary capillary vascular niche to drive lung alveolar regeneration. | Rafii S, Cao Z, Lis R, Siempos II, Chavez D, Shido K, Rabbany SY, Ding BS | Nature cell biology | 25621952 | Nat Cell Biol | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25621952 |
| Outcomes of intermediate-risk patients treated with transcatheter and surgical aortic valve replacement in the Veterans Affairs Healthcare System: A single center 20-year experience. | Garcia S, Kelly R, Mbai M, Gurevich S, Oestreich B, Yannopoulos D, Adabag S | Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions | 29316204 | Catheter Cardiovasc Interv | 2018 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/29316204 |
| Early Access to the Cardiac Catheterization Laboratory for Patients Resuscitated From Cardiac Arrest Due to a Shockable Rhythm: The Minnesota Resuscitation Consortium Twin Cities Unified Protocol. | Garcia S, Drexel T, Bekwelem W, Raveendran G, Caldwell E, Hodgson L, Wang Q, Adabag S, Mahoney B, Frascone R, Helmer G, Lick C, Conterato M, Baran K, Bart B, Bachour F, Roh S, Panetta C, Stark R, Haugland M, Mooney M, Wesley K, Yannopoulos D | Journal of the American Heart Association | 26744380 | J Am Heart Assoc | 2016 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/26744380 |
| Anaesthetic Postconditioning at the Initiation of CPR Improves Myocardial and Mitochondrial Function in a Pig Model of Prolonged Untreated Ventricular Fibrillation. | Riess ML, Matsuura TR, Bartos JA, Bienengraeber M, Aldakkak M, McKnite SH, Rees JN, Aufderheide TP, Sarraf M, Neumar RW, Yannopoulos D | Resuscitation | 25281906 | Resuscitation | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25281906 |
| Simulated traumatic brain injury in in-vitro mouse neuronal and brain endothelial cell culture models. | Meyer LJ, Lotze FP, Riess ML | Journal of pharmacological and toxicological methods | 35149185 | J Pharmacol Toxicol Methods | 2022 Mar-Apr | https://www.ncbi.nlm.nih.gov/pubmed/35149185 |
| Role of epinephrine and extracorporeal membrane oxygenation in the management of ischemic refractory ventricular fibrillation: a randomized trial in pigs. | Bartos JA, Voicu S, Matsuura TR, Tsangaris A, Sideris G, Oestreich BA, George SA, Olson M, Shekar KC, Rees JN, Carlson K, Sebastian P, McKnite S, Raveendran G, Aufderheide TP, Yannopoulos D | JACC. Basic to translational science | 29152600 | JACC Basic Transl Sci | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29152600 |
| Early Effects of Prolonged Cardiac Arrest and Ischemic Postconditioning during Cardiopulmonary Resuscitation on Cardiac and Brain Mitochondrial Function in Pigs. | Matsuura TR, Bartos JA, Tsangaris A, Shekar KC, Olson MD, Riess ML, Bienengraeber M, Aufderheide TP, Neumar RW, Rees JN, McKnite SH, Dikalova AE, Dikalov SI, Douglas HF, Yannopoulos D | Resuscitation | 28408349 | Resuscitation | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28408349 |
| Buffer glucose adjustment affects myocardial function after ischemia-reperfusion in long-term diabetic rat isolated hearts. | Balzer C, Cleveland WJ, Li Z, Riess ML | Physiological reports | 36324287 | Physiol Rep | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36324287 |
| Venous waveform analysis detects acute right ventricular failure in a rat respiratory arrest model. | Lefevre RJ, Barajas MB, Balzer C, Baudenbacher FJ, Riess ML, Staudt G, Hernandez A, Eagle SS | Pediatric research | 36042330 | Pediatr Res | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36042330 |
| Minnesota Resuscitation Consortium's Advanced Perfusion and Reperfusion Cardiac Life Support Strategy for Out-of-Hospital Refractory Ventricular Fibrillation. | Yannopoulos D, Bartos JA, Martin C, Raveendran G, Missov E, Conterato M, Frascone RJ, Trembley A, Sipprell K, John R, George S, Carlson K, Brunsvold ME, Garcia S, Aufderheide TP | Journal of the American Heart Association | 27412906 | J Am Heart Assoc | 2016 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/27412906 |
| Bundled postconditioning therapies improve hemodynamics and neurologic recovery after 17 min of untreated cardiac arrest. | Bartos JA, Matsuura TR, Sarraf M, Youngquist ST, McKnite SH, Rees JN, Sloper DT, Bates FS, Segal N, Debaty G, Lurie KG, Neumar RW, Metzger JM, Riess ML, Yannopoulos D | Resuscitation | 25447036 | Resuscitation | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25447036 |
| Identifying Important Gaps in Randomized Controlled Trials of Adult Cardiac Arrest Treatments: A Systematic Review of the Published Literature. | Sinha SS, Sukul D, Lazarus JJ, Polavarapu V, Chan PS, Neumar RW, Nallamothu BK | Circulation. Cardiovascular quality and outcomes | 27756794 | Circ Cardiovasc Qual Outcomes | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27756794 |
| Mechanical adjuncts for cardiocerebral resuscitation. | Riess ML, Balzer C | Expert review of medical devices | 31353970 | Expert Rev Med Devices | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31353970 |
| Design and Implementation of a Rat Ex Vivo Lung Perfusion Model. | Cleveland WJ, Hees JE, Balzer C, Douglas HF, Stevens T, Riess ML | Journal of visualized experiments : JoVE | 37306411 | J Vis Exp | 2023 May 26 | https://www.ncbi.nlm.nih.gov/pubmed/37306411 |
| Novelties in pharmacological management of cardiopulmonary resuscitation. | Bartos JA, Yannopoulos D | Current opinion in critical care | 23995130 | Curr Opin Crit Care | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23995130 |
| Reperfusion injury protection during Basic Life Support improves circulation and survival outcomes in a porcine model of prolonged cardiac arrest. | Debaty G, Lurie K, Metzger A, Lick M, Bartos JA, Rees JN, McKnite S, Puertas L, Pepe P, Fowler R, Yannopoulos D | Resuscitation | 27211835 | Resuscitation | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27211835 |
| Opioid-induced cardioprotection. | Tanaka K, Kersten JR, Riess ML | Current pharmaceutical design | 24502571 | Curr Pharm Des | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24502571 |
| Sodium nitroprusside enhanced cardiopulmonary resuscitation improves short term survival in a porcine model of ischemic refractory ventricular fibrillation. | Yannopoulos D, Bartos JA, George SA, Sideris G, Voicu S, Oestreich B, Matsuura T, Shekar K, Rees J, Aufderheide TP | Resuscitation | 27771299 | Resuscitation | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27771299 |
| Lipid emulsion enhances cardiac performance after ischemia-reperfusion in isolated hearts from summer-active arctic ground squirrels. | Salzman MM, Cheng Q, Deklotz RJ, Dulai GK, Douglas HF, Dikalova AE, Weihrauch D, Barnes BM, Riess ML | Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology | 28364393 | J Comp Physiol B | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28364393 |
| Surgical Field Visualization during Functional Endoscopic Sinus Surgery: Comparison of Propofol- vs Desflurane-Based Anesthesia. | Gollapudy S, Gashkoff DA, Poetker DM, Loehrl TA, Riess ML | Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery | 32450733 | Otolaryngol Head Neck Surg | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32450733 |
| Cardioprotection by poloxamer 188 is mediated through increased endothelial nitric oxide production. | Chen G, Douglas HF, Li Z, Cleveland WJ, Balzer C, Yannopoulos D, Chen IY, Obal D, Riess ML | Scientific reports | 40307302 | Sci Rep | 2025 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/40307302 |
| Video laryngoscopic oral intubation in rats: a simple and effective method. | Balzer C, Cleveland WJ, Jinka TR, Riess ML | American journal of physiology. Lung cellular and molecular physiology | 32233786 | Am J Physiol Lung Cell Mol Physiol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/32233786 |
| Intralipid Increases Nitric Oxide Release from Human Endothelial Cells During Oxidative Stress. | Weihrauch D, Shumpert SD, Larson ME, McVey N, Krolikowski JG, Bamkole O, Riess ML | JPEN. Journal of parenteral and enteral nutrition | 32291784 | JPEN J Parenter Enteral Nutr | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32291784 |
| New Developments in Cardiac Arrest Management. | Riess ML | Advances in anesthesia | 28867873 | Adv Anesth | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/28867873 |
| PPARγ-Independent Side Effects of Thiazolidinediones on Mitochondrial Redox State in Rat Isolated Hearts. | Riess ML, Elorbany R, Weihrauch D, Stowe DF, Camara AKS | Cells | 31968546 | Cells | 2020 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/31968546 |
| MicroRNA-21 Mediates Isoflurane-induced Cardioprotection against Ischemia-Reperfusion Injury via Akt/Nitric Oxide Synthase/Mitochondrial Permeability Transition Pore Pathway. | Qiao S, Olson JM, Paterson M, Yan Y, Zaja I, Liu Y, Riess ML, Kersten JR, Liang M, Warltier DC, Bosnjak ZJ, Ge ZD | Anesthesiology | 26259139 | Anesthesiology | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26259139 |
| Potential Effects of Poloxamer 188 on Rat Isolated Brain Mitochondria after Oxidative Stress In Vivo and In Vitro. | Pille JA, Riess ML | Brain sciences | 33477541 | Brain Sci | 2021 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/33477541 |
| Poloxamer 188 Exerts Direct Protective Effects on Mouse Brain Microvascular Endothelial Cells in an In Vitro Traumatic Brain Injury Model. | Lotze FP, Riess ML | Biomedicines | 34440247 | Biomedicines | 2021 Aug 19 | https://www.ncbi.nlm.nih.gov/pubmed/34440247 |
| High central venous pressure amplitude predicts successful defibrillation in a porcine model of cardiac arrest. | Balzer C, Eagle SS, Yannopoulos D, Aufderheide TP, Riess ML | Resuscitation | 36736947 | Resuscitation | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/36736947 |
| Therapeutic Hypothermia in Children. | Riess ML, Aufderheide TP, Yannopoulos D | The New England journal of medicine | 26332560 | N Engl J Med | 2015 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/26332560 |
| Noninvasively Measured Hemoglobin Concentration Reflects Arterial Hemoglobin Concentration Before but Not After Cardiopulmonary Bypass in Patients Undergoing Coronary Artery or Valve Surgery. | Riess ML, Pagel PS | Journal of cardiothoracic and vascular anesthesia | 27475734 | J Cardiothorac Vasc Anesth | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27475734 |
| Identifying Candidates for Advanced Hemodynamic Support After Cardiac Arrest. | Bartos JA, Doonan AL, Yannopoulos D | Circulation | 29335287 | Circulation | 2018 Jan 16 | https://www.ncbi.nlm.nih.gov/pubmed/29335287 |
| Venous Waveform Analysis Correlates With Echocardiography in Detecting Hypovolemia in a Rat Hemorrhage Model. | Lefevre RJ, Balzer C, Baudenbacher FJ, Riess ML, Hernandez A, Eagle SS | Seminars in cardiothoracic and vascular anesthesia | 32957831 | Semin Cardiothorac Vasc Anesth | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32957831 |
| Arterial flow waveforms, vascular tone, and chronic fatigue: a case report. | Zundel MT, Pattyn M, Chelimsky TC, Riess ML | Autonomic neuroscience : basic & clinical | 25817901 | Auton Neurosci | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25817901 |
| Total intravenous versus inhaled anesthesia in transsphenoidal tumor surgery. | Gollapudy S, Poetker DM, Sidhu J, Riess ML | American journal of otolaryngology | 30017373 | Am J Otolaryngol | 2018 Sep-Oct | https://www.ncbi.nlm.nih.gov/pubmed/30017373 |
| Sounds Impossible, but It's Knot. | Smith LE, Heath DR, Riess ML | Anesthesiology | 30632983 | Anesthesiology | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30632983 |
| Poloxamer 188 Protects Isolated Adult Mouse Cardiomyocytes from Reoxygenation Injury. | Salzman MM, Bartos JA, Yannopoulos D, Riess ML | Pharmacology research & perspectives | 33073927 | Pharmacol Res Perspect | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33073927 |
| Non-invasive cardiac output monitoring during sinus surgery. | Gollapudy S, Riess ML | Journal of anesthesia | 25543335 | J Anesth | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25543335 |
| Increasing body mass index predicts increasing difficulty, failure rate, and time to discovery of failure of epidural anesthesia in laboring patients. | Kula AO, Riess ML, Ellinas EH | Journal of clinical anesthesia | 28235511 | J Clin Anesth | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28235511 |
| A new method to predict return of spontaneous circulation by peripheral intravenous analysis during cardiopulmonary resuscitation: a rat model pilot study. | Balzer C, Eagle SS, Baudenbacher FJ, Riess ML | Intensive care medicine experimental | 39531090 | Intensive Care Med Exp | 2024 Nov 12 | https://www.ncbi.nlm.nih.gov/pubmed/39531090 |
| Towards bedside washing of stored red blood cells: a prototype of a simple apparatus based on microscale sedimentation in normal gravity. | Khanal G, Huynh RA, Torabian K, Xia H, Vörös E, Shevkoplyas SS | Vox sanguinis | 29067695 | Vox Sang | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/29067695 |
| Washing in hypotonic saline reduces the fraction of irreversibly-damaged cells in stored blood: a proof-of-concept study. | Xia H, Khanal G, Strachan BC, Vörös E, Piety NZ, Gifford SC, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 28686152 | Blood Transfus | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28686152 |
| Substituting Sodium Hydrosulfite with Sodium Metabisulfite Improves Long-Term Stability of a Distributable Paper-Based Test Kit for Point-of-Care Screening for Sickle Cell Anemia. | Torabian K, Lezzar D, Piety NZ, George A, Shevkoplyas SS | Biosensors | 28930183 | Biosensors (Basel) | 2017 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/28930183 |
| A rapid paper-based test for quantifying sickle hemoglobin in blood samples from patients with sickle cell disease. | Piety NZ, Yang X, Lezzar D, George A, Shevkoplyas SS | American journal of hematology | 25689370 | Am J Hematol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25689370 |
| Density-based separation in multiphase systems provides a simple method to identify sickle cell disease. | Kumar AA, Patton MR, Hennek JW, Lee SY, D'Alesio-Spina G, Yang X, Kanter J, Shevkoplyas SS, Brugnara C, Whitesides GM | Proceedings of the National Academy of Sciences of the United States of America | 25197072 | Proc Natl Acad Sci U S A | 2014 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/25197072 |
| A Paper-Based Test for Screening Newborns for Sickle Cell Disease. | Piety NZ, George A, Serrano S, Lanzi MR, Patel PR, Noli MP, Kahan S, Nirenberg D, Camanda JF, Airewele G, Shevkoplyas SS | Scientific reports | 28367971 | Sci Rep | 2017 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/28367971 |
| Traditional and emerging technologies for washing and volume reducing blood products. | Lu M, Lezzar DL, Vörös E, Shevkoplyas SS | Journal of blood medicine | 30655711 | J Blood Med | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30655711 |
| Improved expansion of T cells in culture when isolated with an equipment-free, high-throughput, flow-through microfluidic module versus traditional density gradient centrifugation. | Strachan BC, Xia H, Vörös E, Gifford SC, Shevkoplyas SS | Cytotherapy | 30660490 | Cytotherapy | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30660490 |
| C4d deposits on the surface of RBCs in trauma patients and interferes with their function. | Muroya T, Kannan L, Ghiran IC, Shevkoplyas SS, Paz Z, Tsokos M, Dalle Lucca JJ, Shapiro NI, Tsokos GC | Critical care medicine | 24448198 | Crit Care Med | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24448198 |
| The relationship between red blood cell deformability metrics and perfusion of an artificial microvascular network. | Sosa JM, Nielsen ND, Vignes SM, Chen TG, Shevkoplyas SS | Clinical hemorheology and microcirculation | 23603326 | Clin Hemorheol Microcirc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/23603326 |
| Shape matters: the effect of red blood cell shape on perfusion of an artificial microvascular network. | Piety NZ, Reinhart WH, Pourreau PH, Abidi R, Shevkoplyas SS | Transfusion | 26711854 | Transfusion | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26711854 |
| Deterioration of red blood cell mechanical properties is reduced in anaerobic storage. | Burns JM, Yoshida T, Dumont LJ, Yang X, Piety NZ, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 26674833 | Blood Transfus | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26674833 |
| Quantifying morphological heterogeneity: a study of more than 1 000 000 individual stored red blood cells. | Piety NZ, Gifford SC, Yang X, Shevkoplyas SS | Vox sanguinis | 25900518 | Vox Sang | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25900518 |
| Validation of a Low-Cost Paper-Based Screening Test for Sickle Cell Anemia. | Piety NZ, Yang X, Kanter J, Vignes SM, George A, Shevkoplyas SS | PloS one | 26735691 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26735691 |
| Washing stored red blood cells in an albumin solution improves their morphologic and hemorheologic properties. | Reinhart WH, Piety NZ, Deuel JW, Makhro A, Schulzki T, Bogdanov N, Goede JS, Bogdanova A, Abidi R, Shevkoplyas SS | Transfusion | 25752902 | Transfusion | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25752902 |
| A portable system for processing donated whole blood into high quality components without centrifugation. | Gifford SC, Strachan BC, Xia H, Vörös E, Torabian K, Tomasino TA, Griffin GD, Lichtiger B, Aung FM, Shevkoplyas SS | PloS one | 29346441 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29346441 |
| Dynamics of shape recovery by stored red blood cells during washing at the single cell level. | Lu M, Shevkoplyas SS | Transfusion | 32748970 | Transfusion | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32748970 |
| Centrifugation-free washing: A novel approach for removing immunoglobulin A from stored red blood cells. | Vörös E, Piety NZ, Strachan BC, Lu M, Shevkoplyas SS | American journal of hematology | 29285804 | Am J Hematol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29285804 |
| Optimal hematocrit in an artificial microvascular network. | Piety NZ, Reinhart WH, Stutz J, Shevkoplyas SS | Transfusion | 28681482 | Transfusion | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28681482 |
| Influence of feeding hematocrit and perfusion pressure on hematocrit reduction (Fåhraeus effect) in an artificial microvascular network. | Reinhart WH, Piety NZ, Shevkoplyas SS | Microcirculation (New York, N.Y. : 1994) | 28801994 | Microcirculation | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28801994 |
| Deep ensemble learning enables highly accurate classification of stored red blood cell morphology. | Routt AH, Yang N, Piety NZ, Lu M, Shevkoplyas SS | Scientific reports | 36823298 | Sci Rep | 2023 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/36823298 |
| Microfluidic capillary networks are more sensitive than ektacytometry to the decline of red blood cell deformability induced by storage. | Piety NZ, Stutz J, Yilmaz N, Xia H, Yoshida T, Shevkoplyas SS | Scientific reports | 33436749 | Sci Rep | 2021 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/33436749 |
| Simple paper-based test for measuring blood hemoglobin concentration in resource-limited settings. | Yang X, Piety NZ, Vignes SM, Benton MS, Kanter J, Shevkoplyas SS | Clinical chemistry | 23788584 | Clin Chem | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23788584 |
| Controlled incremental filtration: a simplified approach to design and fabrication of high-throughput microfluidic devices for selective enrichment of particles. | Gifford SC, Spillane AM, Vignes SM, Shevkoplyas SS | Lab on a chip | 25254358 | Lab Chip | 2014 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/25254358 |
| Effect of osmolality on erythrocyte rheology and perfusion of an artificial microvascular network. | Reinhart WH, Piety NZ, Goede JS, Shevkoplyas SS | Microvascular research | 25660474 | Microvasc Res | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25660474 |
| Influence of red blood cell aggregation on perfusion of an artificial microvascular network. | Reinhart WH, Piety NZ, Shevkoplyas SS | Microcirculation (New York, N.Y. : 1994) | 27647727 | Microcirculation | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27647727 |
| A high-throughput microfluidic approach for 1000-fold leukocyte reduction of platelet-rich plasma. | Xia H, Strachan BC, Gifford SC, Shevkoplyas SS | Scientific reports | 27775049 | Sci Rep | 2016 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/27775049 |
| Centrifugation-free washing reduces buildup of potassium and free hemoglobin in washed red blood cells after the procedure. | Vörös E, Lu M, Lezzar D, Shevkoplyas SS | American journal of hematology | 30184257 | Am J Hematol | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30184257 |
| Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa. | Basta DW, Bergkessel M, Newman DK | mBio | 29184024 | mBio | 2017 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/29184024 |
| Sputum glucose and glycemic control in cystic fibrosis-related diabetes: a cross-sectional study. | Van Sambeek L, Cowley ES, Newman DK, Kato R | PloS one | 25803537 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25803537 |
| SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. | Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA | Proceedings of the National Academy of Sciences of the United States of America | 26787849 | Proc Natl Acad Sci U S A | 2016 Feb 2 | https://www.ncbi.nlm.nih.gov/pubmed/26787849 |
| The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. | Kreamer NN, Costa F, Newman DK | mBio | 25714721 | mBio | 2015 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/25714721 |
| Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity. | Gallego-Hernandez AL, DePas WH, Park JH, Teschler JK, Hartmann R, Jeckel H, Drescher K, Beyhan S, Newman DK, Yildiz FH | Proceedings of the National Academy of Sciences of the United States of America | 32355001 | Proc Natl Acad Sci U S A | 2020 May 19 | https://www.ncbi.nlm.nih.gov/pubmed/32355001 |
| Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa. | Racki LR, Tocheva EI, Dieterle MG, Sullivan MC, Jensen GJ, Newman DK | Proceedings of the National Academy of Sciences of the United States of America | 28265086 | Proc Natl Acad Sci U S A | 2017 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/28265086 |
| The Pyruvate and α-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase. | Glasser NR, Wang BX, Hoy JA, Newman DK | The Journal of biological chemistry | 28174304 | J Biol Chem | 2017 Mar 31 | https://www.ncbi.nlm.nih.gov/pubmed/28174304 |
| Ferrous iron is a significant component of bioavailable iron in cystic fibrosis airways. | Hunter RC, Asfour F, Dingemans J, Osuna BL, Samad T, Malfroot A, Cornelis P, Newman DK | mBio | 23963183 | mBio | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/23963183 |
| Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum. | Kopf SH, Sessions AL, Cowley ES, Reyes C, Van Sambeek L, Hu Y, Orphan VJ, Kato R, Newman DK | Proceedings of the National Academy of Sciences of the United States of America | 26715741 | Proc Natl Acad Sci U S A | 2016 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/26715741 |
| Predicting the impact of promoter variability on regulatory outputs. | Kreamer NN, Phillips R, Newman DK, Boedicker JQ | Scientific reports | 26675057 | Sci Rep | 2015 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/26675057 |
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| Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. | Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC | Journal of the American Chemical Society | 25314576 | J Am Chem Soc | 2014 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/25314576 |
| Polymerization of Protecting-Group-Free Peptides via ROMP. | Kammeyer JK, Blum AP, Adamiak L, Hahn ME, Gianneschi NC | Polymer chemistry | 24015154 | Polym Chem | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24015154 |
| Polymerization of a peptide-based enzyme substrate. | Hahn ME, Randolph LM, Adamiak L, Thompson MP, Gianneschi NC | Chemical communications (Cambridge, England) | 23450132 | Chem Commun (Camb) | 2013 Apr 11 | https://www.ncbi.nlm.nih.gov/pubmed/23450132 |
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| Bioactive Peptide Brush Polymers via Photoinduced Reversible-Deactivation Radical Polymerization. | Sun H, Choi W, Zang N, Battistella C, Thompson MP, Cao W, Zhou X, Forman C, Gianneschi NC | Angewandte Chemie (International ed. in English) | 31595626 | Angew Chem Int Ed Engl | 2019 Nov 25 | https://www.ncbi.nlm.nih.gov/pubmed/31595626 |
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| Polymeric Gd-DOTA amphiphiles form spherical and fibril-shaped nanoparticle MRI contrast agents. | Randolph LM, LeGuyader CLM, Hahn ME, Andolina CM, Patterson JP, Mattrey RF, Millstone JE, Botta M, Scadeng M, Gianneschi NC | Chemical science | 30155069 | Chem Sci | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/30155069 |
| pH-Responsive Charge-Conversion Progelator Peptides. | Carlini AS, Choi W, McCallum NC, Gianneschi NC | Advanced functional materials | 36530181 | Adv Funct Mater | 2021 Mar 24 | https://www.ncbi.nlm.nih.gov/pubmed/36530181 |
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| 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 |
| Enzyme-Targeted Nanoparticles for Delivery to Ischemic Skeletal Muscle. | Ungerleider JL, Kammeyer JK, Braden RL, Christman KL, Gianneschi NC | Polymer chemistry | 29098018 | Polym Chem | 2017 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/29098018 |
| Enzyme-Responsive Nanoparticles for Targeted Accumulation and Prolonged Retention in Heart Tissue after Myocardial Infarction. | Nguyen MM, Carlini AS, Chien MP, Sonnenberg S, Luo C, Braden RL, Osborn KG, Li Y, Gianneschi NC, Christman KL | Advanced materials (Deerfield Beach, Fla.) | 26305446 | Adv Mater | 2015 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/26305446 |
| Development of a Synthetic 3-ketosteroid Δ(1)-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells. | D'Arcy BM, Swingle MR, Schambeau L, Pannell L, Prakash A, Honkanen RE | Scientific reports | 30979909 | Sci Rep | 2019 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/30979909 |
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| Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy. | Schain AJ, Hill RA, Grutzendler J | Nature medicine | 24681598 | Nat Med | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24681598 |
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| Regional Blood Flow in the Normal and Ischemic Brain Is Controlled by Arteriolar Smooth Muscle Cell Contractility and Not by Capillary Pericytes. | Hill RA, Tong L, Yuan P, Murikinati S, Gupta S, Grutzendler J | Neuron | 26119027 | Neuron | 2015 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/26119027 |
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| Angiophagy prevents early embolus washout but recanalizes microvessels through embolus extravasation. | Grutzendler J, Murikinati S, Hiner B, Ji L, Lam CK, Yoo T, Gupta S, Hafler BP, Adelman RA, Yuan P, Rodriguez G | Science translational medicine | 24598589 | Sci Transl Med | 2014 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/24598589 |
| TREM2 Haplodeficiency in Mice and Humans Impairs the Microglia Barrier Function Leading to Decreased Amyloid Compaction and Severe Axonal Dystrophy. | Yuan P, Condello C, Keene CD, Wang Y, Bird TD, Paul SM, Luo W, Colonna M, Baddeley D, Grutzendler J | Neuron | 27196974 | Neuron | 2016 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/27196974 |
| Attenuation of β-Amyloid Deposition and Neurotoxicity by Chemogenetic Modulation of Neural Activity. | Yuan P, Grutzendler J | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26758850 | J Neurosci | 2016 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/26758850 |
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| Microtubule dynamics regulate cyclic stretch-induced cell alignment in human airway smooth muscle cells. | Morioka M, Parameswaran H, Naruse K, Kondo M, Sokabe M, Hasegawa Y, Suki B, Ito S | PloS one | 22022610 | PLoS One | 2011 | https://www.ncbi.nlm.nih.gov/pubmed/22022610 |
| Correlated variability in the breathing pattern and end-expiratory lung volumes in conscious humans. | Dellaca RL, Aliverti A, Lo Mauro A, Lutchen KR, Pedotti A, Suki B | PloS one | 25803710 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25803710 |
| Complexity and emergent phenomena. | Suki B, Bates JH, Frey U | Comprehensive Physiology | 23737210 | Compr Physiol | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/23737210 |
| Aging impairs smooth muscle-mediated regulation of aortic stiffness: a defect in shock absorption function? | Gao YZ, Saphirstein RJ, Yamin R, Suki B, Morgan KG | American journal of physiology. Heart and circulatory physiology | 25128168 | Am J Physiol Heart Circ Physiol | 2014 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/25128168 |
| Regulation of Gastrointestinal Smooth Muscle Function by Interstitial Cells. | Sanders KM, Kito Y, Hwang SJ, Ward SM | Physiology (Bethesda, Md.) | 27488743 | Physiology (Bethesda) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27488743 |
| Proteoglycans maintain lung stability in an elastase-treated mouse model of emphysema. | Takahashi A, Majumdar A, Parameswaran H, Bartolák-Suki E, Suki B | American journal of respiratory cell and molecular biology | 24450478 | Am J Respir Cell Mol Biol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24450478 |
| Epithelial and endothelial damage induced by mechanical ventilation modes. | Suki B, Hubmayr R | Current opinion in critical care | 24300621 | Curr Opin Crit Care | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24300621 |
| Combined effects of ventilation mode and positive end-expiratory pressure on mechanics, gas exchange and the epithelium in mice with acute lung injury. | Thammanomai A, Hamakawa H, Bartolák-Suki E, Suki B | PloS one | 23326543 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23326543 |
| Homeostatic maintenance via degradation and repair of elastic fibers under tension. | Alves C, Araújo AD, Oliveira CL, Imsirovic J, Bartolák-Suki E, Andrade JS, Suki B | Scientific reports | 27279029 | Sci Rep | 2016 Jun 9 | https://www.ncbi.nlm.nih.gov/pubmed/27279029 |
| Scale dependence of structure-function relationship in the emphysematous mouse lung. | Sato S, Bartolák-Suki E, Parameswaran H, Hamakawa H, Suki B | Frontiers in physiology | 26029115 | Front Physiol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26029115 |
| Variable ventilation enhances ventilation without exacerbating injury in preterm lambs with respiratory distress syndrome. | Berry CA, Suki B, Polglase GR, Pillow JJ | Pediatric research | 22805999 | Pediatr Res | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22805999 |
| Computational modeling helps uncover mechanisms related to the progression of emphysema. | Suki B, Parameswaran H | Drug discovery today. Disease models | 24904681 | Drug Discov Today Dis Models | 2014 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/24904681 |
| Lung tissue mechanics as an emergent phenomenon. | Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21212247 | J Appl Physiol (1985) | 2011 Apr | https://www.ncbi.nlm.nih.gov/pubmed/21212247 |
| Tidal stretches differently regulate the contractile and cytoskeletal elements in intact airways. | Bartolák-Suki E, LaPrad AS, Harvey BC, Suki B, Lutchen KR | PloS one | 24740101 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24740101 |
| Regulatory Roles of Fluctuation-Driven Mechanotransduction in Cell Function. | Suki B, Parameswaran H, Imsirovic J, Bartolák-Suki E | Physiology (Bethesda, Md.) | 27511461 | Physiology (Bethesda) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27511461 |
| The major transitions of life from a network perspective. | Suki B | Frontiers in physiology | 22514542 | Front Physiol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22514542 |
| A novel device to stretch multiple tissue samples with variable patterns: application for mRNA regulation in tissue-engineered constructs. | Imsirovic J, Derricks K, Buczek-Thomas JA, Rich CB, Nugent MA, Suki B | Biomatter | 23628870 | Biomatter | 2013 Jul-Sep | https://www.ncbi.nlm.nih.gov/pubmed/23628870 |
| Monitoring the temporal changes of respiratory resistance: a novel test for the management of asthma. | Gulotta C, Suki B, Brusasco V, Pellegrino R, Gobbi A, Pedotti A, Dellacà RL | American journal of respiratory and critical care medicine | 22707741 | Am J Respir Crit Care Med | 2012 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/22707741 |
| Effects of recruitment/derecruitment dynamics on the efficacy of variable ventilation. | Ma B, Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21372101 | J Appl Physiol (1985) | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21372101 |
| A mechanical design principle for tissue structure and function in the airway tree. | LaPrad AS, Lutchen KR, Suki B | PLoS computational biology | 23737742 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23737742 |
| Variable ventilation improves ventilation and lung compliance in preterm lambs. | Pillow JJ, Musk GC, McLean CM, Polglase GR, Dalton RG, Jobe AH, Suki B | Intensive care medicine | 21567115 | Intensive Care Med | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21567115 |
| Acute mechanical forces cause deterioration in lung structure and function in elastase-induced emphysema. | Szabari MV, Parameswaran H, Sato S, Hantos Z, Bartolák-Suki E, Suki B | American journal of physiology. Lung cellular and molecular physiology | 22865550 | Am J Physiol Lung Cell Mol Physiol | 2012 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/22865550 |
| Design of a Novel Equi-Biaxial Stretcher for Live Cellular and Subcellular Imaging. | Imsirovic J, Wellman TJ, Mondoñedo JR, Bartolák-Suki E, Suki B | PloS one | 26466363 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26466363 |
| Fluctuation-driven mechanotransduction regulates mitochondrial-network structure and function. | Bartolák-Suki E, Imsirovic J, Parameswaran H, Wellman TJ, Martinez N, Allen PG, Frey U, Suki B | Nature materials | 26213900 | Nat Mater | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/26213900 |
| Emphysema and mechanical stress-induced lung remodeling. | Suki B, Sato S, Parameswaran H, Szabari MV, Takahashi A, Bartolák-Suki E | Physiology (Bethesda, Md.) | 24186935 | Physiology (Bethesda) | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/24186935 |
| A network model of correlated growth of tissue stiffening in pulmonary fibrosis. | Oliveira CL, Bates JH, Suki B | New journal of physics | 25484613 | New J Phys | 2014 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/25484613 |
| A computational model of the response of adherent cells to stretch and changes in substrate stiffness. | Parameswaran H, Lutchen KR, Suki B | Journal of applied physiology (Bethesda, Md. : 1985) | 24408996 | J Appl Physiol (1985) | 2014 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/24408996 |
| Efficient formation of single-copy human artificial chromosomes. | Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE | Science (New York, N.Y.) | 38513017 | Science | 2024 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/38513017 |
| Efficient Formation of Single-copy Human Artificial Chromosomes. | Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE | bioRxiv : the preprint server for biology | 37546784 | bioRxiv | 2023 Jun 30 | https://www.ncbi.nlm.nih.gov/pubmed/37546784 |
| Independent phenotypic plasticity axes define distinct obesity sub-types. | Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, PERMUTE, Pospisilik JA | Nature metabolism | 36097183 | Nat Metab | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36097183 |
| Epigenetic dosage identifies two major and functionally distinct β cell subtypes. | Dror E, Fagnocchi L, Wegert V, Apostle S, Grimaldi B, Gruber T, Panzeri I, Heyne S, Höffler KD, Kreiner V, Ching R, Tsai-Hsiu Lu T, Semwal A, Johnson B, Senapati P, Lempradl A, Schones D, Imhof A, Shen H, Pospisilik JA | Cell metabolism | 36948185 | Cell Metab | 2023 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/36948185 |
| An acute microglial metabolic response controls metabolism and improves memory. | Drougard A, Ma EH, Wegert V, Sheldon R, Panzeri I, Vatsa N, Apostle S, Fagnocchi L, Schaf J, Gossens K, Völker J, Pang S, Bremser A, Dror E, Giacona F, Sagar S, Henderson MX, Prinz M, Jones RG, Pospisilik JA | eLife | 39625057 | Elife | 2024 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/39625057 |
| BifurcatoR: A Framework for Revealing Clinically Actionable Signal in Variance Masquerading as Noise. | Madaj Z, Ding M, Khoo C, Tokarski E, Fagnocchi L, PERMUTE, Li Z, Riordan J, Pospisilik JA, Nadeau JH, Lary CW, Triche TJ | bioRxiv : the preprint server for biology | 40502166 | bioRxiv | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40502166 |
| TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states. | Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Yang CH, Bergsma A, Drougard A, Dror E, PERMUTE, Chandler DP, Schramek D, Triche TJ Jr, Pospisilik JA | Nature cancer | 39856421 | Nat Cancer | 2025 Feb | https://www.ncbi.nlm.nih.gov/pubmed/39856421 |
| Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies. | Rastegari F, Driscoll M, Riordan JD, Nadeau JH, Johnson JS, Weinstock GM | International journal of molecular sciences | 39940948 | Int J Mol Sci | 2025 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/39940948 |
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| The DECON pilot project investigates predictive markers for successful bariatric surgery. | Seifert G, Fagnocchi L, Edozie M, Herrmann S, Baumann H, Panzeri I, Mewes S, Aicher D, Runkel M, Lässle C, Fink J, Marjanovic G, Fichtner-Feigl S, Pospisilik JA | Scientific reports | 37591977 | Sci Rep | 2023 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/37591977 |
| Chronic obesity does not alter cancer incidence in Trp53 (R270H/+) mice. | Panzeri I, Madaj Z, Fagnocchi L, Apostle S, Tompkins M, Hostetter G, Pospisilik JA | bioRxiv : the preprint server for biology | 39463991 | bioRxiv | 2025 Mar 17 | https://www.ncbi.nlm.nih.gov/pubmed/39463991 |
| Isolation and Processing of Murine White Adipocytes for Transcriptome and Epigenome Analyses. | Yang CH, Longinotto J, Panzeri I, Arrigoni L, Wegert V, Heyne S, Seifert G, Lempradl A, Bönisch U, Pospisilik JA | Journal of visualized experiments : JoVE | 35786676 | J Vis Exp | 2022 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/35786676 |
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| D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. | Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M | bioRxiv : the preprint server for biology | 37131803 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/37131803 |
| AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. | Banhos Danneskiold-Samsøe N, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ | Cell systems | 39541981 | Cell Syst | 2024 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/39541981 |
| Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. | Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC | Science (New York, N.Y.) | 37499032 | Science | 2023 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/37499032 |
| TRILL: ORCHESTRATING MODULAR DEEP-LEARNING WORKFLOWS FOR DEMOCRATIZED, SCALABLE PROTEIN ANALYSIS AND ENGINEERING. | Martinez ZA, Murray RM, Thomson MW | bioRxiv : the preprint server for biology | 37986952 | bioRxiv | 2023 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/37986952 |
| Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. | Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC | eLife | 36178190 | Elife | 2022 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/36178190 |
| AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. | Danneskiold-Samsøe NB, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ | bioRxiv : the preprint server for biology | 36993313 | bioRxiv | 2023 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36993313 |
| Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models. | Subramanian AM, Martinez ZA, Lourenço AL, Liu S, Thomson M | bioRxiv : the preprint server for biology | 38187750 | bioRxiv | 2025 Jan 13 | https://www.ncbi.nlm.nih.gov/pubmed/38187750 |
| Protein CREATE enables closed-loop design of de novo synthetic protein binders. | Lourenço A, Subramanian A, Spencer R, Anaya M, Miao J, Fu W, Chow E, Thomson M | bioRxiv : the preprint server for biology | 39803556 | bioRxiv | 2025 Jan 2 | https://www.ncbi.nlm.nih.gov/pubmed/39803556 |
| Nanoarchitecture and molecular interactions of epithelial cell junction proteins revealed by super-resolution microscopy. | Naser AN, Guiler W, Lu Q, Chen YH | Annals of the New York Academy of Sciences | 35819053 | Ann N Y Acad Sci | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35819053 |
| TRPV4: En RhoA To a Cure? | Lu Q, Chen YH | BioEssays : news and reviews in molecular, cellular and developmental biology | 35441721 | Bioessays | 2022 Jun | https://www.ncbi.nlm.nih.gov/pubmed/35441721 |
| Therapeutic Effect of Y-27632 on Tumorigenesis and Cisplatin-Induced Peripheral Sensory Loss through RhoA-NF-κB. | Zhu Y, Howard GA, Pittman K, Boykin C, Herring LE, Wilkerson EM, Verbanac K, Lu Q | Molecular cancer research : MCR | 31189689 | Mol Cancer Res | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31189689 |
| RhoA-LIMK Signaling Axis Reveals Rostral-Caudal Plane and Spatial Dysregulation in the Brain of Alzheimer's Disease Mouse Models. | Nik Akhtar S, Lu Q | Journal of Alzheimer's disease : JAD | 37718806 | J Alzheimers Dis | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37718806 |
| Enabling systemic identification and functionality profiling for Cdc42 homeostatic modulators. | Malasala S, Azimian F, Chen YH, Twiss JL, Boykin C, Akhtar SN, Lu Q | Communications chemistry | 39562759 | Commun Chem | 2024 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/39562759 |
| Spatial and planar profiling of Rac1/Cdc42 signaling in Alzheimer's disease brain. | Akhtar SN, Tran TD, Chen YH, Lu Q | Journal of Alzheimer's disease : JAD | 39610278 | J Alzheimers Dis | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/39610278 |
| G-Protein Signaling in Alzheimer's Disease: Spatial Expression Validation of Semi-supervised Deep Learning-Based Computational Framework. | Zhang DF, Penwell T, Chen YH, Koehler A, Wu R, Nik Akhtar S, Lu Q | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39327003 | J Neurosci | 2024 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/39327003 |
| Selective axonal translation of the mRNA isoform encoding prenylated Cdc42 supports axon growth. | Lee SJ, Zdradzinski MD, Sahoo PK, Kar AN, Patel P, Kawaguchi R, Aguilar BJ, Lantz KD, McCain CR, Coppola G, Lu Q, Twiss JL | Journal of cell science | 33674450 | J Cell Sci | 2021 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/33674450 |
| Trans-Compartmental Regulation of Tight Junction Barrier Function. | Naser AN, Lu Q, Chen YH | Tissue barriers | 36220768 | Tissue Barriers | 2023 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/36220768 |
| Crosstalk between the Rho and Rab family of small GTPases in neurodegenerative disorders. | Nik Akhtar S, Bunner WP, Brennan E, Lu Q, Szatmari EM | Frontiers in cellular neuroscience | 36779014 | Front Cell Neurosci | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/36779014 |
| KHSRP-mediated Decay of Axonally Localized Prenyl-Cdc42 mRNA Slows Nerve Regeneration. | Zdradzinski MD, Vaughn LS, Matoo S, Trumbull K, Loomis A, Thames E, Lee SJ, Perrone-Bizzozero N, Lu Q, Larsen JM, Twiss JL | bioRxiv : the preprint server for biology | 39975228 | bioRxiv | 2025 Feb 8 | https://www.ncbi.nlm.nih.gov/pubmed/39975228 |
| 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 |
| FZD2 Regulates Murine Hair Follicle Function and Maintenance. | Brennan-Crispi DM, Frankfurter M, Murphy C, Sheng E, Xu M, Morrisey EE, Millar SE, Leung TH | The Journal of investigative dermatology | 35051380 | J Invest Dermatol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35051380 |
| 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 |
| Systematically quantifying morphological features reveals constraints on organoid phenotypes. | Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A | Cell systems | 35705097 | Cell Syst | 2022 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/35705097 |
| Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. | Sanford EM, Emert BL, Coté A, Raj A | eLife | 33284110 | Elife | 2020 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/33284110 |
| Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. | Kiani K, Sanford EM, Goyal Y, Raj A | Molecular systems biology | 36069349 | Mol Syst Biol | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36069349 |
| 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 |
| Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states. | Reffsin S, Miller J, Ayyanathan K, Dunagin MC, Jain N, Schultz DC, Cherry S, Raj A | bioRxiv : the preprint server for biology | 37461472 | bioRxiv | 2023 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/37461472 |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene. | Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A | eLife | 38577979 | Elife | 2024 Apr 5 | https://www.ncbi.nlm.nih.gov/pubmed/38577979 |
| Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. | Boe RH, Triandafillou CG, Lazcano R, Wargo JA, Raj A | bioRxiv : the preprint server for biology | 39005406 | bioRxiv | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/39005406 |
| Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A | Cell systems | 38335955 | Cell Syst | 2024 Feb 21 | https://www.ncbi.nlm.nih.gov/pubmed/38335955 |
| Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A | bioRxiv : the preprint server for biology | 36798299 | bioRxiv | 2023 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/36798299 |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A | Nature genetics | 33398196 | Nat Genet | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33398196 |
| Innate Immune Memory is Stimulus Specific. | O'Farrell A, Niu Z, Li J, Van Eyndhoven LC, Sarma K, Raj A | bioRxiv : the preprint server for biology | 39896612 | bioRxiv | 2025 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/39896612 |
| AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance. | Li J, Ravindran PT, O'Farrell A, Busch GT, Boe RH, Niu Z, Woo S, Dunagin MC, Jain N, Goyal Y, Sarma K, Herlyn M, Raj A | bioRxiv : the preprint server for biology | 39091739 | bioRxiv | 2024 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/39091739 |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y | Cell systems | 32325034 | Cell Syst | 2020 Apr 22 | https://www.ncbi.nlm.nih.gov/pubmed/32325034 |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A | Nature biotechnology | 33619394 | Nat Biotechnol | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/33619394 |
| ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. | Dardani I, Emert BL, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A | Nature methods | 36280724 | Nat Methods | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36280724 |
| Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. | Boe RH, Ayyappan V, Schuh L, Raj A | Cell systems | 36450286 | Cell Syst | 2022 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/36450286 |
| Social reprogramming in ants induces longevity-associated glia remodeling. | Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R | Science advances | 32875108 | Sci Adv | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/32875108 |
| Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. | Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A | Cell | 32735851 | Cell | 2020 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/32735851 |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. | Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A | Cell systems | 34352221 | Cell Syst | 2021 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/34352221 |
| 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 |
| Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. | Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A | Nature | 37468627 | Nature | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37468627 |
| Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190. | Dickson P, Abegg D, Vinogradova E, Takaya J, An H, Simanski S, Cravatt BF, Adibekian A, Kodadek T | Cell chemical biology | 32857985 | Cell Chem Biol | 2020 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/32857985 |
| Applications and Limitations of Oxime-Linked "Split PROTACs". | Gui W, Kodadek T | Chembiochem : a European journal of chemical biology | 35802347 | Chembiochem | 2022 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/35802347 |
| Facile Synthesis of Homodimeric Protein Ligands. | Gui W, Kodadek T | Chembiochem : a European journal of chemical biology | 37449865 | Chembiochem | 2023 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/37449865 |
| Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin. | McEnaney P , Balzarini M , Park H , Kodadek T | Chemical communications (Cambridge, England) | 32785302 | Chem Commun (Camb) | 2020 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/32785302 |
| Beyond protein binding: recent advances in screening DNA-encoded libraries. | Kodadek T, Paciaroni NG, Balzarini M, Dickson P | Chemical communications (Cambridge, England) | 31633708 | Chem Commun (Camb) | 2019 Nov 18 | https://www.ncbi.nlm.nih.gov/pubmed/31633708 |
| Solid-phase synthesis of DNA-encoded libraries via an "aldehyde explosion" strategy. | Paciaroni NG , Ndungu JM , Kodadek T | Chemical communications (Cambridge, England) | 32215395 | Chem Commun (Camb) | 2020 Apr 30 | https://www.ncbi.nlm.nih.gov/pubmed/32215395 |
| Reversible Assembly of Proteolysis Targeting Chimeras. | Gui W, Giardina SF, Balzarini M, Barany F, Kodadek T | ACS chemical biology | 37422908 | ACS Chem Biol | 2023 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/37422908 |
| Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11. | Dickson P, Simanski S, Ngundu JM, Kodadek T | Cell chemical biology | 32857986 | Cell Chem Biol | 2020 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/32857986 |
| Chemical composition of DNA-encoded libraries, past present and future. | Dickson P, Kodadek T | Organic & biomolecular chemistry | 31017595 | Org Biomol Chem | 2019 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/31017595 |
| Synthesis and Screening of a DNA-Encoded Library of Non-Peptidic Macrocycles. | Koesema E, Roy A, Paciaroni NG, Coito C, Tokmina-Roszyk M, Kodadek T | Angewandte Chemie (International ed. in English) | 35192245 | Angew Chem Int Ed Engl | 2022 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/35192245 |
| Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets. | Li Y, Abraham C, Suslov O, Yaren O, Shaw RW, Kim MJ, Wan S, Marliere P, Benner SA | ACS synthetic biology | 37227319 | ACS Synth Biol | 2023 Jun 16 | https://www.ncbi.nlm.nih.gov/pubmed/37227319 |
| Ligand-Guided Selection with Artificially Expanded Genetic Information Systems against TCR-CD3ε. | Zumrut H, Yang Z, Williams N, Arizala J, Batool S, Benner SA, Mallikaratchy P | Biochemistry | 31880917 | Biochemistry | 2020 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/31880917 |
| Hachimoji DNA and RNA: A genetic system with eight building blocks. | Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE Jr, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J Jr, Georgiadis MM, Benner SA | Science (New York, N.Y.) | 30792304 | Science | 2019 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/30792304 |
| Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. | Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM | Nucleic acids research | 29986111 | Nucleic Acids Res | 2018 Sep 6 | https://www.ncbi.nlm.nih.gov/pubmed/29986111 |
| Electrochemical Reduction and Oxidation of Eight Unnatural 2'-Deoxynucleosides at a Pyrolytic Graphite Electrode. | Špaček J, Karalkar N, Fojta M, Wang J, Benner SA | Electrochimica acta | 33087943 | Electrochim Acta | 2020 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/33087943 |
| A folding motif formed with an expanded genetic alphabet. | Wang B, Rocca JR, Hoshika S, Chen C, Yang Z, Esmaeeli R, Wang J, Pan X, Lu J, Wang KK, Cao YC, Tan W, Benner SA | Nature chemistry | 38858518 | Nat Chem | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38858518 |
| Building better polymerases: Engineering the replication of expanded genetic alphabets. | Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ | The Journal of biological chemistry | 33004440 | J Biol Chem | 2020 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/33004440 |
| Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. | Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW | Molecules (Basel, Switzerland) | 38474636 | Molecules | 2024 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/38474636 |
| Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. | Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA | Nature communications | 37884513 | Nat Commun | 2023 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/37884513 |
| Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. | Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH | Journal of the American Chemical Society | 37036666 | J Am Chem Soc | 2023 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/37036666 |
| An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. | Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W | Angewandte Chemie (International ed. in English) | 31650689 | Angew Chem Int Ed Engl | 2020 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/31650689 |
| The processivity factor Pol32 mediates nuclear localization of DNA polymerase delta and prevents chromosomal fragile site formation in Drosophila development. | Ji J, Tang X, Hu W, Maggert KA, Rong YS | PLoS genetics | 31100062 | PLoS Genet | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31100062 |
| Under the magnifying glass: The ups and downs of rDNA copy number. | Kindelay SM, Maggert KA | Seminars in cell & developmental biology | 35595601 | Semin Cell Dev Biol | 2023 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/35595601 |
| Stress: An evolutionary mutagen. | Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 31434787 | Proc Natl Acad Sci U S A | 2019 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/31434787 |
| The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. | Bughio F, Maggert KA | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 30511202 | Chromosome Res | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30511202 |
| Human rDNA copy number is unstable in metastatic breast cancers. | Valori V, Tus K, Laukaitis C, Harris DT, LeBeau L, Maggert KA | Epigenetics | 31352858 | Epigenetics | 2020 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/31352858 |
| Live analysis of position-effect variegation in Drosophila reveals different modes of action for HP1a and Su(var)3-9. | Bughio FJ, Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 35704756 | Proc Natl Acad Sci U S A | 2022 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/35704756 |
| Monitoring of switches in heterochromatin-induced silencing shows incomplete establishment and developmental instabilities. | Bughio F, Huckell GR, Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 31527269 | Proc Natl Acad Sci U S A | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31527269 |
| Proteins for increased surface expression of the α6β4 nicotinic acetylcholine receptor: nothing but good news? | Grant S, Lester HA | The Journal of clinical investigation | 33074245 | J Clin Invest | 2020 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/33074245 |
| 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 |
| Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors. | Shivange AV, Borden PM, Muthusamy AK, Nichols AL, Bera K, Bao H, Bishara I, Jeon J, Mulcahy MJ, Cohen B, O'Riordan SL, Kim C, Dougherty DA, Chapman ER, Marvin JS, Looger LL, Lester HA | The Journal of general physiology | 30718376 | J Gen Physiol | 2019 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/30718376 |
| Correction: Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands. | Nichols AL, Blumenfeld Z, Fan C, Luebbert L, Blom AEM, Cohen BN, Marvin JS, Borden PM, Kim CH, Muthusamy AK, Shivange AV, Knox HJ, Campello HR, Wang JH, Dougherty DA, Looger LL, Gallagher T, Rees DC, Lester HA | eLife | 36520038 | Elife | 2022 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/36520038 |
| Fluorescence Screens for Identifying Central Nervous System-Acting Drug-Biosensor Pairs for Subcellular and Supracellular Pharmacokinetics. | Beatty ZG, Muthusamy AK, Unger EK, Dougherty DA, Tian L, Looger LL, Shivange AV, Bera K, Lester HA, Nichols AL | Bio-protocol | 36532688 | Bio Protoc | 2022 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/36532688 |
| Antidepressants enter cells, organelles, and membranes. | Blumenfeld Z, Bera K, Castrén E, Lester HA | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 37783840 | Neuropsychopharmacology | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37783840 |
| Chronic Menthol Does Not Change Stoichiometry or Functional Plasma Membrane Levels of Mouse α3β4-Containing Nicotinic Acetylcholine Receptors. | Bavan S, Kim CH, Henderson BJ, Lester HA | Molecular pharmacology | 30670481 | Mol Pharmacol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/30670481 |
| Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. | Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA | bioRxiv : the preprint server for biology | 36712031 | bioRxiv | 2024 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/36712031 |
| 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 |
| Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins. | Grant SN, Lester HA | Biophysical journal | 34197807 | Biophys J | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/34197807 |
| Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane. | Nichols AL, Blumenfeld Z, Luebbert L, Knox HJ, Muthusamy AK, Marvin JS, Kim CH, Grant SN, Walton DP, Cohen BN, Hammar R, Looger L, Artursson P, Dougherty DA, Lester HA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 36868853 | J Neurosci | 2023 Mar 29 | https://www.ncbi.nlm.nih.gov/pubmed/36868853 |
| Three Mutations Convert the Selectivity of a Protein Sensor from Nicotinic Agonists to S-Methadone for Use in Cells, Organelles, and Biofluids. | Muthusamy AK, Kim CH, Virgil SC, Knox HJ, Marvin JS, Nichols AL, Cohen BN, Dougherty DA, Looger LL, Lester HA | Journal of the American Chemical Society | 35446570 | J Am Chem Soc | 2022 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/35446570 |
| Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. | Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA | Protein engineering, design & selection : PEDS | 38302088 | Protein Eng Des Sel | 2024 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/38302088 |
| Deconstruction of the Ras switching cycle through saturation mutagenesis. | Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J | eLife | 28686159 | Elife | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28686159 |
| Chronic intermittent ethanol exposure and withdrawal leads to adaptations in nucleus accumbens core postsynaptic density proteome and dendritic spines. | Uys JD, McGuier NS, Gass JT, Griffin WC 3rd, Ball LE, Mulholland PJ | Addiction biology | 25787124 | Addict Biol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/25787124 |
| An evolution-based model for designing chorismate mutase enzymes. | Russ WP, Figliuzzi M, Stocker C, Barrat-Charlaix P, Socolich M, Kast P, Hilvert D, Monasson R, Cocco S, Weigt M, Ranganathan R | Science (New York, N.Y.) | 32703877 | Science | 2020 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/32703877 |
| Three structural solutions for bacterial adhesion pilus stability and superelasticity. | Doran MH, Baker JL, Dahlberg T, Andersson M, Bullitt E | Structure (London, England : 1993) | 37001523 | Structure | 2023 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/37001523 |
| Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. | Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T, Reunanen J | Microbiome | 37953319 | Microbiome | 2023 Nov 13 | https://www.ncbi.nlm.nih.gov/pubmed/37953319 |
| A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components. | Subramanian SK, Russ WP, Ranganathan R | Synthetic biology (Oxford, England) | 32995509 | Synth Biol (Oxf) | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/32995509 |
| Learning the pattern of epistasis linking genotype and phenotype in a protein. | Poelwijk FJ, Socolich M, Ranganathan R | Nature communications | 31527666 | Nat Commun | 2019 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/31527666 |
| Coevolution-based inference of amino acid interactions underlying protein function. | Salinas VH, Ranganathan R | eLife | 30024376 | Elife | 2018 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/30024376 |
| An evolutionary hotspot defines functional differences between CRYPTOCHROMES. | Rosensweig C, Reynolds KA, Gao P, Laothamatas I, Shan Y, Ranganathan R, Takahashi JS, Green CB | Nature communications | 29556064 | Nat Commun | 2018 Mar 19 | https://www.ncbi.nlm.nih.gov/pubmed/29556064 |
| Electric-field-stimulated protein mechanics. | Hekstra DR, White KI, Socolich MA, Henning RW, Šrajer V, Ranganathan R | Nature | 27926732 | Nature | 2016 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/27926732 |
| A Novel EGFRvIII T-Cell Bispecific Antibody for the Treatment of Glioblastoma. | Iurlaro R, Waldhauer I, Planas-Rigol E, Bonfill-Teixidor E, Arias A, Nicolini V, Freimoser-Grundschober A, Cuartas I, Martínez-Moreno A, Martínez-Ricarte F, Cordero E, Cicuendez M, Casalino S, Guardia-Reyes X, Fahrni L, Pöschinger T, Steinhart V, Richard M, Briner S, Mueller J, Osl F, Sam J, Colombetti S, Bacac M, Klein C, Pineda E, Reyes-Figueroa L, Di Somma A, González J, Nuciforo P, Carles J, Vieito M, Tabernero J, Umaña P, Seoane J | Molecular cancer therapeutics | 35915983 | Mol Cancer Ther | 2022 Oct 7 | https://www.ncbi.nlm.nih.gov/pubmed/35915983 |
| 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 |
| Virus-like particle-induced protection against MRSA pneumonia is dependent on IL-13 and enhancement of phagocyte function. | Rynda-Apple A, Dobrinen E, McAlpine M, Read A, Harmsen A, Richert LE, Calverley M, Pallister K, Voyich J, Wiley JA, Johnson B, Young M, Douglas T, Harmsen AG | The American journal of pathology | 22642909 | Am J Pathol | 2012 Jul | https://www.ncbi.nlm.nih.gov/pubmed/22642909 |
| RNA sectors and allosteric function within the ribosome. | Walker AS, Russ WP, Ranganathan R, Schepartz A | Proceedings of the National Academy of Sciences of the United States of America | 32747536 | Proc Natl Acad Sci U S A | 2020 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/32747536 |
| Roadmap on biology in time varying environments. | Murugan A, Husain K, Rust MJ, Hepler C, Bass J, Pietsch JMJ, Swain PS, Jena SG, Toettcher JE, Chakraborty AK, Sprenger KG, Mora T, Walczak AM, Rivoire O, Wang S, Wood KB, Skanata A, Kussell E, Ranganathan R, Shih HY, Goldenfeld N | Physical biology | 33477124 | Phys Biol | 2021 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/33477124 |
| Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase. | Jiang T, Yu K, Hartzell HC, Tajkhorshid E | eLife | 28917060 | Elife | 2017 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/28917060 |
| Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics. | Lam K, Tajkhorshid E | Biophysical journal | 32533943 | Biophys J | 2020 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/32533943 |
| Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein. | Kapoor K, Pant S, Tajkhorshid E | Chemical science | 34084427 | Chem Sci | 2021 Apr 9 | https://www.ncbi.nlm.nih.gov/pubmed/34084427 |
| Relationship among egg quality traits in Japanese quails and prediction of egg weight and color using data mining algorithms. | Çelik Ş, Eyduran E, Şengül AY, Şengül T | Tropical animal health and production | 34195902 | Trop Anim Health Prod | 2021 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/34195902 |
| Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. | Licari G, Dehghani-Ghahnaviyeh S, Tajkhorshid E | Journal of chemical information and modeling | 35104125 | J Chem Inf Model | 2022 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/35104125 |
| Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. | Wu Q, Akhter A, Pant S, Cho E, Zhu JX, Garner A, Ohyama T, Tajkhorshid E, van Meyel DJ, Ryan RM | The Journal of clinical investigation | 35167492 | J Clin Invest | 2022 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/35167492 |
| Molecular mechanism of prestin electromotive signal amplification. | Ge J, Elferich J, Dehghani-Ghahnaviyeh S, Zhao Z, Meadows M, von Gersdorff H, Tajkhorshid E, Gouaux E | Cell | 34390643 | Cell | 2021 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/34390643 |
| Microscopic view of lipids and their diverse biological functions. | Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E | Current opinion in structural biology | 30048836 | Curr Opin Struct Biol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30048836 |
| Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. | Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Science advances | 32998886 | Sci Adv | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/32998886 |
| Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy. | Misra C, Bangru S, Lin F, Lam K, Koenig SN, Lubbers ER, Hedhli J, Murphy NP, Parker DJ, Dobrucki LW, Cooper TA, Tajkhorshid E, Mohler PJ, Kalsotra A | Developmental cell | 32109384 | Dev Cell | 2020 Mar 23 | https://www.ncbi.nlm.nih.gov/pubmed/32109384 |
| Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association. | Smith JW, Jiang X, An H, Barclay AM, Licari G, Tajkhorshid E, Moore EG, Rienstra CM, Moore JS, Chen Q | ACS applied nano materials | 32149271 | ACS Appl Nano Mater | 2020 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/32149271 |
| Interaction of Alpha-Synuclein and Its Mutants with Rigid Lipid Vesicle Mimics of Varying Surface Curvature. | McClain SM, Ojoawo AM, Lin W, Rienstra CM, Murphy CJ | ACS nano | 32672441 | ACS Nano | 2020 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/32672441 |
| Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid. | Muller MP, Morrissey JH, Tajkhorshid E | Biochemistry | 35853076 | Biochemistry | 2022 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/35853076 |
| Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis. | Dehghani-Ghahnaviyeh S, Kapoor K, Tajkhorshid E | FEBS letters | 33159693 | FEBS Lett | 2021 Mar | https://www.ncbi.nlm.nih.gov/pubmed/33159693 |
| Structural Insights into the Lipid A Transport Pathway in MsbA. | Padayatti PS, Lee SC, Stanfield RL, Wen PC, Tajkhorshid E, Wilson IA, Zhang Q | Structure (London, England : 1993) | 31130486 | Structure | 2019 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/31130486 |
| Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. | Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C | Proceedings of the National Academy of Sciences of the United States of America | 31911476 | Proc Natl Acad Sci U S A | 2020 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/31911476 |
| Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. | Tang Q, Sinclair M, Hasdemir HS, Stein RA, Karakas E, Tajkhorshid E, Mchaourab HS | Nature communications | 37938578 | Nat Commun | 2023 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/37938578 |
| Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. | Rasouli A, Yu Q, Dehghani-Ghahnaviyeh S, Wen PC, Kowal J, Locher KP, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 36580587 | Proc Natl Acad Sci U S A | 2023 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/36580587 |
| Phosphatidylthreonine is a procoagulant lipid detected in human blood and elevated in coronary artery disease. | Hajeyah AA, Protty MB, Paul D, Costa D, Omidvar N, Morgan B, Iwasaki Y, McGill B, Jenkins PV, Yousef Z, Allen-Redpath K, Soyama S, Choudhury A, Mitra R, Yaqoob P, Morrissey JH, Collins PW, O'Donnell VB | Journal of lipid research | 38103786 | J Lipid Res | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/38103786 |
| Atomistic characterization of β2-glycoprotein I domain V interaction with anionic membranes. | Hasdemir HS, Pozzi N, Tajkhorshid E | Journal of thrombosis and haemostasis : JTH | 39047943 | J Thromb Haemost | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39047943 |
| Improved Highly Mobile Membrane Mimetic Model for Investigating Protein-Cholesterol Interactions. | Lihan M, Tajkhorshid E | Journal of chemical information and modeling | 38844760 | J Chem Inf Model | 2024 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/38844760 |
| Solid-State NMR (13)C sensitivity at high magnetic field. | Han R, Borcik CG, Wang S, Warmuth OA, Geohring K, Mullen C, Incitti M, Stringer JA, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991265 | J Magn Reson | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38991265 |
| Enhancing Spectrometer Performance with Unsupervised Machine Learning. | Harding BD, Hu Z, Hiett A, Delaglio F, Henzler-Wildman KA, Rienstra CM | The journal of physical chemistry. B | 39395040 | J Phys Chem B | 2024 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/39395040 |
| Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains. | Cheng KJ, De Lio AM, Jain R, Paul D, Morrissey JH, Pogorelov TV | Biochemistry | 37747791 | Biochemistry | 2023 Oct 17 | https://www.ncbi.nlm.nih.gov/pubmed/37747791 |
| Segmental Dynamics of Membranous Cholesterol are Coupled. | Della Ripa LA, Courtney JM, Phinney SM, Borcik CG, Burke MD, Rienstra CM, Pogorelov TV | Journal of the American Chemical Society | 37410392 | J Am Chem Soc | 2023 Jul 19 | https://www.ncbi.nlm.nih.gov/pubmed/37410392 |
| Probing cholesterol binding and translocation in P-glycoprotein. | Thangapandian S, Kapoor K, Tajkhorshid E | Biochimica et biophysica acta. Biomembranes | 31676371 | Biochim Biophys Acta Biomembr | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/31676371 |
| Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. | Jia R, Martens C, Shekhar M, Pant S, Pellowe GA, Lau AM, Findlay HE, Harris NJ, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 33268777 | Nat Commun | 2020 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/33268777 |
| A cancer mutation promotes EphA4 oligomerization and signaling by altering the conformation of the SAM domain. | Light TP, Gomez-Soler M, Wang Z, Karl K, Zapata-Mercado E, Gehring MP, Lechtenberg BC, Pogorelov TV, Hristova K, Pasquale EB | The Journal of biological chemistry | 34139238 | J Biol Chem | 2021 Jul | https://www.ncbi.nlm.nih.gov/pubmed/34139238 |
| Solid-State NMR of highly (13)C-enriched cholesterol in lipid bilayers. | Della Ripa LA, Petros ZA, Cioffi AG, Piehl DW, Courtney JM, Burke MD, Rienstra CM | Methods (San Diego, Calif.) | 29366688 | Methods | 2018 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/29366688 |
| Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. | Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N | Nature communications | 32541820 | Nat Commun | 2020 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/32541820 |
| Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. | Martens C, Shekhar M, Lau AM, Tajkhorshid E, Politis A | Nature protocols | 31605097 | Nat Protoc | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31605097 |
| A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca(2+)-activated Cl(-) channel ANO1 (TMEM16A). | Yu K, Jiang T, Cui Y, Tajkhorshid E, Hartzell HC | Proceedings of the National Academy of Sciences of the United States of America | 31515451 | Proc Natl Acad Sci U S A | 2019 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/31515451 |
| Computational Dissection of Membrane Transport at a Microscopic Level. | Jiang T, Wen PC, Trebesch N, Zhao Z, Pant S, Kapoor K, Shekhar M, Tajkhorshid E | Trends in biochemical sciences | 31813734 | Trends Biochem Sci | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31813734 |
| An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells. | Yadav AK, Reinhardt CJ, Arango AS, Huff HC, Dong L, Malkowski MG, Das A, Tajkhorshid E, Chan J | Angewandte Chemie (International ed. in English) | 31854058 | Angew Chem Int Ed Engl | 2020 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/31854058 |
| Stoichiometric analysis reveals a unique phosphatidylserine binding site in coagulation factor X. | Paul D, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 34894064 | J Thromb Haemost | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34894064 |
| Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. | Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW | The Journal of biological chemistry | 35122790 | J Biol Chem | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/35122790 |
| Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane. | Gorgun D, Lihan M, Kapoor K, Tajkhorshid E | Biophysical journal | 33675757 | Biophys J | 2021 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/33675757 |
| Automated fibril structure calculations in Xplor-NIH. | Barclay AM, Milchberg MH, Warmuth OA, Tuttle MD, Dennis CJ, Schwieters CD, Rienstra CM | Structure (London, England : 1993) | 39662464 | Structure | 2025 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/39662464 |
| Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation. | Jiang X, Halmes AJ, Licari G, Smith JW, Song Y, Moore EG, Chen Q, Tajkhorshid E, Rienstra CM, Moore JS | ACS macro letters | 32149017 | ACS Macro Lett | 2019 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/32149017 |
| Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy. | Zhang J, Kim EC, Chen C, Procko E, Pant S, Lam K, Patel J, Choi R, Hong M, Joshi D, Bolton E, Tajkhorshid E, Chung HJ | Scientific reports | 32179837 | Sci Rep | 2020 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/32179837 |
| A modification of γ-encoded RN symmetry pulses for increasing the scaling factor and more accurate measurements of the strong heteronuclear dipolar couplings. | Nimerovsky E, Soutar CP | Journal of magnetic resonance (San Diego, Calif. : 1997) | 32950918 | J Magn Reson | 2020 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32950918 |
| Peridinin Is an Exceptionally Potent and Membrane-Embedded Inhibitor of Bilayer Lipid Peroxidation. | Haley HMS, Hill AG, Greenwood AI, Woerly EM, Rienstra CM, Burke MD | Journal of the American Chemical Society | 30388000 | J Am Chem Soc | 2018 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/30388000 |
| Structural basis for the reaction cycle of DASS dicarboxylate transporters. | Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN | eLife | 32869741 | Elife | 2020 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/32869741 |
| Structure of the alternative complex III in a supercomplex with cytochrome oxidase. | Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB | Nature | 29695868 | Nature | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29695868 |
| Lipid specificity of the membrane binding domain of coagulation factor X. | Muller MP, Wang Y, Morrissey JH, Tajkhorshid E | Journal of thrombosis and haemostasis : JTH | 28782177 | J Thromb Haemost | 2017 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28782177 |
| Direct protein-lipid interactions shape the conformational landscape of secondary transporters. | Martens C, Shekhar M, Borysik AJ, Lau AM, Reading E, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 30297844 | Nat Commun | 2018 Oct 8 | https://www.ncbi.nlm.nih.gov/pubmed/30297844 |
| Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. | Pant S, Tajkhorshid E | Journal of computational chemistry | 31762060 | J Comput Chem | 2020 Mar 5 | https://www.ncbi.nlm.nih.gov/pubmed/31762060 |
| (31)P-dephased, (13)C-detected REDOR for NMR crystallography at natural isotopic abundance. | Greenwood AI, Clay MC, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 28319851 | J Magn Reson | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28319851 |
| Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. | Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E | Chemical reviews | 30978005 | Chem Rev | 2019 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/30978005 |
| Fungicidal amphotericin B sponges are assemblies of staggered asymmetric homodimers encasing large void volumes. | Lewandowska A, Soutar CP, Greenwood AI, Nimerovsky E, De Lio AM, Holler JT, Hisao GS, Khandelwal A, Zhang J, SantaMaria AM, Schwieters CD, Pogorelov TV, Burke MD, Rienstra CM | Nature structural & molecular biology | 34887566 | Nat Struct Mol Biol | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34887566 |
| PIP(2)-dependent coupling of voltage sensor and pore domains in K(v)7.2 channel. | Pant S, Zhang J, Kim EC, Lam K, Chung HJ, Tajkhorshid E | Communications biology | 34650221 | Commun Biol | 2021 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/34650221 |
| Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. | Maji A, Soutar CP, Zhang J, Lewandowska A, Uno BE, Yan S, Shelke Y, Murhade G, Nimerovsky E, Borcik CG, Arango AS, Lange JD, Marin-Toledo JP, Lyu Y, Bailey KL, Roady PJ, Holler JT, Khandelwal A, SantaMaria AM, Sanchez H, Juvvadi PR, Johns G, Hageman MJ, Krise J, Gebremariam T, Youssef EG, Bartizal K, Marr KA, Steinbach WJ, Ibrahim AS, Patterson TF, Wiederhold NP, Andes DR, Pogorelov TV, Schwieters CD, Fan TM, Rienstra CM, Burke MD | Nature | 37938782 | Nature | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37938782 |
| Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. | Gose T, Rasouli A, Dehghani-Ghahnaviyeh S, Wen PC, Wang Y, Lynch J, Fukuda Y, Shafi T, Ford RC, Tajkhorshid E, Schuetz JD | Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy | 38387283 | Drug Resist Updat | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38387283 |
| Structures of the TMC-1 complex illuminate mechanosensory transduction. | Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E | Nature | 36224384 | Nature | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/36224384 |
| Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia. | Singaram I, Sharma A, Pant S, Lihan M, Park MJ, Pergande M, Buwaneka P, Hu Y, Mahmud N, Kim YM, Cologna S, Gevorgyan V, Khan I, Tajkhorshid E, Cho W | Nature chemical biology | 36229686 | Nat Chem Biol | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36229686 |
| Backbone amides are determinants of Cl(-) selectivity in CLC ion channels. | Leisle L, Lam K, Dehghani-Ghahnaviyeh S, Fortea E, Galpin JD, Ahern CA, Tajkhorshid E, Accardi A | Nature communications | 36473856 | Nat Commun | 2022 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/36473856 |
| Topological Learning Approach to Characterizing Biological Membranes. | Arango AS, Park H, Tajkhorshid E | Journal of chemical information and modeling | 38912752 | J Chem Inf Model | 2024 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/38912752 |
| APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. | Park H, Patel P, Haas R, Huerta EA | Proceedings of the National Academy of Sciences of the United States of America | 38913887 | Proc Natl Acad Sci U S A | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/38913887 |
| Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism. | Thangapandian S, Fakharzadeh A, Moradi M, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 40042900 | Proc Natl Acad Sci U S A | 2025 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/40042900 |
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| A serine loop in tissue factor mediates substrate selectivity by the tissue factor-factor VIIa complex. | Birkle F, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 32885882 | J Thromb Haemost | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32885882 |
| Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. | Kapoor K, Chen T, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 35737823 | Proc Natl Acad Sci U S A | 2022 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/35737823 |
| Probing key elements of teixobactin-lipid II interactions in membranes. | Wen PC, Vanegas JM, Rempe SB, Tajkhorshid E | Chemical science | 30210775 | Chem Sci | 2018 Sep 14 | https://www.ncbi.nlm.nih.gov/pubmed/30210775 |
| Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. | Coleman JA, Yang D, Zhao Z, Wen PC, Yoshioka C, Tajkhorshid E, Gouaux E | Nature | 31019304 | Nature | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/31019304 |
| Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane. | Hallock MJ, Greenwood AI, Wang Y, Morrissey JH, Tajkhorshid E, Rienstra CM, Pogorelov TV | Biochemistry | 30456950 | Biochemistry | 2018 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/30456950 |
| Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR. | Grohe K, Nimerovsky E, Singh H, Vasa SK, Söldner B, Vögeli B, Rienstra CM, Linser R | Chemical communications (Cambridge, England) | 31199417 | Chem Commun (Camb) | 2019 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/31199417 |
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| Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. | Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Nature communications | 37989735 | Nat Commun | 2023 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/37989735 |
| The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. | Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO | The Journal of biological chemistry | 38211817 | J Biol Chem | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38211817 |
| Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. | Le LTM, Thompson JR, Dehghani-Ghahnaviyeh S, Pant S, Dang PX, French JB, Kanikeyo T, Tajkhorshid E, Alam A | The EMBO journal | 36484366 | EMBO J | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36484366 |
| Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. | Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA | Nature communications | 36599844 | Nat Commun | 2023 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/36599844 |
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| Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X. | Muller MP, Mortenson A, Sedzro JC, Wen PC, Morrissey JH, Tajkhorshid E | Blood advances | 39671302 | Blood Adv | 2025 Feb 25 | https://www.ncbi.nlm.nih.gov/pubmed/39671302 |
| Cross polarization stability in multidimensional NMR spectroscopy of biological solids. | Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991266 | J Magn Reson | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38991266 |
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| Establishment of human pluripotent stem cell-derived pancreatic β-like cells in the mouse pancreas. | Ma H, Wert KJ, Shvartsman D, Melton DA, Jaenisch R | Proceedings of the National Academy of Sciences of the United States of America | 29599125 | Proc Natl Acad Sci U S A | 2018 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/29599125 |
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| RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. | Gupta S, Lafontaine DL, Vigneau S, Mendelevich A, Vinogradova S, Igarashi KJ, Bortvin A, Alves-Pereira CF, Nag A, Gimelbrant AA | G3 (Bethesda, Md.) | 35100361 | G3 (Bethesda) | 2022 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/35100361 |
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| Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages. | Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko BN, Gimelbrant AA, Kramnik I | Science advances | 37756395 | Sci Adv | 2023 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/37756395 |
| Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. | Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA | bioRxiv : the preprint server for biology | 36798258 | bioRxiv | 2023 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/36798258 |
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| Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. | Dunford A, Weinstock DM, Savova V, Schumacher SE, Cleary JP, Yoda A, Sullivan TJ, Hess JM, Gimelbrant AA, Beroukhim R, Lawrence MS, Getz G, Lane AA | Nature genetics | 27869828 | Nat Genet | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27869828 |
| Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene. | Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, Hnisz D, Li CH, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R | Cell | 29456084 | Cell | 2018 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/29456084 |
| Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. | Savova V, Vinogradova S, Pruss D, Gimelbrant AA, Weiss LA | Molecular psychiatry | 28265118 | Mol Psychiatry | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28265118 |
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| Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. | Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R | Molecular cell | 31422875 | Mol Cell | 2019 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/31422875 |
| Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility. | Yabaji SM, Zhernovkov V, Araveti PB, Lata S, Rukhlenko OS, Abdullatif SA, Vanvalkenburg A, Alekseev Y, Ma Q, Dayama G, Lau NC, Johnson WE, Bishai WR, Crossland NA, Campbell JD, Kholodenko BN, Gimelbrant AA, Kobzik L, Kramnik I | bioRxiv : the preprint server for biology | 38496444 | bioRxiv | 2025 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38496444 |
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| Value-Based Standards Guide Sexism Inferences for Self and Others. | Mitamura C, Erickson L, Devine PG | Journal of experimental social psychology | 29230069 | J Exp Soc Psychol | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29230069 |
| Low agreement among reviewers evaluating the same NIH grant applications. | Pier EL, Brauer M, Filut A, Kaatz A, Raclaw J, Nathan MJ, Ford CE, Carnes M | Proceedings of the National Academy of Sciences of the United States of America | 29507248 | Proc Natl Acad Sci U S A | 2018 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/29507248 |
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| Women Are Less Likely Than Men to Be Full Professors in Cardiology: Why Does This Happen and How Can We Fix It? | Carnes M, Bairey Merz CN | Circulation | 28153988 | Circulation | 2017 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/28153988 |
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| Fair Play: A Study of Scientific Workforce Trainers' Experience Playing an Educational Video Game about Racial Bias. | Kaatz A, Carnes M, Gutierrez B, Savoy J, Samuel C, Filut A, Pribbenow CM | CBE life sciences education | 28450447 | CBE Life Sci Educ | 2017 Summer | https://www.ncbi.nlm.nih.gov/pubmed/28450447 |
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| Who Resembles a Scientific Leader-Jack or Jill? How Implicit Bias Could Influence Research Grant Funding. | Kolehmainen C, Carnes M | Circulation | 29459461 | Circulation | 2018 Feb 20 | https://www.ncbi.nlm.nih.gov/pubmed/29459461 |
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| A Psychological Profile of the Alt-Right. | Forscher PS, Kteily NS | Perspectives on psychological science : a journal of the Association for Psychological Science | 31747343 | Perspect Psychol Sci | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31747343 |
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| A meta-analysis of procedures to change implicit measures. | Forscher PS, Lai CK, Axt JR, Ebersole CR, Herman M, Devine PG, Nosek BA | Journal of personality and social psychology | 31192631 | J Pers Soc Psychol | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31192631 |
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| Are Female Applicants Disadvantaged in National Institutes of Health Peer Review? Combining Algorithmic Text Mining and Qualitative Methods to Detect Evaluative Differences in R01 Reviewers' Critiques. | Magua W, Zhu X, Bhattacharya A, Filut A, Potvien A, Leatherberry R, Lee YG, Jens M, Malikireddy D, Carnes M, Kaatz A | Journal of women's health (2002) | 28281870 | J Womens Health (Larchmt) | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28281870 |
| A Gender Bias Habit-Breaking Intervention Led to Increased Hiring of Female Faculty in STEMM Departments. | Devine PG, Forscher PS, Cox WTL, Kaatz A, Sheridan J, Carnes M | Journal of experimental social psychology | 29249837 | J Exp Soc Psychol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29249837 |
| Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference? | Kaatz A, Lee YG, Potvien A, Magua W, Filut A, Bhattacharya A, Leatherberry R, Zhu X, Carnes M | Academic medicine :, journal of the Association of American Medical Colleges.. | 27276003 | Acad Med | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27276003 |
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| Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. | Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A | Proceedings of the National Academy of Sciences of the United States of America | 26374839 | Proc Natl Acad Sci U S A | 2015 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/26374839 |
| Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity. | Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ | Molecular cell | 30503773 | Mol Cell | 2019 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/30503773 |
| Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. | Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S | Cell | 28985564 | Cell | 2017 Oct 5 | https://www.ncbi.nlm.nih.gov/pubmed/28985564 |
| Structure and function of the bacterial decapping enzyme NudC. | Höfer K, Li S, Abele F, Frindert J, Schlotthauer J, Grawenhoff J, Du J, Patel DJ, Jäschke A | Nature chemical biology | 27428510 | Nat Chem Biol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27428510 |
| FMRP targets distinct mRNA sequence elements to regulate protein expression. | Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T | Nature | 23235829 | Nature | 2012 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/23235829 |
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| The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. | Meyer C, Garzia A, Mazzola M, Gerstberger S, Molina H, Tuschl T | Molecular cell | 29429924 | Mol Cell | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29429924 |
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| The RNA-binding protein vigilin regulates VLDL secretion through modulation of Apob mRNA translation. | Mobin MB, Gerstberger S, Teupser D, Campana B, Charisse K, Heim MH, Manoharan M, Tuschl T, Stoffel M | Nature communications | 27665711 | Nat Commun | 2016 Sep 26 | https://www.ncbi.nlm.nih.gov/pubmed/27665711 |
| The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. | Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T, Sonenberg N | Nature communications | 28685749 | Nat Commun | 2017 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/28685749 |
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| Multicolor microRNA FISH effectively differentiates tumor types. | Renwick N, Cekan P, Masry PA, McGeary SE, Miller JB, Hafner M, Li Z, Mihailovic A, Morozov P, Brown M, Gogakos T, Mobin MB, Snorrason EL, Feilotter HE, Zhang X, Perlis CS, Wu H, Suárez-Fariñas M, Feng H, Shuda M, Moore PS, Tron VA, Chang Y, Tuschl T | The Journal of clinical investigation | 23728175 | J Clin Invest | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23728175 |
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| tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa. | Sun J, Wu J, Yuan Y, Fan L, Chua WLP, Ling YHS, Balamkundu S, Priya D, Suen HCS, de Crécy-Lagard V, Dziergowska A, Dedon PC | bioRxiv : the preprint server for biology | 39005467 | bioRxiv | 2024 Jul 2 | https://www.ncbi.nlm.nih.gov/pubmed/39005467 |
| 5-Methyluridine is Ubiquitous in Pseudomonas aeruginosa tRNA and Modulates Antimicrobial Resistance and Virulence. | Chittrakanwong J, Chen R, Wu J, Demott MS, Sun J, Phatinuwat K, Jaroensuk J, Atichartpongkul S, Mongkolsuk S, Begley T, Dedon PC, Fuangthong M | Journal of molecular biology | 40055058 | J Mol Biol | 2025 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/40055058 |
| Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. | Cao B, Wu X, Zhou J, Wu H, Liu L, Zhang Q, DeMott MS, Gu C, Wang L, You D, Dedon PC | Nucleic acids research | 32484547 | Nucleic Acids Res | 2020 Jul 9 | https://www.ncbi.nlm.nih.gov/pubmed/32484547 |
| Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome. | Yuan Y, DeMott MS, Byrne SR, Flores K, Poyet M, Groussin M, Microbiome Conservancy G, Berdy B, Comstock L, Alm EJ, Dedon PC | bioRxiv : the preprint server for biology | 38895356 | bioRxiv | 2024 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/38895356 |
| Genomic Tools for Environmental Epigenetics and Implications for Public Health. | Perera BPU, Svoboda L, Dolinoy DC | Current opinion in toxicology | 31763499 | Curr Opin Toxicol | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31763499 |
| Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements. | Colwell M, Drown M, Showel K, Drown C, Palowski A, Faulk C | Epigenetics | 29372669 | Epigenetics | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29372669 |
| The role of environmental exposures and the epigenome in health and disease. | Perera BPU, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC | Environmental and molecular mutagenesis | 31177562 | Environ Mol Mutagen | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31177562 |
| Paradoxical whole genome DNA methylation dynamics of 5'aza-deoxycytidine in chronic low-dose exposure in mice. | Colwell M, Wanner NM, Drown C, Drown M, Dolinoy DC, Faulk C | Epigenetics | 32619143 | Epigenetics | 2021 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/32619143 |
| piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. | Wang K, Perera BPU, Morgan RK, Sala-Hamrick K, Geron V, Svoboda LK, Faulk C, Dolinoy DC, Sartor MA | Database : the journal of biological databases and curation | 38204359 | Database (Oxford) | 2024 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/38204359 |
| The evolution of CpG density and lifespan in conserved primate and mammalian promoters. | McLain AT, Faulk C | Aging | 29661983 | Aging (Albany NY) | 2018 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/29661983 |
| Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA. | Perera BPU, Tsai ZT, Colwell ML, Jones TR, Goodrich JM, Wang K, Sartor MA, Faulk C, Dolinoy DC | Epigenetics | 30955436 | Epigenetics | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30955436 |
| Mechanistic validation. | Hartung T, Hoffmann S, Stephens M | ALTEX | 23665802 | ALTEX | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23665802 |
| Metabolomics in toxicology and preclinical research. | Ramirez T, Daneshian M, Kamp H, Bois FY, Clench MR, Coen M, Donley B, Fischer SM, Ekman DR, Fabian E, Guillou C, Heuer J, Hogberg HT, Jungnickel H, Keun HC, Krennrich G, Krupp E, Luch A, Noor F, Peter E, Riefke B, Seymour M, Skinner N, Smirnova L, Verheij E, Wagner S, Hartung T, van Ravenzwaay B, Leist M | ALTEX | 23665807 | ALTEX | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23665807 |
| Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. | Hogberg HT, de Cássia da Silveira E Sá R, Kleensang A, Bouhifd M, Cemiloglu Ulker O, Smirnova L, Behl M, Maertens A, Zhao L, Hartung T | Archives of toxicology | 33078273 | Arch Toxicol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33078273 |
| Morphologic effects of estrogen stimulation on 3D MCF-7 microtissues. | Vantangoli MM, Wilson S, Madnick SJ, Huse SM, Boekelheide K | Toxicology letters | 26921789 | Toxicol Lett | 2016 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/26921789 |
| Application of the TGx-28.65 transcriptomic biomarker to classify genotoxic and non-genotoxic chemicals in human TK6 cells in the presence of rat liver S9. | Yauk CL, Buick JK, Williams A, Swartz CD, Recio L, Li HH, Fornace AJ Jr, Thomson EM, Aubrecht J | Environmental and molecular mutagenesis | 26946220 | Environ Mol Mutagen | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26946220 |
| 21st Century Cell Culture for 21st Century Toxicology. | Pamies D, Hartung T | Chemical research in toxicology | 28092941 | Chem Res Toxicol | 2017 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/28092941 |
| Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs. | Li HH, Chen R, Hyduke DR, Williams A, Frötschl R, Ellinger-Ziegelbauer H, O'Lone R, Yauk CL, Aubrecht J, Fornace AJ Jr | Proceedings of the National Academy of Sciences of the United States of America | 29203651 | Proc Natl Acad Sci U S A | 2017 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/29203651 |
| Transcriptional and metabolic adaptation of human neurons to the mitochondrial toxicant MPP(+). | Krug AK, Gutbier S, Zhao L, Pöltl D, Kullmann C, Ivanova V, Förster S, Jagtap S, Meiser J, Leparc G, Schildknecht S, Adam M, Hiller K, Farhan H, Brunner T, Hartung T, Sachinidis A, Leist M | Cell death & disease | 24810058 | Cell Death Dis | 2014 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/24810058 |
| Immunotoxicology: challenges in the 21st century and in vitro opportunities. | Hartung T, Corsini E | ALTEX | 24173166 | ALTEX | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24173166 |
| Metabolomic network analysis of estrogen-stimulated MCF-7 cells: a comparison of overrepresentation analysis, quantitative enrichment analysis and pathway analysis versus metabolite network analysis. | Maertens A, Bouhifd M, Zhao L, Odwin-DaCosta S, Kleensang A, Yager JD, Hartung T | Archives of toxicology | 27039105 | Arch Toxicol | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27039105 |
| Exploring new technologies in biomedical research. | Benam KH, Gilchrist S, Kleensang A, Satz AB, Willett C, Zhang Q | Drug discovery today | 30953865 | Drug Discov Today | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/30953865 |
| Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics. | Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD | Analytical chemistry | 28221771 | Anal Chem | 2017 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/28221771 |
| Systems Toxicology: The Future of Risk Assessment. | Sauer JM, Hartung T, Leist M, Knudsen TB, Hoeng J, Hayes AW | International journal of toxicology | 25804424 | Int J Toxicol | 2015 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/25804424 |
| Quality assurance of metabolomics. | Bouhifd M, Beger R, Flynn T, Guo L, Harris G, Hogberg H, Kaddurah-Daouk R, Kamp H, Kleensang A, Maertens A, Odwin-DaCosta S, Pamies D, Robertson D, Smirnova L, Sun J, Zhao L, Hartung T | ALTEX | 26536290 | ALTEX | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26536290 |
| Ultrasensitive response motifs: basic amplifiers in molecular signalling networks. | Zhang Q, Bhattacharya S, Andersen ME | Open biology | 23615029 | Open Biol | 2013 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/23615029 |
| Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity. | Pendse SN, Maertens A, Rosenberg M, Roy D, Fasani RA, Vantangoli MM, Madnick SJ, Boekelheide K, Fornace AJ, Odwin SA, Yager JD, Hartung T, Andersen ME, McMullen PD | Archives of toxicology | 27592001 | Arch Toxicol | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27592001 |
| Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function. | Kleensang A, Vantangoli MM, Odwin-DaCosta S, Andersen ME, Boekelheide K, Bouhifd M, Fornace AJ Jr, Li HH, Livi CB, Madnick S, Maertens A, Rosenberg M, Yager JD, Zhao L, Hartung T | Scientific reports | 27456714 | Sci Rep | 2016 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/27456714 |
| 3D - a new dimension of in vitro research. | Hartung T | Advanced drug delivery reviews | 24721291 | Adv Drug Deliv Rev | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24721291 |
| Pathways of Toxicity. | Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ Jr, Gaido K, Gerhold D, Haw R, Henney A, Ma'ayan A, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Patton GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T | ALTEX | 24127042 | ALTEX | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24127042 |
| Systems Toxicology: Real World Applications and Opportunities. | Hartung T, FitzGerald RE, Jennings P, Mirams GR, Peitsch MC, Rostami-Hodjegan A, Shah I, Wilks MF, Sturla SJ | Chemical research in toxicology | 28362102 | Chem Res Toxicol | 2017 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/28362102 |
| Perspectives on In Vitro to In Vivo Extrapolations. | Hartung T | Applied in vitro toxicology | 31890748 | Appl In Vitro Toxicol | 2018 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/31890748 |
| Arsenite and cadmium promote the development of mammary tumors. | Divekar SD, Li HH, Parodi DA, Ghafouri TB, Chen R, Cyrus K, Foxworth AE, Fornace AJ, Byrne C, Martin MB | Carcinogenesis | 31646340 | Carcinogenesis | 2020 Jul 14 | https://www.ncbi.nlm.nih.gov/pubmed/31646340 |
| Estradiol Exposure Differentially Alters Monolayer versus Microtissue MCF-7 Human Breast Carcinoma Cultures. | Vantangoli MM, Madnick SJ, Wilson S, Boekelheide K | PloS one | 27379522 | PLoS One | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27379522 |
| Integrated testing strategies for safety assessments. | Hartung T, Luechtefeld T, Maertens A, Kleensang A | ALTEX | 23338803 | ALTEX | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23338803 |
| The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. | Fasani RA, Livi CB, Choudhury DR, Kleensang A, Bouhifd M, Pendse SN, McMullen PD, Andersen ME, Hartung T, Rosenberg M | Frontiers in pharmacology | 26924983 | Front Pharmacol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26924983 |
| Look back in anger - what clinical studies tell us about preclinical work. | Hartung T | ALTEX | 23861075 | ALTEX | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23861075 |
| Review: toxicometabolomics. | Bouhifd M, Hartung T, Hogberg HT, Kleensang A, Zhao L | Journal of applied toxicology : JAT | 23722930 | J Appl Toxicol | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/23722930 |
| Mapping the human toxome by systems toxicology. | Bouhifd M, Hogberg HT, Kleensang A, Maertens A, Zhao L, Hartung T | Basic & clinical pharmacology & toxicology | 24443875 | Basic Clin Pharmacol Toxicol | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24443875 |
| Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. | Moffat I, Chepelev N, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, Lemieux F, Williams A, Halappanavar S, Malik A, Luijten M, Aubrecht J, Hyduke DR, Fornace AJ Jr, Swartz CD, Recio L, Yauk CL | Critical reviews in toxicology | 25605026 | Crit Rev Toxicol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25605026 |
| MPTP's pathway of toxicity indicates central role of transcription factor SP1. | Maertens A, Luechtefeld T, Kleensang A, Hartung T | Archives of toxicology | 25851821 | Arch Toxicol | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25851821 |
| Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells. | Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ Jr | Environmental and molecular mutagenesis | 25733355 | Environ Mol Mutagen | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25733355 |
| The human toxome project. | Bouhifd M, Andersen ME, Baghdikian C, Boekelheide K, Crofton KM, Fornace AJ Jr, Kleensang A, Li H, Livi C, Maertens A, McMullen PD, Rosenberg M, Thomas R, Vantangoli M, Yager JD, Zhao L, Hartung T | ALTEX | 25742299 | ALTEX | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25742299 |
| MCF-7 Human Breast Cancer Cells Form Differentiated Microtissues in Scaffold-Free Hydrogels. | Vantangoli MM, Madnick SJ, Huse SM, Weston P, Boekelheide K | PloS one | 26267486 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26267486 |
| Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells. | Buick JK, Moffat I, Williams A, Swartz CD, Recio L, Hyduke DR, Li HH, Fornace AJ Jr, Aubrecht J, Yauk CL | Environmental and molecular mutagenesis | 25733247 | Environ Mol Mutagen | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25733247 |
| CAR-T Entering a New "Phase": Improving CAR-T Function by Harnessing Phase Separation. | Su X | Cancer research | 39879116 | Cancer Res | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/39879116 |
| Hyperactive PLCG1 drives non-canonical signaling to promote cell survival. | Zeng L, Zhang X, Xiong Y, Sato K, Hajicek N, Sondek J, Su X | bioRxiv : the preprint server for biology | 39763946 | bioRxiv | 2024 Dec 18 | https://www.ncbi.nlm.nih.gov/pubmed/39763946 |
| Ultrasmall InGa(As)P Dielectric and Plasmonic Nanolasers. | Sarkar D, Cho S, Yan H, Martino N, Dannenberg PH, Yun SH | ACS nano | 37523588 | ACS Nano | 2023 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/37523588 |
| Laser particle activated cell sorting in microfluidics. | Dannenberg PH, Kang J, Martino N, Kashiparekh A, Forward S, Wu J, Liapis AC, Wang J, Yun SH | Lab on a chip | 35621381 | Lab Chip | 2022 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/35621381 |
| Facile layer-by-layer fabrication of semiconductor microdisk laser particles. | Dannenberg PH, Liapis AC, Martino N, Sarkar D, Kim KH, Yun SH | APL photonics | 38031595 | APL Photonics | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/38031595 |
| Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles. | Cho S, Moon W, Martino N, Yun SH | bioRxiv : the preprint server for biology | 39677764 | bioRxiv | 2024 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/39677764 |
| High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding. | Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH | Nature biomedical engineering | 38036616 | Nat Biomed Eng | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38036616 |
| Large-scale combinatorial optical barcoding of cells with laser particles. | Martino N, Yan H, Abbott G, Fahlberg M, Forward S, Kim KH, Wu Y, Zhu H, Kwok SJJ, Yun SH | Light, science & applications | 40169572 | Light Sci Appl | 2025 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/40169572 |
| Plasmonic Hinge Modes in Metal-Coated Nanolasers. | Cho S, Yang Y, Soljačić M, Yun SH | Nano letters | 39414245 | Nano Lett | 2024 Oct 30 | https://www.ncbi.nlm.nih.gov/pubmed/39414245 |
| Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition. | Fahlberg MD, Forward S, Assita ER, Mazzola M, Kiem A, Handley M, Yun SH, Kwok SJJ | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 39467031 | Cytometry A | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39467031 |
| Precise photoelectrochemical tuning of semiconductor microdisk lasers. | Sarkar D, Dannenberg PH, Martino N, Kim KH, Yun SH | Advanced photonics | 38993283 | Adv Photonics | 2023 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38993283 |
| Aggregation-Induced Stimulated Emission of 100% Dye Microspheres. | Kim KH, Yan H, Yun SH | Advanced optical materials | 38107448 | Adv Opt Mater | 2023 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/38107448 |
| Single-cell transcriptomics of a dynamic cell behavior in murine airways. | Kwok SJJ, Montoro DT, Haber AL, Yun SH, Vinarsky V | eLife | 37083555 | Elife | 2023 Apr 21 | https://www.ncbi.nlm.nih.gov/pubmed/37083555 |
| Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition. | Fahlberg MD, Forward S, Assita ER, Mazzola M, Kiem A, Handley M, Yun SH, Kwok SJJ | bioRxiv : the preprint server for biology | 39185194 | bioRxiv | 2024 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/39185194 |
| Half-wave nanolasers and intracellular plasmonic lasing particles. | Cho S, Martino N, Yun SH | Nature nanotechnology | 39747602 | Nat Nanotechnol | 2025 Mar | https://www.ncbi.nlm.nih.gov/pubmed/39747602 |
| Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles. | Cho S, Moon W, Martino N, Yun SH | Advanced materials (Deerfield Beach, Fla.) | 40434228 | Adv Mater | 2025 May 28 | https://www.ncbi.nlm.nih.gov/pubmed/40434228 |
| Extensively drug-resistant tuberculosis in a young child after travel to India. | Salazar-Austin N, Ordonez AA, Hsu AJ, Benson JE, Mahesh M, Menachery E, Razeq JH, Salfinger M, Starke JR, Milstone AM, Parrish N, Nuermberger EL, Jain SK | The Lancet. Infectious diseases | 26607130 | Lancet Infect Dis | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26607130 |
| SPECT/CT Imaging of Mycobacterium tuberculosis Infection with [(125)I]anti-C3d mAb. | Foss CA, Kulik L, Ordonez AA, Jain SK, Michael Holers V, Thurman JM, Pomper MG | Molecular imaging and biology | 29998399 | Mol Imaging Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29998399 |
| Noninvasive (11)C-rifampin positron emission tomography reveals drug biodistribution in tuberculous meningitis. | Tucker EW, Guglieri-Lopez B, Ordonez AA, Ritchie B, Klunk MH, Sharma R, Chang YS, Sanchez-Bautista J, Frey S, Lodge MA, Rowe SP, Holt DP, Gobburu JVS, Peloquin CA, Mathews WB, Dannals RF, Pardo CA, Kannan S, Ivaturi VD, Jain SK | Science translational medicine | 30518610 | Sci Transl Med | 2018 Dec 5 | https://www.ncbi.nlm.nih.gov/pubmed/30518610 |
| Matrix Metalloproteinases in Pulmonary and Central Nervous System Tuberculosis-A Review. | Rohlwink UK, Walker NF, Ordonez AA, Li YJ, Tucker EW, Elkington PT, Wilkinson RJ, Wilkinson KA | International journal of molecular sciences | 30889803 | Int J Mol Sci | 2019 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/30889803 |
| Imaging Enterobacterales infections in patients using pathogen-specific positron emission tomography. | Ordonez AA, Wintaco LM, Mota F, Restrepo AF, Ruiz-Bedoya CA, Reyes CF, Uribe LG, Abhishek S, D'Alessio FR, Holt DP, Dannals RF, Rowe SP, Castillo VR, Pomper MG, Granados U, Jain SK | Science translational medicine | 33853931 | Sci Transl Med | 2021 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/33853931 |
| Efficient ribcage segmentation from CT scans using shape features. | Xu Z, Bagci U, Jonsson C, Jain S, Mollura DJ | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 25570597 | Annu Int Conf IEEE Eng Med Biol Soc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25570597 |
| Radiosynthesis and Biodistribution of (18)F-Linezolid in Mycobacterium tuberculosis-Infected Mice Using Positron Emission Tomography. | Mota F, Jadhav R, Ruiz-Bedoya CA, Ordonez AA, Klunk MH, Freundlich JS, Jain SK | ACS infectious diseases | 32243132 | ACS Infect Dis | 2020 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/32243132 |
| Radiotracer Development for Bacterial Imaging. | Mota F, Ordonez AA, Firth G, Ruiz-Bedoya CA, Ma MT, Jain SK | Journal of medicinal chemistry | 32048838 | J Med Chem | 2020 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/32048838 |
| The Promise of Molecular Imaging in the Study and Treatment of Infectious Diseases. | Jain SK | Molecular imaging and biology | 28155078 | Mol Imaging Biol | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28155078 |
| High-dose rifampin improves bactericidal activity without increased intracerebral inflammation in animal models of tuberculous meningitis. | Ruiz-Bedoya CA, Mota F, Tucker EW, Mahmud FJ, Reyes-Mantilla MI, Erice C, Bahr M, Flavahan K, de Jesus P, Kim J, Foss CA, Peloquin CA, Hammoud DA, Ordonez AA, Pardo CA, Jain SK | The Journal of clinical investigation | 35085105 | J Clin Invest | 2022 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/35085105 |
| 11C-Para-aminobenzoic acid PET imaging of S. aureus and MRSA infection in preclinical models and humans. | Ordonez AA, Parker MF, Miller RJ, Plyku D, Ruiz-Bedoya CA, Tucker EW, Luu JM, Dikeman DA, Lesniak WG, Holt DP, Dannals RF, Miller LS, Rowe SP, Wilson DM, Jain SK | JCI insight | 35014627 | JCI Insight | 2022 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/35014627 |
| Pathogen-Specific Bacterial Imaging in Nuclear Medicine. | Ordonez AA, Jain SK | Seminars in nuclear medicine | 29452620 | Semin Nucl Med | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29452620 |
| Imaging Macrophage-associated Inflammation. | Foss CA, Sanchez-Bautista J, Jain SK | Seminars in nuclear medicine | 29626941 | Semin Nucl Med | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29626941 |
| A Systematic Approach for Developing Bacteria-Specific Imaging Tracers. | Ordonez AA, Weinstein EA, Bambarger LE, Saini V, Chang YS, DeMarco VP, Klunk MH, Urbanowski ME, Moulton KL, Murawski AM, Pokkali S, Kalinda AS, Jain SK | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 27635025 | J Nucl Med | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27635025 |
| Re: Increased 18F-2-Fluorodeoxysorbitol (18F-FDS) Activity in a Pituitary Spindle Cell Carcinoma. | Javadi MS, Ordonez AA, Jain SK | Clinical nuclear medicine | 28319504 | Clin Nucl Med | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28319504 |
| The biodistribution of 5-[18F]fluoropyrazinamide in Mycobacterium tuberculosis-infected mice determined by positron emission tomography. | Zhang Z, Ordonez AA, Smith-Jones P, Wang H, Gogarty KR, Daryaee F, Bambarger LE, Chang YS, Jain SK, Tonge PJ | PloS one | 28151985 | PLoS One | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28151985 |
| Delamanid Central Nervous System Pharmacokinetics in Tuberculous Meningitis in Rabbits and Humans. | Tucker EW, Pieterse L, Zimmerman MD, Udwadia ZF, Peloquin CA, Gler MT, Ganatra S, Tornheim JA, Chawla P, Caoili JC, Ritchie B, Jain SK, Dartois V, Dooley KE | Antimicrobial agents and chemotherapy | 31383662 | Antimicrob Agents Chemother | 2019 Oct | https://www.ncbi.nlm.nih.gov/pubmed/31383662 |
| Stability and Viability of SARS-CoV-2. | Rubens JH, Karakousis PC, Jain SK | The New England journal of medicine | 32283575 | N Engl J Med | 2020 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/32283575 |
| Flagging Bacteria with Radiolabeled d-Amino Acids. | Mota F, Jain SK | ACS central science | 32123728 | ACS Cent Sci | 2020 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/32123728 |
| Imaging Chronic Tuberculous Lesions Using Sodium [(18)F]Fluoride Positron Emission Tomography in Mice. | Ordonez AA, DeMarco VP, Klunk MH, Pokkali S, Jain SK | Molecular imaging and biology | 25750032 | Mol Imaging Biol | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25750032 |
| Determination of [11C]rifampin pharmacokinetics within Mycobacterium tuberculosis-infected mice by using dynamic positron emission tomography bioimaging. | DeMarco VP, Ordonez AA, Klunk M, Prideaux B, Wang H, Zhuo Z, Tonge PJ, Dannals RF, Holt DP, Lee CK, Weinstein EA, Dartois V, Dooley KE, Jain SK | Antimicrobial agents and chemotherapy | 26169396 | Antimicrob Agents Chemother | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26169396 |
| Dynamic imaging in patients with tuberculosis reveals heterogeneous drug exposures in pulmonary lesions. | Ordonez AA, Wang H, Magombedze G, Ruiz-Bedoya CA, Srivastava S, Chen A, Tucker EW, Urbanowski ME, Pieterse L, Fabian Cardozo E, Lodge MA, Shah MR, Holt DP, Mathews WB, Dannals RF, Gobburu JVS, Peloquin CA, Rowe SP, Gumbo T, Ivaturi VD, Jain SK | Nature medicine | 32066976 | Nat Med | 2020 Apr | https://www.ncbi.nlm.nih.gov/pubmed/32066976 |
| Imaging Pulmonary Foreign Body Reaction Using [(125)I]iodo-DPA-713 SPECT/CT in Mice. | Sanchez-Bautista J, Foss CA, Ordonez AA, Klunk MH, Jain SK | Molecular imaging and biology | 29987615 | Mol Imaging Biol | 2019 Apr | https://www.ncbi.nlm.nih.gov/pubmed/29987615 |
| Tuberculous meningitis: a roadmap for advancing basic and translational research. | Jain SK, Tobin DM, Tucker EW, Venketaraman V, Ordonez AA, Jayashankar L, Siddiqi OK, Hammoud DA, Prasadarao NV, Sandor M, Hafner R, Fabry Z, NIH Tuberculous Meningitis Writing Group | Nature immunology | 29777209 | Nat Immunol | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29777209 |
| The integrated stress response mediates necrosis in murine Mycobacterium tuberculosis granulomas. | Bhattacharya B, Xiao S, Chatterjee S, Urbanowski M, Ordonez A, Ihms EA, Agrahari G, Lun S, Berland R, Pichugin A, Gao Y, Connor J, Ivanov AR, Yan BS, Kobzik L, Koo BB, Jain S, Bishai W, Kramnik I | The Journal of clinical investigation | 33301427 | J Clin Invest | 2021 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/33301427 |
| Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. | Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O'Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M | ACS infectious diseases | 27739665 | ACS Infect Dis | 2016 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/27739665 |
| Polymeric nanofiber coating with tunable combinatorial antibiotic delivery prevents biofilm-associated infection in vivo. | Ashbaugh AG, Jiang X, Zheng J, Tsai AS, Kim WS, Thompson JM, Miller RJ, Shahbazian JH, Wang Y, Dillen CA, Ordonez AA, Chang YS, Jain SK, Jones LC, Sterling RS, Mao HQ, Miller LS | Proceedings of the National Academy of Sciences of the United States of America | 27791154 | Proc Natl Acad Sci U S A | 2016 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/27791154 |
| Mouse model of pulmonary cavitary tuberculosis and expression of matrix metalloproteinase-9. | Ordonez AA, Tasneen R, Pokkali S, Xu Z, Converse PJ, Klunk MH, Mollura DJ, Nuermberger EL, Jain SK | Disease models & mechanisms | 27482816 | Dis Model Mech | 2016 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/27482816 |
| Balancing the Risks of Radiation and Anesthesia in Pediatric Patients. | Tucker EW, Jain SK, Mahesh M | Journal of the American College of Radiology : JACR | 28750847 | J Am Coll Radiol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28750847 |
| Novel vaccine strategies against tuberculosis: a road less travelled. | Pokkali S, Jain S | Expert review of vaccines | 24195477 | Expert Rev Vaccines | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24195477 |
| Capsules for biomedical image segmentation. | LaLonde R, Xu Z, Irmakci I, Jain S, Bagci U | Medical image analysis | 33246227 | Med Image Anal | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33246227 |
| Visualizing the dynamics of tuberculosis pathology using molecular imaging. | Ordonez AA, Tucker EW, Anderson CJ, Carter CL, Ganatra S, Kaushal D, Kramnik I, Lin PL, Madigan CA, Mendez S, Rao J, Savic RM, Tobin DM, Walzl G, Wilkinson RJ, Lacourciere KA, Via LE, Jain SK | The Journal of clinical investigation | 33645551 | J Clin Invest | 2021 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/33645551 |
| Pharmacokinetics of rifapentine and rifampin in a rabbit model of tuberculosis and correlation with clinical trial data. | Rifat D, Prideaux B, Savic RM, Urbanowski ME, Parsons TL, Luna B, Marzinke MA, Ordonez AA, DeMarco VP, Jain SK, Dartois V, Bishai WR, Dooley KE | Science translational medicine | 29618565 | Sci Transl Med | 2018 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/29618565 |
| Dynamic PET-facilitated modeling and high-dose rifampin regimens for Staphylococcus aureus orthopedic implant-associated infections. | Gordon O, Lee DE, Liu B, Langevin B, Ordonez AA, Dikeman DA, Shafiq B, Thompson JM, Sponseller PD, Flavahan K, Lodge MA, Rowe SP, Dannals RF, Ruiz-Bedoya CA, Read TD, Peloquin CA, Archer NK, Miller LS, Davis KM, Gobburu JVS, Jain SK | Science translational medicine | 34851697 | Sci Transl Med | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34851697 |
| In vivo prediction of tuberculosis-associated cavity formation in rabbits. | Luna B, Kubler A, Larsson C, Foster B, Bagci U, Mollura DJ, Jain SK, Bishai WR | The Journal of infectious diseases | 25117755 | J Infect Dis | 2015 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/25117755 |
| Microglia activation in a pediatric rabbit model of tuberculous meningitis. | Tucker EW, Pokkali S, Zhang Z, DeMarco VP, Klunk M, Smith ES, Ordonez AA, Penet MF, Bhujwalla Z, Jain SK, Kannan S | Disease models & mechanisms | 27935825 | Dis Model Mech | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27935825 |
| Cavitary tuberculosis: the gateway of disease transmission. | Urbanowski ME, Ordonez AA, Ruiz-Bedoya CA, Jain SK, Bishai WR | The Lancet. Infectious diseases | 32482293 | Lancet Infect Dis | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32482293 |
| Kit-based synthesis of 2-deoxy-2-[(18)F]-fluoro-D-sorbitol for bacterial imaging. | Mota F, De Jesus P, Jain SK | Nature protocols | 34686858 | Nat Protoc | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34686858 |
| Radiosynthesis and validation of [Carboxy-(11) C]4-Aminobenzoic acid ([(11) C]PABA), a PET radiotracer for imaging bacterial infections. | Holt DP, Kalinda AS, Bambarger LE, Jain SK, Dannals RF | Journal of labelled compounds & radiopharmaceuticals | 30089334 | J Labelled Comp Radiopharm | 2019 Jan | https://www.ncbi.nlm.nih.gov/pubmed/30089334 |
| Matrix Metalloproteinase Inhibition in a Murine Model of Cavitary Tuberculosis Paradoxically Worsens Pathology. | Ordonez AA, Pokkali S, Sanchez-Bautista J, Klunk MH, Urbanowski ME, Kübler A, Bishai WR, Elkington PT, Jain SK | The Journal of infectious diseases | 29920600 | J Infect Dis | 2019 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/29920600 |
| [(11)C]Para-Aminobenzoic Acid: A Positron Emission Tomography Tracer Targeting Bacteria-Specific Metabolism. | Mutch CA, Ordonez AA, Qin H, Parker M, Bambarger LE, Villanueva-Meyer JE, Blecha J, Carroll V, Taglang C, Flavell R, Sriram R, VanBrocklin H, Rosenberg O, Ohliger MA, Jain SK, Neumann KD, Wilson DM | ACS infectious diseases | 29712422 | ACS Infect Dis | 2018 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/29712422 |
| Joint solution for PET image segmentation, denoising, and partial volume correction. | Xu Z, Gao M, Papadakis GZ, Luna B, Jain S, Mollura DJ, Bagci U | Medical image analysis | 29627687 | Med Image Anal | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29627687 |
| Successful cure of extensively drug-resistant pulmonary tuberculosis in a young child. | Salazar-Austin N, Akinboyo I, Jain SK | The Lancet. Infectious diseases | 28845790 | Lancet Infect Dis | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28845790 |
| Positron Emission Tomography Imaging with 2-[(18)F]F- p-Aminobenzoic Acid Detects Staphylococcus aureus Infections and Monitors Drug Response. | Zhang Z, Ordonez AA, Wang H, Li Y, Gogarty KR, Weinstein EA, Daryaee F, Merino J, Yoon GE, Kalinda AS, Mease RC, Iuliano JN, Smith-Jones PM, Jain SK, Tonge PJ | ACS infectious diseases | 30067329 | ACS Infect Dis | 2018 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/30067329 |
| Computer-aided pulmonary image analysis in small animal models. | Xu Z, Bagci U, Mansoor A, Kramer-Marek G, Luna B, Kubler A, Dey B, Foster B, Papadakis GZ, Camp JV, Jonsson CB, Bishai WR, Jain S, Udupa JK, Mollura DJ | Medical physics | 26133591 | Med Phys | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26133591 |
| Molecular imaging of bacterial infections: Overcoming the barriers to clinical translation. | Ordonez AA, Sellmyer MA, Gowrishankar G, Ruiz-Bedoya CA, Tucker EW, Palestro CJ, Hammoud DA, Jain SK | Science translational medicine | 31484790 | Sci Transl Med | 2019 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/31484790 |
| (11)C-PABA as a PET Radiotracer for Functional Renal Imaging: Preclinical and First-in-Human Study. | Ruiz-Bedoya CA, Ordonez AA, Werner RA, Plyku D, Klunk MH, Leal J, Lesniak WG, Holt DP, Dannals RF, Higuchi T, Rowe SP, Jain SK | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 32198314 | J Nucl Med | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32198314 |
| Molecular Imaging: a Novel Tool To Visualize Pathogenesis of Infections In Situ. | Gordon O, Ruiz-Bedoya CA, Ordonez AA, Tucker EW, Jain SK | mBio | 31662452 | mBio | 2019 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/31662452 |
| Rabbit model of Staphylococcus aureus implant-associated spinal infection. | Gordon O, Miller RJ, Thompson JM, Ordonez AA, Klunk MH, Dikeman DA, Joyce DP, Ruiz-Bedoya CA, Miller LS, Jain SK | Disease models & mechanisms | 32586832 | Dis Model Mech | 2020 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/32586832 |
| Advanced imaging tools for childhood tuberculosis: potential applications and research needs. | Jain SK, Andronikou S, Goussard P, Antani S, Gomez-Pastrana D, Delacourt C, Starke JR, Ordonez AA, Jean-Philippe P, Browning RS, Perez-Velez CM | The Lancet. Infectious diseases | 32589869 | Lancet Infect Dis | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/32589869 |
| Caspase-Based PET for Evaluating Pro-Apoptotic Treatments in a Tuberculosis Mouse Model. | Ordonez AA, Abhishek S, Singh AK, Klunk MH, Azad BB, Aboagye EO, Carroll L, Jain SK | Molecular imaging and biology | 32232626 | Mol Imaging Biol | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/32232626 |
| Molecular Imaging of Diabetic Foot Infections: New Tools for Old Questions. | Ruiz-Bedoya CA, Gordon O, Mota F, Abhishek S, Tucker EW, Ordonez AA, Jain SK | International journal of molecular sciences | 31795077 | Int J Mol Sci | 2019 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/31795077 |
| Radiosynthesis and PET Bioimaging of (76)Br-Bedaquiline in a Murine Model of Tuberculosis. | Ordonez AA, Carroll LS, Abhishek S, Mota F, Ruiz-Bedoya CA, Klunk MH, Singh AK, Freundlich JS, Mease RC, Jain SK | ACS infectious diseases | 31345032 | ACS Infect Dis | 2019 Dec 13 | https://www.ncbi.nlm.nih.gov/pubmed/31345032 |
| PET/CT imaging of CSF1R in a mouse model of tuberculosis. | Foss CA, Ordonez AA, Naik R, Das D, Hall A, Wu Y, Dannals RF, Jain SK, Pomper MG, Horti AG | European journal of nuclear medicine and molecular imaging | 35713665 | Eur J Nucl Med Mol Imaging | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35713665 |
| Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA. | Woehrstein JB, Strauss MT, Ong LL, Wei B, Zhang DY, Jungmann R, Yin P | Science advances | 28691083 | Sci Adv | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28691083 |
| A DNA nanoscope via auto-cycling proximity recording. | Schaus TE, Woo S, Xuan F, Chen X, Yin P | Nature communications | 28947733 | Nat Commun | 2017 Sep 25 | https://www.ncbi.nlm.nih.gov/pubmed/28947733 |
| Complex cellular logic computation using ribocomputing devices. | Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P | Nature | 28746304 | Nature | 2017 Aug 3 | https://www.ncbi.nlm.nih.gov/pubmed/28746304 |
| Single-stranded DNA and RNA origami. | Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P | Science (New York, N.Y.) | 29242318 | Science | 2017 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/29242318 |
| Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. | Ong LL, Hanikel N, Yaghi OK, Grun C, Strauss MT, Bron P, Lai-Kee-Him J, Schueder F, Wang B, Wang P, Kishi JY, Myhrvold C, Zhu A, Jungmann R, Bellot G, Ke Y, Yin P | Nature | 29219968 | Nature | 2017 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/29219968 |
| Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. | Iinuma R, Ke Y, Jungmann R, Schlichthaerle T, Woehrstein JB, Yin P | Science (New York, N.Y.) | 24625926 | Science | 2014 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/24625926 |
| Axial plane single-molecule super-resolution microscopy of whole cells. | An S, Ziegler KF, Zhang P, Wang Y, Kwok T, Xu F, Bi C, Matosevic S, Yin P, Li T, Huang F | Biomedical optics express | 32010528 | Biomed Opt Express | 2020 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/32010528 |
| 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics. | Wade OK, Woehrstein JB, Nickels PC, Strauss S, Stehr F, Stein J, Schueder F, Strauss MT, Ganji M, Schnitzbauer J, Grabmayr H, Yin P, Schwille P, Jungmann R | Nano letters | 30864449 | Nano Lett | 2019 Apr 10 | https://www.ncbi.nlm.nih.gov/pubmed/30864449 |
| Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT. | Schueder F, Lara-Gutiérrez J, Beliveau BJ, Saka SK, Sasaki HM, Woehrstein JB, Strauss MT, Grabmayr H, Yin P, Jungmann R | Nature communications | 29233999 | Nat Commun | 2017 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/29233999 |
| Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane. | Werbin JL, Avendaño MS, Becker V, Jungmann R, Yin P, Danuser G, Sorger PK | Scientific reports | 28939861 | Sci Rep | 2017 Sep 22 | https://www.ncbi.nlm.nih.gov/pubmed/28939861 |
| Super-resolution labelling with Action-PAINT. | Liu N, Dai M, Saka SK, Yin P | Nature chemistry | 31527848 | Nat Chem | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31527848 |
| Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. | Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P | Nature methods | 24487583 | Nat Methods | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24487583 |
| Super-resolution Geometric Barcoding for Multiplexed miRNA Profiling. | Xu W, Yin P, Dai M | Angewandte Chemie (International ed. in English) | 30182521 | Angew Chem Int Ed Engl | 2018 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/30182521 |
| Design space for complex DNA structures. | Wei B, Dai M, Myhrvold C, Ke Y, Jungmann R, Yin P | Journal of the American Chemical Society | 24256506 | J Am Chem Soc | 2013 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/24256506 |
| Optical imaging of individual biomolecules in densely packed clusters. | Dai M, Jungmann R, Yin P | Nature nanotechnology | 27376244 | Nat Nanotechnol | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27376244 |
| Reconfigurable Three-Dimensional Gold Nanorod Plasmonic Nanostructures Organized on DNA Origami Tripod. | Zhan P, Dutta PK, Wang P, Song G, Dai M, Zhao SX, Wang ZG, Yin P, Zhang W, Ding B, Ke Y | ACS nano | 28056172 | ACS Nano | 2017 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/28056172 |
| DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. | Agasti SS, Wang Y, Schueder F, Sukumar A, Jungmann R, Yin P | Chemical science | 28451377 | Chem Sci | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28451377 |
| Toehold switches: de-novo-designed regulators of gene expression. | Green AA, Silver PA, Collins JJ, Yin P | Cell | 25417166 | Cell | 2014 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/25417166 |
| Quantitative super-resolution imaging with qPAINT. | Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P | Nature methods | 27018580 | Nat Methods | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/27018580 |
| SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P | Nature methods | 31110282 | Nat Methods | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31110282 |
| The emerging landscape of single-molecule protein sequencing technologies. | Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C | Nature methods | 34099939 | Nat Methods | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/34099939 |
| Universal Super-Resolution Multiplexing by DNA Exchange. | Schueder F, Strauss MT, Hoerl D, Schnitzbauer J, Schlichthaerle T, Strauss S, Yin P, Harz H, Leonhardt H, Jungmann R | Angewandte Chemie (International ed. in English) | 28256790 | Angew Chem Int Ed Engl | 2017 Mar 27 | https://www.ncbi.nlm.nih.gov/pubmed/28256790 |
| Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. | Song W, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, Jaffrey SR | Nature chemical biology | 28945233 | Nat Chem Biol | 2017 Nov | https://www.ncbi.nlm.nih.gov/pubmed/28945233 |
| Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval. | Xu F, Ma D, MacPherson KP, Liu S, Bu Y, Wang Y, Tang Y, Bi C, Kwok T, Chubykin AA, Yin P, Calve S, Landreth GE, Huang F | Nature methods | 32371980 | Nat Methods | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/32371980 |
| Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. | Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT | Nature communications | 25962338 | Nat Commun | 2015 May 12 | https://www.ncbi.nlm.nih.gov/pubmed/25962338 |
| A Compact DNA Cube with Side Length 10 nm. | Scheible MB, Ong LL, Woehrstein JB, Jungmann R, Yin P, Simmel FC | Small (Weinheim an der Bergstrasse, Germany) | 26294348 | Small | 2015 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/26294348 |
| Ribocomputing: Cellular Logic Computation Using RNA Devices. | Kim J, Yin P, Green AA | Biochemistry | 29256603 | Biochemistry | 2018 Feb 13 | https://www.ncbi.nlm.nih.gov/pubmed/29256603 |
| Programmable autonomous synthesis of single-stranded DNA. | Kishi JY, Schaus TE, Gopalkrishnan N, Xuan F, Yin P | Nature chemistry | 29359755 | Nat Chem | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29359755 |
| Long-Term In Vivo Oxygen Sensors for Peripheral Artery Disease Monitoring. | Nichols SP, Balaconis MK, Gant RM, Au-Yeung KY, Wisniewski NA | Advances in experimental medicine and biology | 30178370 | Adv Exp Med Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30178370 |
| The First-in-Man "Si Se Puede" Study for the use of micro-oxygen sensors (MOXYs) to determine dynamic relative oxygen indices in the feet of patients with limb-threatening ischemia during endovascular therapy. | Montero-Baker MF, Au-Yeung KY, Wisniewski NA, Gamsey S, Morelli-Alvarez L, Mills JL Sr, Campos M, Helton KL | Journal of vascular surgery | 26004327 | J Vasc Surg | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26004327 |
| Enzymatic Glucose Sensor Compensation for Variations in Ambient Oxygen Concentration. | Collier BB, McShane MJ | Proceedings of SPIE--the International Society for Optical Engineering | 26257458 | Proc SPIE Int Soc Opt Eng | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26257458 |
| Continuous monitoring of interstitial tissue oxygen using subcutaneous oxygen microsensors: In vivo characterization in healthy volunteers. | Kanick SC, Schneider PA, Klitzman B, Wisniewski NA, Rebrin K | Microvascular research | 30742844 | Microvasc Res | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30742844 |
| A Versatile Multichannel Instrument for Measurement of Ratiometric Fluorescence Intensity and Phosphorescence Lifetime. | Zavareh AT, Ko B, Roberts J, Elahi S, McShane MJ | IEEE access : practical innovations, open solutions | 34858770 | IEEE Access | 2021 | https://www.ncbi.nlm.nih.gov/pubmed/34858770 |
| Temperature Compensation of Oxygen Sensing Films Utilizing a Dynamic Dual Lifetime Calculation Technique. | Collier BB, McShane MJ | IEEE sensors journal | 26566384 | IEEE Sens J | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26566384 |
| Characterization of Lactate Sensors Based on Lactate Oxidase and Palladium Benzoporphyrin Immobilized in Hydrogels. | Andrus LP, Unruh R, Wisniewski NA, McShane MJ | Biosensors | 26198251 | Biosensors (Basel) | 2015 Jul 7 | https://www.ncbi.nlm.nih.gov/pubmed/26198251 |
| Modification of PEGylated enzyme with glutaraldehyde can enhance stability while avoiding intermolecular crosslinking. | Ritter DW, Newton JM, McShane MJ | RSC advances | 26052433 | RSC Adv | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/26052433 |
| Preclinical Evaluation of Poly(HEMA-co-acrylamide) Hydrogels Encapsulating Glucose Oxidase and Palladium Benzoporphyrin as Fully Implantable Glucose Sensors. | Unruh RM, Roberts JR, Nichols SP, Gamsey S, Wisniewski NA, McShane MJ | Journal of diabetes science and technology | 26085565 | J Diabetes Sci Technol | 2015 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/26085565 |
| A Design Full of Holes: Functional Nanofilm-Coated Microdomains in Alginate Hydrogels. | Roberts JR, Ritter DW, McShane MJ | Journal of materials chemistry. B | 24040514 | J Mater Chem B | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24040514 |
| Near-Infrared Optical Nanosensors for Continuous Detection of Glucose. | Le LV, Chendke GS, Gamsey S, Wisniewski N, Desai TA | Journal of diabetes science and technology | 31709808 | J Diabetes Sci Technol | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31709808 |
| Composite Hydrogels with Engineered Microdomains for Optical Glucose Sensing at Low Oxygen Conditions. | Bornhoeft LR, Biswas A, McShane MJ | Biosensors | 28117762 | Biosensors (Basel) | 2017 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/28117762 |
| Tissue-Integrating Oxygen Sensors: Continuous Tracking of Tissue Hypoxia. | Wisniewski NA, Nichols SP, Gamsey SJ, Pullins S, Au-Yeung KY, Klitzman B, Helton KL | Advances in experimental medicine and biology | 28685468 | Adv Exp Med Biol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28685468 |
| Inorganic-Organic Interpenetrating Network Hydrogels as Tissue-Integrating Luminescent Implants: Physicochemical Characterization and Preclinical Evaluation. | Unruh RM, Bornhoeft LR, Nichols SP, Wisniewski NA, McShane MJ | Macromolecular bioscience | 34847287 | Macromol Biosci | 2022 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34847287 |
| In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. | Filonov GS, Kam CW, Song W, Jaffrey SR | Chemistry & biology | 26000751 | Chem Biol | 2015 May 21 | https://www.ncbi.nlm.nih.gov/pubmed/26000751 |
| A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. | Strack RL, Disney MD, Jaffrey SR | Nature methods | 24162923 | Nat Methods | 2013 Dec | https://www.ncbi.nlm.nih.gov/pubmed/24162923 |
| Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. | Strack RL, Song W, Jaffrey SR | Nature protocols | 24356773 | Nat Protoc | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24356773 |
| Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. | Filonov GS, Moon JD, Svensen N, Jaffrey SR | Journal of the American Chemical Society | 25337688 | J Am Chem Soc | 2014 Nov 19 | https://www.ncbi.nlm.nih.gov/pubmed/25337688 |
| RNA-Based Fluorescent Biosensors for Detecting Metabolites in vitro and in Living Cells. | Jaffrey SR | Advances in pharmacology (San Diego, Calif.) | 29413520 | Adv Pharmacol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29413520 |
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| Plug-and-play fluorophores extend the spectral properties of Spinach. | Song W, Strack RL, Svensen N, Jaffrey SR | Journal of the American Chemical Society | 24393009 | J Am Chem Soc | 2014 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/24393009 |
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| Fibroblasts in heart scar tissue directly regulate cardiac excitability and arrhythmogenesis. | Wang Y, Li Q, Tao B, Angelini M, Ramadoss S, Sun B, Wang P, Krokhaleva Y, Ma F, Gu Y, Espinoza A, Yamauchi K, Pellegrini M, Novitch B, Olcese R, Qu Z, Song Z, Deb A | Science (New York, N.Y.) | 37769108 | Science | 2023 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/37769108 |
| Differential Susceptibility of Fetal Retinal Pigment Epithelial Cells, hiPSC- Retinal Stem Cells, and Retinal Organoids to Zika Virus Infection. | Contreras D, Garcia G Jr, Jones MK, Martinez LE, Jayakarunakaran A, Gangalapudi V, Tang J, Wu Y, Zhao JJ, Chen Z, Ramaiah A, Tsui I, Kumar A, Nielsen-Saines K, Wang S, Arumugaswami V | Viruses | 36680182 | Viruses | 2023 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/36680182 |
| ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling. | Wu B, Ramaiah A, Garcia G Jr, Hasiakos S, Arumugaswami V, Srikanth S | Journal of immunology (Baltimore, Md. : 1950) | 34819389 | J Immunol | 2022 Jan 1 | https://www.ncbi.nlm.nih.gov/pubmed/34819389 |
| Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition. | Liu X, Verma A, Garcia G Jr, Ramage H, Lucas A, Myers RL, Michaelson JJ, Coryell W, Kumar A, Charney AW, Kazanietz MG, Rader DJ, Ritchie MD, Berrettini WH, Schultz DC, Cherry S, Damoiseaux R, Arumugaswami V, Klein PS | Proceedings of the National Academy of Sciences of the United States of America | 34593624 | Proc Natl Acad Sci U S A | 2021 Oct 19 | https://www.ncbi.nlm.nih.gov/pubmed/34593624 |
| Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: a comparative analysis. | Chakravarty N, Senthilnathan T, Paiola S, Gyani P, Castillo Cario S, Urena E, Jeysankar A, Jeysankar P, Ignatius Irudayam J, Natesan Subramanian S, Lavretsky H, Joshi S, Garcia G Jr, Ramaiah A, Arumugaswami V | FEBS letters | 34757622 | FEBS Lett | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/34757622 |
| Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses. | Jeyachandran AV, Irudayam JI, Dubey S, Chakravarty N, Konda B, Shah A, Su B, Wang C, Cui Q, Williams KJ, Srikanth S, Shi Y, Deb A, Damoiseaux R, Stripp BR, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 37577539 | bioRxiv | 2023 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/37577539 |
| Envelope protein-specific B cell receptors direct lentiviral vector tropism in vivo. | Takano KA, Wong AAL, Brown R, Situ K, Chua BA, Abu AE, Pham TT, Reyes GC, Ramachandran S, Kamata M, Li MMH, Wu TT, Rao DS, Arumugaswami V, Dorshkind K, Cole S, Morizono K | Molecular therapy : the journal of the American Society of Gene Therapy | 38449314 | Mol Ther | 2024 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/38449314 |
| Mpox Virus and its ocular surface manifestations. | Chakravarty N, Hemani D, Paravastu R, Ahmad Z, Palani SN, Arumugaswami V, Kumar A | The ocular surface | 38972544 | Ocul Surf | 2024 Oct | https://www.ncbi.nlm.nih.gov/pubmed/38972544 |
| Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses. | Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Cario SC, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells M, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 36711787 | bioRxiv | 2023 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/36711787 |
| Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses. | Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Castillo Cario S, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells MS, Ramaiah A, Arumugaswami V | Cell reports. Medicine | 37119814 | Cell Rep Med | 2023 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/37119814 |
| Differential Susceptibility of Ex Vivo Primary Glioblastoma Tumors to Oncolytic Effect of Modified Zika Virus. | Garcia G Jr, Chakravarty N, Paiola S, Urena E, Gyani P, Tse C, French SW, Danielpour M, Breunig JJ, Nathanson DA, Arumugaswami V | Cells | 37830597 | Cells | 2023 Sep 29 | https://www.ncbi.nlm.nih.gov/pubmed/37830597 |
| Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response. | Garcia G Jr, Wang Y, Ignatius Irudayam J, Jeyachandran AV, Cario SC, Sen C, Li S, Li Y, Kumar A, Nielsen-Saines K, French SW, Shah PS, Morizono K, Gomperts B, Deb A, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 35441167 | bioRxiv | 2022 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/35441167 |
| In Silico Genome Analysis Reveals the Evolution and Potential Impact of SARS-CoV-2 Omicron Structural Changes on Host Immune Evasion and Antiviral Therapeutics. | Chauhan D, Chakravarty N, Jeyachandran AV, Jayakarunakaran A, Sinha S, Mishra R, Arumugaswami V, Ramaiah A | Viruses | 36366559 | Viruses | 2022 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/36366559 |
| Longitudinal Evaluation of Antibody Persistence in Mother-Infant Dyads After Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Pregnancy. | Cambou MC, Liu CM, Mok T, Fajardo-Martinez V, Paiola SG, Ibarrondo FJ, Kerin T, Fuller T, Tobin NH, Garcia G, Bhattacharya D, Aldrovandi GM, Arumugaswami V, Foo SS, Jung JU, Vasconcelos Z, Brasil P, Brendolin M, Yang OO, Rao R, Nielsen-Saines K | The Journal of infectious diseases | 36082433 | J Infect Dis | 2023 Jan 11 | https://www.ncbi.nlm.nih.gov/pubmed/36082433 |
| Replication-Deficient Zika Vector-Based Vaccine Provides Maternal and Fetal Protection in Mouse Model. | Garcia G Jr, Chakravarty N, Abu AE, Jeyachandran AV, Takano KA, Brown R, Morizono K, Arumugaswami V | Microbiology spectrum | 36169338 | Microbiol Spectr | 2022 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/36169338 |
| Drug screen reveals new potent host-targeted antivirals against Mpox virus. | Jeyachandran AV, Zaiss AK, Chakravarty N, Singh S, Delgado Y, Paravastu R, Satheeshkumar N, Gerald E, Jeysankar A, Thomas J, Fuller L, Lee N, Taylor C, Joshi S, Parcells M, French SW, Date A, Bouhaddou M, Garcia G Jr, Kumar A, Damoiseaux R, Arumugaswami V | bioRxiv : the preprint server for biology | 40400715 | bioRxiv | 2025 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/40400715 |
| SARS-CoV-2 and its beta variant of concern infect human conjunctival epithelial cells and induce differential antiviral innate immune response. | Singh S, Garcia G Jr, Shah R, Kramerov AA, Wright RE 3rd, Spektor TM, Ljubimov AV, Arumugaswami V, Kumar A | The ocular surface | 34583089 | Ocul Surf | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34583089 |
| Cardiomyocytes disrupt pyrimidine biosynthesis in nonmyocytes to regulate heart repair. | Li S, Yokota T, Wang P, Ten Hoeve J, Ma F, Le TM, Abt ER, Zhou Y, Wu R, Nanthavongdouangsy M, Rodriguez A, Wang Y, Lin YJ, Muranaka H, Sharpley M, Braddock DT, MacRae VE, Banerjee U, Chiou PY, Seldin M, Huang D, Teitell M, Gertsman I, Jung M, Bensinger SJ, Damoiseaux R, Faull K, Pellegrini M, Lusis AJ, Graeber TG, Radu CG, Deb A | The Journal of clinical investigation | 34813507 | J Clin Invest | 2022 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/34813507 |
| Development of a blocker of the universal phosphatidylserine- and phosphatidylethanolamine-dependent viral entry pathways. | Song DH, Garcia G Jr, Situ K, Chua BA, Hong MLO, Do EA, Ramirez CM, Harui A, Arumugaswami V, Morizono K | Virology | 34020328 | Virology | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34020328 |
| Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. | Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G Jr, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS | Nature communications | 37185252 | Nat Commun | 2023 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/37185252 |
| The Apolipoprotein E neutralizing antibody inhibits SARS-CoV-2 infection by blocking cellular entry of lipoviral particles. | Cui Q, Jeyachandran AV, Garcia G, Qin C, Zhou Y, Zhang M, Wang C, Sun G, Liu W, Zhou T, Feng L, Palmer C, Li Z, Aziz A, Gomperts BN, Feng P, Arumugaswami V, Shi Y | MedComm | 37822714 | MedComm (2020) | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37822714 |
| A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. | Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A | Communications biology | 37923961 | Commun Biol | 2023 Nov 3 | https://www.ncbi.nlm.nih.gov/pubmed/37923961 |
| Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response. | Garcia G Jr, Jeyachandran AV, Wang Y, Irudayam JI, Cario SC, Sen C, Li S, Li Y, Kumar A, Nielsen-Saines K, French SW, Shah PS, Morizono K, Gomperts BN, Deb A, Ramaiah A, Arumugaswami V | PLoS biology | 36346780 | PLoS Biol | 2022 Nov | https://www.ncbi.nlm.nih.gov/pubmed/36346780 |
| Drug screen reveals new potent host-targeted antivirals against Mpox virus. | Jeyachandran AV, Zaiss AK, Chakravarty N, Singh S, Delgado Y, Paravastu R, Satheeshkumar N, Gerald E, Jeysankar A, Thomas J, Fuller L, Lee N, Taylor C, Joshi S, Parcells M, French SW, Date A, Bouhaddou M, Garcia G Jr, Kumar A, Damoiseaux R, Arumugaswami V | Research square | 40502772 | Res Sq | 2025 Jun 5 | https://www.ncbi.nlm.nih.gov/pubmed/40502772 |
| Regulation of insulin and adipokinetic hormone/glucagon production in flies. | Ahmad M, He L, Perrimon N | Wiley interdisciplinary reviews. Developmental biology | 31379062 | Wiley Interdiscip Rev Dev Biol | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/31379062 |
| Deciphering molecular interactions by proximity labeling. | Qin W, Cho KF, Cavanagh PE, Ting AY | Nature methods | 33432242 | Nat Methods | 2021 Feb | https://www.ncbi.nlm.nih.gov/pubmed/33432242 |
| Split-TurboID enables contact-dependent proximity labeling in cells. | Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY | Proceedings of the National Academy of Sciences of the United States of America | 32424107 | Proc Natl Acad Sci U S A | 2020 Jun 2 | https://www.ncbi.nlm.nih.gov/pubmed/32424107 |
| Proximal tubule responses to injury: interrogation by single-cell transcriptomics. | Cippà PE, McMahon AP | Current opinion in nephrology and hypertension | 37074682 | Curr Opin Nephrol Hypertens | 2023 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/37074682 |
| Dynamic mapping of proteome trafficking within and between living cells by TransitID. | Qin W, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY | Cell | 37385249 | Cell | 2023 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/37385249 |
| Protein phosphatase 1 regulates core PCP signaling. | Song S, Cho B, Weiner AT, Nissen SB, Ojeda Naharros I, Sanchez Bosch P, Suyama K, Hu Y, He L, Svinkina T, Udeshi ND, Carr SA, Perrimon N, Axelrod JD | EMBO reports | 37975164 | EMBO Rep | 2023 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/37975164 |
| Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. | Qin W, Myers SA, Carey DK, Carr SA, Ting AY | Nature communications | 34404792 | Nat Commun | 2021 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/34404792 |
| 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 |
| A genetic model for in vivo proximity labelling of the mammalian secretome. | Yang R, Meyer AS, Droujinine IA, Udeshi ND, Hu Y, Guo J, McMahon JA, Carey DK, Xu C, Fang Q, Sha J, Qin S, Rocco D, Wohlschlegel J, Ting AY, Carr SA, Perrimon N, McMahon AP | Open biology | 35946312 | Open Biol | 2022 Aug | https://www.ncbi.nlm.nih.gov/pubmed/35946312 |
| Repairing the blood-brain barrier. | McMahon AP, Ichida JK | Science (New York, N.Y.) | 35175806 | Science | 2022 Feb 18 | https://www.ncbi.nlm.nih.gov/pubmed/35175806 |
| Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code. | Xie Q, Li J, Li H, Udeshi ND, Svinkina T, Orlin D, Kohani S, Guajardo R, Mani DR, Xu C, Li T, Han S, Wei W, Shuster SA, Luginbuhl DJ, Quake SR, Murthy SE, Ting AY, Carr SA, Luo L | Neuron | 35613619 | Neuron | 2022 Jul 20 | https://www.ncbi.nlm.nih.gov/pubmed/35613619 |
| Proximity-dependent labeling methods for proteomic profiling in living cells: An update. | Bosch JA, Chen CL, Perrimon N | Wiley interdisciplinary reviews. Developmental biology | 32909689 | Wiley Interdiscip Rev Dev Biol | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/32909689 |
| In situ cell-type-specific cell-surface proteomic profiling in mice. | Shuster SA, Li J, Chon U, Sinantha-Hu MC, Luginbuhl DJ, Udeshi ND, Carey DK, Takeo YH, Xie Q, Xu C, Mani DR, Han S, Ting AY, Carr SA, Luo L | Neuron | 36220098 | Neuron | 2022 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/36220098 |
| RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. | Han S, Zhao BS, Myers SA, Carr SA, He C, Ting AY | Proceedings of the National Academy of Sciences of the United States of America | 32839320 | Proc Natl Acad Sci U S A | 2020 Sep 8 | https://www.ncbi.nlm.nih.gov/pubmed/32839320 |
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| Coordination of tumor growth and host wasting by tumor-derived Upd3. | Ding G, Xiang X, Hu Y, Xiao G, Chen Y, Binari R, Comjean A, Li J, Rushworth E, Fu Z, Mohr SE, Perrimon N, Song W | Cell reports | 34407411 | Cell Rep | 2021 Aug 17 | https://www.ncbi.nlm.nih.gov/pubmed/34407411 |
| Identifying Common Molecular Mechanisms in Experimental and Human Acute Kidney Injury. | Gerhardt LMS, McMahon AP | Seminars in nephrology | 36402654 | Semin Nephrol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/36402654 |
| Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. | Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY | Nature methods | 37188954 | Nat Methods | 2023 Jun | https://www.ncbi.nlm.nih.gov/pubmed/37188954 |
| Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Toxoplasma Parasitophorous Vacuole Membrane. | Cygan AM, Jean Beltran PM, Mendoza AG, Branon TC, Ting AY, Carr SA, Boothroyd JC | mBio | 34749525 | mBio | 2021 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/34749525 |
| Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. | Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, Quake SR, Carr SA, Ting AY, Luo L | Cell | 31955847 | Cell | 2020 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/31955847 |
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| Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching. | Xu C, Li Z, Lyu C, Hu Y, McLaughlin CN, Wong KKL, Xie Q, Luginbuhl DJ, Li H, Udeshi ND, Svinkina T, Mani DR, Han S, Li T, Li Y, Guajardo R, Ting AY, Carr SA, Li J, Luo L | Cell | 38996528 | Cell | 2024 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/38996528 |
| Protein phosphatase 1 regulates core PCP signaling. | Song S, Cho B, Weiner AT, Nissen SB, Naharros IO, Bosch PS, Suyama K, Hu Y, He L, Svinkina T, Udeshi ND, Carr SA, Perrimon N, Axelrod JD | bioRxiv : the preprint server for biology | 37745534 | bioRxiv | 2023 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/37745534 |
| Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. | Cheng LC, Zhang X, Abhinav K, Nguyen JA, Baboo S, Martinez-Bartolomé S, Branon TC, Ting AY, Loose E, Yates JR 3rd, Gerace L | Journal of proteome research | 35972904 | J Proteome Res | 2022 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/35972904 |
| Dietary Amino Acids Promote Glucagon-like Hormone Release to Generate Novel Calcium Waves in Adipose Tissues. | He L, Ahmad M, Wu S, Luo S, Shi W, Guo X, Cao Y, Perrimon N | Research square | 38947048 | Res Sq | 2024 Jun 12 | https://www.ncbi.nlm.nih.gov/pubmed/38947048 |
| Cell-death induced immune response and coagulopathy promote cachexia in Drosophila. | Singh A, Hu Y, Lopes RF, Lane L, Woldemichael H, Xu C, Udeshi ND, Carr SA, Perrimon N | bioRxiv : the preprint server for biology | 39829769 | bioRxiv | 2025 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/39829769 |
| Taf2 mediates DNA binding of Taf14. | Klein BJ, Feigerle JT, Zhang J, Ebmeier CC, Fan L, Singh RK, Wang WW, Schmitt LR, Lee T, Hansen KC, Liu WR, Wang YX, Strahl BD, Anthony Weil P, Kutateladze TG | Nature communications | 35676274 | Nat Commun | 2022 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/35676274 |
| Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. | Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD | eLife | 33904398 | Elife | 2021 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/33904398 |
| 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 |
| Primary Role of the Nucleosome. | Kornberg RD, Lorch Y | Molecular cell | 32763226 | Mol Cell | 2020 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/32763226 |
| Structure of mitotic chromosomes. | Beel AJ, Azubel M, Matteï PJ, Kornberg RD | Molecular cell | 34520722 | Mol Cell | 2021 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/34520722 |
| Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy. | Jagota M, Townshend RJL, Kang LW, Bushnell DA, Dror RO, Kornberg RD, Azubel M | Ultramicroscopy | 34062386 | Ultramicroscopy | 2021 Aug | https://www.ncbi.nlm.nih.gov/pubmed/34062386 |
| Microbiota modulate sympathetic neurons via a gut-brain circuit. | Muller PA, Schneeberger M, Matheis F, Wang P, Kerner Z, Ilanges A, Pellegrino K, Del Mármol J, Castro TBR, Furuichi M, Perkins M, Han W, Rao A, Pickard AJ, Cross JR, Honda K, de Araujo I, Mucida D | Nature | 32641826 | Nature | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32641826 |
| Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections. | Ahrends T, Aydin B, Matheis F, Classon CH, Marchildon F, Furtado GC, Lira SA, Mucida D | Cell | 34717799 | Cell | 2021 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/34717799 |
| Adrenergic Signaling in Muscularis Macrophages Limits Infection-Induced Neuronal Loss. | Matheis F, Muller PA, Graves CL, Gabanyi I, Kerner ZJ, Costa-Borges D, Ahrends T, Rosenstiel P, Mucida D | Cell | 31923400 | Cell | 2020 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/31923400 |
| Microbiota-modulated CART(+) enteric neurons autonomously regulate blood glucose. | Muller PA, Matheis F, Schneeberger M, Kerner Z, Jové V, Mucida D | Science (New York, N.Y.) | 32855216 | Science | 2020 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/32855216 |
| Gut macrophages: key players in intestinal immunity and tissue physiology. | Muller PA, Matheis F, Mucida D | Current opinion in immunology | 31841704 | Curr Opin Immunol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31841704 |
| Tunable dynamics of B cell selection in gut germinal centres. | Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP, Araki T, Schiepers A, Lockhart AAK, Bilate AM, Mucida D, Victora GD | Nature | 33116306 | Nature | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33116306 |
| A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. | Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM | Science (New York, N.Y.) | 35926021 | Science | 2022 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/35926021 |
| Citrobacter rodentium(ϕStx2dact), a murine infection model for enterohemorrhagic Escherichia coli. | Thorpe CM, Pulsifer AR, Osburne MS, Vanaja SK, Leong JM | Current opinion in microbiology | 34929548 | Curr Opin Microbiol | 2022 Feb | https://www.ncbi.nlm.nih.gov/pubmed/34929548 |
| PROT(3)EcT, engineered Escherichia coli for the targeted delivery of therapeutics. | González-Prieto C, Lynch JP, Lesser CF | Trends in molecular medicine | 37574350 | Trends Mol Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37574350 |
| Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. | Lynch JP, Goers L, Lesser CF | Trends in pharmacological sciences | 35232591 | Trends Pharmacol Sci | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35232591 |
| Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. | Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS | PLoS pathogens | 36107831 | PLoS Pathog | 2022 Sep | https://www.ncbi.nlm.nih.gov/pubmed/36107831 |
| Living Engineered Bacterial Therapeutics: Emerging Affordable Precision Interventions. | Srivastava R, Lesser CF | Microbial biotechnology | 39579048 | Microb Biotechnol | 2024 Nov | https://www.ncbi.nlm.nih.gov/pubmed/39579048 |
| Rationale redesign of type III secretion systems: toward the development of non-pathogenic E. coli for in vivo delivery of therapeutic payloads. | González-Prieto C, Lesser CF | Current opinion in microbiology | 29141238 | Curr Opin Microbiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29141238 |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo ME, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | PNAS nexus | 39262854 | PNAS Nexus | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39262854 |
| A host metabolite promotes Salmonella survival. | Lynch JP, Lesser CF | Science (New York, N.Y.) | 33479138 | Science | 2021 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/33479138 |
| Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut. | Lynch JP, González-Prieto C, Reeves AZ, Bae S, Powale U, Godbole NP, Tremblay JM, Schmidt FI, Ploegh HL, Kansra V, Glickman JN, Leong JM, Shoemaker CB, Garrett WS, Lesser CF | Cell host & microbe | 37003258 | Cell Host Microbe | 2023 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/37003258 |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo M, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | bioRxiv : the preprint server for biology | 39131305 | bioRxiv | 2024 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/39131305 |
| Rational Design of Silicon-Based Zinc Ionophores. | Yamada K, Deb A, Shoba VM, Lim D, Maji B, Modell AE, Choudhary A | Angewandte Chemie (International ed. in English) | 35385189 | Angew Chem Int Ed Engl | 2022 Jun 7 | https://www.ncbi.nlm.nih.gov/pubmed/35385189 |
| Native Zinc Catalyzes Selective and Traceless Release of Small Molecules in β-Cells. | Lee M, Maji B, Manna D, Kahraman S, Elgamal RM, Small J, Kokkonda P, Vetere A, Goldberg JM, Lippard SJ, Kulkarni RN, Wagner BK, Choudhary A | Journal of the American Chemical Society | 32175731 | J Am Chem Soc | 2020 Apr 8 | https://www.ncbi.nlm.nih.gov/pubmed/32175731 |
| Engineering designer beta cells with a CRISPR-Cas9 conjugation platform. | Lim D, Sreekanth V, Cox KJ, Law BK, Wagner BK, Karp JM, Choudhary A | Nature communications | 32792475 | Nat Commun | 2020 Aug 13 | https://www.ncbi.nlm.nih.gov/pubmed/32792475 |
| Excess pancreatic elastase alters acinar-β cell communication by impairing the mechano-signaling and the PAR2 pathways. | Basile G, Vetere A, Hu J, Ijaduola O, Zhang Y, Liu KC, Eltony AM, De Jesus DF, Fukuda K, Doherty G, Leech CA, Chepurny OG, Holz GG, Yun SH, Andersson O, Choudhary A, Wagner BK, Kulkarni RN | Cell metabolism | 37339634 | Cell Metab | 2023 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/37339634 |
| Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. | Andrew AL, Perry BW, Card DC, Schield DR, Ruggiero RP, McGaugh SE, Choudhary A, Secor SM, Castoe TA | BMC genomics | 28464824 | BMC Genomics | 2017 May 2 | https://www.ncbi.nlm.nih.gov/pubmed/28464824 |
| A 3D culture platform enables development of zinc-binding prodrugs for targeted proliferation of β cells. | Yang K, Lee M, Jones PA, Liu SS, Zhou A, Xu J, Sreekanth V, Wu JLY, Vo L, Lee EA, Pop R, Lee Y, Wagner BK, Melton DA, Choudhary A, Karp JM | Science advances | 33208361 | Sci Adv | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33208361 |
| Enterochromaffin Cell-Enriched Monolayer Platform for Assaying Serotonin Release from Human Primary Intestinal Cells. | Wang Y, Sims CE, Allbritton NL | Analytical chemistry | 32819098 | Anal Chem | 2020 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/32819098 |
| An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. | Kim R, Attayek PJ, Wang Y, Furtado KL, Tamayo R, Sims CE, Allbritton NL | Biofabrication | 31519008 | Biofabrication | 2019 Nov 6 | https://www.ncbi.nlm.nih.gov/pubmed/31519008 |
| In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels. | Hinman SS, Wang Y, Kim R, Allbritton NL | Nature protocols | 33299154 | Nat Protoc | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33299154 |
| Primary Cell-Derived Intestinal Models: Recapitulating Physiology. | Dutton JS, Hinman SS, Kim R, Wang Y, Allbritton NL | Trends in biotechnology | 30591184 | Trends Biotechnol | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30591184 |
| Nonsteroidal Anti-Inflammatory Drug-Induced Leaky Gut Modeled Using Polarized Monolayers of Primary Human Intestinal Epithelial Cells. | Bhatt AP, Gunasekara DB, Speer J, Reed MI, Peña AN, Midkiff BR, Magness ST, Bultman SJ, Allbritton NL, Redinbo MR | ACS infectious diseases | 29094594 | ACS Infect Dis | 2018 Jan 12 | https://www.ncbi.nlm.nih.gov/pubmed/29094594 |
| In Vitro Generation of Mouse Colon Crypts. | Wang Y, Gunasekara DB, Attayek PJ, Reed MI, DiSalvo M, Nguyen DL, Dutton JS, Lebhar MS, Bultman SJ, Sims CE, Magness ST, Allbritton NL | ACS biomaterials science & engineering | 30854421 | ACS Biomater Sci Eng | 2017 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/30854421 |
| TGFB1 induces fetal reprogramming and enhances intestinal regeneration. | Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP | Cell stem cell | 37865088 | Cell Stem Cell | 2023 Nov 2 | https://www.ncbi.nlm.nih.gov/pubmed/37865088 |
| 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 |
| Hypoxia Primes Human ISCs for Interleukin-Dependent Rescue of Stem Cell Activity. | Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Deal HE, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST | Cellular and molecular gastroenterology and hepatology | 37562653 | Cell Mol Gastroenterol Hepatol | 2023 | https://www.ncbi.nlm.nih.gov/pubmed/37562653 |
| Use of liquid lithography to form in vitro intestinal crypts with varying microcurvature surrounding the stem cell niche. | Logan Howard R, Wang Y, Allbritton NL | Journal of micromechanics and microengineering : structures, devices, and systems | 35241878 | J Micromech Microeng | 2021 Dec | https://www.ncbi.nlm.nih.gov/pubmed/35241878 |
| "Fix and Click" for Assay of Sphingolipid Signaling in Single Primary Human Intestinal Epithelial Cells. | Gallion LA, Wang Y, Massaro A, Yao M, Petersen BV, Zhang Q, Huang W, Carr AJ, Zhang Q, Allbritton NL | Analytical chemistry | 35020354 | Anal Chem | 2022 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/35020354 |
| Analysis of Interleukin 8 Secretion by a Stem-Cell-Derived Human-Intestinal-Epithelial-Monolayer Platform. | Wang Y, Kim R, Hwang SJ, Dutton J, Sims CE, Allbritton NL | Analytical chemistry | 30199234 | Anal Chem | 2018 Oct 2 | https://www.ncbi.nlm.nih.gov/pubmed/30199234 |
| The role of the microbiome in cancer development and therapy. | Bhatt AP, Redinbo MR, Bultman SJ | CA: a cancer journal for clinicians | 28481406 | CA Cancer J Clin | 2017 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/28481406 |
| A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. | Wang Y, Gunasekara DB, Reed MI, DiSalvo M, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Biomaterials | 28288348 | Biomaterials | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28288348 |
| Photopatterned Membranes and Chemical Gradients Enable Scalable Phenotypic Organization of Primary Human Colon Epithelial Models. | Hinman SS, Wang Y, Allbritton NL | Analytical chemistry | 31692334 | Anal Chem | 2019 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/31692334 |
| Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer. | Bultman SJ | Molecular nutrition & food research | 27138454 | Mol Nutr Food Res | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/27138454 |
| Hyperglycemia minimally alters primary self-renewing human colonic epithelial cells while TNFα-promotes severe intestinal epithelial dysfunction. | Dutton JS, Hinman SS, Kim R, Attayek PJ, Maurer M, Sims CS, Allbritton NL | Integrative biology : quantitative biosciences from nano to macro | 33989405 | Integr Biol (Camb) | 2021 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/33989405 |
| Integrative microphysiological tissue systems of cancer metastasis to the liver. | Clark AM, Allbritton NL, Wells A | Seminars in cancer biology | 32580025 | Semin Cancer Biol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32580025 |
| Formation of arrays of planar, murine, intestinal crypts possessing a stem/proliferative cell compartment and differentiated cell zone. | Kim R, Wang Y, Hwang SJ, Attayek PJ, Smiddy NM, Reed MI, Sims CE, Allbritton NL | Lab on a chip | 29944153 | Lab Chip | 2018 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/29944153 |
| Microphysiological System Design: Simplicity Is Elegance. | Hinman SS, Kim R, Wang Y, Phillips KS, Attayek PJ, Allbritton NL | Current opinion in biomedical engineering | 32095672 | Curr Opin Biomed Eng | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32095672 |
| A new microphysiological system shows hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity. | Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST | bioRxiv : the preprint server for biology | 36778265 | bioRxiv | 2023 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/36778265 |
| Development of Arrayed Colonic Organoids for Screening of Secretagogues Associated with Enterotoxins. | Gunasekara DB, DiSalvo M, Wang Y, Nguyen DL, Reed MI, Speer J, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 29281259 | Anal Chem | 2018 Feb 6 | https://www.ncbi.nlm.nih.gov/pubmed/29281259 |
| Reserve Stem Cells in Intestinal Homeostasis and Injury. | Bankaitis ED, Ha A, Kuo CJ, Magness ST | Gastroenterology | 30118745 | Gastroenterology | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/30118745 |
| Bioengineered Systems and Designer Matrices That Recapitulate the Intestinal Stem Cell Niche. | Wang Y, Kim R, Hinman SS, Zwarycz B, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29675459 | Cell Mol Gastroenterol Hepatol | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29675459 |
| Butyrate consumption of differentiated colonocytes in the upper crypt promotes homeostatic proliferation of stem and progenitor cells near the crypt base. | Bultman SJ | Translational cancer research | 30568890 | Transl Cancer Res | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/30568890 |
| Magnetically-propelled fecal surrogates for modeling the impact of solid-induced shear forces on primary colonic epithelial cells. | Hinman SS, Huling J, Wang Y, Wang H, Bretherton RC, DeForest CA, Allbritton NL | Biomaterials | 34412014 | Biomaterials | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34412014 |
| Molecular transport through primary human small intestinal monolayers by culture on a collagen scaffold with a gradient of chemical cross-linking. | Speer JE, Gunasekara DB, Wang Y, Fallon JK, Attayek PJ, Smith PC, Sims CE, Allbritton NL | Journal of biological engineering | 31061676 | J Biol Eng | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31061676 |
| Recombination drives the evolution of mutational robustness. | Singhal S, Gomez SM, Burch CL | Current opinion in systems biology | 31572829 | Curr Opin Syst Biol | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31572829 |
| An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells. | Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora K, Tang CY, Zheng A, Magness ST, Burclaff J | bioRxiv : the preprint server for biology | 37873351 | bioRxiv | 2023 Oct 10 | https://www.ncbi.nlm.nih.gov/pubmed/37873351 |
| Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells. | Sarma S, Catella CM, San Pedro ET, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK | Communications biology | 37634026 | Commun Biol | 2023 Aug 26 | https://www.ncbi.nlm.nih.gov/pubmed/37634026 |
| The microbiome and its potential as a cancer preventive intervention. | Bultman SJ | Seminars in oncology | 26970128 | Semin Oncol | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26970128 |
| Stem/Proliferative and Differentiated Cells within Primary Murine Colonic Epithelium Display Distinct Intracellular Free Ca(2+) Signal Codes. | Mestril S, Kim R, Hinman SS, Gomez SM, Allbritton NL | Advanced healthcare materials | 34510822 | Adv Healthc Mater | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34510822 |
| A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. | Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST | Cellular and molecular gastroenterology and hepatology | 30123820 | Cell Mol Gastroenterol Hepatol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30123820 |
| "Fix and assay": separating in-cellulo sphingolipid reactions from analytical assay in time and space using an aldehyde-based fixative. | Proctor A , Allbritton NL | The Analyst | 30207332 | Analyst | 2019 Jan 28 | https://www.ncbi.nlm.nih.gov/pubmed/30207332 |
| Formation of Human Colonic Crypt Array by Application of Chemical Gradients Across a Shaped Epithelial Monolayer. | Wang Y, Kim R, Gunasekara DB, Reed MI, DiSalvo M, Nguyen DL, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29693040 | Cell Mol Gastroenterol Hepatol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29693040 |
| Self-renewing Monolayer of Primary Colonic or Rectal Epithelial Cells. | Wang Y, DiSalvo M, Gunasekara DB, Dutton J, Proctor A, Lebhar MS, Williamson IA, Speer J, Howard RL, Smiddy NM, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29204504 | Cell Mol Gastroenterol Hepatol | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29204504 |
| Building a Thick Mucus Hydrogel Layer to Improve the Physiological Relevance of In Vitro Primary Colonic Epithelial Models. | Wang Y, Kim R, Sims CE, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 31356887 | Cell Mol Gastroenterol Hepatol | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/31356887 |
| A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies. | Gunasekara DB, Speer J, Wang Y, Nguyen DL, Reed MI, Smiddy NM, Parker JS, Fallon JK, Smith PC, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 30350627 | Anal Chem | 2018 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/30350627 |
| Genomewide CRISPR knockout screen identified PLAC8 as an essential factor for SADS-CoVs infection. | Tse LV, Meganck RM, Araba KC, Yount BL, Shaffer KM, Hou YJ, Munt JE, Adams LE, Wykoff JA, Morowitz JM, Dong S, Magness ST, Marzluff WF, Gonzalez LM, Ehre C, Baric RS | Proceedings of the National Academy of Sciences of the United States of America | 35476513 | Proc Natl Acad Sci U S A | 2022 May 3 | https://www.ncbi.nlm.nih.gov/pubmed/35476513 |
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| The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. | Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23154883 | FASEB J | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/23154883 |
| The impact of Helicobacter pylori on atopic disorders in childhood. | Holster IL, Vila AM, Caudri D, den Hoed CM, Perez-Perez GI, Blaser MJ, de Jongste JC, Kuipers EJ | Helicobacter | 22515362 | Helicobacter | 2012 Jun | https://www.ncbi.nlm.nih.gov/pubmed/22515362 |
| Candida krusei colonization in patients with gastrointestinal diseases. | Huong DT, Zhao Y, Nguyet NT, Loan TT, Binh NT, Thinh NV, Hanh NT, Perez-Perez GI, Perlin DS | Medical mycology | 23815437 | Med Mycol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23815437 |
| Asthma: Undoing millions of years of coevolution in early life? | Dominguez-Bello MG, Blaser MJ | Science translational medicine | 26424565 | Sci Transl Med | 2015 Sep 30 | https://www.ncbi.nlm.nih.gov/pubmed/26424565 |
| Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. | Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ | Genome medicine | 27124954 | Genome Med | 2016 Apr 27 | https://www.ncbi.nlm.nih.gov/pubmed/27124954 |
| Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. | Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL | mBio | 27178263 | mBio | 2016 May 13 | https://www.ncbi.nlm.nih.gov/pubmed/27178263 |
| The microbiome revolution. | Blaser MJ | The Journal of clinical investigation | 25271724 | J Clin Invest | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25271724 |
| A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome. | Bokulich NA, Blaser MJ | Cell metabolism | 25440050 | Cell Metab | 2014 Nov 4 | https://www.ncbi.nlm.nih.gov/pubmed/25440050 |
| Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. | Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ | Cell | 25126780 | Cell | 2014 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/25126780 |
| Detecting a bacterial protein to understand cancer risk. | Blaser MJ | Clinical chemistry | 21586641 | Clin Chem | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21586641 |
| Intergenerational reduction in Helicobacter pylori prevalence is similar between different ethnic groups living in a Western city. | den Hollander WJ, Holster IL, van Gilst B, van Vuuren AJ, Jaddoe VW, Hofman A, Perez-Perez GI, Kuipers EJ, Moll HA, Blaser MJ | Gut | 25192563 | Gut | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25192563 |
| Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. | Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC | Nature medicine | 26828196 | Nat Med | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26828196 |
| Risks of Antibiotic Exposures Early in Life on the Developing Microbiome. | Schulfer A, Blaser MJ | PLoS pathogens | 26135581 | PLoS Pathog | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26135581 |
| Antibiotic use and its consequences for the normal microbiome. | Blaser MJ | Science (New York, N.Y.) | 27126037 | Science | 2016 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/27126037 |
| Helminth infection promotes colonization resistance via type 2 immunity. | Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K | Science (New York, N.Y.) | 27080105 | Science | 2016 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/27080105 |
| Role of childhood infection in the sequelae of H. pylori disease. | Harris PR, Smythies LE, Smith PD, Perez-Perez GI | Gut microbes | 24275060 | Gut Microbes | 2013 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/24275060 |
| Ethnicity is a strong predictor for Helicobacter pylori infection in young women in a multi-ethnic European city. | den Hollander WJ, Holster IL, den Hoed CM, van Deurzen F, van Vuuren AJ, Jaddoe VW, Hofman A, Perez Perez GI, Blaser MJ, Moll HA, Kuipers EJ | Journal of gastroenterology and hepatology | 23808840 | J Gastroenterol Hepatol | 2013 Nov | https://www.ncbi.nlm.nih.gov/pubmed/23808840 |
| Antibiotic exposure and the development of coeliac disease: a nationwide case-control study. | Mårild K, Ye W, Lebwohl B, Green PH, Blaser MJ, Card T, Ludvigsson JF | BMC gastroenterology | 23834758 | BMC Gastroenterol | 2013 Jul 8 | https://www.ncbi.nlm.nih.gov/pubmed/23834758 |
| Evidence for Environmental-Human Microbiota Transfer at a Manufacturing Facility with Novel Work-related Respiratory Disease. | Wu BG, Kapoor B, Cummings KJ, Stanton ML, Nett RJ, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Clemente JC, Gao Z, Coffre M, Meyn P, Heguy A, Li Y, Sulaiman I, Borbet TC, Koralov SB, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Edwards NT, Veillette M, Duchaine C, Warren K, Lundeen S, Blaser MJ, Segal LN | American journal of respiratory and critical care medicine | 32673495 | Am J Respir Crit Care Med | 2020 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/32673495 |
| Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota. | den Hartigh LJ, Gao Z, Goodspeed L, Wang S, Das AK, Burant CF, Chait A, Blaser MJ | The Journal of nutrition | 29659960 | J Nutr | 2018 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/29659960 |
| Predominance of Lactobacillus spp. Among Patients Who Do Not Acquire Multidrug-Resistant Organisms. | Araos R, Tai AK, Snyder GM, Blaser MJ, D'Agata EMC | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 27358350 | Clin Infect Dis | 2016 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/27358350 |
| Association between Helicobacter pylori and mortality in the NHANES III study. | Chen Y, Segers S, Blaser MJ | Gut | 23303440 | Gut | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23303440 |
| The theory of disappearing microbiota and the epidemics of chronic diseases. | Blaser MJ | Nature reviews. Immunology | 28749457 | Nat Rev Immunol | 2017 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/28749457 |
| Risk of Clostridium difficile Infection in Patients With Celiac Disease: A Population-Based Study. | Lebwohl B, Nobel YR, Green PHR, Blaser MJ, Ludvigsson JF | The American journal of gastroenterology | 29087398 | Am J Gastroenterol | 2017 Dec | https://www.ncbi.nlm.nih.gov/pubmed/29087398 |
| Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. | Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward T, Cox LM, Rogers AB, Knights D, Sartor RB, Blaser MJ | Nature microbiology | 29180726 | Nat Microbiol | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29180726 |
| Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. | Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL | Science (New York, N.Y.) | 28839072 | Science | 2017 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/28839072 |
| Microbially Produced Acetate: A "Missing Link" in Understanding Obesity? | Trent CM, Blaser MJ | Cell metabolism | 27411005 | Cell Metab | 2016 Jul 12 | https://www.ncbi.nlm.nih.gov/pubmed/27411005 |
| The gut microbiota influences skeletal muscle mass and function in mice. | Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Gulyás B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S | Science translational medicine | 31341063 | Sci Transl Med | 2019 Jul 24 | https://www.ncbi.nlm.nih.gov/pubmed/31341063 |
| Association of caesarean delivery with child adiposity from age 6 weeks to 15 years. | Blustein J, Attina T, Liu M, Ryan AM, Cox LM, Blaser MJ, Trasande L | International journal of obesity (2005) | 23670220 | Int J Obes (Lond) | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/23670220 |
| Helminth colonization is associated with increased diversity of the gut microbiota. | Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P | PLoS neglected tropical diseases | 24851867 | PLoS Negl Trop Dis | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24851867 |
| Helicobacter pylori colonization and pregnancies complicated by preeclampsia, spontaneous prematurity, and small for gestational age birth. | den Hollander WJ, Schalekamp-Timmermans S, Holster IL, Jaddoe VW, Hofman A, Moll HA, Perez-Perez GI, Blaser MJ, Steegers EA, Kuipers EJ | Helicobacter | 27786400 | Helicobacter | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27786400 |
| The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin. | Francois F, Roper J, Joseph N, Pei Z, Chhada A, Shak JR, de Perez AZ, Perez-Perez GI, Blaser MJ | BMC gastroenterology | 21489301 | BMC Gastroenterol | 2011 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/21489301 |
| Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. | Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R | Gastroenterology | 21530737 | Gastroenterology | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21530737 |
| Association between gastric Helicobacter pylori colonization and glycated hemoglobin levels. | Chen Y, Blaser MJ | The Journal of infectious diseases | 22427676 | J Infect Dis | 2012 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/22427676 |
| Infant antibiotic exposures and early-life body mass. | Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ | International journal of obesity (2005) | 22907693 | Int J Obes (Lond) | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22907693 |
| Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. | Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R | The ISME journal | 22895161 | ISME J | 2013 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22895161 |
| The Human Microbiome before Birth. | Blaser MJ, Dominguez-Bello MG | Cell host & microbe | 27832586 | Cell Host Microbe | 2016 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/27832586 |
| Antibiotics, birth mode, and diet shape microbiome maturation during early life. | Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ | Science translational medicine | 27306664 | Sci Transl Med | 2016 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/27306664 |
| Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. | Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD | Nature microbiology | 27572644 | Nat Microbiol | 2016 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/27572644 |
| Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibaculum rodentium. | Cox LM, Sohn J, Tyrrell KL, Citron DM, Lawson PA, Patel NB, Iizumi T, Perez-Perez GI, Goldstein EJC, Blaser MJ | International journal of systematic and evolutionary microbiology | 28100298 | Int J Syst Evol Microbiol | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28100298 |
| The effects of trans-resveratrol on insulin resistance, inflammation, and microbiota in men with the metabolic syndrome: A pilot randomized, placebo-controlled clinical trial. | Walker JM, Eckardt P, Aleman JO, da Rosa JC, Liang Y, Iizumi T, Etheve S, Blaser MJ, L Breslow J, Holt PR | Journal of clinical and translational research | 30873501 | J Clin Transl Res | 2019 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/30873501 |
| Work-related adverse respiratory health outcomes at a machine manufacturing facility with a cluster of bronchiolitis, alveolar ductitis and emphysema (BADE). | Cummings KJ, Stanton ML, Kreiss K, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Edwards NT, Segal LN, Blaser MJ, Weissman DN, Nett RJ | Occupational and environmental medicine | 32132182 | Occup Environ Med | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32132182 |
| Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion. | Nazzal L, Francois F, Henderson N, Liu M, Li H, Koh H, Wang C, Gao Z, Perez GP, Asplin JR, Goldfarb DS, Blaser MJ | Scientific reports | 34385560 | Sci Rep | 2021 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/34385560 |
| Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. | Segal LN, Blaser MJ | The Journal of pediatrics | 25934071 | J Pediatr | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25934071 |
| Celecoxib does not alter intestinal microbiome in a longitudinal diet-controlled study. | Bokulich NA, Battaglia T, Aleman JO, Walker JM, Blaser MJ, Holt PR | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases | 26806255 | Clin Microbiol Infect | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26806255 |
| Maturation of the gut microbiome and risk of asthma in childhood. | Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H | Nature communications | 29321519 | Nat Commun | 2018 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/29321519 |
| Severe lung disease characterized by lymphocytic bronchiolitis, alveolar ductitis, and emphysema (BADE) in industrial machine-manufacturing workers. | Cummings KJ, Stanton ML, Nett RJ, Segal LN, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Green BJ, LeBouf RF, Blaser MJ, Weissman DN | American journal of industrial medicine | 31461179 | Am J Ind Med | 2019 Nov | https://www.ncbi.nlm.nih.gov/pubmed/31461179 |
| Comparative prevalence of Oxalobacter formigenes in three human populations. | PeBenito A, Nazzal L, Wang C, Li H, Jay M, Noya-Alarcon O, Contreras M, Lander O, Leach J, Dominguez-Bello MG, Blaser MJ | Scientific reports | 30679485 | Sci Rep | 2019 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/30679485 |
| Antibiotics in early life and obesity. | Cox LM, Blaser MJ | Nature reviews. Endocrinology | 25488483 | Nat Rev Endocrinol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25488483 |
| Helicobacter pylori in children with asthmatic conditions at school age, and their mothers. | den Hollander WJ, Sonnenschein-van der Voort AM, Holster IL, de Jongste JC, Jaddoe VW, Hofman A, Perez-Perez GI, Moll HA, Blaser MJ, Duijts L, Kuipers EJ | Alimentary pharmacology & therapeutics | 26932510 | Aliment Pharmacol Ther | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26932510 |
| The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer. | Kwa M, Plottel CS, Blaser MJ, Adams S | Journal of the National Cancer Institute | 27107051 | J Natl Cancer Inst | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27107051 |
| Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum. | Shin H, Martinez KA 2nd, Henderson N, Jay M, Schweizer W, Bogaert D, Park G, Bokulich NA, Blaser MJ, Dominguez-Bello MG | NPJ biofilms and microbiomes | 37311781 | NPJ Biofilms Microbiomes | 2023 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/37311781 |
| Obtaining and estimating kinetic parameters from the literature. | Neves SR | Science signaling | 21934111 | Sci Signal | 2011 Sep 13 | https://www.ncbi.nlm.nih.gov/pubmed/21934111 |
| Modeling of spatial intracellular signaling events in neurons. | Wenderski WC, Neves SR | Methods in enzymology | 22289450 | Methods Enzymol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22289450 |
| Computational analysis of Rho GTPase cycling. | Falkenberg CV, Loew LM | PLoS computational biology | 23326220 | PLoS Comput Biol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23326220 |
| Cross-regulation of Phosphodiesterase 1 and Phosphodiesterase 2 Activities Controls Dopamine-mediated Striatal α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Trafficking. | Song RS, Tolentino R, Sobie EA, Neves-Zaph SR | The Journal of biological chemistry | 27605670 | J Biol Chem | 2016 Oct 28 | https://www.ncbi.nlm.nih.gov/pubmed/27605670 |
| Systems biology of kidney diseases. | He JC, Chuang PY, Ma'ayan A, Iyengar R | Kidney international | 21881558 | Kidney Int | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21881558 |
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| Interconnected network motifs control podocyte morphology and kidney function. | Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R | Science signaling | 24497609 | Sci Signal | 2014 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/24497609 |
| ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion. | Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR | Proceedings of the National Academy of Sciences of the United States of America | 23986500 | Proc Natl Acad Sci U S A | 2013 Sep 17 | https://www.ncbi.nlm.nih.gov/pubmed/23986500 |
| A biomimetic gelatin-based platform elicits a pro-differentiation effect on podocytes through mechanotransduction. | Hu M, Azeloglu EU, Ron A, Tran-Ba KH, Calizo RC, Tavassoly I, Bhattacharya S, Jayaraman G, Chen Y, Rabinovich V, Iyengar R, Hone JC, He JC, Kaufman LJ | Scientific reports | 28262745 | Sci Rep | 2017 Mar 6 | https://www.ncbi.nlm.nih.gov/pubmed/28262745 |
| Cell shape information is transduced through tension-independent mechanisms. | Ron A, Azeloglu EU, Calizo RC, Hu M, Bhattacharya S, Chen Y, Jayaraman G, Lee S, Neves-Zaph SR, Li H, Gordon RE, He JC, Hone JC, Iyengar R | Nature communications | 29247198 | Nat Commun | 2017 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/29247198 |
| G Protein-regulated inducer of neurite outgrowth (GRIN) modulates Sprouty protein repression of mitogen-activated protein kinase (MAPK) activation by growth factor stimulation. | Hwangpo TA, Jordan JD, Premsrirut PK, Jayamaran G, Licht JD, Iyengar R, Neves SR | The Journal of biological chemistry | 22383529 | J Biol Chem | 2012 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/22383529 |
| Modeling of spatially-restricted intracellular signaling. | Neves SR | Wiley interdisciplinary reviews. Systems biology and medicine | 21766466 | Wiley Interdiscip Rev Syst Biol Med | 2012 Jan-Feb | https://www.ncbi.nlm.nih.gov/pubmed/21766466 |
| Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. | Falkenberg CV, Blinov ML, Loew LM | Biophysical journal | 24314076 | Biophys J | 2013 Dec 3 | https://www.ncbi.nlm.nih.gov/pubmed/24314076 |
| Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory. | Havekes R, Park AJ, Tolentino RE, Bruinenberg VM, Tudor JC, Lee Y, Hansen RT, Guercio LA, Linton E, Neves-Zaph SR, Meerlo P, Baillie GS, Houslay MD, Abel T | The Journal of neuroscience : the official journal of the Society for Neuroscience | 27559174 | J Neurosci | 2016 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/27559174 |
| Lipid storage by adipose tissue macrophages regulates systemic glucose tolerance. | Aouadi M, Vangala P, Yawe JC, Tencerova M, Nicoloro SM, Cohen JL, Shen Y, Czech MP | American journal of physiology. Endocrinology and metabolism | 24986598 | Am J Physiol Endocrinol Metab | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/24986598 |
| Local proliferation of macrophages contributes to obesity-associated adipose tissue inflammation. | Amano SU, Cohen JL, Vangala P, Tencerova M, Nicoloro SM, Yawe JC, Shen Y, Czech MP, Aouadi M | Cell metabolism | 24374218 | Cell Metab | 2014 Jan 7 | https://www.ncbi.nlm.nih.gov/pubmed/24374218 |
| CD40 deficiency in mice exacerbates obesity-induced adipose tissue inflammation, hepatic steatosis, and insulin resistance. | Guo CA, Kogan S, Amano SU, Wang M, Dagdeviren S, Friedline RH, Aouadi M, Kim JK, Czech MP | American journal of physiology. Endocrinology and metabolism | 23482447 | Am J Physiol Endocrinol Metab | 2013 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/23482447 |
| Gene silencing in adipose tissue macrophages regulates whole-body metabolism in obese mice. | Aouadi M, Tencerova M, Vangala P, Yawe JC, Nicoloro SM, Amano SU, Cohen JL, Czech MP | Proceedings of the National Academy of Sciences of the United States of America | 23630254 | Proc Natl Acad Sci U S A | 2013 May 14 | https://www.ncbi.nlm.nih.gov/pubmed/23630254 |
| Insulin signalling mechanisms for triacylglycerol storage. | Czech MP, Tencerova M, Pedersen DJ, Aouadi M | Diabetologia | 23443243 | Diabetologia | 2013 May | https://www.ncbi.nlm.nih.gov/pubmed/23443243 |
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| A population of Langerin-positive dendritic cells in murine Peyer's patches involved in sampling β-glucan microparticles. | De Jesus M, Ostroff GR, Levitz SM, Bartling TR, Mantis NJ | PloS one | 24632738 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24632738 |
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| Glucan particles for selective delivery of siRNA to phagocytic cells in mice. | Tesz GJ, Aouadi M, Prot M, Nicoloro SM, Boutet E, Amano SU, Goller A, Wang M, Guo CA, Salomon WE, Virbasius JV, Baum RA, O'Connor MJ Jr, Soto E, Ostroff GR, Czech MP | The Biochemical journal | 21418037 | Biochem J | 2011 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/21418037 |
| Peptide- and Amine-Modified Glucan Particles for the Delivery of Therapeutic siRNA. | Cohen JL, Shen Y, Aouadi M, Vangala P, Tencerova M, Amano SU, Nicoloro SM, Yawe JC, Czech MP | Molecular pharmaceutics | 26815386 | Mol Pharm | 2016 Mar 7 | https://www.ncbi.nlm.nih.gov/pubmed/26815386 |
| Activated Kupffer cells inhibit insulin sensitivity in obese mice. | Tencerova M, Aouadi M, Vangala P, Nicoloro SM, Yawe JC, Cohen JL, Shen Y, Garcia-Menendez L, Pedersen DJ, Gallagher-Dorval K, Perugini RA, Gupta OT, Czech MP | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 25805830 | FASEB J | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25805830 |
| IL-1 signaling in obesity-induced hepatic lipogenesis and steatosis. | Negrin KA, Roth Flach RJ, DiStefano MT, Matevossian A, Friedline RH, Jung D, Kim JK, Czech MP | PloS one | 25216251 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25216251 |
| Activation of the Nlrp3 inflammasome in infiltrating macrophages by endocannabinoids mediates beta cell loss in type 2 diabetes. | Jourdan T, Godlewski G, Cinar R, Bertola A, Szanda G, Liu J, Tam J, Han T, Mukhopadhyay B, Skarulis MC, Ju C, Aouadi M, Czech MP, Kunos G | Nature medicine | 23955712 | Nat Med | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23955712 |
| 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 |
| The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations. | Yan KS, Chia LA, Li X, Ootani A, Su J, Lee JY, Su N, Luo Y, Heilshorn SC, Amieva MR, Sangiorgi E, Capecchi MR, Kuo CJ | Proceedings of the National Academy of Sciences of the United States of America | 22190486 | Proc Natl Acad Sci U S A | 2012 Jan 10 | https://www.ncbi.nlm.nih.gov/pubmed/22190486 |
| 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 |
| 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 |
| Organoids as Models for Neoplastic Transformation. | Neal JT, Kuo CJ | Annual review of pathology | 26907527 | Annu Rev Pathol | 2016 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/26907527 |
| Partial proteasome inhibitors induce hair follicle growth by stabilizing β-catenin. | Yucel G, Van Arnam J, Means PC, Huntzicker E, Altindag B, Lara MF, Yuan J, Kuo C, Oro AE | Stem cells (Dayton, Ohio) | 23963711 | Stem Cells | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/23963711 |
| Dual-stage growth factor release within 3D protein-engineered hydrogel niches promotes adipogenesis. | Greenwood-Goodwin M, Teasley ES, Heilshorn SC | Biomaterials science | 25309741 | Biomater Sci | 2014 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/25309741 |
| Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. | Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD, Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ | Nature medicine | 24859528 | Nat Med | 2014 Jul | https://www.ncbi.nlm.nih.gov/pubmed/24859528 |
| 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 |
| 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 |
| 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 |
| Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche. | Ootani A, Li X, Sangiorgi E, Ho QT, Ueno H, Toda S, Sugihara H, Fujimoto K, Weissman IL, Capecchi MR, Kuo CJ | Nature medicine | 19398967 | Nat Med | 2009 Jun | https://www.ncbi.nlm.nih.gov/pubmed/19398967 |
| 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 |
| 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 |
| Reversible cell-cycle entry in adult kidney podocytes through regulated control of telomerase and Wnt signaling. | Shkreli M, Sarin KY, Pech MF, Papeta N, Chang W, Brockman SA, Cheung P, Lee E, Kuhnert F, Olson JL, Kuo CJ, Gharavi AG, D'Agati VD, Artandi SE | Nature medicine | 22138751 | Nat Med | 2011 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/22138751 |
| 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 |
| 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 |
| Organoid modeling for cancer precision medicine. | Cantrell MA, Kuo CJ | Genome medicine | 25825593 | Genome Med | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25825593 |
| Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. | Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R | Science (New York, N.Y.) | 24311688 | Science | 2013 Dec 6 | https://www.ncbi.nlm.nih.gov/pubmed/24311688 |
| 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 |
| Presentation of BMP-2 mimicking peptides in 3D hydrogels directs cell fate commitment in osteoblasts and mesenchymal stem cells. | Madl CM, Mehta M, Duda GN, Heilshorn SC, Mooney DJ | Biomacromolecules | 24400664 | Biomacromolecules | 2014 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/24400664 |
| 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 |
| 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 |
| Regulation of self-renewal and differentiation by the intestinal stem cell niche. | Yeung TM, Chia LA, Kosinski CM, Kuo CJ | Cellular and molecular life sciences : CMLS | 21509540 | Cell Mol Life Sci | 2011 Aug | https://www.ncbi.nlm.nih.gov/pubmed/21509540 |
| β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. | Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC | Cell | 23245941 | Cell | 2012 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/23245941 |
| 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 |
| 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 |
| 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 |
| Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids. | DiMarco RL, Dewi RE, Bernal G, Kuo C, Heilshorn SC | Biomaterials science | 26371971 | Biomater Sci | 2015 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/26371971 |
| Matrix 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 |
| 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 |
| Improved outcomes in a quality improvement collaborative for pediatric inflammatory bowel disease. | Crandall WV, Margolis PA, Kappelman MD, King EC, Pratt JM, Boyle BM, Duffy LF, Grunow JE, Kim SC, Leibowitz I, Schoen BT, Colletti RB, ImproveCareNow Collaborative | Pediatrics | 22412030 | Pediatrics | 2012 Apr | https://www.ncbi.nlm.nih.gov/pubmed/22412030 |
| Using a network organisational architecture to support the development of Learning Healthcare Systems. | Britto MT, Fuller SC, Kaplan HC, Kotagal U, Lannon C, Margolis PA, Muething SE, Schoettker PJ, Seid M | BMJ quality & safety | 29438072 | BMJ Qual Saf | 2018 Nov | https://www.ncbi.nlm.nih.gov/pubmed/29438072 |
| A maturity grid assessment tool for learning networks. | Lannon C, Schuler CL, Seid M, Provost LP, Fuller S, Purcell D, Forrest CB, Margolis PA | Learning health systems | 33889737 | Learn Health Syst | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33889737 |
| Pilot Development of an Electronic Pediatric Inflammatory Bowel Disease Quiz Game. | Tung J, Grunow JE, Jacobs N | Journal of pediatric gastroenterology and nutrition | 25793902 | J Pediatr Gastroenterol Nutr | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25793902 |
| Collaborative Chronic Care Networks (C3Ns) to transform chronic illness care. | Margolis PA, Peterson LE, Seid M | Pediatrics | 23729764 | Pediatrics | 2013 Jun | https://www.ncbi.nlm.nih.gov/pubmed/23729764 |
| Appreciating the Nuance of Daily Symptom Variation to Individualize Patient Care. | Adler J, Saeed SA, Eslick IS, Provost L, Margolis PA, Kaplan HC | EGEMS (Washington, DC) | 27376097 | EGEMS (Wash DC) | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27376097 |
| Health services innovation: the time is now. | Zuckerman B, Margolis PA, Mate KS | JAMA | 23512055 | JAMA | 2013 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/23512055 |
| What's in a name generator? Choosing the right name generators for social network surveys in healthcare quality and safety research. | Burt RS, Meltzer DO, Seid M, Borgert A, Chung JW, Colletti RB, Dellal G, Kahn SA, Kaplan HC, Peterson LE, Margolis P | BMJ quality & safety | 22942400 | BMJ Qual Saf | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22942400 |
| Learning Health Systems as Facilitators of Precision Medicine. | Ramsey LB, Mizuno T, Vinks AA, Margolis PA | Clinical pharmacology and therapeutics | 27984650 | Clin Pharmacol Ther | 2017 Mar | https://www.ncbi.nlm.nih.gov/pubmed/27984650 |
| Co-Designing a Collaborative Chronic Care Network (C3N) for Inflammatory Bowel Disease: Development of Methods. | Seid M, Dellal G, Peterson LE, Provost L, Gloor PA, Fore DL, Margolis PA | JMIR human factors | 29472173 | JMIR Hum Factors | 2018 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/29472173 |
| "A Guide to Gutsy Living": Patient-Driven Development of a Pediatric Ostomy Toolkit. | David JG, Jofriet A, Seid M, Margolis PA, ImproveCareNow Pediatric IBD Learning Health System | Pediatrics | 29610402 | Pediatrics | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29610402 |
| Coproduction of healthcare service. | Batalden M, Batalden P, Margolis P, Seid M, Armstrong G, Opipari-Arrigan L, Hartung H | BMJ quality & safety | 26376674 | BMJ Qual Saf | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26376674 |
| Engagement, peer production, and the learning healthcare system. | Seid M, Margolis PA, Opipari-Arrigan L | JAMA pediatrics | 24446048 | JAMA Pediatr | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24446048 |
| Measuring engagement in a collaborative learning health system: The case of ImproveCareNow. | Hartley DM, Keck C, Havens M, Margolis PA, Seid M | Learning health systems | 33889734 | Learn Health Syst | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33889734 |
| Transepithelial projections from basal cells are luminal sensors in pseudostratified epithelia. | Shum WW, Da Silva N, McKee M, Smith PJ, Brown D, Breton S | Cell | 19070580 | Cell | 2008 Dec 12 | https://www.ncbi.nlm.nih.gov/pubmed/19070580 |
| Epithelial basal cells are distinct from dendritic cells and macrophages in the mouse epididymis. | Shum WW, Smith TB, Cortez-Retamozo V, Grigoryeva LS, Roy JW, Hill E, Pittet MJ, Breton S, Da Silva N | Biology of reproduction | 24648397 | Biol Reprod | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24648397 |
| High-resolution helium ion microscopy of epididymal epithelial cells and their interaction with spermatozoa. | Păunescu TG, Shum WW, Huynh C, Lechner L, Goetze B, Brown D, Breton S | Molecular human reproduction | 25015675 | Mol Hum Reprod | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25015675 |
| Establishment of cell-cell cross talk in the epididymis: control of luminal acidification. | Shum WW, Ruan YC, Da Silva N, Breton S | Journal of andrology | 21441423 | J Androl | 2011 Nov-Dec | https://www.ncbi.nlm.nih.gov/pubmed/21441423 |
| A dense network of dendritic cells populates the murine epididymis. | Da Silva N, Cortez-Retamozo V, Reinecker HC, Wildgruber M, Hill E, Brown D, Swirski FK, Pittet MJ, Breton S | Reproduction (Cambridge, England) | 21310816 | Reproduction | 2011 May | https://www.ncbi.nlm.nih.gov/pubmed/21310816 |
| ROS1 signaling regulates epithelial differentiation in the epididymis. | Jun HJ, Roy J, Smith TB, Wood LB, Lane K, Woolfenden S, Punko D, Bronson RT, Haigis KM, Breton S, Charest A | Endocrinology | 24971615 | Endocrinology | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/24971615 |
| In vivo imaging of tracheal epithelial cells in mice during airway regeneration. | Kim JK, Vinarsky V, Wain J, Zhao R, Jung K, Choi J, Lam A, Pardo-Saganta A, Breton S, Rajagopal J, Yun SH | American journal of respiratory cell and molecular biology | 22984086 | Am J Respir Cell Mol Biol | 2012 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22984086 |
| Plasticity of basal cells during postnatal development in the rat epididymis. | Shum WW, Hill E, Brown D, Breton S | Reproduction (Cambridge, England) | 23960170 | Reproduction | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23960170 |
| Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy. | Hovelson DH, Liu CJ, Wang Y, Kang Q, Henderson J, Gursky A, Brockman S, Ramnath N, Krauss JC, Talpaz M, Kandarpa M, Chugh R, Tuck M, Herman K, Grasso CS, Quist MJ, Feng FY, Haakenson C, Langmore J, Kamberov E, Tesmer T, Husain H, Lonigro RJ, Robinson D, Smith DC, Alva AS, Hussain MH, Chinnaiyan AM, Tewari M, Mills RE, Morgan TM, Tomlins SA | Oncotarget | 29163793 | Oncotarget | 2017 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/29163793 |
| A functional extracellular transcriptome in animals? Implications for biology, disease and medicine. | Tewari M | Genome biology | 25723626 | Genome Biol | 2015 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/25723626 |
| Circulating microRNA profiling identifies a subset of metastatic prostate cancer patients with evidence of cancer-associated hypoxia. | Cheng HH, Mitchell PS, Kroh EM, Dowell AE, Chéry L, Siddiqui J, Nelson PS, Vessella RL, Knudsen BS, Chinnaiyan AM, Pienta KJ, Morrissey C, Tewari M | PloS one | 23935962 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23935962 |
| Intact microRNA analysis using high resolution mass spectrometry. | Kullolli M, Knouf E, Arampatzidou M, Tewari M, Pitteri SJ | Journal of the American Society for Mass Spectrometry | 24174127 | J Am Soc Mass Spectrom | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/24174127 |
| Quantitative and stoichiometric analysis of the microRNA content of exosomes. | Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova-Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS, Tewari M | Proceedings of the National Academy of Sciences of the United States of America | 25267620 | Proc Natl Acad Sci U S A | 2014 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/25267620 |
| Absolute quantification by droplet digital PCR versus analog real-time PCR. | Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL, Tewari M | Nature methods | 23995387 | Nat Methods | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23995387 |
| Evaluating Serum Markers for Hormone Receptor-Negative Breast Cancer. | Schummer M, Thorpe J, Giraldez MD, Bergan L, Tewari M, Urban N | PloS one | 26565788 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26565788 |
| Ultra-Specific Isolation of Circulating Tumor Cells Enables Rare-Cell RNA Profiling. | Jack RM, Grafton MM, Rodrigues D, Giraldez MD, Griffith C, Cieslak R, Zeinali M, Kumar Sinha C, Azizi E, Wicha M, Tewari M, Simeone DM, Nagrath S | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 27711257 | Adv Sci (Weinh) | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27711257 |
| Release of Cell-free MicroRNA Tumor Biomarkers into the Blood Circulation with Pulsed Focused Ultrasound: A Noninvasive, Anatomically Localized, Molecular Liquid Biopsy. | Chevillet JR, Khokhlova TD, Giraldez MD, Schade GR, Starr F, Wang YN, Gallichotte EN, Wang K, Hwang JH, Tewari M | Radiology | 27802108 | Radiology | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27802108 |
| Plasma processing conditions substantially influence circulating microRNA biomarker levels. | Cheng HH, Yi HS, Kim Y, Kroh EM, Chien JW, Eaton KD, Goodman MT, Tait JF, Tewari M, Pritchard CC | PloS one | 23762257 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23762257 |
| The human TUT1 nucleotidyl transferase as a global regulator of microRNA abundance. | Knouf EC, Wyman SK, Tewari M | PloS one | 23874977 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23874977 |
| Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation. | Kang Q, Parkin B, Giraldez MD, Tewari M | BioTechniques | 27071606 | Biotechniques | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/27071606 |
| Platelet-Synthesized Testosterone in Men with Prostate Cancer Induces Androgen Receptor Signaling. | Zaslavsky AB, Gloeckner-Kalousek A, Adams M, Putluri N, Venghatakrishnan H, Li H, Morgan TM, Feng FY, Tewari M, Sreekumar A, Palapattu GS | Neoplasia (New York, N.Y.) | 26152357 | Neoplasia | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26152357 |
| Kinetic fingerprinting to identify and count single nucleic acids. | Johnson-Buck A, Su X, Giraldez MD, Zhao M, Tewari M, Walter NG | Nature biotechnology | 26098451 | Nat Biotechnol | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26098451 |
| Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. | Pritchard CC, Kroh E, Wood B, Arroyo JD, Dougherty KJ, Miyaji MM, Tait JF, Tewari M | Cancer prevention research (Philadelphia, Pa.) | 22158052 | Cancer Prev Res (Phila) | 2012 Mar | https://www.ncbi.nlm.nih.gov/pubmed/22158052 |
| Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. | Wyman SK, Knouf EC, Parkin RK, Fritz BR, Lin DW, Dennis LM, Krouse MA, Webster PJ, Tewari M | Genome research | 21813625 | Genome Res | 2011 Sep | https://www.ncbi.nlm.nih.gov/pubmed/21813625 |
| Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. | Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F | Nucleic acids research | 24838567 | Nucleic Acids Res | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24838567 |
| Droplet Digital PCR for Absolute Quantification of Extracellular MicroRNAs in Plasma and Serum: Quantification of the Cancer Biomarker hsa-miR-141. | Giraldez MD, Chevillet JR, Tewari M | Methods in molecular biology (Clifton, N.J.) | 29717459 | Methods Mol Biol | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29717459 |
| Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. | Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova-Agadjanyan EL, Stirewalt DL, Tait JF, Tewari M | Proceedings of the National Academy of Sciences of the United States of America | 21383194 | Proc Natl Acad Sci U S A | 2011 Mar 22 | https://www.ncbi.nlm.nih.gov/pubmed/21383194 |
| MicroRNA profiling: approaches and considerations. | Pritchard CC, Cheng HH, Tewari M | Nature reviews. Genetics | 22510765 | Nat Rev Genet | 2012 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/22510765 |
| Tumor characterization by ultrasound-release of multiple protein and microRNA biomarkers, preclinical and clinical evidence. | D'Souza AL, Chevillet JR, Ghanouni P, Yan X, Tewari M, Gambhir SS | PloS one | 29547636 | PLoS One | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/29547636 |
| Systematic design and functional analysis of artificial microRNAs. | Arroyo JD, Gallichotte EN, Tewari M | Nucleic acids research | 24598260 | Nucleic Acids Res | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24598260 |
| Design and Analysis for Studying microRNAs in Human Disease: A Primer on -Omic Technologies. | Nair VS, Pritchard CC, Tewari M, Ioannidis JP | American journal of epidemiology | 24966218 | Am J Epidemiol | 2014 Jul 15 | https://www.ncbi.nlm.nih.gov/pubmed/24966218 |
| Circulating microRNAs and treatment response in the Phase II SWOG S0925 study for patients with new metastatic hormone-sensitive prostate cancer. | Cheng HH, Plets M, Li H, Higano CS, Tangen CM, Agarwal N, Vogelzang NJ, Hussain M, Thompson IM Jr, Tewari M, Yu EY | The Prostate | 29105802 | Prostate | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29105802 |
| Antisense gets a grip on miR-122 in chimpanzees. | Branch AD, Rice CM | Science translational medicine | 20371461 | Sci Transl Med | 2010 Jan 6 | https://www.ncbi.nlm.nih.gov/pubmed/20371461 |
| Hepatitis C virus induces interferon-λ and interferon-stimulated genes in primary liver cultures. | Marukian S, Andrus L, Sheahan TP, Jones CT, Charles ED, Ploss A, Rice CM, Dustin LB | Hepatology (Baltimore, Md.) | 21800339 | Hepatology | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21800339 |
| Modeling hepatitis C virus infection using human induced pluripotent stem cells. | Schwartz RE, Trehan K, Andrus L, Sheahan TP, Ploss A, Duncan SA, Rice CM, Bhatia SN | Proceedings of the National Academy of Sciences of the United States of America | 22308485 | Proc Natl Acad Sci U S A | 2012 Feb 14 | https://www.ncbi.nlm.nih.gov/pubmed/22308485 |
| Teaching new tricks to an old foe: murinizing hepatitis C virus. | Gerold G, Rice CM, Ploss A | Hepatology (Baltimore, Md.) | 21105113 | Hepatology | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/21105113 |
| Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. | Stoddard MB, Li H, Wang S, Saeed M, Andrus L, Ding W, Jiang X, Learn GH, von Schaewen M, Wen J, Goepfert PA, Hahn BH, Ploss A, Rice CM, Shaw GM | mBio | 25714714 | mBio | 2015 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/25714714 |
| Degradable hydrogels derived from PEG-diacrylamide for hepatic tissue engineering. | Stevens KR, Miller JS, Blakely BL, Chen CS, Bhatia SN | Journal of biomedical materials research. Part A | 25851120 | J Biomed Mater Res A | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25851120 |
| Characterization of nonprimate hepacivirus and construction of a functional molecular clone. | Scheel TK, Kapoor A, Nishiuchi E, Brock KV, Yu Y, Andrus L, Gu M, Renshaw RW, Dubovi EJ, McDonough SP, Van de Walle GR, Lipkin WI, Divers TJ, Tennant BC, Rice CM | Proceedings of the National Academy of Sciences of the United States of America | 25646476 | Proc Natl Acad Sci U S A | 2015 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/25646476 |
| Expansion, in vivo-ex vivo cycling, and genetic manipulation of primary human hepatocytes. | Michailidis E, Vercauteren K, Mancio-Silva L, Andrus L, Jahan C, Ricardo-Lax I, Zou C, Kabbani M, Park P, Quirk C, Pyrgaki C, Razooky B, Verhoye L, Zoluthkin I, Lu WY, Forbes SJ, Chiriboga L, Theise ND, Herzog RW, Suemizu H, Schneider WM, Shlomai A, Meuleman P, Bhatia SN, Rice CM, de Jong YP | Proceedings of the National Academy of Sciences of the United States of America | 31915293 | Proc Natl Acad Sci U S A | 2020 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/31915293 |
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| Humanized mice efficiently engrafted with fetal hepatoblasts and syngeneic immune cells develop human monocytes and NK cells. | Billerbeck E, Mommersteeg MC, Shlomai A, Xiao JW, Andrus L, Bhatta A, Vercauteren K, Michailidis E, Dorner M, Krishnan A, Charlton MR, Chiriboga L, Rice CM, de Jong YP | Journal of hepatology | 27151182 | J Hepatol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27151182 |
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| Large-Area, Ultrathin Metal-Oxide Semiconductor Nanoribbon Arrays Fabricated by Chemical Lift-Off Lithography. | Zhao C, Xu X, Bae SH, Yang Q, Liu W, Belling JN, Cheung KM, Rim YS, Yang Y, Andrews AM, Weiss PS | Nano letters | 30060654 | Nano Lett | 2018 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/30060654 |
| Differential Charging in Photoemission from Mercurated DNA Monolayers on Ferromagnetic Films. | Stemer DM, Abendroth JM, Cheung KM, Ye M, El Hadri MS, Fullerton EE, Weiss PS | Nano letters | 31960675 | Nano Lett | 2020 Feb 12 | https://www.ncbi.nlm.nih.gov/pubmed/31960675 |
| Small-Molecule Patterning via Prefunctionalized Alkanethiols. | Cao HH, Nakatsuka N, Deshayes S, Abendroth JM, Yang H, Weiss PS, Kasko AM, Andrews AM | Chemistry of materials : a publication of the American Chemical Society | 30828130 | Chem Mater | 2018 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/30828130 |
| Implantable aptamer-field-effect transistor neuroprobes for in vivo neurotransmitter monitoring. | Zhao C, Cheung KM, Huang IW, Yang H, Nakatsuka N, Liu W, Cao Y, Man T, Weiss PS, Monbouquette HG, Andrews AM | Science advances | 34818033 | Sci Adv | 2021 Nov 26 | https://www.ncbi.nlm.nih.gov/pubmed/34818033 |
| Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors. | Cheung KM, Abendroth JM, Nakatsuka N, Zhu B, Yang Y, Andrews AM, Weiss PS | Nano letters | 32706969 | Nano Lett | 2020 Aug 12 | https://www.ncbi.nlm.nih.gov/pubmed/32706969 |
| Lipid Bicelle Micropatterning Using Chemical Lift-Off Lithography. | Belling JN, Cheung KM, Jackman JA, Sut TN, Allen M, Park JH, Jonas SJ, Cho NJ, Weiss PS | ACS applied materials & interfaces | 32092250 | ACS Appl Mater Interfaces | 2020 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/32092250 |
| Optogenetic Stimulation of Midbrain Dopamine Neurons Produces Striatal Serotonin Release. | Dagher M, Perrotta KA, Erwin SA, Hachisuka A, Iyer R, Masmanidis SC, Yang H, Andrews AM | ACS chemical neuroscience | 35312275 | ACS Chem Neurosci | 2022 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/35312275 |
| Flexible and Implantable Polyimide Aptamer-Field-Effect Transistor Biosensors. | Zhao C, Man T, Cao Y, Weiss PS, Monbouquette HG, Andrews AM | ACS sensors | 36399772 | ACS Sens | 2022 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/36399772 |
| Simultaneous serotonin and dopamine monitoring across timescales by rapid pulse voltammetry with partial least squares regression. | Movassaghi CS, Perrotta KA, Yang H, Iyer R, Cheng X, Dagher M, Fillol MA, Andrews AM | Analytical and bioanalytical chemistry | 34686897 | Anal Bioanal Chem | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34686897 |
| Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. | Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM | ACS applied materials & interfaces | 29851335 | ACS Appl Mater Interfaces | 2018 Jul 18 | https://www.ncbi.nlm.nih.gov/pubmed/29851335 |
| Polyserotonin Nanoparticles as Multifunctional Materials for Biomedical Applications. | Nakatsuka N, Hasani-Sadrabadi MM, Cheung KM, Young TD, Bahlakeh G, Moshaverinia A, Weiss PS, Andrews AM | ACS nano | 29664607 | ACS Nano | 2018 May 22 | https://www.ncbi.nlm.nih.gov/pubmed/29664607 |
| Phenylalanine Monitoring via Aptamer-Field-Effect Transistor Sensors. | Cheung KM, Yang KA, Nakatsuka N, Zhao C, Ye M, Jung ME, Yang H, Weiss PS, Stojanović MN, Andrews AM | ACS sensors | 31631652 | ACS Sens | 2019 Dec 27 | https://www.ncbi.nlm.nih.gov/pubmed/31631652 |
| Interfacing with the Brain: How Nanotechnology Can Contribute. | Ahmed AAA, Alegret N, Almeida B, Alvarez-Puebla R, Andrews AM, Ballerini L, Barrios-Capuchino JJ, Becker C, Blick RH, Bonakdar S, Chakraborty I, Chen X, Cheon J, Chilla G, Coelho Conceicao AL, Delehanty J, Dulle M, Efros AL, Epple M, Fedyk M, Feliu N, Feng M, Fernández-Chacón R, Fernandez-Cuesta I, Fertig N, Förster S, Garrido JA, George M, Guse AH, Hampp N, Harberts J, Han J, Heekeren HR, Hofmann UG, Holzapfel M, Hosseinkazemi H, Huang Y, Huber P, Hyeon T, Ingebrandt S, Ienca M, Iske A, Kang Y, Kasieczka G, Kim DH, Kostarelos K, Lee JH, Lin KW, Liu S, Liu X, Liu Y, Lohr C, Mailänder V, Maffongelli L, Megahed S, Mews A, Mutas M, Nack L, Nakatsuka N, Oertner TG, Offenhäusser A, Oheim M, Otange B, Otto F, Patrono E, Peng B, Picchiotti A, Pierini F, Pötter-Nerger M, Pozzi M, Pralle A, Prato M, Qi B, Ramos-Cabrer P, Genger UR, Ritter N, Rittner M, Roy S, Santoro F, Schuck NW, Schulz F, Şeker E, Skiba M, Sosniok M, Stephan H, Wang R, Wang T, Wegner KD, Weiss PS, Xu M, Yang C, Zargarian SS, Zeng Y, Zhou Y, Zhu D, Zierold R, Parak WJ | ACS nano | 40063703 | ACS Nano | 2025 Mar 25 | https://www.ncbi.nlm.nih.gov/pubmed/40063703 |
| Aerosol-Phase Synthesis and Processing of Luminescent Silicon Nanocrystals. | Li Z, Kortshagen UR | Chemistry of materials : a publication of the American Chemical Society | 34163100 | Chem Mater | 2019 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/34163100 |
| Synthesis of PEG-grafted boron doped Si nanocrystals. | Greenhagen JR, Andaraarachchi HP, Li Z, Kortshagen UR | The Journal of chemical physics | 31822090 | J Chem Phys | 2019 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/31822090 |
| Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. | Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E | Science (New York, N.Y.) | 30655415 | Science | 2019 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/30655415 |
| Single-Shot Quantitative Polarization Imaging of Complex Birefringent Structure Dynamics. | Ge B, Zhang Q, Zhang R, Lin JT, Tseng PH, Chang CW, Dong CY, Zhou R, Yaqoob Z, Bischofberger I, So PTC | ACS photonics | 37292495 | ACS Photonics | 2021 Dec 15 | https://www.ncbi.nlm.nih.gov/pubmed/37292495 |
| Mapping nanoscale topographic features in thick tissues with speckle diffraction tomography. | Kang S, Zhou R, Brelen M, Mak HK, Lin Y, So PTC, Yaqoob Z | Light, science & applications | 37607903 | Light Sci Appl | 2023 Aug 22 | https://www.ncbi.nlm.nih.gov/pubmed/37607903 |
| A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. | Gao R, Yu CJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES | Nature nanotechnology | 33782587 | Nat Nanotechnol | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/33782587 |
| Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging. | Qian Y, Cosio DMO, Piatkevich KD, Aufmkolk S, Su WC, Celiker OT, Schohl A, Murdock MH, Aggarwal A, Chang YF, Wiseman PW, Ruthazer ES, Boyden ES, Campbell RE | PLoS biology | 33232322 | PLoS Biol | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33232322 |
| In situ genome sequencing resolves DNA sequence and structure in intact biological samples. | Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F | Science (New York, N.Y.) | 33384301 | Science | 2021 Feb 26 | https://www.ncbi.nlm.nih.gov/pubmed/33384301 |
| In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui. | McDougal AD, Kang S, Yaqoob Z, So PTC, Kolle M | Proceedings of the National Academy of Sciences of the United States of America | 34845021 | Proc Natl Acad Sci U S A | 2021 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/34845021 |
| Distance-dependent resonance energy transfer in alkyl-terminated Si nanocrystal solids. | Li Z, Robinson ZL, Elvati P, Violi A, Kortshagen UR | The Journal of chemical physics | 35364875 | J Chem Phys | 2022 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/35364875 |
| Structures and topological defects in pressure-driven lyotropic chromonic liquid crystals. | Zhang Q, Zhang R, Ge B, Yaqoob Z, So PTC, Bischofberger I | Proceedings of the National Academy of Sciences of the United States of America | 34446562 | Proc Natl Acad Sci U S A | 2021 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/34446562 |
| Fast light-field 3D microscopy with out-of-distribution detection and adaptation through Conditional Normalizing Flows. | Vizcaíno JP, Symvoulidis P, Wang Z, Jelten J, Favaro P, Boyden ES, Lasser T | ArXiv | 37396615 | ArXiv | 2023 Jun 14 | https://www.ncbi.nlm.nih.gov/pubmed/37396615 |
| Recording of cellular physiological histories along optically readable self-assembling protein chains. | Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C, Park D, Park WM, Ramirez S, Boyden ES | Nature biotechnology | 36593405 | Nat Biotechnol | 2023 May | https://www.ncbi.nlm.nih.gov/pubmed/36593405 |
| Water-Soluble Luminescent Silicon Nanocrystals by Plasma-Induced Acrylic Acid Grafting and PEGylation. | Li Z, Mahajan A, Andaraarachchi HP, Lee Y, Kortshagen UR | ACS applied bio materials | 35014827 | ACS Appl Bio Mater | 2022 Jan 17 | https://www.ncbi.nlm.nih.gov/pubmed/35014827 |
| Multisensory gamma stimulation promotes glymphatic clearance of amyloid. | Murdock MH, Yang CY, Sun N, Pao PC, Blanco-Duque C, Kahn MC, Kim T, Lavoie NS, Victor MB, Islam MR, Galiana F, Leary N, Wang S, Bubnys A, Ma E, Akay LA, Sneve M, Qian Y, Lai C, McCarthy MM, Kopell N, Kellis M, Piatkevich KD, Boyden ES, Tsai LH | Nature | 38418876 | Nature | 2024 Mar | https://www.ncbi.nlm.nih.gov/pubmed/38418876 |
| 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 |
| Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. | Yang JH, Hansen AS | Nature reviews. Molecular cell biology | 38413840 | Nat Rev Mol Cell Biol | 2024 Jul | https://www.ncbi.nlm.nih.gov/pubmed/38413840 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | bioRxiv : the preprint server for biology | 39229045 | bioRxiv | 2024 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/39229045 |
| Molecular models of bidirectional promoter regulation. | Nemsick S, Hansen AS | Current opinion in structural biology | 38905929 | Curr Opin Struct Biol | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38905929 |
| Genome-wide absolute quantification of chromatin looping. | Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny LA, Hansen AS | bioRxiv : the preprint server for biology | 39935886 | bioRxiv | 2025 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/39935886 |
| 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 |
| Catalytic Protein Inhibitors. | Kodadek T | Angewandte Chemie (International ed. in English) | 38064411 | Angew Chem Int Ed Engl | 2024 Mar 11 | https://www.ncbi.nlm.nih.gov/pubmed/38064411 |
| Juneteenth in STEMM and the barriers to equitable science. | Mays A, Byars-Winston A, Hinton A Jr, Marshall AG, Kirabo A, August A, Marlin BJ, Riggs B, Tolbert B, Wanjalla C, Womack C, Evans CS, Barnes C, Starbird C, Williams C, Reynolds C, Taabazuing C, Cameron CE, Murray DD, Applewhite D, Morton DJ, Lee D, Williams DW, Lynch D, Brady D, Lynch E, Rutaganira FUN, Silva GM, Shuler H, Saboor IA, Davis J, Dzirasa K, Hammonds-Odie L, Reyes L, Sweetwyne MT, McReynolds MR, Johnson MDL, Smith NA, Pittman N, Ajijola OA, Smith Q, Robinson RAS, Lewis SC, Murray SA, Black S, Neal SE, Andrisse S, Townsend S, Damo SM, Griffith TN, Lambert WM, Clemons WM Jr | Cell | 37295396 | Cell | 2023 Jun 8 | https://www.ncbi.nlm.nih.gov/pubmed/37295396 |
| RASopathy mutations open new insights into the mechanism of BRAF activation. | Dar AC, Brady DC | Molecular cell | 36400004 | Mol Cell | 2022 Nov 17 | https://www.ncbi.nlm.nih.gov/pubmed/36400004 |
| Alcohol Drinking Without Meals Is Associated With Risk of Gastrointestinal Cancers, Including Early-Onset Cases. | Shi M, Ahmedin NJ, Zong X, Yilmaz ӦH, Bishehsari F, Cao Y | Gastroenterology | 37977310 | Gastroenterology | 2024 Feb | https://www.ncbi.nlm.nih.gov/pubmed/37977310 |
| Early-onset Colon Cancer Shows a Distinct Intestinal Microbiome and a Host-Microbe Interaction. | Adnan D, Trinh JQ, Sharma D, Alsayid M, Bishehsari F | Cancer prevention research (Philadelphia, Pa.) | 37967575 | Cancer Prev Res (Phila) | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/37967575 |
| Reorganization of pancreas circadian transcriptome with aging. | Sharma D, Wessel CR, Mahdavinia M, Preuss F, Bishehsari F | Aging | 37647013 | Aging (Albany NY) | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37647013 |
| Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets. | Sharma D, Adnan D, Abdel-Reheem MK, Anafi RC, Leary DD, Bishehsari F | JCI insight | 38716727 | JCI Insight | 2024 May 8 | https://www.ncbi.nlm.nih.gov/pubmed/38716727 |
| Patient-Derived Organoids as Therapy Screening Platforms in Cancer Patients. | Khorsandi D, Yang JW, Foster S, Khosravi S, Hosseinzadeh Kouchehbaghi N, Zarei F, Lee YB, Runa F, Gangrade A, Voskanian L, Adnan D, Zhu Y, Wang Z, Jucaud V, Dokmeci MR, Shen X, Bishehsari F, Kelber JA, Khademhosseini A, de Barros NR | Advanced healthcare materials | 38359321 | Adv Healthc Mater | 2024 Aug | https://www.ncbi.nlm.nih.gov/pubmed/38359321 |
| Discovery of VH domains that allosterically inhibit ENPP1. | Solomon PE, Bracken CJ, Carozza JA, Wang H, Young EP, Wellner A, Liu CC, Sweet-Cordero EA, Li L, Wells JA | Nature chemical biology | 37400538 | Nat Chem Biol | 2024 Jan | https://www.ncbi.nlm.nih.gov/pubmed/37400538 |
| The M3 Muscarinic Acetylcholine Receptor Can Signal through Multiple G Protein Families. | Smith JS, Hilibrand AS, Skiba MA, Dates AN, Calvillo-Miranda VG, Kruse AC | Molecular pharmacology | 38641412 | Mol Pharmacol | 2024 May 17 | https://www.ncbi.nlm.nih.gov/pubmed/38641412 |
| Rapidly Inducible Yeast Surface Display for Antibody Evolution with OrthoRep. | Paulk AM, Williams RL, Liu CC | ACS synthetic biology | 39052526 | ACS Synth Biol | 2024 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/39052526 |
| Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. | Rix G, Williams RL, Hu VJ, Spinner A, Pisera AO, Marks DS, Liu CC | Science (New York, N.Y.) | 39509492 | Science | 2024 Nov 8 | https://www.ncbi.nlm.nih.gov/pubmed/39509492 |
| Ultra-efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. | Pisera AO, Yu Y, Williams RL, Liu CC | ACS synthetic biology | 40127237 | ACS Synth Biol | 2025 Apr 18 | https://www.ncbi.nlm.nih.gov/pubmed/40127237 |
| Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. | Orenbuch R, Kollasch AW, Spinner HD, Shearer CA, Hopf TA, Franceschi D, Dias M, Frazer J, Marks DS | Research square | 38260496 | Res Sq | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/38260496 |
| Proteome-wide model for human disease genetics. | Orenbuch R, Shearer CA, Kollasch AW, Spinner HD, Hopf TA, van Niekerk L, Franceschi D, Dias M, Frazer J, Marks DS | medRxiv : the preprint server for health sciences | 38076790 | medRxiv | 2025 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/38076790 |
| Antibodies Expand the Scope of Angiotensin Receptor Pharmacology. | Skiba MA, Sterling SM, Rawson S, Gilman MSA, Xu H, Nemeth GR, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Wingler LM, Kruse AC | bioRxiv : the preprint server for biology | 37662341 | bioRxiv | 2023 Aug 24 | https://www.ncbi.nlm.nih.gov/pubmed/37662341 |
| The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. | Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC | Nature chemical biology | 37081311 | Nat Chem Biol | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37081311 |
| Co-evolution of interacting proteins through non-contacting and non-specific mutations. | Ding D, Green AG, Wang B, Lite TV, Weinstein EN, Marks DS, Laub MT | Nature ecology & evolution | 35361892 | Nat Ecol Evol | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35361892 |
| G Protein Selectivity in Dopamine Receptors is Determined before GDP Release. | Tawfeeq C, Hilibrand AS, Smith JS, Portillo J, Kruse AC, Abrol R | Biochemistry | 40358213 | Biochemistry | 2025 Jun 3 | https://www.ncbi.nlm.nih.gov/pubmed/40358213 |
| Decoding protein-peptide interactions using a large, target-agnostic yeast surface display library. | Hurley JD, Shlosman I, Lakshminarayan M, Zhao Z, Yue H, Nowak RP, Fischer ES, Kruse AC | bioRxiv : the preprint server for biology | 40475574 | bioRxiv | 2025 May 23 | https://www.ncbi.nlm.nih.gov/pubmed/40475574 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | bioRxiv : the preprint server for biology | 33200136 | bioRxiv | 2020 Nov 11 | https://www.ncbi.nlm.nih.gov/pubmed/33200136 |
| Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. | Rix G, Williams RL, Spinner H, Hu VJ, Marks DS, Liu CC | bioRxiv : the preprint server for biology | 38014077 | bioRxiv | 2023 Nov 14 | https://www.ncbi.nlm.nih.gov/pubmed/38014077 |
| Antibodies expand the scope of angiotensin receptor pharmacology. | Skiba MA, Sterling SM, Rawson S, Zhang S, Xu H, Jiang H, Nemeth GR, Gilman MSA, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Rockman HA, Barth P, Wingler LM, Kruse AC | Nature chemical biology | 38744986 | Nat Chem Biol | 2024 Dec | https://www.ncbi.nlm.nih.gov/pubmed/38744986 |
| ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers. | Notin P, Marks DS, Weitzman R, Gal Y | bioRxiv : the preprint server for biology | 38106034 | bioRxiv | 2023 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/38106034 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Hu VJ, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | Nature chemical biology | 34168368 | Nat Chem Biol | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34168368 |
| Learning from prepandemic data to forecast viral escape. | Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS | Nature | 37821700 | Nature | 2023 Oct | https://www.ncbi.nlm.nih.gov/pubmed/37821700 |
| Atomically accurate de novo design of antibodies with RFdiffusion. | Bennett NR, Watson JL, Ragotte RJ, Borst AJ, See DL, Weidle C, Biswas R, Yu Y, Shrock EL, Ault R, Leung PJY, Huang B, Goreshnik I, Tam J, Carr KD, Singer B, Criswell C, Wicky BIM, Vafeados D, Sanchez MG, Kim HM, Torres SV, Chan S, Sun SM, Spear T, Sun Y, O'Reilly K, Maris JM, Sgourakis NG, Melnyk RA, Liu CC, Baker D | bioRxiv : the preprint server for biology | 38562682 | bioRxiv | 2025 Feb 28 | https://www.ncbi.nlm.nih.gov/pubmed/38562682 |
| Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape. | Muir DF, Asper GPR, Notin P, Posner JA, Marks DS, Keiser MJ, Pinney MM | bioRxiv : the preprint server for biology | 39484523 | bioRxiv | 2024 Oct 25 | https://www.ncbi.nlm.nih.gov/pubmed/39484523 |
| Epitope-directed selection of GPCR nanobody ligands with evolvable function. | Skiba MA, Canavan C, Nemeth GR, Liu J, Kanso A, Kruse AC | Proceedings of the National Academy of Sciences of the United States of America | 40067891 | Proc Natl Acad Sci U S A | 2025 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/40067891 |
| Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. | Pisera A, Yu Y, Williams RL, Liu CC | bioRxiv : the preprint server for biology | 39651169 | bioRxiv | 2024 Nov 30 | https://www.ncbi.nlm.nih.gov/pubmed/39651169 |
| Guidelines for releasing a variant effect predictor. | Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA | Genome biology | 40234898 | Genome Biol | 2025 Apr 15 | https://www.ncbi.nlm.nih.gov/pubmed/40234898 |
| Protein design and variant prediction using autoregressive generative models. | Shin JE, Riesselman AJ, Kollasch AW, McMahon C, Simon E, Sander C, Manglik A, Kruse AC, Marks DS | Nature communications | 33893299 | Nat Commun | 2021 Apr 23 | https://www.ncbi.nlm.nih.gov/pubmed/33893299 |
| Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. | Nicoludis JM, Green AG, Walujkar S, May EJ, Sotomayor M, Marks DS, Gaudet R | Proceedings of the National Academy of Sciences of the United States of America | 31431536 | Proc Natl Acad Sci U S A | 2019 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/31431536 |
| Guidelines for releasing a variant effect predictor. | Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA | ArXiv | 38699161 | ArXiv | 2024 Apr 16 | https://www.ncbi.nlm.nih.gov/pubmed/38699161 |
| ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. | Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS | bioRxiv : the preprint server for biology | 38106144 | bioRxiv | 2023 Dec 8 | https://www.ncbi.nlm.nih.gov/pubmed/38106144 |
| Protein design using structure-based residue preferences. | Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS | Nature communications | 38388493 | Nat Commun | 2024 Feb 22 | https://www.ncbi.nlm.nih.gov/pubmed/38388493 |
| An Atlas of Variant Effects to understand the genome at nucleotide resolution. | Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME | Genome biology | 37394429 | Genome Biol | 2023 Jul 3 | https://www.ncbi.nlm.nih.gov/pubmed/37394429 |
| An in silico method to assess antibody fragment polyreactivity. | Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC | Nature communications | 36477674 | Nat Commun | 2022 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/36477674 |
| Rapidly inducible yeast surface display for antibody evolution with OrthoRep. | Paulk AM, Williams RL, Liu CC | bioRxiv : the preprint server for biology | 38826191 | bioRxiv | 2024 May 24 | https://www.ncbi.nlm.nih.gov/pubmed/38826191 |
| Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. | Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL | eLife | 37068011 | Elife | 2023 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/37068011 |
| Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis. | Jayasinghe MI, Patel KJ, Jackman JE | RNA (New York, N.Y.) | 38997129 | RNA | 2024 Sep 16 | https://www.ncbi.nlm.nih.gov/pubmed/38997129 |
| Mitochondrial tRNA processing: a neutral evolutionary ratchet innovation. | Lai LB, Jackman JE, Daniels CJ, Gopalan V | Trends in biochemical sciences | 40581570 | Trends Biochem Sci | 2025 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/40581570 |
| Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity. | Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC | Cell reports | 37494187 | Cell Rep | 2023 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/37494187 |
| Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | eLife | 38747717 | Elife | 2024 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/38747717 |
| C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | bioRxiv : the preprint server for biology | 37790392 | bioRxiv | 2024 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/37790392 |
| Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses. | Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC | bioRxiv : the preprint server for biology | 36909515 | bioRxiv | 2023 Apr 3 | https://www.ncbi.nlm.nih.gov/pubmed/36909515 |
| The competitive landscape of the dsRNA world. | Cottrell KA, Andrews RJ, Bass BL | Molecular cell | 38118451 | Mol Cell | 2024 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/38118451 |
| Metal ion requirement for catalysis by 3'-5' RNA polymerases. | Iwaniec BWJ, Allegretti MM, Jackman JE | bioRxiv : the preprint server for biology | 40166239 | bioRxiv | 2025 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/40166239 |
| Pim kinase inhibitor co-treatment decreases alternative non-homologous end-joining DNA repair and genomic instability induced by topoisomerase 2 inhibitors in cells with FLT3 internal tandem duplication. | Scarpa M, Kapoor S, Tvedte ES, Doshi KA, Zou YS, Singh P, Lee JK, Chatterjee A, Ali MKM, Bromley RE, Hotopp JCD, Rassool FV, Baer MR | Oncotarget | 34504649 | Oncotarget | 2021 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/34504649 |
| Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. | Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O'Connor TD | Cancer | 30865299 | Cancer | 2019 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/30865299 |
| TwinBLAST: When Two Is Better than One. | Dunning Hotopp JC, Matsumura J, Bromley RE, Riley DR, Agrawal S, Sparklin B, Mattick J, Crabtree J, Mahurkar A | Microbiology resource announcements | 31467106 | Microbiol Resour Announc | 2019 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/31467106 |
| Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae. | Gasser MT, Chung M, Bromley RE, Nadendla S, Dunning Hotopp JC | Microbiology resource announcements | 31649084 | Microbiol Resour Announc | 2019 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/31649084 |
| Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement. | Tvedte ES, Gasser M, Zhao X, Tallon LJ, Sadzewicz L, Bromley RE, Chung M, Mattick J, Sparklin BC, Dunning Hotopp JC | Current biology : CB | 35671755 | Curr Biol | 2022 Jun 20 | https://www.ncbi.nlm.nih.gov/pubmed/35671755 |
| Aligner optimization increases accuracy and decreases compute times in multi-species sequence data. | Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC | Microbial genomics | 29114401 | Microb Genom | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/29114401 |
| The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont. | Dunning Hotopp JC, Klasson L | G3 (Bethesda, Md.) | 29301977 | G3 (Bethesda) | 2018 Jan 4 | https://www.ncbi.nlm.nih.gov/pubmed/29301977 |
| Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. | Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC | Microbiome | 28118849 | Microbiome | 2017 Jan 25 | https://www.ncbi.nlm.nih.gov/pubmed/28118849 |
| Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. | Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, Thrash JC | Microbiology resource announcements | 32883786 | Microbiol Resour Announc | 2020 Sep 3 | https://www.ncbi.nlm.nih.gov/pubmed/32883786 |
| Grafting or pruning in the animal tree: lateral gene transfer and gene loss? | Dunning Hotopp JC | BMC genomics | 29914363 | BMC Genomics | 2018 Jun 18 | https://www.ncbi.nlm.nih.gov/pubmed/29914363 |
| Modeling the integration of bacterial rRNA fragments into the human cancer genome. | Sieber KB, Gajer P, Dunning Hotopp JC | BMC bioinformatics | 27001685 | BMC Bioinformatics | 2016 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/27001685 |
| Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics. | Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC | Microbial genomics | 31851607 | Microb Genom | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31851607 |
| Updated annotation and meta-analysis of Brugia malayi transcriptomics data reveals consistent transcriptional profiles across time and space with some study-specific differences in adult female worm transcriptional profiles. | Holt CI, Dunning Hotopp JC | PLoS neglected tropical diseases | 39325836 | PLoS Negl Trop Dis | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/39325836 |
| Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes. | Tvedte ES, Gasser M, Sparklin BC, Michalski J, Hjelmen CE, Johnston JS, Zhao X, Bromley R, Tallon LJ, Sadzewicz L, Rasko DA, Dunning Hotopp JC | G3 (Bethesda, Md.) | 33768248 | G3 (Bethesda) | 2021 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/33768248 |
| Lateral gene transfer between prokaryotes and eukaryotes. | Sieber KB, Bromley RE, Dunning Hotopp JC | Experimental cell research | 28189637 | Exp Cell Res | 2017 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/28189637 |
| Development and Evaluation of mini-EXPLORER: A Long Axial Field-of-View PET Scanner for Nonhuman Primate Imaging. | Berg E, Zhang X, Bec J, Judenhofer MS, Patel B, Peng Q, Kapusta M, Schmand M, Casey ME, Tarantal AF, Qi J, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 29419483 | J Nucl Med | 2018 Jun | https://www.ncbi.nlm.nih.gov/pubmed/29419483 |
| Total-Body Quantitative Parametric Imaging of Early Kinetics of (18)F-FDG. | Feng T, Zhao Y, Shi H, Li H, Zhang X, Wang G, Price PM, Badawi RD, Cherry SR, Jones T | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 32948679 | J Nucl Med | 2021 May 10 | https://www.ncbi.nlm.nih.gov/pubmed/32948679 |
| PET Parametric Imaging: Past, Present, and Future. | Wang G, Rahmim A, Gunn RN | IEEE transactions on radiation and plasma medical sciences | 33763624 | IEEE Trans Radiat Plasma Med Sci | 2020 Nov | https://www.ncbi.nlm.nih.gov/pubmed/33763624 |
| Mini EXPLORER II: a prototype high-sensitivity PET/CT scanner for companion animal whole body and human brain scanning. | Lv Y, Lv X, Liu W, Judenhofer MS, Zwingenberger A, Wisner E, Berg E, McKenney S, Leung E, Spencer BA, Cherry SR, Badawi RD | Physics in medicine and biology | 30620929 | Phys Med Biol | 2019 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/30620929 |
| Performance assessment of a software-based coincidence processor for the EXPLORER total-body PET scanner. | Leung EK, Judenhofer MS, Cherry SR, Badawi RD | Physics in medicine and biology | 30152793 | Phys Med Biol | 2018 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/30152793 |
| Relating(18)F-FDG image signal-to-noise ratio to time-of-flight noise-equivalent count rate in total-body PET using the uEXPLORER scanner. | Leung EK, Abdelhafez YG, Berg E, Xie Z, Zhang X, Bayerlein R, Spencer B, Li E, Omidvari N, Selfridge A, Cherry SR, Qi J, Badawi RD | Physics in medicine and biology | 35609588 | Phys Med Biol | 2022 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/35609588 |
| Clinical Implementation of Total-Body PET/CT at University of California, Davis. | Nardo L, Abdelhafez YG, Spencer BA, Badawi RD | PET clinics | 33218600 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218600 |
| Update on the PennPET Explorer: A Whole-body Imager with Scalable Axial Field-of-View. | Pantel AR, Viswanath V, Karp JS | PET clinics | 33218602 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218602 |
| Lutetium background radiation in total-body PET-A simulation study on opportunities and challenges in PET attenuation correction. | Omidvari N, Cheng L, Leung EK, Abdelhafez YG, Badawi RD, Ma T, Qi J, Cherry SR | Frontiers in nuclear medicine | 36172601 | Front Nucl Med | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/36172601 |
| Total-Body Dynamic Reconstruction and Parametric Imaging on the uEXPLORER. | Zhang X, Xie Z, Berg E, Judenhofer MS, Liu W, Xu T, Ding Y, Lv Y, Dong Y, Deng Z, Tang S, Shi H, Hu P, Chen S, Bao J, Li H, Zhou J, Wang G, Cherry SR, Badawi RD, Qi J | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31302637 | J Nucl Med | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31302637 |
| Total-Body Perfusion Imaging with [(11)C]-Butanol. | Li EJ, López JE, Spencer BA, Abdelhafez Y, Badawi RD, Wang G, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37652544 | J Nucl Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37652544 |
| Optimization-derived blood input function using a kernel method and its evaluation with total-body PET for brain parametric imaging. | Zhu Y, Tran Q, Wang Y, Badawi RD, Cherry SR, Qi J, Abbaszadeh S, Wang G | NeuroImage | 38643890 | Neuroimage | 2024 Jun | https://www.ncbi.nlm.nih.gov/pubmed/38643890 |
| High-Temporal-Resolution Lung Kinetic Modeling Using Total-Body Dynamic PET with Time-Delay and Dispersion Corrections. | Wang Y, Spencer BA, Schmall J, Li E, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37116916 | J Nucl Med | 2023 Jul | https://www.ncbi.nlm.nih.gov/pubmed/37116916 |
| Cloud-based serverless computing enables accelerated monte carlo simulations for nuclear medicine imaging. | Bayerlein R, Swarnakar V, Selfridge A, Spencer BA, Nardo L, Badawi RD | Biomedical physics & engineering express | 38876087 | Biomed Phys Eng Express | 2024 Jun 25 | https://www.ncbi.nlm.nih.gov/pubmed/38876087 |
| Numerical investigation reveals challenges in measuring the contrast recovery coefficients in PET. | Bayerlein R, Spencer BA, Abdelhafez YG, Cherry SR, Badawi RD, Omidvari N | Physics in medicine and biology | 37802064 | Phys Med Biol | 2023 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/37802064 |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | Science advances | 37824612 | Sci Adv | 2023 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/37824612 |
| Total-Body Multiparametric PET Quantification of (18)F-FDG Delivery and Metabolism in the Study of Coronavirus Disease 2019 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37591539 | J Nucl Med | 2023 Nov | https://www.ncbi.nlm.nih.gov/pubmed/37591539 |
| Facial Anonymization and Privacy Concerns in Total-Body PET/CT. | Selfridge AR, Spencer BA, Abdelhafez YG, Nakagawa K, Tupin JD, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37268426 | J Nucl Med | 2023 Aug | https://www.ncbi.nlm.nih.gov/pubmed/37268426 |
| Practical joint reconstruction of activity and attenuation with autonomous scaling for time-of-flight PET. | Li Y, Matej S, Karp JS | Physics in medicine and biology | 32340014 | Phys Med Biol | 2020 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/32340014 |
| PennPET Explorer: Design and Preliminary Performance of a Whole-Body Imager. | Karp JS, Viswanath V, Geagan MJ, Muehllehner G, Pantel AR, Parma MJ, Perkins AE, Schmall JP, Werner ME, Daube-Witherspoon ME | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31227573 | J Nucl Med | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31227573 |
| Innovations in Instrumentation for Positron Emission Tomography. | Berg E, Cherry SR | Seminars in nuclear medicine | 29852942 | Semin Nucl Med | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29852942 |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | medRxiv : the preprint server for health sciences | 36993568 | medRxiv | 2023 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/36993568 |
| Total-body PET/CT - First Clinical Experiences and Future Perspectives. | Ng QK, Triumbari EKA, Omidvari N, Cherry SR, Badawi RD, Nardo L | Seminars in nuclear medicine | 35272853 | Semin Nucl Med | 2022 May | https://www.ncbi.nlm.nih.gov/pubmed/35272853 |
| 3D/4D Reconstruction and Quantitative Total Body Imaging. | Qi J, Matej S, Wang G, Zhang X | PET clinics | 33218603 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218603 |
| Analysis of Four-Dimensional Data for Total Body PET Imaging. | Viswanath V, Chitalia R, Pantel AR, Karp JS, Mankoff DA | PET clinics | 33218604 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218604 |
| Total-Body PET: Maximizing Sensitivity to Create New Opportunities for Clinical Research and Patient Care. | Cherry SR, Jones T, Karp JS, Qi J, Moses WW, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 28935835 | J Nucl Med | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28935835 |
| Impact of event positioning algorithm on performance of a whole-body PET scanner using one-to-one coupled detectors. | Surti S, Karp JS | Physics in medicine and biology | 29411709 | Phys Med Biol | 2018 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/29411709 |
| PennPET Explorer: Human Imaging on a Whole-Body Imager. | Pantel AR, Viswanath V, Daube-Witherspoon ME, Dubroff JG, Muehllehner G, Parma MJ, Pryma DA, Schubert EK, Mankoff DA, Karp JS | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31562224 | J Nucl Med | 2020 Jan | https://www.ncbi.nlm.nih.gov/pubmed/31562224 |
| The role of brown adipose tissue in branched-chain amino acid clearance in people. | Abdelhafez YG, Wang G, Li S, Pellegrinelli V, Chaudhari AJ, Ramirez A, Sen F, Vidal-Puig A, Sidossis LS, Klein S, Badawi RD, Chondronikola M | iScience | 39175781 | iScience | 2024 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/39175781 |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39108503 | medRxiv | 2024 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/39108503 |
| Quantitative Total-Body Imaging of Blood Flow with High Temporal Resolution Early Dynamic (18)F-Fluorodeoxyglucose PET Kinetic Modeling. | Chung KJ, Chaudhari AJ, Nardo L, Jones T, Chen MS Jr, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39252929 | medRxiv | 2024 Aug 31 | https://www.ncbi.nlm.nih.gov/pubmed/39252929 |
| Total-body positron emission tomography: a tool for systemic, quantitative evaluation of the inflammatory burden of psoriatic arthritis. | Raychaudhuri SP, Abdelhafez YG, Mazza DF, Raychaudhuri SK, Cherry SR, Nardo L, Badawi RD, Chaudhari AJ | Rheumatology (Oxford, England) | 39714258 | Rheumatology (Oxford) | 2025 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/39714258 |
| Performance Evaluation of the uEXPLORER Total-Body PET/CT Scanner Based on NEMA NU 2-2018 with Additional Tests to Characterize PET Scanners with a Long Axial Field of View. | Spencer BA, Berg E, Schmall JP, Omidvari N, Leung EK, Abdelhafez YG, Tang S, Deng Z, Dong Y, Lv Y, Bao J, Liu W, Li H, Jones T, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 33008932 | J Nucl Med | 2021 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/33008932 |
| Total Body PET: Why, How, What for? | Surti S, Pantel AR, Karp JS | IEEE transactions on radiation and plasma medical sciences | 33134653 | IEEE Trans Radiat Plasma Med Sci | 2020 May | https://www.ncbi.nlm.nih.gov/pubmed/33134653 |
| Total-body imaging: Transforming the role of positron emission tomography. | Cherry SR, Badawi RD, Karp JS, Moses WW, Price P, Jones T | Science translational medicine | 28298419 | Sci Transl Med | 2017 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/28298419 |
| Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner. | Zhang X, Zhou J, Cherry SR, Badawi RD, Qi J | Physics in medicine and biology | 28240215 | Phys Med Biol | 2017 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/28240215 |
| Theoretical study of the benefit of long axial field-of-view PET on region of interest quantification. | Zhang X, Badawi RD, Cherry SR, Qi J | Physics in medicine and biology | 29799814 | Phys Med Biol | 2018 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/29799814 |
| Parallax error in long-axial field-of-view PET scanners-a simulation study. | Schmall JP, Karp JS, Werner M, Surti S | Physics in medicine and biology | 27367971 | Phys Med Biol | 2016 Jul 21 | https://www.ncbi.nlm.nih.gov/pubmed/27367971 |
| Reaching 200-ps timing resolution in a time-of-flight and depth-of-interaction positron emission tomography detector using phosphor-coated crystals and high-density silicon photomultipliers. | Kwon SI, Ferri A, Gola A, Berg E, Piemonte C, Cherry SR, Roncali E | Journal of medical imaging (Bellingham, Wash.) | 27921069 | J Med Imaging (Bellingham) | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/27921069 |
| Total-Body Multiparametric PET Quantification of (18) F-FDG Delivery and Metabolism in the Study of COVID-19 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 37034643 | medRxiv | 2023 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/37034643 |
| First Human Imaging Studies with the EXPLORER Total-Body PET Scanner. | Badawi RD, Shi H, Hu P, Chen S, Xu T, Price PM, Ding Y, Spencer BA, Nardo L, Liu W, Bao J, Jones T, Li H, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 30733314 | J Nucl Med | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30733314 |
| Oncologic Applications of Long Axial Field-of-View PET/Computed Tomography. | Nardo L, Pantel AR | PET clinics | 33218605 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33218605 |
| Total-Body (18)F-FDG PET/CT in Autoimmune Inflammatory Arthritis at Ultra-Low Dose: Initial Observations. | Abdelhafez Y, Raychaudhuri SP, Mazza D, Sarkar S, Hunt HL, McBride K, Nguyen M, Caudle DT, Spencer BA, Omidvari N, Bang H, Cherry SR, Nardo L, Badawi RD, Chaudhari AJ | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 35589405 | J Nucl Med | 2022 Oct | https://www.ncbi.nlm.nih.gov/pubmed/35589405 |
| Total-body Dynamic Imaging and Kinetic Modeling of (18)F-AraG in Healthy Individuals and a Non-Small Cell Lung Cancer Patient Undergoing Anti-PD-1 Immunotherapy. | Omidvari N, Levi J, Abdelhafez YG, Wang Y, Nardo L, Daly ME, Wang G, Cherry SR | medRxiv : the preprint server for health sciences | 37790461 | medRxiv | 2023 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/37790461 |
| Advances in PET Diagnostics for Guiding Targeted Cancer Therapy and Studying In Vivo Cancer Biology. | Mankoff DA, Pantel AR, Viswanath V, Karp JS | Current pathobiology reports | 37092138 | Curr Pathobiol Rep | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/37092138 |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | Nature communications | 40159510 | Nat Commun | 2025 Mar 30 | https://www.ncbi.nlm.nih.gov/pubmed/40159510 |
| Exploring Vessel Wall Biology In Vivo by Ultrasensitive Total-Body PET. | Derlin T, Spencer BA, Mamach M, Abdelhafez Y, Nardo L, Badawi RD, Cherry SR, Bengel FM | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 36175139 | J Nucl Med | 2023 Mar | https://www.ncbi.nlm.nih.gov/pubmed/36175139 |
| Total-Body PET Kinetic Modeling and Potential Opportunities Using Deep Learning. | Wang Y, Li E, Cherry SR, Wang G | PET clinics | 34353745 | PET Clin | 2021 Oct | https://www.ncbi.nlm.nih.gov/pubmed/34353745 |
| Performance Characteristics of Long Axial Field-of-View PET Scanners with Axial Gaps. | Daube-Witherspoon ME, Viswanath V, Werner ME, Karp JS | IEEE transactions on radiation and plasma medical sciences | 34179595 | IEEE Trans Radiat Plasma Med Sci | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/34179595 |
| Quantitative accuracy in total-body imaging using the uEXPLORER PET/CT scanner. | Leung EK, Berg E, Omidvari N, Spencer BA, Li E, Abdelhafez YG, Schmall JP, Liu W, He L, Tang S, Liu Y, Dong Y, Jones T, Cherry SR, Badawi RD | Physics in medicine and biology | 34544074 | Phys Med Biol | 2021 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/34544074 |
| Subsecond total-body imaging using ultrasensitive positron emission tomography. | Zhang X, Cherry SR, Xie Z, Shi H, Badawi RD, Qi J | Proceedings of the National Academy of Sciences of the United States of America | 31964808 | Proc Natl Acad Sci U S A | 2020 Feb 4 | https://www.ncbi.nlm.nih.gov/pubmed/31964808 |
| Numerical observer study of lesion detectability for a long axial field-of-view whole-body PET imager using the PennPET Explorer. | Viswanath V, Daube Witherspoon ME, Karp JS, Surti S | Physics in medicine and biology | 31816616 | Phys Med Biol | 2020 Jan 24 | https://www.ncbi.nlm.nih.gov/pubmed/31816616 |
| Scanner Design Considerations for Long Axial Field-of-View PET Systems. | Daube-Witherspoon ME, Cherry SR | PET clinics | 33160929 | PET Clin | 2021 Jan | https://www.ncbi.nlm.nih.gov/pubmed/33160929 |
| Quantitative PET in the 2020s: a roadmap. | Meikle SR, Sossi V, Roncali E, Cherry SR, Banati R, Mankoff D, Jones T, James M, Sutcliffe J, Ouyang J, Petibon Y, Ma C, El Fakhri G, Surti S, Karp JS, Badawi RD, Yamaya T, Akamatsu G, Schramm G, Rezaei A, Nuyts J, Fulton R, Kyme A, Lois C, Sari H, Price J, Boellaard R, Jeraj R, Bailey DL, Eslick E, Willowson KP, Dutta J | Physics in medicine and biology | 33339012 | Phys Med Biol | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33339012 |
| Multimodal positron emission tomography (PET) imaging in non-oncologic musculoskeletal radiology. | Kogan F, Yoon D, Teeter MG, Chaudhari AJ, Hales L, Barbieri M, Gold GE, Vainberg Y, Goyal A, Watkins L | Skeletal radiology | 38492029 | Skeletal Radiol | 2024 Sep | https://www.ncbi.nlm.nih.gov/pubmed/38492029 |
| EXPLORing Arthritis with Total-body Positron Emission Tomography. | Chaudhari AJ, Abdelhafez YG, Nardo L, Raychaudhuri SP | Seminars in musculoskeletal radiology | 37935209 | Semin Musculoskelet Radiol | 2023 Dec | https://www.ncbi.nlm.nih.gov/pubmed/37935209 |
| Role of Total Body PET/CT in Inflammatory Disorders. | Zoghi S, Mingels C, Badawi RD, Spencer BA, Yarbrough TL, Nardo L, Chaudhari AJ | Seminars in nuclear medicine | 39578110 | Semin Nucl Med | 2025 Jan | https://www.ncbi.nlm.nih.gov/pubmed/39578110 |
| Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. | Roybal KT, Lim WA | Annual review of immunology | 28446063 | Annu Rev Immunol | 2017 Apr 26 | https://www.ncbi.nlm.nih.gov/pubmed/28446063 |
| Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies. | Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA | Cell systems | 32916097 | Cell Syst | 2020 Sep 23 | https://www.ncbi.nlm.nih.gov/pubmed/32916097 |
| T cells selectively filter oscillatory signals on the minutes timescale. | O'Donoghue GP, Bugaj LJ, Anderson W, Daniels KG, Rawlings DJ, Lim WA | Proceedings of the National Academy of Sciences of the United States of America | 33627405 | Proc Natl Acad Sci U S A | 2021 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/33627405 |
| T cell circuits that sense antigen density with an ultrasensitive threshold. | Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Lopez Pazmino MDP, Tonai Y, De Guzman A, Mäkelä A, Saksela K, Gartner ZJ, Lim WA | Science (New York, N.Y.) | 33632893 | Science | 2021 Mar 12 | https://www.ncbi.nlm.nih.gov/pubmed/33632893 |
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| CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. | Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A | Scientific reports | 28389661 | Sci Rep | 2017 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/28389661 |
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| Synthetic cytokine circuits that drive T cells into immune-excluded tumors. | Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, Lim WA | Science (New York, N.Y.) | 36520915 | Science | 2022 Dec 16 | https://www.ncbi.nlm.nih.gov/pubmed/36520915 |
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| SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma. | Choe JH, Watchmaker PB, Simic MS, Gilbert RD, Li AW, Krasnow NA, Downey KM, Yu W, Carrera DA, Celli A, Cho J, Briones JD, Duecker JM, Goretsky YE, Dannenfelser R, Cardarelli L, Troyanskaya O, Sidhu SS, Roybal KT, Okada H, Lim WA | Science translational medicine | 33910979 | Sci Transl Med | 2021 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/33910979 |
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| Precise T cell recognition programs designed by transcriptionally linking multiple receptors. | Williams JZ, Allen GM, Shah D, Sterin IS, Kim KH, Garcia VP, Shavey GE, Yu W, Puig-Saus C, Tsoi J, Ribas A, Roybal KT, Lim WA | Science (New York, N.Y.) | 33243890 | Science | 2020 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/33243890 |
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| Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. | Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY | eLife | 28441135 | Elife | 2017 Apr 25 | https://www.ncbi.nlm.nih.gov/pubmed/28441135 |
| An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. | Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ | Cell | 28388416 | Cell | 2017 Apr 6 | https://www.ncbi.nlm.nih.gov/pubmed/28388416 |
| Atlas of Subcellular RNA Localization Revealed by APEX-Seq. | Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY | Cell | 31230715 | Cell | 2019 Jul 11 | https://www.ncbi.nlm.nih.gov/pubmed/31230715 |
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| Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. | Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC | eLife | 31535972 | Elife | 2019 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/31535972 |
| A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. | Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY | Nature biotechnology | 27240195 | Nat Biotechnol | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27240195 |
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| Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. | Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY | The Plant cell | 36660928 | Plant Cell | 2023 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/36660928 |
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| Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. | Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY | Nature protocols | 28796234 | Nat Protoc | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28796234 |
| Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. | Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, Svinkina T, Deerinck TJ, Ellisman MH, Stevens B, Carr SA, Ting AY | Cell | 27565350 | Cell | 2016 Aug 25 | https://www.ncbi.nlm.nih.gov/pubmed/27565350 |
| Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. | Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY | Cell chemical biology | 28238724 | Cell Chem Biol | 2017 Mar 16 | https://www.ncbi.nlm.nih.gov/pubmed/28238724 |
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| A Mechanical Switch Couples T Cell Receptor Triggering to the Cytoplasmic Juxtamembrane Regions of CD3ζζ. | Lee MS, Glassman CR, Deshpande NR, Badgandi HB, Parrish HL, Uttamapinant C, Stawski PS, Ting AY, Kuhns MS | Immunity | 26231119 | Immunity | 2015 Aug 18 | https://www.ncbi.nlm.nih.gov/pubmed/26231119 |
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| Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution. | Liang J, Wang P, Zhu L, Wang LV | Nature communications | 33067438 | Nat Commun | 2020 Oct 16 | https://www.ncbi.nlm.nih.gov/pubmed/33067438 |
| Transcranial photoacoustic computed tomography based on a layered back-projection method. | Na S, Yuan X, Lin L, Isla J, Garrett D, Wang LV | Photoacoustics | 33134081 | Photoacoustics | 2020 Dec | https://www.ncbi.nlm.nih.gov/pubmed/33134081 |
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| Photoacoustic lymphatic imaging with high spatial-temporal resolution. | Martel C, Yao J, Huang CH, Zou J, Randolph GJ, Wang LV | Journal of biomedical optics | 25408958 | J Biomed Opt | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25408958 |
| A review of snapshot multidimensional optical imaging: measuring photon tags in parallel. | Gao L, Wang LV | Physics reports | 27134340 | Phys Rep | 2016 Feb 29 | https://www.ncbi.nlm.nih.gov/pubmed/27134340 |
| Focusing light through scattering media by full-polarization digital optical phase conjugation. | Shen Y, Liu Y, Ma C, Wang LV | Optics letters | 26977651 | Opt Lett | 2016 Mar 15 | https://www.ncbi.nlm.nih.gov/pubmed/26977651 |
| Lock-in camera based heterodyne holography for ultrasound-modulated optical tomography inside dynamic scattering media. | Liu Y, Shen Y, Ma C, Shi J, Wang LV | Applied physics letters | 27493275 | Appl Phys Lett | 2016 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/27493275 |
| Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. | Li L, Shemetov AA, Baloban M, Hu P, Zhu L, Shcherbakova DM, Zhang R, Shi J, Yao J, Wang LV, Verkhusha VV | Nature communications | 30013153 | Nat Commun | 2018 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/30013153 |
| Photoacoustic computed tomography of human extremities. | Wray P, Lin L, Hu P, Wang LV | Journal of biomedical optics | 30784244 | J Biomed Opt | 2019 Feb | https://www.ncbi.nlm.nih.gov/pubmed/30784244 |
| High-speed alignment optimization of digital optical phase conjugation systems based on autocovariance analysis in conjunction with orthonormal rectangular polynomials. | Hemphill AS, Shen Y, Hwang J, Wang LV | Journal of biomedical optics | 30156064 | J Biomed Opt | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/30156064 |
| Sub-Nyquist sampling boosts targeted light transport through opaque scattering media. | Shen Y, Liu Y, Ma C, Wang LV | Optica | 28670607 | Optica | 2017 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/28670607 |
| Direct measurement of hypoxia in a xenograft multiple myeloma model by optical-resolution photoacoustic microscopy. | Imai T, Muz B, Yeh CH, Yao J, Zhang R, Azab AK, Wang L | Cancer biology & therapy | 28045569 | Cancer Biol Ther | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28045569 |
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| Handheld photoacoustic microscopy to detect melanoma depth in vivo. | Zhou Y, Xing W, Maslov KI, Cornelius LA, Wang LV | Optics letters | 25121860 | Opt Lett | 2014 Aug 15 | https://www.ncbi.nlm.nih.gov/pubmed/25121860 |
| Photoacoustic Computed Tomography of Breast Cancer in Response to Neoadjuvant Chemotherapy. | Lin L, Tong X, Hu P, Invernizzi M, Lai L, Wang LV | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 33854889 | Adv Sci (Weinh) | 2021 Apr | https://www.ncbi.nlm.nih.gov/pubmed/33854889 |
| Integration of Multitargeted Polymer-Based Contrast Agents with Photoacoustic Computed Tomography: An Imaging Technique to Visualize Breast Cancer Intratumor Heterogeneity. | Li L, Patil D, Petruncio G, Harnden KK, Somasekharan JV, Paige M, Wang LV, Salvador-Morales C | ACS nano | 33464827 | ACS Nano | 2021 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/33464827 |
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| Bessel-beam Grueneisen relaxation photoacoustic microscopy with extended depth of field. | Shi J, Wang L, Noordam C, Wang LV | Journal of biomedical optics | 26524679 | J Biomed Opt | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26524679 |
| Wave of single-impulse-stimulated fast initial dip in single vessels of mouse brains imaged by high-speed functional photoacoustic microscopy. | He Y, Shi J, Maslov KI, Cao R, Wang LV | Journal of biomedical optics | 32529816 | J Biomed Opt | 2020 Jun | https://www.ncbi.nlm.nih.gov/pubmed/32529816 |
| Real-time frequency-encoded spatiotemporal focusing through scattering media using a programmable 2D ultrafine optical frequency comb. | Wei X, Shen Y, Jing JC, Hemphill AS, Yang C, Xu S, Yang Z, Wang LV | Science advances | 32128401 | Sci Adv | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32128401 |
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| Focusing light inside live tissue using reversibly switchable bacterial phytochrome as a genetically encoded photochromic guide star. | Yang J, Li L, Shemetov AA, Lee S, Zhao Y, Liu Y, Shen Y, Li J, Oka Y, Verkhusha VV, Wang LV | Science advances | 31844671 | Sci Adv | 2019 Dec | https://www.ncbi.nlm.nih.gov/pubmed/31844671 |
| Single-shot photoacoustic imaging with single-element transducer through a spatiotemporal encoder. | Zhao Y, Wang LV | Journal of biomedical optics | 37065647 | J Biomed Opt | 2023 Apr | https://www.ncbi.nlm.nih.gov/pubmed/37065647 |
| High-speed single-shot optical focusing through dynamic scattering media with full-phase wavefront shaping. | Hemphill AS, Shen Y, Liu Y, Wang LV | Applied physics letters | 29249832 | Appl Phys Lett | 2017 Nov 27 | https://www.ncbi.nlm.nih.gov/pubmed/29249832 |
| Dual-view photoacoustic microscopy for quantitative cell nuclear imaging. | Cai D, Wong TTW, Zhu L, Shi J, Chen SL, Wang LV | Optics letters | 30320772 | Opt Lett | 2018 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/30320772 |
| Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy. | Wong TTW, Zhang R, Zhang C, Hsu HC, Maslov KI, Wang L, Shi J, Chen R, Shung KK, Zhou Q, Wang LV | Nature communications | 29123109 | Nat Commun | 2017 Nov 9 | https://www.ncbi.nlm.nih.gov/pubmed/29123109 |
| High-throughput, label-free, single-cell photoacoustic microscopy of intratumoral metabolic heterogeneity. | Hai P, Imai T, Xu S, Zhang R, Aft RL, Zou J, Wang LV | Nature biomedical engineering | 30936431 | Nat Biomed Eng | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/30936431 |
| Quantitative photoacoustic elastography in humans. | Hai P, Zhou Y, Gong L, Wang LV | Journal of biomedical optics | 27304419 | J Biomed Opt | 2016 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/27304419 |
| Focusing light through biological tissue and tissue-mimicking phantoms up to 9.6 cm in thickness with digital optical phase conjugation. | Shen Y, Liu Y, Ma C, Wang LV | Journal of biomedical optics | 27533439 | J Biomed Opt | 2016 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/27533439 |
| Use of a single xenon flash lamp for photoacoustic computed tomography of multiple-centimeter-thick biological tissue ex vivo and a whole mouse body in vivo. | Wong TT, Zhou Y, Garcia-Uribe A, Li L, Maslov K, Lin L, Wang LV | Journal of biomedical optics | 27775747 | J Biomed Opt | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27775747 |
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| Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse. | Liang J, Ma C, Zhu L, Chen Y, Gao L, Wang LV | Science advances | 28116357 | Sci Adv | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28116357 |
| Dry coupling for whole-body small-animal photoacoustic computed tomography. | Yeh C, Li L, Zhu L, Xia J, Li C, Chen W, Garcia-Uribe A, Maslov KI, Wang LV | Journal of biomedical optics | 28241305 | J Biomed Opt | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/28241305 |
| Spatio-temporal-spectral imaging of non-repeatable dissipative soliton dynamics. | Jing JC, Wei X, Wang LV | Nature communications | 32345966 | Nat Commun | 2020 Apr 28 | https://www.ncbi.nlm.nih.gov/pubmed/32345966 |
| Label-free high-throughput photoacoustic tomography of suspected circulating melanoma tumor cells in patients in vivo. | Hai P, Qu Y, Li Y, Zhu L, Shmuylovich L, Cornelius LA, Wang LV | Journal of biomedical optics | 32170857 | J Biomed Opt | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32170857 |
| Bit-efficient, sub-millisecond wavefront measurement using a lock-in camera for time-reversal based optical focusing inside scattering media. | Liu Y, Ma C, Shen Y, Wang LV | Optics letters | 27192226 | Opt Lett | 2016 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27192226 |
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| Reversibly switchable fluorescence microscopy with enhanced resolution and image contrast. | Yao J, Shcherbakova DM, Li C, Krumholz A, Lorca RA, Reinl E, England SK, Verkhusha VV, Wang LV | Journal of biomedical optics | 25144452 | J Biomed Opt | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25144452 |
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| alphaVbeta3-targeted copper nanoparticles incorporating an Sn 2 lipase-labile fumagillin prodrug for photoacoustic neovascular imaging and treatment. | Zhang R, Pan D, Cai X, Yang X, Senpan A, Allen JS, Lanza GM, Wang LV | Theranostics | 25553103 | Theranostics | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25553103 |
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| In vivo photoacoustic tomography of myoglobin oxygen saturation. | Lin L, Yao J, Li L, Wang LV | Journal of biomedical optics | 26719943 | J Biomed Opt | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26719943 |
| Optical-resolution photoacoustic microscopy for volumetric and spectral analysis of histological and immunochemical samples. | Zhang YS, Yao J, Zhang C, Li L, Wang LV, Xia Y | Angewandte Chemie (International ed. in English) | 24961608 | Angew Chem Int Ed Engl | 2014 Jul 28 | https://www.ncbi.nlm.nih.gov/pubmed/24961608 |
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| In vivo label-free photoacoustic flow cytography and on-the-spot laser killing of single circulating melanoma cells. | He Y, Wang L, Shi J, Yao J, Li L, Zhang R, Huang CH, Zou J, Wang LV | Scientific reports | 28000788 | Sci Rep | 2016 Dec 21 | https://www.ncbi.nlm.nih.gov/pubmed/28000788 |
| High-speed photoacoustic microscopy of mouse cortical microhemodynamics. | Lin L, Yao J, Zhang R, Chen CC, Huang CH, Li Y, Wang L, Chapman W, Zou J, Wang LV | Journal of biophotonics | 28009098 | J Biophotonics | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28009098 |
| Noninvasive Determination of Melanoma Depth using a Handheld Photoacoustic Probe. | Zhou Y, Tripathi SV, Rosman I, Ma J, Hai P, Linette GP, Council ML, Fields RC, Wang LV, Cornelius LA | The Journal of investigative dermatology | 28163070 | J Invest Dermatol | 2017 Jun | https://www.ncbi.nlm.nih.gov/pubmed/28163070 |
| Fast label-free multilayered histology-like imaging of human breast cancer by photoacoustic microscopy. | Wong TTW, Zhang R, Hai P, Zhang C, Pleitez MA, Aft RL, Novack DV, Wang LV | Science advances | 28560329 | Sci Adv | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28560329 |
| High-resolution deep functional imaging of the whole mouse brain by photoacoustic computed tomography in vivo. | Zhang P, Li L, Lin L, Hu P, Shi J, He Y, Zhu L, Zhou Y, Wang LV | Journal of biophotonics | 28635056 | J Biophotonics | 2018 Jan | https://www.ncbi.nlm.nih.gov/pubmed/28635056 |
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| Single-breath-hold photoacoustic computed tomography of the breast. | Lin L, Hu P, Shi J, Appleton CM, Maslov K, Li L, Zhang R, Wang LV | Nature communications | 29907740 | Nat Commun | 2018 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/29907740 |
| Handheld optical-resolution photoacoustic microscopy. | Lin L, Zhang P, Xu S, Shi J, Li L, Yao J, Wang L, Zou J, Wang LV | Journal of biomedical optics | 27775746 | J Biomed Opt | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27775746 |
| Tutorial on photoacoustic tomography. | Zhou Y, Yao J, Wang LV | Journal of biomedical optics | 27086868 | J Biomed Opt | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27086868 |
| Label-free high-throughput detection and quantification of circulating melanoma tumor cell clusters by linear-array-based photoacoustic tomography. | Hai P, Zhou Y, Zhang R, Ma J, Li Y, Shao JY, Wang LV | Journal of biomedical optics | 27832253 | J Biomed Opt | 2017 Apr 1 | https://www.ncbi.nlm.nih.gov/pubmed/27832253 |
| Cuffing-based photoacoustic flowmetry in humans in the optical diffusive regime. | Zhou Y, Liang J, Wang LV | Journal of biophotonics | 26515158 | J Biophotonics | 2016 Mar | https://www.ncbi.nlm.nih.gov/pubmed/26515158 |
| Microcirculatory changes identified by photoacoustic microscopy in patients with complex regional pain syndrome type I after stellate ganglion blocks. | Zhou Y, Yi X, Xing W, Hu S, Maslov KI, Wang LV | Journal of biomedical optics | 25144451 | J Biomed Opt | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25144451 |
| Three-dimensional photoacoustic endoscopic imaging of the rabbit esophagus. | Yang JM, Favazza C, Yao J, Chen R, Zhou Q, Shung KK, Wang LV | PloS one | 25874640 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25874640 |
| Multiview Hilbert transformation for full-view photoacoustic computed tomography using a linear array. | Li G, Li L, Zhu L, Xia J, Wang LV | Journal of biomedical optics | 26112369 | J Biomed Opt | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/26112369 |
| High-speed label-free functional photoacoustic microscopy of mouse brain in action. | Yao J, Wang L, Yang JM, Maslov KI, Wong TT, Li L, Huang CH, Zou J, Wang LV | Nature methods | 25822799 | Nat Methods | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25822799 |
| In vivo deep brain imaging of rats using oral-cavity illuminated photoacoustic computed tomography. | Lin L, Xia J, Wong TT, Li L, Wang LV | Journal of biomedical optics | 25611865 | J Biomed Opt | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25611865 |
| Multiscale Functional and Molecular Photoacoustic Tomography. | Yao J, Xia J, Wang LV | Ultrasonic imaging | 25933617 | Ultrason Imaging | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25933617 |
| Multiview Hilbert transformation in full-ring transducer array-based photoacoustic computed tomography. | Li L, Zhu L, Shen Y, Wang LV | Journal of biomedical optics | 28745385 | J Biomed Opt | 2017 Jul 1 | https://www.ncbi.nlm.nih.gov/pubmed/28745385 |
| High-throughput ultraviolet photoacoustic microscopy with multifocal excitation. | Imai T, Shi J, Wong TTW, Li L, Zhu L, Wang LV | Journal of biomedical optics | 29546734 | J Biomed Opt | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/29546734 |
| Calibration-free absolute quantification of particle concentration by statistical analyses of photoacoustic signals in vivo. | Zhou Y, Yao J, Maslov KI, Wang LV | Journal of biomedical optics | 24589987 | J Biomed Opt | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24589987 |
| Three-dimensional arbitrary trajectory scanning photoacoustic microscopy. | Yeh C, Soetikno B, Hu S, Maslov KI, Wang LV | Journal of biophotonics | 25077689 | J Biophotonics | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25077689 |
| Amplitude-masked photoacoustic wavefront shaping and application in flowmetry. | Tay JW, Liang J, Wang LV | Optics letters | 25360912 | Opt Lett | 2014 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/25360912 |
| Breakthrough in Photonics 2013: Photoacoustic Tomography in Biomedicine. | Yao J, Wang LV | IEEE photonics journal | 25383143 | IEEE Photonics J | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25383143 |
| Sensitivity of photoacoustic microscopy. | Yao J, Wang LV | Photoacoustics | 25302158 | Photoacoustics | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25302158 |
| Optical focusing deep inside dynamic scattering media with near-infrared time-reversed ultrasonically encoded (TRUE) light. | Liu Y, Lai P, Ma C, Xu X, Grabar AA, Wang LV | Nature communications | 25556918 | Nat Commun | 2015 Jan 5 | https://www.ncbi.nlm.nih.gov/pubmed/25556918 |
| Dependence of optical scattering from Intralipid in gelatin-gel based tissue-mimicking phantoms on mixing temperature and time. | Lai P, Xu X, Wang LV | Journal of biomedical optics | 24604534 | J Biomed Opt | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24604534 |
| Handheld photoacoustic probe to detect both melanoma depth and volume at high speed in vivo. | Zhou Y, Li G, Zhu L, Li C, Cornelius LA, Wang LV | Journal of biophotonics | 25676898 | J Biophotonics | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25676898 |
| Dichroism-sensitive photoacoustic computed tomography. | Qu Y, Li L, Shen Y, Wei X, Wong TTW, Hu P, Yao J, Maslov K, Wang LV | Optica | 30820444 | Optica | 2018 Apr 20 | https://www.ncbi.nlm.nih.gov/pubmed/30820444 |
| Recent progress in photoacoustic molecular imaging. | Yao J, Wang LV | Current opinion in chemical biology | 29631120 | Curr Opin Chem Biol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29631120 |
| Single-shot ultrafast imaging attaining 70 trillion frames per second. | Wang P, Liang J, Wang LV | Nature communications | 32350256 | Nat Commun | 2020 Apr 29 | https://www.ncbi.nlm.nih.gov/pubmed/32350256 |
| High-resolution, high-contrast mid-infrared imaging of fresh biological samples with ultraviolet-localized photoacoustic microscopy. | Shi J, Wong TTW, He Y, Li L, Zhang R, Yung CS, Hwang J, Maslov K, Wang LV | Nature photonics | 31440304 | Nat Photonics | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31440304 |
| Single-shot real-time femtosecond imaging of temporal focusing. | Liang J, Zhu L, Wang LV | Light, science & applications | 30839588 | Light Sci Appl | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30839588 |
| In vivo superresolution photoacoustic computed tomography by localization of single dyed droplets. | Zhang P, Li L, Lin L, Shi J, Wang LV | Light, science & applications | 30962922 | Light Sci Appl | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30962922 |
| Fighting against fast speckle decorrelation for light focusing inside live tissue by photon frequency shifting. | Yang J, Li L, Li J, Cheng Z, Liu Y, Wang LV | ACS photonics | 34113691 | ACS Photonics | 2020 Mar 18 | https://www.ncbi.nlm.nih.gov/pubmed/34113691 |
| Label-free intraoperative histology of bone tissue via deep-learning-assisted ultraviolet photoacoustic microscopy. | Cao R, Nelson SD, Davis S, Liang Y, Luo Y, Zhang Y, Crawford B, Wang LV | Nature biomedical engineering | 36123403 | Nat Biomed Eng | 2023 Feb | https://www.ncbi.nlm.nih.gov/pubmed/36123403 |
| Encrypted Three-dimensional Dynamic Imaging using Snapshot Time-of-flight Compressed Ultrafast Photography. | Liang J, Gao L, Hai P, Li C, Wang LV | Scientific reports | 26503834 | Sci Rep | 2015 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/26503834 |
| Photoacoustic tomography of vascular compliance in humans. | Hai P, Zhou Y, Liang J, Li C, Wang LV | Journal of biomedical optics | 26720875 | J Biomed Opt | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26720875 |
| Photoacoustic microscopy of arteriovenous shunts and blood diffusion in early-stage tumors. | Yeh C, Liang J, Zhou Y, Hu S, Sohn RE, Arbeit JM, Wang LV | Journal of biomedical optics | 26882446 | J Biomed Opt | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/26882446 |
| Grueneisen relaxation photoacoustic microscopy in vivo. | Ma J, Shi J, Hai P, Zhou Y, Wang LV | Journal of biomedical optics | 27272096 | J Biomed Opt | 2016 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/27272096 |
| Continuous scanning of a time-reversed ultrasonically encoded optical focus by reflection-mode digital phase conjugation. | Suzuki Y, Tay JW, Yang Q, Wang LV | Optics letters | 24978506 | Opt Lett | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24978506 |
| Label-free photoacoustic nanoscopy. | Danielli A, Maslov K, Garcia-Uribe A, Winkler AM, Li C, Wang L, Chen Y, Dorn GW 2nd, Wang LV | Journal of biomedical optics | 25104412 | J Biomed Opt | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/25104412 |
| Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe. | Yao J, Kaberniuk AA, Li L, Shcherbakova DM, Zhang R, Wang L, Li G, Verkhusha VV, Wang LV | Nature methods | 26550774 | Nat Methods | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26550774 |
| Photoacoustic tomography: principles and advances. | Xia J, Yao J, Wang LV | Electromagnetic waves (Cambridge, Mass.) | 25642127 | Electromagn Waves (Camb) | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25642127 |
| Tripling the detection view of high-frequency linear-array-based photoacoustic computed tomography by using two planar acoustic reflectors. | Li G, Xia J, Wang K, Maslov K, Anastasio MA, Wang LV | Quantitative imaging in medicine and surgery | 25694954 | Quant Imaging Med Surg | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25694954 |
| Dual-Modality Photoacoustic and Ultrasound Imaging System for Noninvasive Sentinel Lymph Node Detection in Patients with Breast Cancer. | Garcia-Uribe A, Erpelding TN, Krumholz A, Ke H, Maslov K, Appleton C, Margenthaler JA, Wang LV | Scientific reports | 26510774 | Sci Rep | 2015 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/26510774 |
| Multiscale Photoacoustic Tomography of a Genetically Encoded Near-Infrared FRET Biosensor. | Li L, Hsu HC, Verkhusha VV, Wang LV, Shcherbakova DM | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 34533889 | Adv Sci (Weinh) | 2021 Nov | https://www.ncbi.nlm.nih.gov/pubmed/34533889 |
| Harnessing a multi-dimensional fibre laser using genetic wavefront shaping. | Wei X, Jing JC, Shen Y, Wang LV | Light, science & applications | 32884678 | Light Sci Appl | 2020 | https://www.ncbi.nlm.nih.gov/pubmed/32884678 |
| Photoacoustic topography through an ergodic relay for functional imaging and biometric application in vivo. | Li Y, Li L, Zhu L, Shi J, Maslov K, Wang LV | Journal of biomedical optics | 32648387 | J Biomed Opt | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32648387 |
| High-speed three-dimensional photoacoustic computed tomography for preclinical research and clinical translation. | Lin L, Hu P, Tong X, Na S, Cao R, Yuan X, Garrett DC, Shi J, Maslov K, Wang LV | Nature communications | 33563996 | Nat Commun | 2021 Feb 9 | https://www.ncbi.nlm.nih.gov/pubmed/33563996 |
| In vivo photoacoustic microscopy of human cuticle microvasculature with single-cell resolution. | Hsu HC, Wang L, Wang LV | Journal of biomedical optics | 27207113 | J Biomed Opt | 2016 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/27207113 |
| Label-free cell nuclear imaging by Grüneisen relaxation photoacoustic microscopy. | Liu X, Wong TTW, Shi J, Ma J, Yang Q, Wang LV | Optics letters | 29444034 | Opt Lett | 2018 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/29444034 |
| Single-impulse Panoramic Photoacoustic Computed Tomography of Small-animal Whole-body Dynamics at High Spatiotemporal Resolution. | Li L, Zhu L, Ma C, Lin L, Yao J, Wang L, Maslov K, Zhang R, Chen W, Shi J, Wang LV | Nature biomedical engineering | 29333331 | Nat Biomed Eng | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29333331 |
| Dual-axis illumination for virtually augmenting the detection view of optical-resolution photoacoustic microscopy. | Hsu HC, Li L, Yao J, Wong TTW, Shi J, Chen R, Zhou Q, Wang L | Journal of biomedical optics | 29981225 | J Biomed Opt | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29981225 |
| In vivo characterization of connective tissue remodeling using infrared photoacoustic spectra. | Qu Y, Hu P, Shi J, Maslov K, Zhao P, Li C, Ma J, Garcia-Uribe A, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Altieri E, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Stout MJ, Tuuli M, Wang LV | Journal of biomedical optics | 30520275 | J Biomed Opt | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30520275 |
| Transvaginal fast-scanning optical-resolution photoacoustic endoscopy. | Qu Y, Li C, Shi J, Chen R, Xu S, Rafsanjani H, Maslov K, Krigman H, Garvey L, Hu P, Zhao P, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Zhou Q, Shung KK, Zou J, Stout MJ, Tuuli M, Wang LV | Journal of biomedical optics | 30520276 | J Biomed Opt | 2018 Dec | https://www.ncbi.nlm.nih.gov/pubmed/30520276 |
| Space- and intensity-constrained reconstruction for compressed ultrafast photography. | Zhu L, Chen Y, Liang J, Xu Q, Gao L, Ma C, Wang LV | Optica | 28775997 | Optica | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28775997 |
| Single-exposure optical focusing inside scattering media using binarized time-reversed adapted perturbation. | Ma C, Zhou F, Liu Y, Wang LV | Optica | 30221184 | Optica | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/30221184 |
| Nonlinear photoacoustic spectroscopy of hemoglobin. | Danielli A, Maslov K, Favazza CP, Xia J, Wang LV | Applied physics letters | 26045627 | Appl Phys Lett | 2015 May 18 | https://www.ncbi.nlm.nih.gov/pubmed/26045627 |
| Optical drug monitoring: photoacoustic imaging of nanosensors to monitor therapeutic lithium in vivo. | Cash KJ, Li C, Xia J, Wang LV, Clark HA | ACS nano | 25588028 | ACS Nano | 2015 Feb 24 | https://www.ncbi.nlm.nih.gov/pubmed/25588028 |
| Photoacoustically guided wavefront shaping for enhanced optical focusing in scattering media. | Lai P, Wang L, Tay JW, Wang LV | Nature photonics | 25914725 | Nat Photonics | 2015 Feb | https://www.ncbi.nlm.nih.gov/pubmed/25914725 |
| Optical-resolution photoacoustic endomicroscopy in vivo. | Yang JM, Li C, Chen R, Rao B, Yao J, Yeh CH, Danielli A, Maslov K, Zhou Q, Shung KK, Wang LV | Biomedical optics express | 25798315 | Biomed Opt Express | 2015 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/25798315 |
| Ultrasonic-heating-encoded photoacoustic tomography with virtually augmented detection view. | Wang L, Li G, Xia J, Wang LV | Optica | 25984555 | Optica | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25984555 |
| Noninvasive photoacoustic microscopy of methemoglobin in vivo. | Tang M, Zhou Y, Zhang R, Wang LV | Journal of biomedical optics | 25760655 | J Biomed Opt | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25760655 |
| Single-shot ultrafast optical imaging. | Liang J, Wang LV | Optica | 30820445 | Optica | 2018 Sep 20 | https://www.ncbi.nlm.nih.gov/pubmed/30820445 |
| Dual-polarization analog optical phase conjugation for focusing light through scattering media. | Cheng Z, Yang J, Wang LV | Applied physics letters | 31312071 | Appl Phys Lett | 2019 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/31312071 |
| Snapshot Photoacoustic Topography Through an Ergodic Relay for High-throughput Imaging of Optical Absorption. | Li Y, Li L, Zhu L, Maslov K, Shi J, Hu P, Bo E, Yao J, Liang J, Wang L, Wang LV | Nature photonics | 34178097 | Nat Photonics | 2020 Mar | https://www.ncbi.nlm.nih.gov/pubmed/34178097 |
| Single-shot time-reversed optical focusing into and through scattering media. | Cheng Z, Yang J, Wang LV | ACS photonics | 34337103 | ACS Photonics | 2020 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/34337103 |
| LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. | Wang J, Telese F, Tan Y, Li W, Jin C, He X, Basnet H, Ma Q, Merkurjev D, Zhu X, Liu Z, Zhang J, Ohgi K, Taylor H, White RR, Tazearslan C, Suh Y, Macfarlan TS, Pfaff SL, Rosenfeld MG | Nature neuroscience | 26214369 | Nat Neurosci | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26214369 |
| Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program. | Yang F, Ma Q, Liu Z, Li W, Tan Y, Jin C, Ma W, Hu Y, Shen J, Ohgi KA, Telese F, Liu W, Rosenfeld MG | Molecular cell | 28475868 | Mol Cell | 2017 May 4 | https://www.ncbi.nlm.nih.gov/pubmed/28475868 |
| SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. | Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK | Cell metabolism | 28041958 | Cell Metab | 2017 Feb 7 | https://www.ncbi.nlm.nih.gov/pubmed/28041958 |
| Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. | Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S | Nucleic acids research | 25352550 | Nucleic Acids Res | 2014 Nov 10 | https://www.ncbi.nlm.nih.gov/pubmed/25352550 |
| Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. | Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK | Nature neuroscience | 24584051 | Nat Neurosci | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24584051 |
| Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program. | Zhang F, Tanasa B, Merkurjev D, Lin C, Song X, Li W, Tan Y, Liu Z, Zhang J, Ohgi KA, Krones A, Skowronska-Krawczyk D, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 25605944 | Proc Natl Acad Sci U S A | 2015 Feb 3 | https://www.ncbi.nlm.nih.gov/pubmed/25605944 |
| Ligand-dependent enhancer activation regulated by topoisomerase-I activity. | Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, Ohgi KA, Zhang J, Aggarwal AK, Rosenfeld MG | Cell | 25619691 | Cell | 2015 Jan 29 | https://www.ncbi.nlm.nih.gov/pubmed/25619691 |
| Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. | Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK | Cell | 25480297 | Cell | 2014 Dec 4 | https://www.ncbi.nlm.nih.gov/pubmed/25480297 |
| Patient-derived xenograft (PDX) models in basic and translational breast cancer research. | Dobrolecki LE, Airhart SD, Alferez DG, Aparicio S, Behbod F, Bentires-Alj M, Brisken C, Bult CJ, Cai S, Clarke RB, Dowst H, Ellis MJ, Gonzalez-Suarez E, Iggo RD, Kabos P, Li S, Lindeman GJ, Marangoni E, McCoy A, Meric-Bernstam F, Piwnica-Worms H, Poupon MF, Reis-Filho J, Sartorius CA, Scabia V, Sflomos G, Tu Y, Vaillant F, Visvader JE, Welm A, Wicha MS, Lewis MT | Cancer metastasis reviews | 28025748 | Cancer Metastasis Rev | 2016 Dec | https://www.ncbi.nlm.nih.gov/pubmed/28025748 |
| Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. | Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK | eLife | 27462873 | Elife | 2016 Jul 27 | https://www.ncbi.nlm.nih.gov/pubmed/27462873 |
| Required enhancer-matrin-3 network interactions for a homeodomain transcription program. | Skowronska-Krawczyk D, Ma Q, Schwartz M, Scully K, Li W, Liu Z, Taylor H, Tollkuhn J, Ohgi KA, Notani D, Kohwi Y, Kohwi-Shigematsu T, Rosenfeld MG | Nature | 25119036 | Nature | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25119036 |
| Enhancer activation requires trans-recruitment of a mega transcription factor complex. | Liu Z, Merkurjev D, Yang F, Li W, Oh S, Friedman MJ, Song X, Zhang F, Ma Q, Ohgi KA, Krones A, Rosenfeld MG | Cell | 25303530 | Cell | 2014 Oct 9 | https://www.ncbi.nlm.nih.gov/pubmed/25303530 |
| Exploiting genomics and natural genetic variation to decode macrophage enhancers. | Romanoski CE, Link VM, Heinz S, Glass CK | Trends in immunology | 26298065 | Trends Immunol | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/26298065 |
| Vespucci: a system for building annotated databases of nascent transcripts. | Allison KA, Kaikkonen MU, Gaasterland T, Glass CK | Nucleic acids research | 24304890 | Nucleic Acids Res | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24304890 |
| Genome-Wide Approaches to Defining Macrophage Identity and Function. | Fonseca GJ, Seidman JS, Glass CK | Microbiology spectrum | 28087927 | Microbiol Spectr | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/28087927 |
| Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens. | Jin C, Yang L, Xie M, Lin C, Merkurjev D, Yang JC, Tanasa B, Oh S, Zhang J, Ohgi KA, Zhou H, Li W, Evans CP, Ding S, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 24928520 | Proc Natl Acad Sci U S A | 2014 Jun 24 | https://www.ncbi.nlm.nih.gov/pubmed/24928520 |
| Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation. | Li W, Hu Y, Oh S, Ma Q, Merkurjev D, Song X, Zhou X, Liu Z, Tanasa B, He X, Chen AY, Ohgi K, Zhang J, Liu W, Rosenfeld MG | Molecular cell | 26166704 | Mol Cell | 2015 Jul 16 | https://www.ncbi.nlm.nih.gov/pubmed/26166704 |
| Genetic and genomic approaches to understanding macrophage identity and function. | Glass CK | Arteriosclerosis, thrombosis, and vascular biology | 25745059 | Arterioscler Thromb Vasc Biol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25745059 |
| Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock. | Wang J, Saijo K, Skola D, Jin C, Ma Q, Merkurjev D, Glass CK, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 29263096 | Proc Natl Acad Sci U S A | 2018 Jan 9 | https://www.ncbi.nlm.nih.gov/pubmed/29263096 |
| Enhancer RNAs and regulated transcriptional programs. | Lam MT, Li W, Rosenfeld MG, Glass CK | Trends in biochemical sciences | 24674738 | Trends Biochem Sci | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24674738 |
| Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. | Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang J, Aggarwal A, Rosenfeld MG | Cell | 24360279 | Cell | 2013 Dec 19 | https://www.ncbi.nlm.nih.gov/pubmed/24360279 |
| Effect of natural genetic variation on enhancer selection and function. | Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK | Nature | 24121437 | Nature | 2013 Nov 28 | https://www.ncbi.nlm.nih.gov/pubmed/24121437 |
| Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation. | Basnet H, Su XB, Tan Y, Meisenhelder J, Merkurjev D, Ohgi KA, Hunter T, Pillus L, Rosenfeld MG | Nature | 25252977 | Nature | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25252977 |
| The selection and function of cell type-specific enhancers. | Heinz S, Romanoski CE, Benner C, Glass CK | Nature reviews. Molecular cell biology | 25650801 | Nat Rev Mol Cell Biol | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25650801 |
| Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. | Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG | Nature | 23728302 | Nature | 2013 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/23728302 |
| Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. | Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK | Nature | 23728303 | Nature | 2013 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/23728303 |
| Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers. | Link VM, Gosselin D, Glass CK | Cold Spring Harbor symposia on quantitative biology | 26582787 | Cold Spring Harb Symp Quant Biol | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26582787 |
| Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program. | Tan Y, Jin C, Ma W, Hu Y, Tanasa B, Oh S, Gamliel A, Ma Q, Yao L, Zhang J, Ohgi K, Liu W, Aggarwal AK, Rosenfeld MG | Molecular cell | 30118678 | Mol Cell | 2018 Aug 16 | https://www.ncbi.nlm.nih.gov/pubmed/30118678 |
| Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. | Nair SJ, Yang L, Meluzzi D, Oh S, Yang F, Friedman MJ, Wang S, Suter T, Alshareedah I, Gamliel A, Ma Q, Zhang J, Hu Y, Tan Y, Ohgi KA, Jayani RS, Banerjee PR, Aggarwal AK, Rosenfeld MG | Nature structural & molecular biology | 30833784 | Nat Struct Mol Biol | 2019 Mar | https://www.ncbi.nlm.nih.gov/pubmed/30833784 |
| Molecular control of activation and priming in macrophages. | Glass CK, Natoli G | Nature immunology | 26681459 | Nat Immunol | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26681459 |
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| Intraoperative molecular imaging can identify lung adenocarcinomas during pulmonary resection. | Okusanya OT, DeJesus EM, Jiang JX, Judy RP, Venegas OG, Deshpande CG, Heitjan DF, Nie S, Low PS, Singhal S | The Journal of thoracic and cardiovascular surgery | 26126457 | J Thorac Cardiovasc Surg | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26126457 |
| Variance Regularized Counterfactual Risk Minimizationvia Variational Divergence Minimization. | Wu H, Wang MD | Proceedings of machine learning research | 32789292 | Proc Mach Learn Res | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/32789292 |
| Effect of low-expression gene filtering on detection of differentially expressed genes in RNA-seq data. | Sha Y, Phan JH, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26737772 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26737772 |
| Near-infrared operating lamp for intraoperative molecular imaging of a mediastinal tumor. | Keating J, Judy R, Newton A, Singhal S | BMC medical imaging | 26883511 | BMC Med Imaging | 2016 Feb 17 | https://www.ncbi.nlm.nih.gov/pubmed/26883511 |
| Near-infrared Intraoperative Molecular Imaging Can Identify Metastatic Lymph Nodes in Prostate Cancer. | Xia L, Zeh R, Mizelle J, Newton A, Predina J, Nie S, Singhal S, Guzzo TJ | Urology | 28438626 | Urology | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28438626 |
| -Omic and Electronic Health Record Big Data Analytics for Precision Medicine. | Wu PY, Cheng CW, Kaddi CD, Venugopalan J, Hoffman R, Wang MD | IEEE transactions on bio-medical engineering | 27740470 | IEEE Trans Biomed Eng | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27740470 |
| MotifMark: Finding regulatory motifs in DNA sequences. | Hassanzadeh HR, Kolhe P, Isbell CL, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 29060747 | Annu Int Conf IEEE Eng Med Biol Soc | 2017 Jul | https://www.ncbi.nlm.nih.gov/pubmed/29060747 |
| Tumor-associated neutrophils stimulate T cell responses in early-stage human lung cancer. | Eruslanov EB, Bhojnagarwala PS, Quatromoni JG, Stephen TL, Ranganathan A, Deshpande C, Akimova T, Vachani A, Litzky L, Hancock WW, Conejo-Garcia JR, Feldman M, Albelda SM, Singhal S | The Journal of clinical investigation | 25384214 | J Clin Invest | 2014 Dec | https://www.ncbi.nlm.nih.gov/pubmed/25384214 |
| Intraoperative near-infrared imaging can distinguish cancer from normal tissue but not inflammation. | Holt D, Okusanya O, Judy R, Venegas O, Jiang J, DeJesus E, Eruslanov E, Quatromoni J, Bhojnagarwala P, Deshpande C, Albelda S, Nie S, Singhal S | PloS one | 25072388 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25072388 |
| The More Exotic Shapes of Semiconductor Nanocrystals: Emerging Applications in Bioimaging. | Lim SJ, Smith A, Nie S | Current opinion in chemical engineering | 24982823 | Curr Opin Chem Eng | 2014 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/24982823 |
| Histological image classification using biologically interpretable shape-based features. | Kothari S, Phan JH, Young AN, Wang MD | BMC medical imaging | 23497380 | BMC Med Imaging | 2013 Mar 13 | https://www.ncbi.nlm.nih.gov/pubmed/23497380 |
| Intraoperative Molecular Imaging of Lung Adenocarcinoma Can Identify Residual Tumor Cells at the Surgical Margins. | Keating JJ, Okusanya OT, De Jesus E, Judy R, Jiang J, Deshpande C, Nie S, Low P, Singhal S | Molecular imaging and biology | 26228697 | Mol Imaging Biol | 2016 Apr | https://www.ncbi.nlm.nih.gov/pubmed/26228697 |
| Molecular imaging to identify tumor recurrence following chemoradiation in a hostile surgical environment. | Okusanya OT, Deshpande C, Barbosa EM Jr, Aggarwal C, Simone CB 2nd, Jiang J, Judy R, DeJesus E, Albelda S, Nie S, Low PS, Singhal S | Molecular imaging | 25442640 | Mol Imaging | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25442640 |
| Exploration of Genomic, Proteomic, and Histopathological Image Data Integration Methods for Clinical Prediction. | Poruthoor A, Phan JH, Kothari S, Wang MD | IEEE China Summit & International Conference on Signal and Information Processing. IEEE China Summit & International Conference on Signal and Information Processing | 28393144 | IEEE China Summit Int Conf Signal Inf Process | 2013 Jul | https://www.ncbi.nlm.nih.gov/pubmed/28393144 |
| PEPCOR - A Risk Prediction Model for Pediatric Intensive Care Units Utilizing Ventilator Days and Length of Stay. | Pethiyagoda T, Chanani N, Cheng C, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 28164175 | IEEE EMBS Int Conf Biomed Health Inform | 2016 Feb | https://www.ncbi.nlm.nih.gov/pubmed/28164175 |
| Intraoperative near-infrared imaging of surgical wounds after tumor resections can detect residual disease. | Madajewski B, Judy BF, Mouchli A, Kapoor V, Holt D, Wang MD, Nie S, Singhal S | Clinical cancer research : an official journal of the American Association for Cancer Research | 22932668 | Clin Cancer Res | 2012 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/22932668 |
| A fast least-squares algorithm for population inference. | Parry RM, Wang MD | BMC bioinformatics | 23343408 | BMC Bioinformatics | 2013 Jan 23 | https://www.ncbi.nlm.nih.gov/pubmed/23343408 |
| Models for Predicting Stage in Head and Neck Squamous Cell Carcinoma Using Proteomic and Transcriptomic Data. | Kaddi CD, Wang MD | IEEE journal of biomedical and health informatics | 26462248 | IEEE J Biomed Health Inform | 2017 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26462248 |
| Comparison of Folate Receptor Targeted Optical Contrast Agents for Intraoperative Molecular Imaging. | De Jesus E, Keating JJ, Kularatne SA, Jiang J, Judy R, Predina J, Nie S, Low P, Singhal S | International journal of molecular imaging | 26491562 | Int J Mol Imaging | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26491562 |
| Physical chemistry of nanomedicine: understanding the complex behaviors of nanoparticles in vivo. | Lane LA, Qian X, Smith AM, Nie S | Annual review of physical chemistry | 25622189 | Annu Rev Phys Chem | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25622189 |
| Compact and blinking-suppressed quantum dots for single-particle tracking in live cells. | Lane LA, Smith AM, Lian T, Nie S | The journal of physical chemistry. B | 25157589 | J Phys Chem B | 2014 Dec 11 | https://www.ncbi.nlm.nih.gov/pubmed/25157589 |
| SERS Nanoparticles in Medicine: From Label-Free Detection to Spectroscopic Tagging. | Lane LA, Qian X, Nie S | Chemical reviews | 26313254 | Chem Rev | 2015 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/26313254 |
| CD38-Expressing Myeloid-Derived Suppressor Cells Promote Tumor Growth in a Murine Model of Esophageal Cancer. | Karakasheva TA, Waldron TJ, Eruslanov E, Kim SB, Lee JS, O'Brien S, Hicks PD, Basu D, Singhal S, Malavasi F, Rustgi AK | Cancer research | 26294209 | Cancer Res | 2015 Oct 1 | https://www.ncbi.nlm.nih.gov/pubmed/26294209 |
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| Detection of blur artifacts in histopathological whole-slide images of endomyocardial biopsies. | Hang Wu, Phan JH, Bhatia AK, Cundiff CA, Shehata BM, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736365 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26736365 |
| Prediction of Heart Transplant Rejection Using Histopathological Whole-Slide Imaging. | Dooley AE, Tong L, Deshpande SR, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32551442 | IEEE EMBS Int Conf Biomed Health Inform | 2018 Mar | https://www.ncbi.nlm.nih.gov/pubmed/32551442 |
| Improved Prediction on Heart Transplant Rejection Using Convolutional Autoencoder and Multiple Instance Learning on Whole-Slide Imaging. | Zhu Y, Wang MD, Tong L, Deshpande SR | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32577622 | IEEE EMBS Int Conf Biomed Health Inform | 2019 May | https://www.ncbi.nlm.nih.gov/pubmed/32577622 |
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| Combination of an Integrin-Targeting NIR Tracer and an Ultrasensitive Spectroscopic Device for Intraoperative Detection of Head and Neck Tumor Margins and Metastatic Lymph Nodes. | Yoon Y, Mohs AM, Mancini MC, Nie S, Shim H | Tomography (Ann Arbor, Mich.) | 27738656 | Tomography | 2016 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27738656 |
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| icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care units. | Cheng CW, Chanani N, Maher K, Wang | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 27532061 | ACM BCB | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27532061 |
| Intraoperative near-infrared fluorescence imaging and spectroscopy identifies residual tumor cells in wounds. | Holt D, Parthasarathy AB, Okusanya O, Keating J, Venegas O, Deshpande C, Karakousis G, Madajewski B, Durham A, Nie S, Yodh AG, Singhal S | Journal of biomedical optics | 26160347 | J Biomed Opt | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/26160347 |
| Mapping the spatial distribution of charge carriers in quantum-confined heterostructures. | Smith AM, Lane LA, Nie S | Nature communications | 25080298 | Nat Commun | 2014 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/25080298 |
| Intraoperative near-infrared imaging can identify pulmonary nodules. | Okusanya OT, Holt D, Heitjan D, Deshpande C, Venegas O, Jiang J, Judy R, DeJesus E, Madajewski B, Oh K, Wang M, Albelda SM, Nie S, Singhal S | The Annals of thoracic surgery | 25106680 | Ann Thorac Surg | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25106680 |
| An integrated widefield imaging and spectroscopy system for contrast-enhanced, image-guided resection of tumors. | Mohs AM, Mancini MC, Provenzale JM, Saba CF, Cornell KK, Howerth EW, Nie S | IEEE transactions on bio-medical engineering | 25585410 | IEEE Trans Biomed Eng | 2015 May | https://www.ncbi.nlm.nih.gov/pubmed/25585410 |
| An optimized disaggregation method for human lung tumors that preserves the phenotype and function of the immune cells. | Quatromoni JG, Singhal S, Bhojnagarwala P, Hancock WW, Albelda SM, Eruslanov E | Journal of leukocyte biology | 25359999 | J Leukoc Biol | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25359999 |
| CAESNet: Convolutional AutoEncoder based Semi-supervised Network for improving multiclass classification of endomicroscopic images. | Tong L, Wu H, Wang MD | Journal of the American Medical Informatics Association : JAMIA | 31260038 | J Am Med Inform Assoc | 2019 Nov 1 | https://www.ncbi.nlm.nih.gov/pubmed/31260038 |
| Deep learning based feature-level integration of multi-omics data for breast cancer patients survival analysis. | Tong L, Mitchel J, Chatlin K, Wang MD | BMC medical informatics and decision making | 32933515 | BMC Med Inform Decis Mak | 2020 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/32933515 |
| Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer. | Tong L, Wu H, Wang MD | Methods (San Diego, Calif.) | 32763377 | Methods | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/32763377 |
| InterVisAR: An Interactive Visualization for Association Rule Search. | Cheng CW, Sha Y, Wang MD | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 32789305 | ACM BCB | 2016 Oct | https://www.ncbi.nlm.nih.gov/pubmed/32789305 |
| Intraoperative Near-infrared Imaging Can Identify Neoplasms and Aid in Real-time Margin Assessment During Pancreatic Resection. | Newton AD, Predina JD, Shin MH, Frenzel-Sulyok LG, Vollmer CM, Drebin JA, Singhal S, Lee MK 4th | Annals of surgery | 31188797 | Ann Surg | 2019 Jul | https://www.ncbi.nlm.nih.gov/pubmed/31188797 |
| Targeted Drug Delivery and Image-Guided Therapy of Heterogeneous Ovarian Cancer Using HER2-Targeted Theranostic Nanoparticles. | Satpathy M, Wang L, Zielinski RJ, Qian W, Wang YA, Mohs AM, Kairdolf BA, Ji X, Capala J, Lipowska M, Nie S, Mao H, Yang L | Theranostics | 30809308 | Theranostics | 2019 | https://www.ncbi.nlm.nih.gov/pubmed/30809308 |
| Emerging technologies and their impact on regulatory science. | Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GE, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJ, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, Eijnden-van-Raaij JVD, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker W Jr | Experimental biology and medicine (Maywood, N.J.) | 34783606 | Exp Biol Med (Maywood) | 2022 Jan | https://www.ncbi.nlm.nih.gov/pubmed/34783606 |
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| A High-Resolution Tile-Based Approach for Classifying Biological Regions in Whole-Slide Histopathological Images. | Hoffman RA, Kothari S, Phan JH, Wang MD | IFMBE proceedings | 27532012 | IFMBE Proc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/27532012 |
| Integration of multimodal RNA-seq data for prediction of kidney cancer survival. | Schwartzi M, Parkl M, Phanl JH, Wang MD | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 27532026 | Proceedings (IEEE Int Conf Bioinformatics Biomed) | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27532026 |
| Improving Personalized Clinical Risk Prediction Based on Causality-Based Association Rules. | Cheng CW, Wang MD | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 27532063 | ACM BCB | 2015 Sep | https://www.ncbi.nlm.nih.gov/pubmed/27532063 |
| Targeted delivery of siRNA-generating DNA nanocassettes using multifunctional nanoparticles. | Cho YS, Lee GY, Sajja HK, Qian W, Cao Z, He W, Karna P, Chen X, Mao H, Wang YA, Yang L | Small (Weinheim an der Bergstrasse, Germany) | 23292656 | Small | 2013 Jun 10 | https://www.ncbi.nlm.nih.gov/pubmed/23292656 |
| Integrating image analysis algorithms in a web interface for the quantification of microtubule dynamics. | Kong KY, Marcus AI, Giannakakou P, Wang MD | International journal of computational biology and drug design | 23013655 | Int J Comput Biol Drug Des | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23013655 |
| Feasibility of multiplex quantum dot stain using primary antibodies from four distinct host animals. | Tran JK, Hubbard EN, Stokes TH, Moffitt RA, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23367436 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/23367436 |
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| Near-Infrared Intraoperative Molecular Imaging Can Locate Metastases to the Lung. | Keating J, Newton A, Venegas O, Nims S, Zeh R, Predina J, Deshpande C, Kucharczuk J, Nie S, Delikatny EJ, Singhal S | The Annals of thoracic surgery | 27793401 | Ann Thorac Surg | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27793401 |
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| Removing batch effects from histopathological images for enhanced cancer diagnosis. | Kothari S, Phan JH, Stokes TH, Osunkoya AO, Young AN, Wang MD | IEEE journal of biomedical and health informatics | 24808220 | IEEE J Biomed Health Inform | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24808220 |
| Small portable interchangeable imager of fluorescence for fluorescence guided surgery and research. | Okusanya OT, Madajewski B, Segal E, Judy BF, Venegas OG, Judy RP, Quatromoni JG, Wang MD, Nie S, Singhal S | Technology in cancer research & treatment | 24354756 | Technol Cancer Res Treat | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24354756 |
| Predicting Heart Rejection Using Histopathological Whole-Slide Imaging and Deep Neural Network with Dropout. | Tong L, Hoffman R, Deshpande SR, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32601619 | IEEE EMBS Int Conf Biomed Health Inform | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/32601619 |
| Emergence of two near-infrared windows for in vivo and intraoperative SERS. | Lane LA, Xue R, Nie S | Current opinion in chemical biology | 29631122 | Curr Opin Chem Biol | 2018 Aug | https://www.ncbi.nlm.nih.gov/pubmed/29631122 |
| Local recurrence following lung cancer surgery: incidence, risk factors, and outcomes. | Fedor D, Johnson WR, Singhal S | Surgical oncology | 23702313 | Surg Oncol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23702313 |
| Eliminating tissue-fold artifacts in histopathological whole-slide images for improved image-based prediction of cancer grade. | Kothari S, Phan JH, Wang MD | Journal of pathology informatics | 24083057 | J Pathol Inform | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24083057 |
| uPAR-targeted optical imaging contrasts as theranostic agents for tumor margin detection. | Yang L, Sajja HK, Cao Z, Qian W, Bender L, Marcus AI, Lipowska M, Wood WC, Wang YA | Theranostics | 24396518 | Theranostics | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24396518 |
| Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction. | Tong L, Wu PY, Phan JH, Hassazadeh HR, SEQC Consortium, Tong W, Wang MD | Scientific reports | 33087762 | Sci Rep | 2020 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/33087762 |
| Micro-Inversions In Human Cancer Genomes. | Qu L, Zhu H, Wang M | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 30440635 | Annu Int Conf IEEE Eng Med Biol Soc | 2018 Jul | https://www.ncbi.nlm.nih.gov/pubmed/30440635 |
| A SIRT2-Selective Inhibitor Promotes c-Myc Oncoprotein Degradation and Exhibits Broad Anticancer Activity. | Jing H, Hu J, He B, Negrón Abril YL, Stupinski J, Weiser K, Carbonaro M, Chiang YL, Southard T, Giannakakou P, Weiss RS, Lin H | Cancer cell | 26977881 | Cancer Cell | 2016 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/26977881 |
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| Tumour endothelial marker 1/endosialin-mediated targeting of human sarcoma. | Guo Y, Hu J, Wang Y, Peng X, Min J, Wang J, Matthaiou E, Cheng Y, Sun K, Tong X, Fan Y, Zhang PJ, Kandalaft LE, Irving M, Coukos G, Li C | European journal of cancer (Oxford, England : 1990) | 29304474 | Eur J Cancer | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29304474 |
| A fusion-protein approach enabling mammalian cell production of tumor targeting protein domains for therapeutic development. | Hu J, Chen X, Zhang X, Yuan X, Yang M, Dai H, Yang W, Zhou Q, Wen W, Wang Q, Qin W, Zhao A | Protein science : a publication of the Protein Society | 29500915 | Protein Sci | 2018 May | https://www.ncbi.nlm.nih.gov/pubmed/29500915 |
| Mass spectrometry-based antigen discovery for cancer immunotherapy. | Bassani-Sternberg M, Coukos G | Current opinion in immunology | 27155075 | Curr Opin Immunol | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27155075 |
| Development, optimization, and validation of novel anti-TEM1/CD248 affinity agent for optical imaging in cancer. | Li C, Wang J, Hu J, Feng Y, Hasegawa K, Peng X, Duan X, Zhao A, Mikitsh JL, Muzykantov VR, Chacko AM, Pryma DA, Dunn SM, Coukos G | Oncotarget | 25051365 | Oncotarget | 2014 Aug 30 | https://www.ncbi.nlm.nih.gov/pubmed/25051365 |
| Development of 124I immuno-PET targeting tumor vascular TEM1/endosialin. | Chacko AM, Li C, Nayak M, Mikitsh JL, Hu J, Hou C, Grasso L, Nicolaides NC, Muzykantov VR, Divgi CR, Coukos G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 24525208 | J Nucl Med | 2014 Mar | https://www.ncbi.nlm.nih.gov/pubmed/24525208 |
| Deciphering and reversing tumor immune suppression. | Motz GT, Coukos G | Immunity | 23890064 | Immunity | 2013 Jul 25 | https://www.ncbi.nlm.nih.gov/pubmed/23890064 |
| T cells bearing a chimeric antigen receptor against prostate-specific membrane antigen mediate vascular disruption and result in tumor regression. | Santoro SP, Kim S, Motz GT, Alatzoglou D, Li C, Irving M, Powell DJ Jr, Coukos G | Cancer immunology research | 25358763 | Cancer Immunol Res | 2015 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25358763 |
| Interrogating open issues in cancer precision medicine with patient-derived xenografts. | Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L | Nature reviews. Cancer | 28104906 | Nat Rev Cancer | 2017 Apr | https://www.ncbi.nlm.nih.gov/pubmed/28104906 |
| Targeting the undruggable: immunotherapy meets personalized oncology in the genomic era. | Martin SD, Coukos G, Holt RA, Nelson BH | Annals of oncology : official journal of the European Society for Medical Oncology | 26371284 | Ann Oncol | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26371284 |
| T-cell and NK-cell infiltration into solid tumors: a key limiting factor for efficacious cancer immunotherapy. | Melero I, Rouzaut A, Motz GT, Coukos G | Cancer discovery | 24795012 | Cancer Discov | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24795012 |
| Combine and Conquer: Double CTLA-4 and PD-1 Blockade Combined with Whole Tumor Antigen Vaccine Cooperate to Eradicate Tumors. | Homicsko K, Duraiswamy J, Doucey MA, Coukos G | Cancer research | 27909064 | Cancer Res | 2016 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/27909064 |
| Targeting the tumor vasculature to enhance T cell activity. | Lanitis E, Irving M, Coukos G | Current opinion in immunology | 25665467 | Curr Opin Immunol | 2015 Apr | https://www.ncbi.nlm.nih.gov/pubmed/25665467 |
| Shikonin-loaded antibody-armed nanoparticles for targeted therapy of ovarian cancer. | Matthaiou EI, Barar J, Sandaltzopoulos R, Li C, Coukos G, Omidi Y | International journal of nanomedicine | 24790428 | Int J Nanomedicine | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24790428 |
| Tumor endothelium FasL establishes a selective immune barrier promoting tolerance in tumors. | Motz GT, Santoro SP, Wang LP, Garrabrant T, Lastra RR, Hagemann IS, Lal P, Feldman MD, Benencia F, Coukos G | Nature medicine | 24793239 | Nat Med | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24793239 |
| Antibody-based tumor vascular theranostics targeting endosialin/TEM1 in a new mouse tumor vascular model. | Li C, Chacko AM, Hu J, Hasegawa K, Swails J, Grasso L, El-Deiry WS, Nicolaides N, Muzykantov VR, Divgi CR, Coukos G | Cancer biology & therapy | 24553243 | Cancer Biol Ther | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24553243 |
| Correction to: Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. | Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A, Scholler N, Coukos G | Cancer immunology, immunotherapy : CII | 29313073 | Cancer Immunol Immunother | 2018 Feb | https://www.ncbi.nlm.nih.gov/pubmed/29313073 |
| Two forms of loops generate the chromatin conformation of the immunoglobulin heavy-chain gene locus. | Guo C, Gerasimova T, Hao H, Ivanova I, Chakraborty T, Selimyan R, Oltz EM, Sen R | Cell | 21982154 | Cell | 2011 Oct 14 | https://www.ncbi.nlm.nih.gov/pubmed/21982154 |
| cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent. | Huang Y, Koues OI, Zhao JY, Liu R, Pyfrom SC, Payton JE, Oltz EM | Cell reports | 28329684 | Cell Rep | 2017 Mar 21 | https://www.ncbi.nlm.nih.gov/pubmed/28329684 |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T | G3 (Bethesda, Md.) | 26888867 | G3 (Bethesda) | 2016 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/26888867 |
| BCALM (AC099524.1) Is a Human B Lymphocyte-Specific Long Noncoding RNA That Modulates B Cell Receptor-Mediated Calcium Signaling. | Pyfrom SC, Quinn CC, Dorando HK, Luo H, Payton JE | Journal of immunology (Baltimore, Md. : 1950) | 32571842 | J Immunol | 2020 Aug 1 | https://www.ncbi.nlm.nih.gov/pubmed/32571842 |
| Targeted epigenetic repression of a lymphoma oncogene by sequence-specific histone modifiers induces apoptosis in DLBCL. | Luo H, Schmidt JA, Lee YS, Oltz EM, Payton JE | Leukemia & lymphoma | 27268204 | Leuk Lymphoma | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27268204 |
| Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma. | Koues OI, Kowalewski RA, Chang LW, Pyfrom SC, Schmidt JA, Luo H, Sandoval LE, Hughes TB, Bednarski JJ, Cashen AF, Payton JE, Oltz EM | Immunity | 25607463 | Immunity | 2015 Jan 20 | https://www.ncbi.nlm.nih.gov/pubmed/25607463 |
| Short-Circuiting Gene Regulatory Networks: Origins of B Cell Lymphoma. | Koues OI, Oltz EM, Payton JE | Trends in genetics : TIG | 26604030 | Trends Genet | 2015 Dec | https://www.ncbi.nlm.nih.gov/pubmed/26604030 |
| Unifying model for molecular determinants of the preselection Vβ repertoire. | Gopalakrishnan S, Majumder K, Predeus A, Huang Y, Koues OI, Verma-Gaur J, Loguercio S, Su AI, Feeney AJ, Artyomov MN, Oltz EM | Proceedings of the National Academy of Sciences of the United States of America | 23918392 | Proc Natl Acad Sci U S A | 2013 Aug 20 | https://www.ncbi.nlm.nih.gov/pubmed/23918392 |
| Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. | Andrews JM, Pyfrom SC, Schmidt JA, Koues OI, Kowalewski RA, Grams NR, Sun JJ, Berman LR, Duncavage EJ, Lee YS, Cashen AF, Oltz EM, Payton JE | EBioMedicine | 34461601 | EBioMedicine | 2021 Sep | https://www.ncbi.nlm.nih.gov/pubmed/34461601 |
| NKG2D-NKG2D Ligand Interaction Inhibits the Outgrowth of Naturally Arising Low-Grade B Cell Lymphoma In Vivo. | Raju S, Kretzmer LZ, Koues OI, Payton JE, Oltz EM, Cashen A, Polic B, Schreiber RD, Shaw AS, Markiewicz MA | Journal of immunology (Baltimore, Md. : 1950) | 27183590 | J Immunol | 2016 Jun 1 | https://www.ncbi.nlm.nih.gov/pubmed/27183590 |
| Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci. | Predeus AV, Gopalakrishnan S, Huang Y, Tang J, Feeney AJ, Oltz EM, Artyomov MN | Journal of immunology (Baltimore, Md. : 1950) | 24353267 | J Immunol | 2014 Feb 1 | https://www.ncbi.nlm.nih.gov/pubmed/24353267 |
| PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities. | Pyfrom SC, Luo H, Payton JE | BMC genomics | 30767760 | BMC Genomics | 2019 Feb 15 | https://www.ncbi.nlm.nih.gov/pubmed/30767760 |
| Humanized hemato-lymphoid system mice. | Theocharides AP, Rongvaux A, Fritsch K, Flavell RA, Manz MG | Haematologica | 26721800 | Haematologica | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26721800 |
| Clonal Immunoglobulin against Lysolipids in the Origin of Myeloma. | Nair S, Branagan AR, Liu J, Boddupalli CS, Mistry PK, Dhodapkar MV | The New England journal of medicine | 26863356 | N Engl J Med | 2016 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/26863356 |
| Peripheral blood CD34(+) cells efficiently engraft human cytokine knock-in mice. | Saito Y, Ellegast JM, Rafiei A, Song Y, Kull D, Heikenwalder M, Rongvaux A, Halene S, Flavell RA, Manz MG | Blood | 27543436 | Blood | 2016 Oct 6 | https://www.ncbi.nlm.nih.gov/pubmed/27543436 |
| Nanoparticle-mediated combinatorial targeting of multiple human dendritic cell (DC) subsets leads to enhanced T cell activation via IL-15-dependent DC crosstalk. | Sehgal K, Ragheb R, Fahmy TM, Dhodapkar MV, Dhodapkar KM | Journal of immunology (Baltimore, Md. : 1950) | 25080481 | J Immunol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25080481 |
| Type II NKT-TFH cells against Gaucher lipids regulate B-cell immunity and inflammation. | Nair S, Boddupalli CS, Verma R, Liu J, Yang R, Pastores GM, Mistry PK, Dhodapkar MV | Blood | 25499455 | Blood | 2015 Feb 19 | https://www.ncbi.nlm.nih.gov/pubmed/25499455 |
| A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies. | Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S | Nature communications | 30664659 | Nat Commun | 2019 Jan 21 | https://www.ncbi.nlm.nih.gov/pubmed/30664659 |
| inv(16) and NPM1mut AMLs engraft human cytokine knock-in mice. | Ellegast JM, Rauch PJ, Kovtonyuk LV, Müller R, Wagner U, Saito Y, Wildner-Verhey van Wijk N, Fritz C, Rafiei A, Lysenko V, Dudkiewicz E, Theocharides AP, Soldini D, Goede JS, Flavell RA, Manz MG | Blood | 27581357 | Blood | 2016 Oct 27 | https://www.ncbi.nlm.nih.gov/pubmed/27581357 |
| Development and function of human innate immune cells in a humanized mouse model. | Rongvaux A, Willinger T, Martinek J, Strowig T, Gearty SV, Teichmann LL, Saito Y, Marches F, Halene S, Palucka AK, Manz MG, Flavell RA | Nature biotechnology | 24633240 | Nat Biotechnol | 2014 Apr | https://www.ncbi.nlm.nih.gov/pubmed/24633240 |
| BRAFV 600E or mutant MAP2K1 human CD34+ cells establish Langerhans cell-like histiocytosis in immune-deficient mice. | Rafiei A, Wilk CM, Helbling PM, Myburgh R, Saito Y, Haralambieva E, Soldini D, Chakraborty R, Merad M, Allen CE, Nombela-Arrieta C, Manz MG | Blood advances | 33035332 | Blood Adv | 2020 Oct 13 | https://www.ncbi.nlm.nih.gov/pubmed/33035332 |
| Microenvironment-dependent growth of preneoplastic and malignant plasma cells in humanized mice. | Das R, Strowig T, Verma R, Koduru S, Hafemann A, Hopf S, Kocoglu MH, Borsotti C, Zhang L, Branagan A, Eynon E, Manz MG, Flavell RA, Dhodapkar MV | Nature medicine | 27723723 | Nat Med | 2016 Nov | https://www.ncbi.nlm.nih.gov/pubmed/27723723 |
| Human hemato-lymphoid system mice: current use and future potential for medicine. | Rongvaux A, Takizawa H, Strowig T, Willinger T, Eynon EE, Flavell RA, Manz MG | Annual review of immunology | 23330956 | Annu Rev Immunol | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/23330956 |
| Targeting human dendritic cells in situ to improve vaccines. | Sehgal K, Dhodapkar KM, Dhodapkar MV | Immunology letters | 25072116 | Immunol Lett | 2014 Nov | https://www.ncbi.nlm.nih.gov/pubmed/25072116 |
| A novel humanized mouse model with significant improvement of class-switched, antigen-specific antibody production. | Yu H, Borsotti C, Schickel JN, Zhu S, Strowig T, Eynon EE, Frleta D, Gurer C, Murphy AJ, Yancopoulos GD, Meffre E, Manz MG, Flavell RA | Blood | 28077418 | Blood | 2017 Feb 23 | https://www.ncbi.nlm.nih.gov/pubmed/28077418 |
| Using a Culturally Tailored Narrative to Increase Cervical Cancer Detection Among Spanish-Speaking Mexican-American Women. | Ochoa CY, Murphy ST, Frank LB, Baezconde-Garbanati LA | Journal of cancer education : the official journal of the American Association for Cancer Education | 31020621 | J Cancer Educ | 2020 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31020621 |
| Implementation of HPV vaccination guidelines in a diverse population in Los Angeles: Results from an environmental scan of local HPV resources and needs. | Baezconde-Garbanati L, Lienemann BA, Robles M, Johnson E, Sanchez K, Singhal R, Steinberg J, Jaque JM, Pentz MA, Gruber S | Vaccine | 28774559 | Vaccine | 2017 Sep 5 | https://www.ncbi.nlm.nih.gov/pubmed/28774559 |
| Public Diplomacy in Prime Time: Exploring the Potential of Entertainment Education in International Public Diplomacy. | Murphy ST, Hether HJ, Felt LJ, de Castro Buffington S | American journal of media psychology | 24489980 | Am J Media Psychol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/24489980 |
| Telling stories, saving lives: creating narrative health messages. | Frank LB, Murphy ST, Chatterjee JS, Moran MB, Baezconde-Garbanati L | Health communication | 25470440 | Health Commun | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/25470440 |
| Each Medium Tells a Different Story: The Effect of Message Channel on Narrative Persuasion. | Walter N, Murphy ST, Frank LB, Baezconde-Garbanati L | Communication research reports : CRR | 30739986 | Commun Res Rep | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/30739986 |
| Narrative versus Non-narrative: The Role of Identification, Transportation and Emotion in Reducing Health Disparities. | Murphy ST, Frank LB, Chatterjee JS, Baezconde-Garbanati L | The Journal of communication | 24347679 | J Commun | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24347679 |
| A pilot test of the acceptability and efficacy of narrative and non-narrative health education materials in a low health literacy population. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Journal of communication in healthcare | 27872657 | J Commun Healthc | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27872657 |
| Self-Construal as a Predictor of Korean American Women's Intention to Vaccinate Daughters against Human Papillomavirus. | Zhao N, Huh J, Murphy ST, Chatterjee JS, Baezconde-Garbanati L | Asian American journal of psychology | 25558309 | Asian Am J Psychol | 2014 Jan | https://www.ncbi.nlm.nih.gov/pubmed/25558309 |
| Reducing the Excess Burden of Cervical Cancer Among Latinas: Translating Science into Health Promotion Initiatives. | Baezconde-Garbanati L, Murphy ST, Moran MB, Cortessis VK | Californian journal of health promotion | 24587769 | Calif J Health Promot | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24587769 |
| Information scanning and vaccine safety concerns among African American, Mexican American, and non-Hispanic White women. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Patient education and counseling | 26321294 | Patient Educ Couns | 2016 Jan | https://www.ncbi.nlm.nih.gov/pubmed/26321294 |
| Portrayals of reproductive and sexual health on prime-time television. | Pariera KL, Hether HJ, Murphy ST, Buffington Sde C, Baezconde-Garbanati L | Health communication | 24156468 | Health Commun | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24156468 |
| The Ability of Narrative Communication to Address Health-related Social Norms. | Moran MB, Murphy ST, Frank L, Baezconde-Garbanati L | International Review of Social Research | 24179677 | Int Rev Soc Res | 2013 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24179677 |
| Comparing the Relative Efficacy of Narrative vs Nonnarrative Health Messages in Reducing Health Disparities Using a Randomized Trial. | Murphy ST, Frank LB, Chatterjee JS, Moran MB, Zhao N, Amezola de Herrera P, Baezconde-Garbanati LA | American journal of public health | 25905845 | Am J Public Health | 2015 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25905845 |
| Barriers and innovative interventions for early detection of cervical cancer. | Baezconde-Garbanati L, Agurto I, Gravitt PE, Luciani S, Murphy S, Ochoa C, Gallegos K, Barahona R, Rodríguez Y | Salud publica de Mexico | 31430087 | Salud Publica Mex | 2019 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/31430087 |
| Assessing impact of a community-based screening campaign to address social determinants of cervical cancer. | Po J, Bookstein A, Lee W, Barahona R, Baezconde-Garbanati L | JNCI cancer spectrum | 39888858 | JNCI Cancer Spectr | 2025 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/39888858 |
| Expression of human endogenous retrovirus type K (HML-2) is activated by the Tat protein of HIV-1. | Gonzalez-Hernandez MJ, Swanson MD, Contreras-Galindo R, Cookinham S, King SR, Noel RJ Jr, Kaplan MH, Markovitz DM | Journal of virology | 22593154 | J Virol | 2012 Aug | https://www.ncbi.nlm.nih.gov/pubmed/22593154 |
| The strategy, organization, and progress of the HUPO Human Proteome Project. | Omenn GS | Journal of proteomics | 24145142 | J Proteomics | 2014 Apr 4 | https://www.ncbi.nlm.nih.gov/pubmed/24145142 |
| Susceptibility of Human Endogenous Retrovirus Type K to Reverse Transcriptase Inhibitors. | Contreras-Galindo R, Dube D, Fujinaga K, Kaplan MH, Markovitz DM | Journal of virology | 28931682 | J Virol | 2017 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/28931682 |
| "Reverse genomics" and human endogenous retroviruses. | Markovitz DM | Transactions of the American Clinical and Climatological Association | 25125718 | Trans Am Clin Climatol Assoc | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25125718 |
| Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans. | Zahn J, Kaplan MH, Fischer S, Dai M, Meng F, Saha AK, Cervantes P, Chan SM, Dube D, Omenn GS, Markovitz DM, Contreras-Galindo R | Genome biology | 25886262 | Genome Biol | 2015 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/25886262 |
| Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. | Contreras-Galindo R, Kaplan MH, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Ferlenghi I, Giusti F, Lorenzo E, Gitlin SD, Dosik MH, Yamamura Y, Markovitz DM | Journal of virology | 22031938 | J Virol | 2012 Jan | https://www.ncbi.nlm.nih.gov/pubmed/22031938 |
| NGSQC: cross-platform quality analysis pipeline for deep sequencing data. | Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F | BMC genomics | 21143816 | BMC Genomics | 2010 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/21143816 |
| Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. | Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM | Nature chemical biology | 21706033 | Nat Chem Biol | 2011 Jun 26 | https://www.ncbi.nlm.nih.gov/pubmed/21706033 |
| Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. | Omenn GS, Menon R, Zhang Y | Journal of proteomics | 23603631 | J Proteomics | 2013 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/23603631 |
| HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. | Contreras-Galindo R, Kaplan MH, He S, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Kappes F, Dube D, Chan SM, Robinson D, Meng F, Dai M, Gitlin SD, Chinnaiyan AM, Omenn GS, Markovitz DM | Genome research | 23657884 | Genome Res | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23657884 |
| Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. | Monde K, Contreras-Galindo R, Kaplan MH, Markovitz DM, Ono A | Journal of virology | 22855497 | J Virol | 2012 Oct | https://www.ncbi.nlm.nih.gov/pubmed/22855497 |
| Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. | Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM | Journal of virology | 24872592 | J Virol | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24872592 |
| A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. | Omenn GS, Guan Y, Menon R | Journal of proteomics | 24802673 | J Proteomics | 2014 Jul 31 | https://www.ncbi.nlm.nih.gov/pubmed/24802673 |
| Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity. | Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM | Cell | 26496612 | Cell | 2015 Oct 22 | https://www.ncbi.nlm.nih.gov/pubmed/26496612 |
| Strategies for Genomic and Proteomic Profiling of Cancers. | Omenn GS | Statistics in biosciences | 27594925 | Stat Biosci | 2016 Jun | https://www.ncbi.nlm.nih.gov/pubmed/27594925 |
| Genomic flexibility of human endogenous retrovirus type K. | Dube D, Contreras-Galindo R, He S, King SR, Gonzalez-Hernandez MJ, Gitlin SD, Kaplan MH, Markovitz DM | Journal of virology | 24920813 | J Virol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/24920813 |
| Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. | Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS | Journal of proteome research | 24364385 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24364385 |
| Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. | Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS | Journal of proteome research | 24111759 | J Proteome Res | 2014 Jan 3 | https://www.ncbi.nlm.nih.gov/pubmed/24111759 |
| Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. | Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM | Journal of virology | 25926654 | J Virol | 2015 Jul | https://www.ncbi.nlm.nih.gov/pubmed/25926654 |
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| Gun violence incidence during the COVID-19 pandemic is higher than before the pandemic in the United States. | Ssentongo P, Fronterre C, Ssentongo AE, Advani S, Heilbrunn ES, Hazelton JP, Oh JS, McCall-Hosenfeld JS, Chinchilli VM | Scientific reports | 34675321 | Sci Rep | 2021 Oct 21 | https://www.ncbi.nlm.nih.gov/pubmed/34675321 |
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| Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. | Hehnly C, Shi A, Ssentongo P, Zhang L, Isaacs A, Morton SU, Streck N, Erdmann-Gilmore P, Tolstoy I, Townsend RR, Limbrick DD, Paulson JN, Ericson JE, Galperin MY, Schiff SJ, Broach JR | mBio | 36374038 | mBio | 2022 Dec 20 | https://www.ncbi.nlm.nih.gov/pubmed/36374038 |
| mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. | Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN | BMC genomics | 35698050 | BMC Genomics | 2022 Jun 13 | https://www.ncbi.nlm.nih.gov/pubmed/35698050 |
| Identification of White Matter Hyperintensities in Routine Emergency Department Visits Using Portable Bedside Magnetic Resonance Imaging. | de Havenon A, Parasuram NR, Crawford AL, Mazurek MH, Chavva IR, Yadlapalli V, Iglesias JE, Rosen MS, Falcone GJ, Payabvash S, Sze G, Sharma R, Schiff SJ, Safdar B, Wira C, Kimberly WT, Sheth KN | Journal of the American Heart Association | 37218590 | J Am Heart Assoc | 2023 Jun 6 | https://www.ncbi.nlm.nih.gov/pubmed/37218590 |
| Brain growth after surgical treatment for infant postinfectious hydrocephalus in Sub-Saharan Africa: 2-year results of a randomized trial. | Schiff SJ, Kulkarni AV, Mbabazi-Kabachelor E, Mugamba J, Ssenyonga P, Donnelly R, Levenbach J, Monga V, Peterson M, Cherukuri V, Warf BC | Journal of neurosurgery. Pediatrics | 34243157 | J Neurosurg Pediatr | 2021 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/34243157 |
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| A Bcl6 Intronic Element Regulates T Follicular Helper Cell Differentiation. | Lai CY, Marcel N, Yaldiko AW, Delpoux A, Hedrick SM | Journal of immunology (Baltimore, Md. : 1950) | 35948398 | J Immunol | 2022 Sep 15 | https://www.ncbi.nlm.nih.gov/pubmed/35948398 |
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| Caspase-8 restricts natural killer cell accumulation during MCMV Infection. | Feng Y, Daley-Bauer LP, Roback L, Potempa M, Lanier LL, Mocarski ES | Medical microbiology and immunology | 31115653 | Med Microbiol Immunol | 2019 Aug | https://www.ncbi.nlm.nih.gov/pubmed/31115653 |
| Retinoic Acid Inducible Gene 1 Protein (RIG1)-Like Receptor Pathway Is Required for Efficient Nuclear Reprogramming. | Sayed N, Ospino F, Himmati F, Lee J, Chanda P, Mocarski ES, Cooke JP | Stem cells (Dayton, Ohio) | 28276156 | Stem Cells | 2017 May | https://www.ncbi.nlm.nih.gov/pubmed/28276156 |
| Caspase-8 modulates dectin-1 and complement receptor 3-driven IL-1β production in response to β-glucans and the fungal pathogen, Candida albicans. | Ganesan S, Rathinam VAK, Bossaller L, Army K, Kaiser WJ, Mocarski ES, Dillon CP, Green DR, Mayadas TN, Levitz SM, Hise AG, Silverman N, Fitzgerald KA | Journal of immunology (Baltimore, Md. : 1950) | 25063877 | J Immunol | 2014 Sep 1 | https://www.ncbi.nlm.nih.gov/pubmed/25063877 |
| TNFR1-dependent cell death drives inflammation in Sharpin-deficient mice. | Rickard JA, Anderton H, Etemadi N, Nachbur U, Darding M, Peltzer N, Lalaoui N, Lawlor KE, Vanyai H, Hall C, Bankovacki A, Gangoda L, Wong WW, Corbin J, Huang C, Mocarski ES, Murphy JM, Alexander WS, Voss AK, Vaux DL, Kaiser WJ, Walczak H, Silke J | eLife | 25443632 | Elife | 2014 Dec 2 | https://www.ncbi.nlm.nih.gov/pubmed/25443632 |
| Remarkably Robust Antiviral Immune Response despite Combined Deficiency in Caspase-8 and RIPK3. | Feng Y, Livingston-Rosanoff D, Roback L, Sundararajan A, Speck SH, Mocarski ES, Daley-Bauer LP | Journal of immunology (Baltimore, Md. : 1950) | 30194111 | J Immunol | 2018 Oct 15 | https://www.ncbi.nlm.nih.gov/pubmed/30194111 |
| Caspase-8 Collaborates with Caspase-11 to Drive Tissue Damage and Execution of Endotoxic Shock. | Mandal P, Feng Y, Lyons JD, Berger SB, Otani S, DeLaney A, Tharp GK, Maner-Smith K, Burd EM, Schaeffer M, Hoffman S, Capriotti C, Roback L, Young CB, Liang Z, Ortlund EA, DiPaolo NC, Bosinger S, Bertin J, Gough PJ, Brodsky IE, Coopersmith CM, Shayakhmetov DM, Mocarski ES | Immunity | 30021146 | Immunity | 2018 Jul 17 | https://www.ncbi.nlm.nih.gov/pubmed/30021146 |
| Herpes simplex virus 1 ICP6 impedes TNF receptor 1-induced necrosome assembly during compartmentalization to detergent-resistant membrane vesicles. | Ali M, Roback L, Mocarski ES | The Journal of biological chemistry | 30504227 | J Biol Chem | 2019 Jan 18 | https://www.ncbi.nlm.nih.gov/pubmed/30504227 |
| T cell-intrinsic ASC critically promotes T(H)17-mediated experimental autoimmune encephalomyelitis. | Martin BN, Wang C, Zhang CJ, Kang Z, Gulen MF, Zepp JA, Zhao J, Bian G, Do JS, Min B, Pavicic PG Jr, El-Sanadi C, Fox PL, Akitsu A, Iwakura Y, Sarkar A, Wewers MD, Kaiser WJ, Mocarski ES, Rothenberg ME, Hise AG, Dubyak GR, Ransohoff RM, Li X | Nature immunology | 26998763 | Nat Immunol | 2016 May | https://www.ncbi.nlm.nih.gov/pubmed/26998763 |
| Herpes simplex virus suppresses necroptosis in human cells. | Guo H, Omoto S, Harris PA, Finger JN, Bertin J, Gough PJ, Kaiser WJ, Mocarski ES | Cell host & microbe | 25674983 | Cell Host Microbe | 2015 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/25674983 |
| Caspase-8 and RIP kinases regulate bacteria-induced innate immune responses and cell death. | Weng D, Marty-Roix R, Ganesan S, Proulx MK, Vladimer GI, Kaiser WJ, Mocarski ES, Pouliot K, Chan FK, Kelliher MA, Harris PA, Bertin J, Gough PJ, Shayakhmetov DM, Goguen JD, Fitzgerald KA, Silverman N, Lien E | Proceedings of the National Academy of Sciences of the United States of America | 24799678 | Proc Natl Acad Sci U S A | 2014 May 20 | https://www.ncbi.nlm.nih.gov/pubmed/24799678 |
| RIP1 suppresses innate immune necrotic as well as apoptotic cell death during mammalian parturition. | Kaiser WJ, Daley-Bauer LP, Thapa RJ, Mandal P, Berger SB, Huang C, Sundararajan A, Guo H, Roback L, Speck SH, Bertin J, Gough PJ, Balachandran S, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 24821786 | Proc Natl Acad Sci U S A | 2014 May 27 | https://www.ncbi.nlm.nih.gov/pubmed/24821786 |
| Cutting Edge: RIP1 kinase activity is dispensable for normal development but is a key regulator of inflammation in SHARPIN-deficient mice. | Berger SB, Kasparcova V, Hoffman S, Swift B, Dare L, Schaeffer M, Capriotti C, Cook M, Finger J, Hughes-Earle A, Harris PA, Kaiser WJ, Mocarski ES, Bertin J, Gough PJ | Journal of immunology (Baltimore, Md. : 1950) | 24821972 | J Immunol | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24821972 |
| Manipulation of apoptosis and necroptosis signaling by herpesviruses. | Guo H, Kaiser WJ, Mocarski ES | Medical microbiology and immunology | 25828583 | Med Microbiol Immunol | 2015 Jun | https://www.ncbi.nlm.nih.gov/pubmed/25828583 |
| RIPK3 Activates Parallel Pathways of MLKL-Driven Necroptosis and FADD-Mediated Apoptosis to Protect against Influenza A Virus. | Nogusa S, Thapa RJ, Dillon CP, Liedmann S, Oguin TH 3rd, Ingram JP, Rodriguez DA, Kosoff R, Sharma S, Sturm O, Verbist K, Gough PJ, Bertin J, Hartmann BM, Sealfon SC, Kaiser WJ, Mocarski ES, López CB, Thomas PG, Oberst A, Green DR, Balachandran S | Cell host & microbe | 27321907 | Cell Host Microbe | 2016 Jul 13 | https://www.ncbi.nlm.nih.gov/pubmed/27321907 |
| Caspase-8 as an Effector and Regulator of NLRP3 Inflammasome Signaling. | Antonopoulos C, Russo HM, El Sanadi C, Martin BN, Li X, Kaiser WJ, Mocarski ES, Dubyak GR | The Journal of biological chemistry | 26100631 | J Biol Chem | 2015 Aug 14 | https://www.ncbi.nlm.nih.gov/pubmed/26100631 |
| Suppression of RIP3-dependent necroptosis by human cytomegalovirus. | Omoto S, Guo H, Talekar GR, Roback L, Kaiser WJ, Mocarski ES | The Journal of biological chemistry | 25778401 | J Biol Chem | 2015 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/25778401 |
| RIP3 induces apoptosis independent of pronecrotic kinase activity. | Mandal P, Berger SB, Pillay S, Moriwaki K, Huang C, Guo H, Lich JD, Finger J, Kasparcova V, Votta B, Ouellette M, King BW, Wisnoski D, Lakdawala AS, DeMartino MP, Casillas LN, Haile PA, Sehon CA, Marquis RW, Upton J, Daley-Bauer LP, Roback L, Ramia N, Dovey CM, Carette JE, Chan FK, Bertin J, Gough PJ, Mocarski ES, Kaiser WJ | Molecular cell | 25459880 | Mol Cell | 2014 Nov 20 | https://www.ncbi.nlm.nih.gov/pubmed/25459880 |
| Mouse cytomegalovirus M36 and M45 death suppressors cooperate to prevent inflammation resulting from antiviral programmed cell death pathways. | Daley-Bauer LP, Roback L, Crosby LN, McCormick AL, Feng Y, Kaiser WJ, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 28292903 | Proc Natl Acad Sci U S A | 2017 Mar 28 | https://www.ncbi.nlm.nih.gov/pubmed/28292903 |
| Proteasome inhibition blocks necroptosis by attenuating death complex aggregation. | Ali M, Mocarski ES | Cell death & disease | 29497034 | Cell Death Dis | 2018 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/29497034 |
| Species-independent contribution of ZBP1/DAI/DLM-1-triggered necroptosis in host defense against HSV1. | Guo H, Gilley RP, Fisher A, Lane R, Landsteiner VJ, Ragan KB, Dovey CM, Carette JE, Upton JW, Mocarski ES, Kaiser WJ | Cell death & disease | 30050136 | Cell Death Dis | 2018 Jul 26 | https://www.ncbi.nlm.nih.gov/pubmed/30050136 |
| Inhibition of DAI-dependent necroptosis by the Z-DNA binding domain of the vaccinia virus innate immune evasion protein, E3. | Koehler H, Cotsmire S, Langland J, Kibler KV, Kalman D, Upton JW, Mocarski ES, Jacobs BL | Proceedings of the National Academy of Sciences of the United States of America | 29073079 | Proc Natl Acad Sci U S A | 2017 Oct 24 | https://www.ncbi.nlm.nih.gov/pubmed/29073079 |
| Caspase-8 restricts antiviral CD8 T cell hyperaccumulation. | Feng Y, Daley-Bauer LP, Roback L, Guo H, Koehler HS, Potempa M, Lanier LL, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 31285326 | Proc Natl Acad Sci U S A | 2019 Jul 23 | https://www.ncbi.nlm.nih.gov/pubmed/31285326 |
| Subpopulations of myeloid-derived suppressor cells impair T cell responses through independent nitric oxide-related pathways. | Raber PL, Thevenot P, Sierra R, Wyczechowska D, Halle D, Ramirez ME, Ochoa AC, Fletcher M, Velasco C, Wilk A, Reiss K, Rodriguez PC | International journal of cancer | 24259296 | Int J Cancer | 2014 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/24259296 |
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| Inhibition of Fatty Acid Oxidation Modulates Immunosuppressive Functions of Myeloid-Derived Suppressor Cells and Enhances Cancer Therapies. | Hossain F, Al-Khami AA, Wyczechowska D, Hernandez C, Zheng L, Reiss K, Valle LD, Trillo-Tinoco J, Maj T, Zou W, Rodriguez PC, Ochoa AC | Cancer immunology research | 26025381 | Cancer Immunol Res | 2015 Nov | https://www.ncbi.nlm.nih.gov/pubmed/26025381 |
| Fuelling the mechanisms of asthma: Increased fatty acid oxidation in inflammatory immune cells may represent a novel therapeutic target. | Al-Khami AA, Ghonim MA, Del Valle L, Ibba SV, Zheng L, Pyakurel K, Okpechi SC, Garay J, Wyczechowska D, Sanchez-Pino MD, Rodriguez PC, Boulares AH, Ochoa AC | Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology | 28456994 | Clin Exp Allergy | 2017 Sep | https://www.ncbi.nlm.nih.gov/pubmed/28456994 |
| Development and evaluation of SYBR Green-I based quantitative PCR assays for herpes simplex virus type 1 whole transcriptome analysis. | Garvey CE, McGowin CL, Foster TP | Journal of virological methods | 24607486 | J Virol Methods | 2014 Jun | https://www.ncbi.nlm.nih.gov/pubmed/24607486 |
| Expression of arginase I in myeloid cells limits control of residual disease after radiation therapy of tumors in mice. | Crittenden MR, Savage T, Cottam B, Baird J, Rodriguez PC, Newell P, Young K, Jackson AM, Gough MJ | Radiation research | 24992164 | Radiat Res | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24992164 |
| Arginase I levels are decreased in the plasma of pediatric patients with atopic dermatitis. | Dimitriades V, Rodriguez PC, Zabaleta J, Ochoa AC | Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology | 25027824 | Ann Allergy Asthma Immunol | 2014 Sep | https://www.ncbi.nlm.nih.gov/pubmed/25027824 |
| l-Arginine depletion blunts antitumor T-cell responses by inducing myeloid-derived suppressor cells. | Fletcher M, Ramirez ME, Sierra RA, Raber P, Thevenot P, Al-Khami AA, Sanchez-Pino D, Hernandez C, Wyczechowska DD, Ochoa AC, Rodriguez PC | Cancer research | 25406192 | Cancer Res | 2015 Jan 15 | https://www.ncbi.nlm.nih.gov/pubmed/25406192 |
| Design, validation and evaluation of a SYBR green-based quantitative PCR array for comprehensive analysis of adenovirus type 5 transcriptional patterns. | Nebeluk N, Foster TP | Journal of virological methods | 32413477 | J Virol Methods | 2020 Jul | https://www.ncbi.nlm.nih.gov/pubmed/32413477 |
| Metabolic reprogramming of myeloid-derived suppressor cells (MDSC) in cancer. | Al-Khami AA, Rodriguez PC, Ochoa AC | Oncoimmunology | 27622069 | Oncoimmunology | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27622069 |
| Arginine Metabolism in Myeloid Cells Shapes Innate and Adaptive Immunity. | Rodriguez PC, Ochoa AC, Al-Khami AA | Frontiers in immunology | 28223985 | Front Immunol | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/28223985 |
| Molecular and Structural Traits of Insulin Receptor Substrate 1/LC3 Nuclear Structures and Their Role in Autophagy Control and Tumor Cell Survival. | Lassak A, Dean M, Wyczechowska D, Wilk A, Marrero L, Trillo-Tinoco J, Boulares AH, Sarkaria JN, Del Valle L, Peruzzi F, Ochoa A, Reiss K | Molecular and cellular biology | 29483302 | Mol Cell Biol | 2018 May 15 | https://www.ncbi.nlm.nih.gov/pubmed/29483302 |
| Exogenous lipid uptake induces metabolic and functional reprogramming of tumor-associated myeloid-derived suppressor cells. | Al-Khami AA, Zheng L, Del Valle L, Hossain F, Wyczechowska D, Zabaleta J, Sanchez MD, Dean MJ, Rodriguez PC, Ochoa AC | Oncoimmunology | 29123954 | Oncoimmunology | 2017 | https://www.ncbi.nlm.nih.gov/pubmed/29123954 |
| The antimicrobial agent C31G is effective for therapy for HSV-1 ocular keratitis in the rabbit eye model. | Hill JM, Stern EM, Bhattacharjee PS, Malamud D, Clement C, Rodriguez P, Lukiw WJ, Ochoa AC, Foster TP, Velasco C, McFerrin HE Jr | Antiviral research | 23860013 | Antiviral Res | 2013 Oct | https://www.ncbi.nlm.nih.gov/pubmed/23860013 |
| Rescue of notch-1 signaling in antigen-specific CD8+ T cells overcomes tumor-induced T-cell suppression and enhances immunotherapy in cancer. | Sierra RA, Thevenot P, Raber PL, Cui Y, Parsons C, Ochoa AC, Trillo-Tinoco J, Del Valle L, Rodriguez PC | Cancer immunology research | 24830414 | Cancer Immunol Res | 2014 Aug | https://www.ncbi.nlm.nih.gov/pubmed/24830414 |
| Herpes Simplex Virus-1 Induced Serotonin-Associated Metabolic Pathways Correlate With Severity of Virus- and Inflammation-Associated Ocular Disease. | Battaglia DM, Sanchez-Pino MD, Nichols CD, Foster TP | Frontiers in microbiology | 35391733 | Front Microbiol | 2022 | https://www.ncbi.nlm.nih.gov/pubmed/35391733 |
| Antibiotics and the gut microbiota. | Modi SR, Collins JJ, Relman DA | The Journal of clinical investigation | 25271726 | J Clin Invest | 2014 Oct | https://www.ncbi.nlm.nih.gov/pubmed/25271726 |
| Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. | Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP | F1000Research | 27508062 | F1000Res | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/27508062 |
| Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. | Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ | Microbiome | 30558668 | Microbiome | 2018 Dec 17 | https://www.ncbi.nlm.nih.gov/pubmed/30558668 |
| Ten quick tips for effective dimensionality reduction. | Nguyen LH, Holmes S | PLoS computational biology | 31220072 | PLoS Comput Biol | 2019 Jun | https://www.ncbi.nlm.nih.gov/pubmed/31220072 |
| Interactive Visualization of Hierarchically Structured Data. | Sankaran K, Holmes S | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 30416327 | J Comput Graph Stat | 2018 | https://www.ncbi.nlm.nih.gov/pubmed/30416327 |
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| Measuring multivariate association and beyond. | Josse J, Holmes S | Statistics surveys | 29081877 | Stat Surv | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/29081877 |
| Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. | Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman DA, Holmes SP | PLoS computational biology | 28821012 | PLoS Comput Biol | 2017 Aug | https://www.ncbi.nlm.nih.gov/pubmed/28821012 |
| Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. | Gorvitovskaia A, Holmes SP, Huse SM | Microbiome | 27068581 | Microbiome | 2016 Apr 12 | https://www.ncbi.nlm.nih.gov/pubmed/27068581 |
| DADA2: High-resolution sample inference from Illumina amplicon data. | Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP | Nature methods | 27214047 | Nat Methods | 2016 Jul | https://www.ncbi.nlm.nih.gov/pubmed/27214047 |
| Unrest at home: diarrheal disease and microbiota disturbance. | Bik EM, Relman DA | Genome biology | 25002208 | Genome Biol | 2014 Jun 27 | https://www.ncbi.nlm.nih.gov/pubmed/25002208 |
| REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA. | Callahan B, Proctor D, Relman D, Fukuyama J, Holmes S | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 26776185 | Pac Symp Biocomput | 2016 | https://www.ncbi.nlm.nih.gov/pubmed/26776185 |
| Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. | Yaffe E, Relman DA | Nature microbiology | 31873203 | Nat Microbiol | 2020 Feb | https://www.ncbi.nlm.nih.gov/pubmed/31873203 |
| A Statistical Perspective on the Challenges in Molecular Microbial Biology. | Jeganathan P, Holmes SP | Journal of agricultural, biological, and environmental statistics | 36398283 | J Agric Biol Environ Stat | 2021 Jun | https://www.ncbi.nlm.nih.gov/pubmed/36398283 |
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| Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. | Gavrish E, Sit CS, Cao S, Kandror O, Spoering A, Peoples A, Ling L, Fetterman A, Hughes D, Bissell A, Torrey H, Akopian T, Mueller A, Epstein S, Goldberg A, Clardy J, Lewis K | Chemistry & biology | 24684906 | Chem Biol | 2014 Apr 24 | https://www.ncbi.nlm.nih.gov/pubmed/24684906 |
| A screen for and validation of prodrug antimicrobials. | Fleck LE, North EJ, Lee RE, Mulcahy LR, Casadei G, Lewis K | Antimicrobial agents and chemotherapy | 24342644 | Antimicrob Agents Chemother | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/24342644 |
| Persister-promoting bacterial toxin TisB produces anion-selective pores in planar lipid bilayers. | Gurnev PA, Ortenberg R, Dörr T, Lewis K, Bezrukov SM | FEBS letters | 22728134 | FEBS Lett | 2012 Jul 30 | https://www.ncbi.nlm.nih.gov/pubmed/22728134 |
| HipBA-promoter structures reveal the basis of heritable multidrug tolerance. | Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulić M, Lewis K, Brennan RG | Nature | 26222023 | Nature | 2015 Aug 6 | https://www.ncbi.nlm.nih.gov/pubmed/26222023 |
| A new antibiotic kills pathogens without detectable resistance. | Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K | Nature | 25561178 | Nature | 2015 Jan 22 | https://www.ncbi.nlm.nih.gov/pubmed/25561178 |
| Activated ClpP kills persisters and eradicates a chronic biofilm infection. | Conlon BP, Nakayasu ES, Fleck LE, LaFleur MD, Isabella VM, Coleman K, Leonard SN, Smith RD, Adkins JN, Lewis K | Nature | 24226776 | Nature | 2013 Nov 21 | https://www.ncbi.nlm.nih.gov/pubmed/24226776 |
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| Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis. | Hansen S, Vulić M, Min J, Yen TJ, Schumacher MA, Brennan RG, Lewis K | PloS one | 22720069 | PLoS One | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22720069 |
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| Genetic basis of persister tolerance to aminoglycosides in Escherichia coli. | Shan Y, Lazinski D, Rowe S, Camilli A, Lewis K | mBio | 25852159 | mBio | 2015 Apr 7 | https://www.ncbi.nlm.nih.gov/pubmed/25852159 |
| Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. | Mulcahy LR, Burns JL, Lory S, Lewis K | Journal of bacteriology | 20935098 | J Bacteriol | 2010 Dec | https://www.ncbi.nlm.nih.gov/pubmed/20935098 |
| Staphylococcus aureus persisters tolerant to bactericidal antibiotics. | Lechner S, Lewis K, Bertram R | Journal of molecular microbiology and biotechnology | 22986269 | J Mol Microbiol Biotechnol | 2012 | https://www.ncbi.nlm.nih.gov/pubmed/22986269 |
| Potentiation of azole antifungals by 2-adamantanamine. | Lafleur MD, Sun L, Lister I, Keating J, Nantel A, Long L, Ghannoum M, North J, Lee RE, Coleman K, Dahl T, Lewis K | Antimicrobial agents and chemotherapy | 23689724 | Antimicrob Agents Chemother | 2013 Aug | https://www.ncbi.nlm.nih.gov/pubmed/23689724 |
| Borrelia burgdorferi, the Causative Agent of Lyme Disease, Forms Drug-Tolerant Persister Cells. | Sharma B, Brown AV, Matluck NE, Hu LT, Lewis K | Antimicrobial agents and chemotherapy | 26014929 | Antimicrob Agents Chemother | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26014929 |
| Type II fatty acid biosynthesis is essential for Plasmodium falciparum sporozoite development in the midgut of Anopheles mosquitoes. | van Schaijk BC, Kumar TR, Vos MW, Richman A, van Gemert GJ, Li T, Eappen AG, Williamson KC, Morahan BJ, Fishbaugher M, Kennedy M, Camargo N, Khan SM, Janse CJ, Sim KL, Hoffman SL, Kappe SH, Sauerwein RW, Fidock DA, Vaughan AM | Eukaryotic cell | 24297444 | Eukaryot Cell | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24297444 |
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| Multicolor bioluminescence boosts malaria research: quantitative dual-color assay and single-cell imaging in Plasmodium falciparum parasites. | Cevenini L, Camarda G, Michelini E, Siciliano G, Calabretta MM, Bona R, Kumar TR, Cara A, Branchini BR, Fidock DA, Roda A, Alano P | Analytical chemistry | 25102353 | Anal Chem | 2014 Sep 2 | https://www.ncbi.nlm.nih.gov/pubmed/25102353 |
| Yeast-based high-throughput screen identifies Plasmodium falciparum equilibrative nucleoside transporter 1 inhibitors that kill malaria parasites. | Frame IJ, Deniskin R, Rinderspacher A, Katz F, Deng SX, Moir RD, Adjalley SH, Coburn-Flynn O, Fidock DA, Willis IM, Landry DW, Akabas MH | ACS chemical biology | 25602169 | ACS Chem Biol | 2015 Mar 20 | https://www.ncbi.nlm.nih.gov/pubmed/25602169 |
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| A key role for lipoic acid synthesis during Plasmodium liver stage development. | Falkard B, Kumar TR, Hecht LS, Matthews KA, Henrich PP, Gulati S, Lewis RE, Manary MJ, Winzeler EA, Sinnis P, Prigge ST, Heussler V, Deschermeier C, Fidock D | Cellular microbiology | 23490300 | Cell Microbiol | 2013 Sep | https://www.ncbi.nlm.nih.gov/pubmed/23490300 |
| How can we identify parasite genes that underlie antimalarial drug resistance? | Anderson T, Nkhoma S, Ecker A, Fidock D | Pharmacogenomics | 21174623 | Pharmacogenomics | 2011 Jan | https://www.ncbi.nlm.nih.gov/pubmed/21174623 |
| Parasite-induced ER stress response in hepatocytes facilitates Plasmodium liver stage infection. | Inácio P, Zuzarte-Luís V, Ruivo MT, Falkard B, Nagaraj N, Rooijers K, Mann M, Mair G, Fidock DA, Mota MM | EMBO reports | 26113366 | EMBO Rep | 2015 Aug | https://www.ncbi.nlm.nih.gov/pubmed/26113366 |
| Discrimination of potent inhibitors of Toxoplasma gondii enoyl-acyl carrier protein reductase by a thermal shift assay. | Afanador GA, Muench SP, McPhillie M, Fomovska A, Schön A, Zhou Y, Cheng G, Stec J, Freundlich JS, Shieh HM, Anderson JW, Jacobus DP, Fidock DA, Kozikowski AP, Fishwick CW, Rice DW, Freire E, McLeod R, Prigge ST | Biochemistry | 24295325 | Biochemistry | 2013 Dec 23 | https://www.ncbi.nlm.nih.gov/pubmed/24295325 |
| Profiling the Essential Nature of Lipid Metabolism in Asexual Blood and Gametocyte Stages of Plasmodium falciparum. | Gulati S, Ekland EH, Ruggles KV, Chan RB, Jayabalasingham B, Zhou B, Mantel PY, Lee MC, Spottiswoode N, Coburn-Flynn O, Hjelmqvist D, Worgall TS, Marti M, Di Paolo G, Fidock DA | Cell host & microbe | 26355219 | Cell Host Microbe | 2015 Sep 9 | https://www.ncbi.nlm.nih.gov/pubmed/26355219 |
| Plasmodium falciparum LipB mutants display altered redox and carbon metabolism in asexual stages and cannot complete sporogony in Anopheles mosquitoes. | Biddau M, Santha Kumar TR, Henrich P, Laine LM, Blackburn GJ, Chokkathukalam A, Li T, Lee Sim K, King L, Hoffman SL, Barrett MP, Coombs GH, McFadden GI, Fidock DA, Müller S, Sheiner L | International journal for parasitology | 33713652 | Int J Parasitol | 2021 May | https://www.ncbi.nlm.nih.gov/pubmed/33713652 |
| In vitro and in vivo activity of frenolicin B against Plasmodium falciparum and P berghei. | Fitzgerald JT, Henrich PP, O'Brien C, Krause M, Ekland EH, Mattheis C, Sá JM, Fidock D, Khosla C | The Journal of antibiotics | 22008701 | J Antibiot (Tokyo) | 2011 Dec | https://www.ncbi.nlm.nih.gov/pubmed/22008701 |
| An integrated strategy for efficient vector construction and multi-gene expression in Plasmodium falciparum. | Wagner JC, Goldfless SJ, Ganesan SM, Lee MC, Fidock DA, Niles JC | Malaria journal | 24160265 | Malar J | 2013 Oct 26 | https://www.ncbi.nlm.nih.gov/pubmed/24160265 |
| Characterization of the ATG8-conjugation system in 2 Plasmodium species with special focus on the liver stage: possible linkage between the apicoplastic and autophagic systems? | Jayabalasingham B, Voss C, Ehrenman K, Romano JD, Smith ME, Fidock DA, Bosch J, Coppens I | Autophagy | 24342964 | Autophagy | 2014 Feb | https://www.ncbi.nlm.nih.gov/pubmed/24342964 |
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| α1-FANGs: Protein Ligands Selective for the α-Bungarotoxin Site of the α1-Nicotinic Acetylcholine Receptor. | Nichols AL, Noridomi K, Hughes CR, Jalali-Yazdi F, Eaton JB, Lai LH, Advani G, Lukas RJ, Lester HA, Chen L, Roberts RW | ACS chemical biology | 30059207 | ACS Chem Biol | 2018 Sep 21 | https://www.ncbi.nlm.nih.gov/pubmed/30059207 |
| Serum stable natural peptides designed by mRNA display. | Howell SM, Fiacco SV, Takahashi TT, Jalali-Yazdi F, Millward SW, Hu B, Wang P, Roberts RW | Scientific reports | 25234472 | Sci Rep | 2014 Sep 19 | https://www.ncbi.nlm.nih.gov/pubmed/25234472 |
| Single-round, multiplexed antibody mimetic design through mRNA display. | Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R | Angewandte Chemie (International ed. in English) | 23125174 | Angew Chem Int Ed Engl | 2012 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/23125174 |
| Recombinant probes reveal dynamic localization of CaMKIIα within somata of cortical neurons. | Mora RJ, Roberts RW, Arnold DB | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24005308 | J Neurosci | 2013 Sep 4 | https://www.ncbi.nlm.nih.gov/pubmed/24005308 |
| Recombinant probes for visualizing endogenous synaptic proteins in living neurons. | Gross GG, Junge JA, Mora RJ, Kwon HB, Olson CA, Takahashi TT, Liman ER, Ellis-Davies GC, McGee AW, Sabatini BL, Roberts RW, Arnold DB | Neuron | 23791193 | Neuron | 2013 Jun 19 | https://www.ncbi.nlm.nih.gov/pubmed/23791193 |
| Particle display: a quantitative screening method for generating high-affinity aptamers. | Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT | Angewandte Chemie (International ed. in English) | 24644057 | Angew Chem Int Ed Engl | 2014 May 5 | https://www.ncbi.nlm.nih.gov/pubmed/24644057 |
| An E3-ligase-based method for ablating inhibitory synapses. | Gross GG, Straub C, Perez-Sanchez J, Dempsey WP, Junge JA, Roberts RW, Trinh le A, Fraser SE, De Koninck Y, De Koninck P, Sabatini BL, Arnold DB | Nature methods | 27271196 | Nat Methods | 2016 Aug | https://www.ncbi.nlm.nih.gov/pubmed/27271196 |
| Importance of controlling nanotube density for highly sensitive and reliable biosensors functional in physiological conditions. | Ishikawa FN, Curreli M, Olson CA, Liao HI, Sun R, Roberts RW, Cote RJ, Thompson ME, Zhou C | ACS nano | 21028792 | ACS Nano | 2010 Nov 23 | https://www.ncbi.nlm.nih.gov/pubmed/21028792 |
| Rapid mRNA-display selection of an IL-6 inhibitor using continuous-flow magnetic separation. | Olson CA, Adams JD, Takahashi TT, Qi H, Howell SM, Wu TT, Roberts RW, Sun R, Soh HT | Angewandte Chemie (International ed. in English) | 21761516 | Angew Chem Int Ed Engl | 2011 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/21761516 |
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| General, Label-Free Method for Determining K(d) and Ligand Concentration Simultaneously. | Jalali-Yazdi F, Takahashi TT, Roberts RW | Analytical chemistry | 26485531 | Anal Chem | 2015 Dec 1 | https://www.ncbi.nlm.nih.gov/pubmed/26485531 |
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| RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS. | Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE | Proceedings. IEEE International Symposium on Biomedical Imaging | 21383863 | Proc IEEE Int Symp Biomed Imaging | 2010 Jun 21 | https://www.ncbi.nlm.nih.gov/pubmed/21383863 |
| Pseudomonas aeruginosa RhlR is required to neutralize the cellular immune response in a Drosophila melanogaster oral infection model. | Limmer S, Haller S, Drenkard E, Lee J, Yu S, Kocks C, Ausubel FM, Ferrandon D | Proceedings of the National Academy of Sciences of the United States of America | 21987808 | Proc Natl Acad Sci U S A | 2011 Oct 18 | https://www.ncbi.nlm.nih.gov/pubmed/21987808 |
| A Defensin from the Model Beetle Tribolium castaneum Acts Synergistically with Telavancin and Daptomycin against Multidrug Resistant Staphylococcus aureus. | Rajamuthiah R, Jayamani E, Conery AL, Fuchs BB, Kim W, Johnston T, Vilcinskas A, Ausubel FM, Mylonakis E | PloS one | 26062137 | PLoS One | 2015 | https://www.ncbi.nlm.nih.gov/pubmed/26062137 |
| A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence. | Kirienko DR, Revtovich AV, Kirienko NV | mSphere | 27579370 | mSphere | 2016 Jul-Aug | https://www.ncbi.nlm.nih.gov/pubmed/27579370 |
| Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. | McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM | BMC biology | 27927200 | BMC Biol | 2016 Dec 7 | https://www.ncbi.nlm.nih.gov/pubmed/27927200 |
| Mitophagy confers resistance to siderophore-mediated killing by Pseudomonas aeruginosa. | Kirienko NV, Ausubel FM, Ruvkun G | Proceedings of the National Academy of Sciences of the United States of America | 25624506 | Proc Natl Acad Sci U S A | 2015 Feb 10 | https://www.ncbi.nlm.nih.gov/pubmed/25624506 |
| Insect-derived cecropins display activity against Acinetobacter baumannii in a whole-animal high-throughput Caenorhabditis elegans model. | Jayamani E, Rajamuthiah R, Larkins-Ford J, Fuchs BB, Conery AL, Vilcinskas A, Ausubel FM, Mylonakis E | Antimicrobial agents and chemotherapy | 25583713 | Antimicrob Agents Chemother | 2015 Mar | https://www.ncbi.nlm.nih.gov/pubmed/25583713 |
| Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile. | Rajamuthiah R, Jayamani E, Majed H, Conery AL, Kim W, Kwon B, Fuchs BB, Kelso MJ, Ausubel FM, Mylonakis E | Bioorganic & medicinal chemistry letters | 26459212 | Bioorg Med Chem Lett | 2015 Nov 15 | https://www.ncbi.nlm.nih.gov/pubmed/26459212 |
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| Investment in secreted enzymes during nutrient-limited growth is utility dependent. | Cezairliyan B, Ausubel FM | Proceedings of the National Academy of Sciences of the United States of America | 28847943 | Proc Natl Acad Sci U S A | 2017 Sep 12 | https://www.ncbi.nlm.nih.gov/pubmed/28847943 |
| High-throughput screening for novel anti-infectives using a C. elegans pathogenesis model. | Conery AL, Larkins-Ford J, Ausubel FM, Kirienko NV | Current protocols in chemical biology | 24652621 | Curr Protoc Chem Biol | 2014 Mar 14 | https://www.ncbi.nlm.nih.gov/pubmed/24652621 |
| Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. | Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM | Cell host & microbe | 23601103 | Cell Host Microbe | 2013 Apr 17 | https://www.ncbi.nlm.nih.gov/pubmed/23601103 |
| The evolutionarily conserved mediator subunit MDT-15/MED15 links protective innate immune responses and xenobiotic detoxification. | Pukkila-Worley R, Feinbaum RL, McEwan DL, Conery AL, Ausubel FM | PLoS pathogens | 24875643 | PLoS Pathog | 2014 May | https://www.ncbi.nlm.nih.gov/pubmed/24875643 |
| Morphology-guided graph search for untangling objects: C. elegans analysis. | Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879454 | Med Image Comput Comput Assist Interv | 2010 | https://www.ncbi.nlm.nih.gov/pubmed/20879454 |
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| Axonal regeneration proceeds through specific axonal fusion in transected C. elegans neurons. | Neumann B, Nguyen KC, Hall DH, Ben-Yakar A, Hilliard MA | Developmental dynamics : an official publication of the American Association of Anatomists | 21416556 | Dev Dyn | 2011 Jun | https://www.ncbi.nlm.nih.gov/pubmed/21416556 |
| Ultrafast laser nanosurgery in microfluidics for genome-wide screenings. | Ben-Yakar A, Bourgeois F | Current opinion in biotechnology | 19278850 | Curr Opin Biotechnol | 2009 Feb | https://www.ncbi.nlm.nih.gov/pubmed/19278850 |
| Femtosecond laser nanoaxotomy properties and their effect on axonal recovery in C. elegans. | Bourgeois F, Ben-Yakar A | Optics express | 18725955 | Opt Express | 2008 Apr 14 | https://www.ncbi.nlm.nih.gov/pubmed/18725955 |
| Planar Laser Activated Neuronal Scanning (PLANS) System for in vivo Flow Cytometry. | Watson N, Mondal S, DuPlissis A, Kim KH, Ben-Yakar A | Frontiers in optics. Annual Meeting of the Optical Society of America | 35350105 | Front Opt | 2020 Sep | https://www.ncbi.nlm.nih.gov/pubmed/35350105 |
| Microfluidics for the analysis of behavior, nerve regeneration, and neural cell biology in C. elegans. | Ben-Yakar A, Chronis N, Lu H | Current opinion in neurobiology | 19896831 | Curr Opin Neurobiol | 2009 Oct | https://www.ncbi.nlm.nih.gov/pubmed/19896831 |
| Ultrasound measurements of cavitation bubble radius for femtosecond laser-induced breakdown in water. | Aglyamov SR, Karpiouk AB, Bourgeois F, Ben-Yakar A, Emelianov SY | Optics letters | 18552957 | Opt Lett | 2008 Jun 15 | https://www.ncbi.nlm.nih.gov/pubmed/18552957 |
| Femtosecond laser nanoaxotomy lab-on-a-chip for in vivo nerve regeneration studies. | Guo SX, Bourgeois F, Chokshi T, Durr NJ, Hilliard MA, Chronis N, Ben-Yakar A | Nature methods | 18408725 | Nat Methods | 2008 Jun | https://www.ncbi.nlm.nih.gov/pubmed/18408725 |
| High-Content Microfluidic Screening Platform Used To Identify σ2R/Tmem97 Binding Ligands that Reduce Age-Dependent Neurodegeneration in C. elegans SC_APP Model. | Mondal S, Hegarty E, Sahn JJ, Scott LL, Gökçe SK, Martin C, Ghorashian N, Satarasinghe PN, Iyer S, Sae-Lee W, Hodges TR, Pierce JT, Martin SF, Ben-Yakar A | ACS chemical neuroscience | 29426225 | ACS Chem Neurosci | 2018 May 16 | https://www.ncbi.nlm.nih.gov/pubmed/29426225 |
| Line excitation array detection fluorescence microscopy at 0.8 million frames per second. | Martin C, Li T, Hegarty E, Zhao P, Mondal S, Ben-Yakar A | Nature communications | 30374138 | Nat Commun | 2018 Oct 29 | https://www.ncbi.nlm.nih.gov/pubmed/30374138 |
| A multi-trap microfluidic chip enabling longitudinal studies of nerve regeneration in Caenorhabditis elegans. | Gokce SK, Hegarty EM, Mondal S, Zhao P, Ghorashian N, Hilliard MA, Ben-Yakar A | Scientific reports | 28852096 | Sci Rep | 2017 Aug 29 | https://www.ncbi.nlm.nih.gov/pubmed/28852096 |
| Small-molecule-mediated axonal branching in Caenorhabditis elegans. | Zlotkowski K, Pierce-Shimomura J, Siegel D | Chembiochem : a European journal of chemical biology | 23362121 | Chembiochem | 2013 Feb 11 | https://www.ncbi.nlm.nih.gov/pubmed/23362121 |
| Worming our way to Alzheimer's disease drug discovery. | Iyer S, Pierce-Shimomura JT | Biological psychiatry | 23399470 | Biol Psychiatry | 2013 Mar 1 | https://www.ncbi.nlm.nih.gov/pubmed/23399470 |
| An automated microfluidic multiplexer for fast delivery of C. elegans populations from multiwells. | Ghorashian N, Gökçe SK, Guo SX, Everett WN, Ben-Yakar A | PloS one | 24069313 | PLoS One | 2013 | https://www.ncbi.nlm.nih.gov/pubmed/24069313 |
| Small molecule modulator of sigma 2 receptor is neuroprotective and reduces cognitive deficits and neuroinflammation in experimental models of Alzheimer's disease. | Yi B, Sahn JJ, Ardestani PM, Evans AK, Scott LL, Chan JZ, Iyer S, Crisp A, Zuniga G, Pierce JT, Martin SF, Shamloo M | Journal of neurochemistry | 27926996 | J Neurochem | 2017 Feb | https://www.ncbi.nlm.nih.gov/pubmed/27926996 |
| APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans. | Sae-Lee W, Scott LL, Brose L, Encarnacion AJ, Shi T, Kore P, Oyibo LO, Ye C, Rozmiarek SK, Pierce JT | G3 (Bethesda, Md.) | 32580938 | G3 (Bethesda) | 2020 Aug 5 | https://www.ncbi.nlm.nih.gov/pubmed/32580938 |
| Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans. | Nordquist SK, Smith SR, Pierce JT | G3 (Bethesda, Md.) | 29367452 | G3 (Bethesda) | 2018 Mar 2 | https://www.ncbi.nlm.nih.gov/pubmed/29367452 |
| An automated microfluidic device for time-lapse imaging of mouse embryonic stem cells. | Laing AF, Tirumala V, Hegarty E, Mondal S, Zhao P, Hamilton WB, Brickman JM, Ben-Yakar A | Biomicrofluidics | 31558920 | Biomicrofluidics | 2019 Sep | https://www.ncbi.nlm.nih.gov/pubmed/31558920 |
| Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. | Cohn JA, Cebul ER, Valperga G, Brose L, de Bono M, Heiman MG, Pierce JT | Developmental biology | 31945343 | Dev Biol | 2020 May 1 | https://www.ncbi.nlm.nih.gov/pubmed/31945343 |
| Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model. | Mondal S, Hegarty E, Martin C, Gökçe SK, Ghorashian N, Ben-Yakar A | Nature communications | 27725672 | Nat Commun | 2016 Oct 11 | https://www.ncbi.nlm.nih.gov/pubmed/27725672 |
| Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans. | Vidal-Gadea A, Ward K, Beron C, Ghorashian N, Gokce S, Russell J, Truong N, Parikh A, Gadea O, Ben-Yakar A, Pierce-Shimomura J | eLife | 26083711 | Elife | 2015 Jun 17 | https://www.ncbi.nlm.nih.gov/pubmed/26083711 |
| A fully automated microfluidic femtosecond laser axotomy platform for nerve regeneration studies in C. elegans. | Gokce SK, Guo SX, Ghorashian N, Everett WN, Jarrell T, Kottek A, Bovik AC, Ben-Yakar A | PloS one | 25470130 | PLoS One | 2014 | https://www.ncbi.nlm.nih.gov/pubmed/25470130 |
| Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene egl-1 in a Living Neuron Pair in Caenorhabditis elegans. | Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT | G3 (Bethesda, Md.) | 31519744 | G3 (Bethesda) | 2019 Nov 5 | https://www.ncbi.nlm.nih.gov/pubmed/31519744 |
| Quantitative ultrasound method to detect and monitor laser-induced cavitation bubbles. | Karpiouk AB, Aglyamov SR, Bourgeois F, Ben-Yakar A, Emelianov SY | Journal of biomedical optics | 18601556 | J Biomed Opt | 2008 May-Jun | https://www.ncbi.nlm.nih.gov/pubmed/18601556 |
