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Mark Gerstein

yale university

191H-index
1.2KPaper Count
25.7WCitation Count
Published Papers 361
Publication Date
MedicalAgentsBench for complex medical reasoning: Comparing internalized reasoning models versus externalized agent-based frameworks
err2026-07-08
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errOAAI
errYanjun Shao; Xiangru Tang; Jiwoong Sohn; Jiapeng Chen; Yuxuan Liao; Jiayi Zhang; Jinyu Xiang; Fang Wu; Yilun Zhao; Chenglin Wu; Wenqi Shi; Arman Cohan; Mark Gerstein
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Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms
err2026-05-21
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errOAAI
errKate R. Bowie; Irvan Luhung; Taylor R. Burke; Scott C. Roberts; Richard A. Martinello; Mark Gerstein; Jordan Peccia; Hannah G. Healy
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Transcriptomic and phenotypic convergence of neurodevelopmental disorder risk genes in vitro and in vivo
err2026-04-24
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errOAAI
errMeilin Fernandez Garcia; Kayla Retallick-Townsley; April Pruitt; Elizabeth A. Davidson; Novin Balafkan; Jonathan Warrell; Tzu-Chieh Huang; Alfred Kibowen; Zhiyuan Chu; Yi Dai; Sarah E. Fitzpatrick; Ran Meng; Annabel Sen; Sophie Cohen; Olivia Livoti; Suha Khan; Charlotte Becker; Andre Luiz Teles e Silva; Jenny Liu; Grace Dossou; Jen Cheung; Susanna Liu; Sadaf Ghorbani; P. J. Michael Deans; Marisa DeCiucis; Prashant Emani; Huanyao Gao; Hongying Shen; Mark Gerstein; Zuoheng Wang; Laura M. Huckins; Ellen J. Hoffman; Kristen Brennand
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Interpretability and implicit model semantics in biomedicine and deep learning
err2026-03-23
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PREAI
errJonathan Warrell; Michael Gancz; Hussein Mohsen; Prashant Emani; Mark Gerstein
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Homomorphic encryption enables privacy preserving polygenic risk scores
err2026-01-08
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errOAAI
errElizabeth Knight; Jiaqi Li; Matthew Jensen; Israel Yolou; Can Kockan; Mark Gerstein
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An expanded registry of candidate cis-regulatory elements
errNature
IF48.5
err2026-01-07
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errOAAI
errJill E. Moore; Henry E. Pratt; Kaili Fan; Nishigandha Phalke; Jonathan Fisher; Shaimae I. Elhajjajy; Gregory Andrews; Mingshi Gao; Nicole Shedd; Yu Fu; Matthew C. Lacadie; Jair Meza; Mansi Khandpekar; Mohit Ganna; Eva Choudhury; Ross Swofford; Huong Phan; Christian C. Ramirez; Maxwell Campbell; Mary Likhite; Nina P. Farrell; Annika K. Weimer; Anusri Pampari; Vivekanandan Ramalingam; Fairlie Reese; Beatrice Borsari; Xuezhu Yu; Eve Wattenberg; Marina Ruiz-Romero; Milad Razavi-Mohseni; Jinrui Xu; Timur Galeev; Andres Colubri; Michael A. Beer; Roderic Guigó; Mark B. Gerstein; Jesse M. Engreitz; Mats Ljungman; Timothy E. Reddy; Michael P. Snyder; Charles B. Epstein; Elizabeth Gaskell; Bradley E. Bernstein; Diane E. Dickel; Axel Visel; Len A. Pennacchio; Ali Mortazavi; Anshul Kundaje; Zhiping Weng
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The IGVF catalog-from genetic variation to function
err2025-12-01
err1
PREAI
errLi, Daofeng; Liu, Shane; Assis, Pedro R.; Li, Mingjie; Dong, Shengcheng; Whaling, Ian; Jolanki, Otto; Kagda, Meenakshi; Zhang, Wenjin; Macias-Velasco, Juan F.; Liu, Tianjie; Cody, Sarah; Antonacci-Fulton, Lucinda; Huang, Yuanhao; Liu, Jie; Montgomery, Michael T.; Zeiberg, Daniel; Jain, Shantanu; Pejaver, Vikas; Bergquist, Timothy; Chen, Yile; Radivojac, Predrag; Gersbach, Charles A.; Sherpa, Rintsen N.; Castro, Christopher P.; Boyle, Alan P.; Starita, Lea M.; Fowler, Douglas M.; Ahituv, Nadav; Dey, Kushal K.; Majoros, William H.; Reddy, Timothy E.; Craven, Mark; Sinha, Riya; Sverchkov, Yuriy; Cai, Xiangmeng; Nzima, Mpathi Z.; Calderwood, Michael A.; Rozowsky, Joel; Gerstein, Mark; Ma, Jian; Yue, Feng; Cherry, J. Michael; Love, Michael, I; Engreitz, Jesse M.; Hitz, Benjamin C.; Wang, Ting
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FAVOR 2.0: A reengineered functional annotation of variants online resource for interpreting genomic variation
err2025-12-01
err1
PREAI
errZhou, Hufeng; Verma, Vineet; Li, Xihao; Li, Zilin; Shedd, Nicole; Li, Thomas Cheng; Yang, Haoyu; Zhang, Alvin; Borsari, Beatrice; Buyske, Steven; Gerstein, Mark; Matise, Tara; Zody, Michael C.; Neale, Benjamin; Weng, Zhiping; Sunyaev, Shamil R.; Lin, Xihong
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Aerosol-based Exposure to Opportunistic Pathogens Originating from Hospital Sink Drains
err2025-11-04
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PREAI
errLucien Dieter; Kate Bowie; Irvan Luhung; Hannah Greenwald Healy; Scott C. Roberts; Trini Mathew; David Peaper; Richard A. Martinello; Mark B. Gerstein; Jordan Peccia
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Network-based drug repurposing for psychiatric disorders using single-cell genomics
err2025-09-18
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PREAI
errChirag Gupta; Noah Cohen Kalafut; Declan Clarke; Jerome J. Choi; Kalpana Hanthanan Arachchilage; Saniya Khullar; Yan Xia; Xiao Zhou; Cagatay Dursun; Mark Gerstein; Daifeng Wang
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Regulatory genome annotation
err2025-09-16
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PREAI
errSushant Kumar; Mark Gerstein
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Author Correction: Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-08-26
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
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Recent advances and future prospects for blockchain in biomedicine
err2025-07-25
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errOAAI
errEric Ni; Xiangru Tang; Xiao Zhou; Danielle Lee; Ahmed Elhussein; Elizabeth Knight; Gamze Gürsoy; Mark Gerstein
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Complex genetic variation in nearly complete human genomes
errNature
IF48.5
err2025-07-23
err0
errOAAI
errGlennis A. Logsdon; Peter Ebert; Peter A. Audano; Mark Loftus; David Porubsky; Jana Ebler; Feyza Yilmaz; Pille Hallast; Timofey Prodanov; DongAhn Yoo; Carolyn A. Paisie; William T. Harvey; Xuefang Zhao; Gianni V. Martino; Mir Henglin; Katherine M. Munson; Keon Rabbani; Chen-Shan Chin; Bida Gu; Hufsah Ashraf; Stephan Scholz; Olanrewaju Austine-Orimoloye; Parithi Balachandran; Marc Jan Bonder; Haoyu Cheng; Zechen Chong; Jonathan Crabtree; Mark Gerstein; Lisbeth A. Guethlein; Patrick Hasenfeld; Glenn Hickey; Kendra Hoekzema; Sarah E. Hunt; Matthew Jensen; Yunzhe Jiang; Sergey Koren; Youngjun Kwon; Chong Li; Heng Li; Jiaqi Li; Paul J. Norman; Keisuke K. Oshima; Benedict Paten; Adam M. Phillippy; Nicholas R. Pollock; Tobias Rausch; Mikko Rautiainen; Yuwei Song; Arda Söylev; Arvis Sulovari; Likhitha Surapaneni; Vasiliki Tsapalou; Weichen Zhou; Ying Zhou; Qihui Zhu; Michael C. Zody; Ryan E. Mills; Scott E. Devine; Xinghua Shi; Michael E. Talkowski; Mark J. P. Chaisson; Alexander T. Dilthey; Miriam K. Konkel; Jan O. Korbel; Charles Lee; Christine R. Beck; Evan E. Eichler; Tobias Marschall
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A discard-and-restart MD algorithm for the sampling of protein intermediate states
err2025-03-28
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PREAI
errAlan Ianeselli; Jonathon Howard; Mark B. Gerstein
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A variational graph-partitioning approach to modeling protein liquid-liquid phase separation
err2024-11-01
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errOAAI
errWang, Gaoyuan; Warrell, Jonathan; Zheng, Suchen; Gerstein, Mark
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REliable PIcking by Consensus (REPIC): a consensus methodology for harnessing multiple cryo-EM particle pickers
err2024-10-31
err0
errOAAI
errCameron, Christopher J. F.; Seager, Sebastian J. H.; Sigworth, Fred J.; Tagare, Hemant D.; Gerstein, Mark B.
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