Jimin Tan, PhD

Institute for Systems Genetics

Research Assistant Professor, Department of Medicine

Positions

Research Assistant Professor, Department of Medicine at NYU Grossman School of Medicine

Graduate Education

PhD from New York University

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Serologic Testing and Genomic Analysis of Autoimmune Immune-Mediated and Rheumatic Patients with COVID-19 (SAGA)

ELLIPSS: ELucidating the Landscape of Immunoendotypes in Psoriatic Skin and Synovium

See All Studies (2)

Characterization of tumour heterogeneity through segmentation-free representation learning on multiplexed imaging data

Tan, Jimin; Le, Hortense; Deng, Jiehui; Liu, Yingzhuo; Hao, Yuan; Hollenberg, Michelle; Liu, Wenke; Wang, Joshua M; Xia, Bo; Ramaswami, Sitharam; Mezzano, Valeria; Loomis, Cynthia; Murrell, Nina; Moreira, Andre L; Cho, Kyunghyun; Pass, Harvey I; Wong, Kwok-Kin; Ban, Yi; Neel, Benjamin G; Tsirigos, Aristotelis; Fenyö, David

Nature biomedical engineering. 2025 Mar; 9(3):405-419

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia

Gambi, Giovanni; Boccalatte, Francesco; Rodriguez Hernaez, Javier; Lin, Ziyan; Nadorp, Bettina; Polyzos, Alexander; Tan, Jimin; Avrampou, Kleopatra; Inghirami, Giorgio; Kentsis, Alex; Apostolou, Effie; Aifantis, Iannis; Tsirigos, Aristotelis

Molecular cell. 2025 Jan 02; 85(1):42-60.e7

A foundation model of transcription across human cell types

Fu, Xi; Mo, Shentong; Buendia, Alejandro; Laurent, Anouchka P; Shao, Anqi; Alvarez-Torres, Maria Del Mar; Yu, Tianji; Tan, Jimin; Su, Jiayu; Sagatelian, Romella; Ferrando, Adolfo A; Ciccia, Alberto; Lan, Yanyan; Owens, David M; Palomero, Teresa; Xing, Eric P; Rabadan, Raul

Nature. 2025 Jan; 637(8047):965-973

Characterization of tumor heterogeneity through segmentation-free representation learning

Tan, Jimin; Le, Hortense; Deng, Jiehui; Liu, Yingzhuo; Hao, Yuan; Hollenberg, Michelle; Liu, Wenke; Wang, Joshua M; Xia, Bo; Ramaswami, Sitharam; Mezzano, Valeria; Loomis, Cynthia; Murrell, Nina; Moreira, Andre L; Cho, Kyunghyun; Pass, Harvey; Wong, Kwok-Kin; Ban, Yi; Neel, Benjamin G; Tsirigos, Aristotelis; Fenyö, David

bioRxiv.org : the preprint server for biology. 2024 Sep 06;

Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Wang, Joshua M; Hong, Runyu; Demicco, Elizabeth G; Tan, Jimin; Lazcano, Rossana; Moreira, Andre L; Li, Yize; Calinawan, Anna; Razavian, Narges; Schraink, Tobias; Gillette, Michael A; Omenn, Gilbert S; An, Eunkyung; Rodriguez, Henry; Tsirigos, Aristotelis; Ruggles, Kelly V; Ding, Li; Robles, Ana I; Mani, D R; Rodland, Karin D; Lazar, Alexander J; Liu, Wenke; Fenyö, David; ,

Cell reports. Medicine. 2023 Sep 19; 4(9):101173

Proteogenomic insights suggest druggable pathways in endometrial carcinoma

Dou, Yongchao; Katsnelson, Lizabeth; Gritsenko, Marina A; Hu, Yingwei; Reva, Boris; Hong, Runyu; Wang, Yi-Ting; Kolodziejczak, Iga; Lu, Rita Jui-Hsien; Tsai, Chia-Feng; Bu, Wen; Liu, Wenke; Guo, Xiaofang; An, Eunkyung; Arend, Rebecca C; Bavarva, Jasmin; Chen, Lijun; Chu, Rosalie K; Czekański, Andrzej; Davoli, Teresa; Demicco, Elizabeth G; DeLair, Deborah; Devereaux, Kelly; Dhanasekaran, Saravana M; Dottino, Peter; Dover, Bailee; Fillmore, Thomas L; Foxall, McKenzie; Hermann, Catherine E; Hiltke, Tara; Hostetter, Galen; Jędryka, Marcin; Jewell, Scott D; Johnson, Isabelle; Kahn, Andrea G; Ku, Amy T; Kumar-Sinha, Chandan; Kurzawa, Paweł; Lazar, Alexander J; Lazcano, Rossana; Lei, Jonathan T; Li, Yi; Liao, Yuxing; Lih, Tung-Shing M; Lin, Tai-Tu; Martignetti, John A; Masand, Ramya P; Matkowski, Rafał; McKerrow, Wilson; Mesri, Mehdi; Monroe, Matthew E; Moon, Jamie; Moore, Ronald J; Nestor, Michael D; Newton, Chelsea; Omelchenko, Tatiana; Omenn, Gilbert S; Payne, Samuel H; Petyuk, Vladislav A; Robles, Ana I; Rodriguez, Henry; Ruggles, Kelly V; Rykunov, Dmitry; Savage, Sara R; Schepmoes, Athena A; Shi, Tujin; Shi, Zhiao; Tan, Jimin; Taylor, Mason; Thiagarajan, Mathangi; Wang, Joshua M; Weitz, Karl K; Wen, Bo; Williams, C M; Wu, Yige; Wyczalkowski, Matthew A; Yi, Xinpei; Zhang, Xu; Zhao, Rui; Mutch, David; Chinnaiyan, Arul M; Smith, Richard D; Nesvizhskii, Alexey I; Wang, Pei; Wiznerowicz, Maciej; Ding, Li; Mani, D R; Zhang, Hui; Anderson, Matthew L; Rodland, Karin D; Zhang, Bing; Liu, Tao; Fenyö, David; ,

Cancer cell. 2023 Sep 11; 41(9):1586-1605.e15

Cell-type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

Tan, Jimin; Shenker-Tauris, Nina; Rodriguez-Hernaez, Javier; Wang, Eric; Sakellaropoulos, Theodore; Boccalatte, Francesco; Thandapani, Palaniraja; Skok, Jane; Aifantis, Iannis; Fenyö, David; Xia, Bo; Tsirigos, Aristotelis

Nature biotechnology. 2023 Aug; 41(8):1140-1150

A critical look at the current train/test split in machine learning

Tan, Jimin; Yang, Jianan; Wu, Sai; Chen, Gang; Zhao, Jake

arXiv. 2021;

See All Publications (12)