Thomas Gingeras
Professor
Cancer Center Member
Ph.D., New York University, 1976
gingeras@cshl.edu | 516-422-4105
Faculty ProfileOnly a small portion of the RNAs encoded in any genome are used to make proteins. My lab investigates what these noncoding RNAs (ncRNAs) do within and outside of cells, where regulators of their expression are located in the genome. This is particularly important in cancer. Our laboratory works on endometrial cancer and its relationship to age and obesity.
Thomas Gingeras and colleagues study where and how functional information is stored in genomes. These efforts help explain the biological and clinical effects of disease-causing gene mutations in humans and other organisms. Gingeras is a leader of the ENCODE (ENCyclopedia of DNA Elements) and the mouseENCODE and modENCODE (model genome ENCODE) projects of the National Institutes of Health. His research has altered our understanding of the traditional boundaries of genes, revealing that almost the entire lengths of genomes in organisms ranging from bacteria to humans can be transcribed into RNA (pervasive transcription) and that most RNA products made by a cell are not destined to be translated into proteins (noncoding, or ncRNAs). In fact, ncRNAs are proving to be involved in a variety of other important biological functions. Some have been shown to be critical components in the pre- and posttranscriptional and translational processes, as scaffolds upon which large protein complexes are assembled and as extracellular signals. The initial studies that led to these observations have been extended to cover the entire human genome. The initial studies that led to these observations have been extended to cover the entire human genome. The maps of where and what types of RNA are transcribed serves as a foundation by many areas of disease diagnosis and treatment. In particular non-protein coding (nc)RNAs are responsible for the expression of the regulatory gene, PTEN. In endometrial cancer dysregulation of PTEN via overexpression of a lncRNA (HOTAIR) binding to PTEN. Such overexpression of HOTAIR occurs in obese individuals due to dysregulation of adipogenesis and lipid metabolism leading to endometrial cancer.
At the Lab Episode 26: The golden grail of genomics
October 1, 2024
For our Season 1 finale, we invite you to step inside EN-TEx, a catalog of more than one million genomic variants.
CSHL’s Thomas Gingeras awarded $2 million NSF grant
April 3, 2024
Climate change threatens crops with acidic soils and aluminum toxicity. Gingeras leads an international team tackling this problem head-on.
Genome analysis just got personal
March 30, 2023
A new algorithm created by CSHL researchers can help predict the health effects of millions of genetic variants found within a single person’s genome.
ENCODE3: Interpreting the human and mouse genomes
July 29, 2020
Researchers report on 900,000 regulatory elements in our genomes that could influence our health.
CSHL investigators rank among world’s most highly cited
December 11, 2019
Seven researchers affiliated with CSHL are among the scientists producing the top 1 percent of the most highly-cited research in the world.
Base Pairs Episode 9.5: Redefining biologists, redefining genes
May 16, 2017
We talk with Molly Hammell about peering into deep space using a high-tech telescope, we also talk to Tom Gingeras about redefining the gene.
Redefining biologists, redefining genes
May 16, 2017
Drs. Molly Hammell and Thomas Gingeras talk about redefining what a biologist is and what genes are.
Base Pairs Episode 9: Dark matter of the genome, part 2
April 15, 2017
In this episode of Base Pairs, we question the mythos that is “junk DNA” and explore the mysterious non-coding portions of the genome.
Dark matter of the genome, part 2
April 15, 2017
This episode of Base Pairs deals with the myth of "junk DNA" and why scientists are interested in non-coding portions of the genome.
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Researchers have identified some 6600 genes whose level of expression varies within a comparatively restricted range in humans and mice
All Publications
High-quality chromosome scale genome assemblies of two important Sorghum inbred lines, Tx2783 and RTx436
Sep 2024 | NAR Genomics and Bioinformatics | 6(3):lqae097
Wang, Bo; Chougule, Kapeel; Jiao, Yinping; Olson, Andrew; Kumar, Vivek; Gladman, Nicholas; Huang, Jian; Llaca, Victor; Fengler, Kevin; Wei, Xuehong; Wang, Liya; Wang, Xiaofei; Regulski, Michael; Drenkow, Jorg; Gingeras, Thomas; Hayes, Chad; Armstrong, J; Huang, Yinghua; Xin, Zhanguo; Ware, Doreen;
The status of the human gene catalogue
Oct 2023 | Nature | 622(7981):41-47
Amaral, Paulo; Carbonell-Sala, Silvia; De La Vega, Francisco; Faial, Tiago; Frankish, Adam; Gingeras, Thomas; Guigo, Roderic; Harrow, Jennifer; Hatzigeorgiou, Artemis; Johnson, Rory; Murphy, Terence; Pertea, Mihaela; Pruitt, Kim; Pujar, Shashikant; Takahashi, Hazuki; Ulitsky, Igor; Varabyou, Ales; Wells, Christine; Yandell, Mark; Carninci, Piero; Salzberg, Steven;
The ENCODE Uniform Analysis Pipelines
19 Jul 2023
Hitz, Benjamin; Lee, Jin-Wook; Jolanki, Otto; Kagda, Meenakshi; Graham, Keenan; Sud, Paul; Gabdank, Idan; Strattan, J; Sloan, Cricket; Dreszer, Timothy; Rowe, Laurence; Podduturi, Nikhil; Malladi, Venkat; Chan, Esther; Davidson, Jean; Ho, Marcus; Miyasato, Stuart; Simison, Matt; Tanaka, Forrest; Luo, Yunhai; Wahling, Ian; Lin, Khine; Jou, Jennifer; Hong, Eurie; Lee, Brian; Sandstrom, Richard; Rynes, Eric; Nelson, Jemma; Nishida, Andrew; Ingersoll, Alyssa; Buckley, Michael; Frerker, Mark; Kim, Daniel; Boley, Nathan; Trout, Diane; Dobin, Alexander; Rahmanian, Sorena; Wyman, Dana; Balderrama-Gutierrez, Gabriela; Reese, Fairlie; Durand, Neva; Dudchenko, Olga; Weisz, David; Rao, Suhas; Blackburn, Alyssa; Gkountaroulis, Dimos; Sadr, Mahdi; Olshansky, Moshe; Eliaz, Yossi; Nguyen, Dat; Bochkov, Ivan; Shamim, Muhammad; Mahajan, Ragini; Aiden, Erez; Gingeras, Thomas; Heath, Simon; Hirst, Martin; Kent, W; Kundaje, Anshul; Mortazavi, Ali; Wold, Barbara; Cherry, J;
The ENCODE Uniform Analysis Pipelines.
6 Apr 2023 | bioRxiv
Hitz, Benjamin; Lee, Jin-Wook; Jolanki, Otto; Kagda, Meenakshi; Graham, Keenan; Sud, Paul; Gabdank, Idan; Seth Strattan, J; Sloan, Cricket; Dreszer, Timothy; Rowe, Laurence; Podduturi, Nikhil; Malladi, Venkat; Chan, Esther; Davidson, Jean; Ho, Marcus; Miyasato, Stuart; Simison, Matt; Tanaka, Forrest; Luo, Yunhai; Whaling, Ian; Hong, Eurie; Lee, Brian; Sandstrom, Richard; Rynes, Eric; Nelson, Jemma; Nishida, Andrew; Ingersoll, Alyssa; Buckley, Michael; Frerker, Mark; Kim, Daniel; Boley, Nathan; Trout, Diane; Dobin, Alex; Rahmanian, Sorena; Wyman, Dana; Balderrama-Gutierrez, Gabriela; Reese, Fairlie; Durand, Neva; Dudchenko, Olga; Weisz, David; Rao, Suhas; Blackburn, Alyssa; Gkountaroulis, Dimos; Sadr, Mahdi; Olshansky, Moshe; Eliaz, Yossi; Nguyen, Dat; Bochkov, Ivan; Shamim, Muhammad; Mahajan, Ragini; Aiden, Erez; Gingeras, Tom; Heath, Simon; Hirst, Martin; James Kent, W; Kundaje, Anshul; Mortazavi, Ali; Wold, Barbara; Cherry, J;
The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
30 Mar 2023 | Cell | 186(7):1493-1511.e40
Rozowsky, Joel; Gao, Jiahao; Borsari, Beatrice; Yang, Yucheng; Galeev, Timur; Gürsoy, Gamze; Epstein, Charles; Xiong, Kun; Xu, Jinrui; Li, Tianxiao; Liu, Jason; Yu, Keyang; Berthel, Ana; Chen, Zhanlin; Navarro, Fabio; Sun, Maxwell; Wright, James; Chang, Justin; Cameron, Christopher; Shoresh, Noam; Gaskell, Elizabeth; Drenkow, Jorg; Adrian, Jessika; Aganezov, Sergey; Aguet, François; Balderrama-Gutierrez, Gabriela; Banskota, Samridhi; Corona, Guillermo; Chee, Sora; Chhetri, Surya; Cortez Martins, Gabriel; Danyko, Cassidy; Davis, Carrie; Farid, Daniel; Farrell, Nina; Gabdank, Idan; Gofin, Yoel; Gorkin, David; Gu, Mengting; Hecht, Vivian; Hitz, Benjamin; Issner, Robbyn; Jiang, Yunzhe; Kirsche, Melanie; Kong, Xiangmeng; Lam, Bonita; Li, Shantao; Li, Bian; Li, Xiqi; Lin, Khine; Luo, Ruibang; Mackiewicz, Mark; Meng, Ran; Moore, Jill; Mudge, Jonathan; Nelson, Nicholas; Nusbaum, Chad; Popov, Ioann; Pratt, Henry; Qiu, Yunjiang; Ramakrishnan, Srividya; Raymond, Joe; Salichos, Leonidas; Scavelli, Alexandra; Schreiber, Jacob; Sedlazeck, Fritz; See, Lei; Sherman, Rachel; Shi, Xu; Shi, Minyi; Sloan, Cricket; Strattan, J; Tan, Zhen; Tanaka, Forrest; Vlasova, Anna; Wang, Jun; Werner, Jonathan; Williams, Brian; Xu, Min; Yan, Chengfei; Yu, Lu; Zaleski, Christopher; Zhang, Jing; Ardlie, Kristin; Cherry, J; Mendenhall, Eric; Noble, William; Weng, Zhiping; Levine, Morgan; Dobin, Alexander; Wold, Barbara; Mortazavi, Ali; Ren, Bing; Gillis, Jesse; Myers, Richard; Snyder, Michael; Choudhary, Jyoti; Milosavljevic, Aleksandar; Schatz, Michael; Bernstein, Bradley; Guigó, Roderic; Gingeras, Thomas; Gerstein, Mark;
The status of the human gene catalogue
24 Mar 2023
Amaral, Paulo; Carbonell-Sala, Silvia; De La Vega, Francisco; Faial, Tiago; Frankish, Adam; Gingeras, Thomas; Guigo, Roderic; Harrow, Jennifer; Hatzigeorgiou, Artemis; Johnson, Rory; Murphy, Terence; Pertea, Mihaela; Pruitt, Kim; Pujar, Shashikant; Takahashi, Hazuki; Ulitsky, Igor; Varabyou, Ales; Wells, Christine; Yandell, Mark; Carninci, Piero; Salzberg, Steven;
Long non-coding RNAs: definitions, functions, challenges and recommendations
3 Jan 2023 | Nature Reviews Molecular Cell Biology
Mattick, John; Amaral, Paulo; Carninci, Piero; Carpenter, Susan; Chang, Howard; Chen, Ling-Ling; Chen, Runsheng; Dean, Caroline; Dinger, Marcel; Fitzgerald, Katherine; Gingeras, Thomas; Guttman, Mitchell; Hirose, Tetsuro; Huarte, Maite; Johnson, Rory; Kanduri, Chandrasekhar; Kapranov, Philipp; Lawrence, Jeanne; Lee, Jeannie; Mendell, Joshua; Mercer, Timothy; Moore, Kathryn; Nakagawa, Shinichi; Rinn, John; Spector, David; Ulitsky, Igor; Wan, Yue; Wilusz, Jeremy; Wu, Mian;
Author Correction: Perspectives on ENCODE
May 2022 | Nature | 605(7909):E4
ENCODE Project Consortium; Snyder, Michael; Gingeras, Thomas; Moore, Jill; Weng, Zhiping; Gerstein, Mark; Ren, Bing; Hardison, Ross; Stamatoyannopoulos, John; Graveley, Brenton; Feingold, Elise; Pazin, Michael; Pagan, Michael; Gilchrist, Daniel; Hitz, Benjamin; Cherry, J; Bernstein, Bradley; Mendenhall, Eric; Zerbino, Daniel; Frankish, Adam; Flicek, Paul; Myers, Richard;
Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes
May 2022 | Nature | 605(7909):E3
ENCODE Project Consortium; Moore, Jill; Purcaro, Michael; Pratt, Henry; Epstein, Charles; Shoresh, Noam; Adrian, Jessika; Kawli, Trupti; Davis, Carrie; Dobin, Alexander; Kaul, Rajinder; Halow, Jessica; Van Nostrand, Eric; Freese, Peter; Gorkin, David; Shen, Yin; He, Yupeng; Mackiewicz, Mark; Pauli-Behn, Florencia; Williams, Brian; Mortazavi, Ali; Keller, Cheryl; Zhang, Xiao-Ou; Elhajjajy, Shaimae; Huey, Jack; Dickel, Diane; Snetkova, Valentina; Wei, Xintao; Wang, Xiaofeng; Rivera-Mulia, Juan; Rozowsky, Joel; Zhang, Jing; Chhetri, Surya; Zhang, Jialing; Victorsen, Alec; White, Kevin; Visel, Axel; Yeo, Gene; Burge, Christopher; Lécuyer, Eric; Gilbert, David; Dekker, Job; Rinn, John; Mendenhall, Eric; Ecker, Joseph; Kellis, Manolis; Klein, Robert; Noble, William; Kundaje, Anshul; Guigó, Roderic; Farnham, Peggy; Cherry, J; Myers, Richard; Ren, Bing; Graveley, Brenton; Gerstein, Mark; Pennacchio, Len; Snyder, Michael; Bernstein, Bradley; Wold, Barbara; Hardison, Ross; Gingeras, Thomas; Stamatoyannopoulos, John; Weng, Zhiping;
Author Correction: Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
1 Mar 2022 | Nature Communications | 13(1):1200
Grapotte, Mathys; Saraswat, Manu; Bessière, Chloé; Menichelli, Christophe; Ramilowski, Jordan; Severin, Jessica; Hayashizaki, Yoshihide; Itoh, Masayoshi; Tagami, Michihira; Murata, Mitsuyoshi; Kojima-Ishiyama, Miki; Noma, Shohei; Noguchi, Shuhei; Kasukawa, Takeya; Hasegawa, Akira; Suzuki, Harukazu; Nishiyori-Sueki, Hiromi; Frith, Martin; FANTOM consortium; Chatelain, Clément; Carninci, Piero; de Hoon, Michiel; Wasserman, Wyeth; Bréhélin, Laurent; Lecellier, Charles-Henri;