Thomas Gingeras
Professor
Cancer Center Member
Ph.D., New York University, 1976
[email protected] | 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.
The location, function and the regulation of information stored in genomes are critical areas of research for biology and medicine. Dr. Thomas Gingeras and his laboratory colleagues seek to discover and study these functional genome elements to help explain the biological and clinical effects of disease-causing gene mutations in humans and other organisms. Gingeras has been 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 organization 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 (ncRNAs) but have regulatory functions. 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, such as scaffolds upon which large protein complexes are assembled and as extracellular signals. These studies have led to a fundamental understanding of why genomes are pervasively transcribed. Pervasive transcription is a genome design principle built into genomes in which transcription begets regulators. The maps of where and what types of RNA are transcribed serve as a foundation by many areas of disease diagnosis and treatment. In particular, individual ncRNAs are responsible for regulating the expression levels of individual genes locally and hundreds of genes at a genome-wide level. ncRNAs are positioned in antisense, divergent, intronic, and intergenic configurations, yet no model currently links these topological arrangements to match their regulatory scope. We have proposed a Topological Regulatory Logic (TRL) model to formalize a coherent conceptual basis for lncRNA-mediated regulation.
Cocktails & Chromosomes: Heresy in genetics
June 17, 2025
Imagine everything you learned about DNA wasn’t quite wrong, but was only a fraction of the truth. Now, get more of the whole story.
Corn’s ancient ancestors are calling
February 6, 2025
Cold Spring Harbor Laboratory Professors Thomas Gingeras and Rob Martienssen have launched a new genomic encyclopedia called MaizeCODE.
At the Lab Season 1 Research Rewind: Genetics
October 22, 2024
It’s the code for all life on Earth. This week At the Lab, we’re hacking it with the help of Cold Spring Harbor Laboratory’s geneticists.
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.
All Publications
Author Correction: MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication.
23 Jul 2025 | Nature Communications | 16(1):6790
Cahn, Jonathan; Regulski, Michael; Lynn, Jason; Ernst, Evan; de Santis Alves, Cristiane; Ramakrishnan, Srividya; Chougule, Kapeel; Wei, Sharon; Lu, Zhenyuan; Xu, Xiaosa; Ramu, Umamaheswari; Drenkow, Jorg; Danyko, Cassidy; Kramer, Melissa; Seetharam, Arun; Hufford, Matthew; McCombie, W; Ware, Doreen; Jackson, David; Schatz, Michael; Gingeras, Thomas; Martienssen, Robert;
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
30 Dec 2024 | Nature Communications | 15(1):10854
Cahn, Jonathan; Regulski, Michael; Lynn, Jason; Ernst, Evan; de Santis Alves, Cristiane; Ramakrishnan, Srividya; Chougule, Kapeel; Wei, Sharon; Lu, Zhenyuan; Xu, Xiaosa; Ramu, Umamaheswari; Drenkow, Jorg; Kramer, Melissa; Seetharam, Arun; Hufford, Matthew; McCombie, W; Ware, Doreen; Jackson, David; Schatz, Michael; Gingeras, Thomas; Martienssen, Robert;
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;
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication
23 Feb 2024 | bioRxiv
Cahn, Jonathan; Regulski, Michael; Lynn, Jason; Ernst, Evan; Alves, Cristiane; Ramakrishnan, Srividya; Chougule, Kapeel; Wei, Sharon; Lu, Zhenyuan; Xu, Xiaosa; Drenkow, Jorg; Kramer, Melissa; Seetharam, Arun; Hufford, Matthew; McCombie, Richard; Ware, Doreen; Jackson, David; Schatz, Michael; Gingeras, Thomas; Martienssen, Robert;
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;