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Thomas Gingeras

Thomas Gingeras

Professor
Cancer Center Member

Ph.D., New York University, 1976

gingeras@cshl.edu | 516-422-4105

Faculty Profile

Only 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.

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All Publications

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;  

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;  

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