Ph.D., New York University, 1976
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, and how perturbations of ncRNAs and their regulators contribute to disease.
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.
Yue, F. and Cheng, Y. and Breschi, A. and Vierstra, J. and Wu, W. and Ryba, T. and Sandstrom, R. and Ma, Z. and Davis, C. and Pope, B. D. and Shen, Y. and Pervouchine, D. D. and Djebali, S. and Thurman, R. E. and Kaul, R. and Rynes, E. and Kirilusha, A. and Marinov, G. K. and Williams, B. A. and Trout, D. and Amrhein, H. and Fisher-Aylor, K. and Antoshechkin, I. and DeSalvo, G. and See, L. H. and Fastuca, M. and Drenkow, J. and Zaleski, C. and Dobin, A. and Prieto, P. and Lagarde, J. and Bussotti, G. and Tanzer, A. and Denas, O. and Li, K. and Bender, M. A. and Zhang, M. and Byron, R. and Groudine, M. T. and McCleary, D. and Pham, L. and Ye, Z. and Kuan, S. and Edsall, L. and Wu, Y. C. and Rasmussen, M. D. and Bansal, M. S. and Kellis, M. and Keller, C. A. and Morrissey, C. S. and Mishra, T. and Jain, D. and Dogan, N. and Harris, R. S. and Cayting, P. and Kawli, T. and Boyle, A. P. and Euskirchen, G. and Kundaje, A. and Lin, S. and Lin, Y. and Jansen, C. and Malladi, V. S. and Cline, M. S. and Erickson, D. T. and Kirkup, V. M. and Learned, K. and Sloan, C. A. and Rosenbloom, K. R. and Lacerda de Sousa, B. and Beal, K. and Pignatelli, M. and Flicek, P. and Lian, J. and Kahveci, T. and Lee, D. and Kent, W. J. and Ramalho Santos, M. and Herrero, J. and Notredame, C. and Johnson, A. and Vong, S. and Lee, K. and Bates, D. and Neri, F. and Diegel, M. and Canfield, T. and Sabo, P. J. and Wilken, M. S. and Reh, T. A. and Giste, E. and Shafer, A. and Kutyavin, T. and Haugen, E. and Dunn, D. and Reynolds, A. P. and Neph, S. and Humbert, R. and Hansen, R. S. and De Bruijn, M. (2014) A comparative encyclopedia of DNA elements in the mouse genome. Nature 515(7527) pp. 355-64.
Gerstein, M. B. and Rozowsky, J. and Yan, K. K. and Wang, D. and Cheng, C. and Brown, J. B. and Davis, C. A. and Hillier, L. and Sisu, C. and Li, J. J. and Pei, B. and Harmanci, A. O. and Duff, M. O. and Djebali, S. and Alexander, R. P. and Alver, B. H. and Auerbach, R. and Bell, K. and Bickel, P. J. and Boeck, M. E. and Boley, N. P. and Booth, B. W. and Cherbas, L. and Cherbas, P. and Di, C. and Dobin, A. and Drenkow, J. and Ewing, B. and Fang, G. and Fastuca, M. and Feingold, E. A. and Frankish, A. and Gao, G. and Good, P. J. and Guigo, R. and Hammonds, A. and Harrow, J. and Hoskins, R. A. and Howald, C. and Hu, L. and Huang, H. and Hubbard, T. J. and Huynh, C. and Jha, S. and Kasper, D. and Kato, M. and Kaufman, T. C. and Kitchen, R. R. and Ladewig, E. and Lagarde, J. and Lai, E. and Leng, J. and Lu, Z. and MacCoss, M. and May, G. and McWhirter, R. and Merrihew, G. and Miller, D. M. and Mortazavi, A. and Murad, R. and Oliver, B. and Olson, S. and Park, P. J. and Pazin, M. J. and Perrimon, N. and Pervouchine, D. and Reinke, V. and Reymond, A. and Robinson, G. and Samsonova, A. and Saunders, G. I. and Schlesinger, F. and Sethi, A. and Slack, F. J. and Spencer, W. C. and Stoiber, M. H. and Strasbourger, P. and Tanzer, A. and Thompson, O. A. and Wan, K. H. and Wang, G. and Wang, H. and Watkins, K. L. and Wen, J. and Wen, K. and Xue, C. and Yang, L. and Yip, K. and Zaleski, C. and Zhang, Y. and Zheng, H. and Brenner, S. E. and Graveley, B. R. and Celniker, S. E. and Gingeras, T. R. and Waterston, R. (2014) Comparative analysis of the transcriptome across distant species. Nature 512(7515) pp. 445-8.
Dobin, A. and Davis, C. A. and Schlesinger, F. and Drenkow, J. and Zaleski, C. and Jha, S. and Batut, P. and Chaisson, M. and Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1) pp. 15-21.
Djebali, S. and Davis, C. A. and Merkel, A. and Dobin, A. and Lassmann, T. and Mortazavi, A. and Tanzer, A. and Lagarde, J. and Lin, W. and Schlesinger, F. and Xue, C. and Marinov, G. K. and Khatun, J. and Williams, B. A. and Zaleski, C. and Rozowsky, J. and Röder, M. and Kokocinski, F. and Abdelhamid, R. F. and Alioto, T. and Antoshechkin, I. and Baer, M. T. and Bar, N. S. and Batut, P. and Bell, K. and Bell, I. and Chakrabortty, S. and Chen, X. and Chrast, J. and Curado, J. and Derrien, T. and Drenkow, J. and Dumais, E. and Dumais, J. and Duttagupta, R. and Falconnet, E. and Fastuca, M. and Fejes-Toth, K. and Ferreira, P. and Foissac, S. and Fullwood, M. J. and Gao, H. and Gonzalez, D. and Gordon, A. and Gunawardena, H. and Howald, C. and Jha, S. and Johnson, R. and Kapranov, P. and King, B. and Kingswood, C. and Luo, O. J. and Park, E. and Persaud, K. and Preall, J. B. and Ribeca, P. and Risk, B. and Robyr, D. and Sammeth, M. and Schaffer, L. and See, L. H. and Shahab, A. and Skancke, J. and Suzuki, A. M. and Takahashi, H. and Tilgner, H. and Trout, D. and Walters, N. and Wang, H. and Wrobel, J. and Yu, Y. and Ruan, X. and Hayashizaki, Y. and Harrow, J. and Gerstein, M. and Hubbard, T. and Reymond, A. and Antonarakis, S. E. and Hannon, G. and Giddings, M. C. and Ruan, Y. and Wold, B. and Carninci, P. and Guig, R. and Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature 489(7414) pp. 101-108.
Dunham, I. and Kundaje, A. and Aldred, S. F. and Collins, P. J. and Davis, C. and Doyle, F. and Epstein, C. B. and Frietze, S. and Harrow, J. and Kaul, R. and Khatun, J. and Lajoie, B. R. and Landt, S. G. and Lee, B. K. and Pauli, F. and Rosenbloom, K. R. and Sabo, P. and Safi, A. and Sanyal, A. and Shoresh, N. and Simon, J. M. and Song, L. and Trinklein, N. D. and Altshuler, R. C. and Birney, E. and Brown, J. B. and Cheng, C. and Djebali, S. and Dong, X. J. and Ernst, J. and Furey, T. S. and Gerstein, M. and Giardine, B. and Greven, M. and Hardison, R. C. and Harris, R. S. and Herrero, J. and Hoffman, M. M. and Iyer, S. and Kellis, M. and Kheradpour, P. and Lassmann, T. and Li, Q. H. and Lin, X. and Marinov, G. K. and Merkel, A. and Mortazavi, A. and Parker, S. C. J. and Reddy, T. E. and Rozowsky, J. and Schlesinger, F. and Thurman, R. E. and Wang, J. and Ward, L. D. and Whitfield, T. W. and Wilder, S. P. and Wu, W. and Xi, H. L. S. and Yip, K. Y. and Zhuang, J. L. and Bernstein, B. E. and Green, E. D. and Gunter, C. and Snyder, M. and Pazin, M. J. and Lowdon, R. F. and Dillon, L. A. L. and Adams, L. B. and Kelly, C. J. and Zhang, J. and Wexler, J. R. and Good, P. J. and Feingold, E. A. and Crawford, G. E. and Dekker, J. and Elnitski, L. and Farnham, P. J. and Giddings, M. C. and Gingeras, T. R. and Guigo, R. and Hubbard, T. J. and Kent, W. J. and Lieb, J. D. and Margulies, E. H. and Myers, R. M. and Stamatoyannopoulos, J. A. and Tenenbaum, S. A. and Weng, Z. P. and White, K. P. and Wold, B. and Yu, Y. and Wrobel, J. and Risk, B. A. and Gunawardena, H. P. and Kuiper, H. C. and Maier, C. W. and Xie, L. and Chen, X. and Mikkelsen, T. S. and Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414) pp. 57-74.Additional materials of the author at
CSHL Institutional Repository