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., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., et al. 2014. A comparative encyclopedia of DNA elements in the mouse genome. Nature 515: 371-375.
Gerstein, M.B., Rozowsky, J., Yan, K.K., Wang, D., Cheng, C., Brown, J.B., et al. 2014. Comparative analysis of the transcriptome across distant species. Nature 512:445-448
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15–21.
The ENCODE Consortium Project. 2012. An integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489:57-74.
Djebali, S.*, Davis, C.A. *, Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A. M., et al. 2012. Landscape of transcription in human cells. Nature 489: 101-108.
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Scientists looking across human, fly and worm genomes find shared biology
September 8, 2014
In massive genome analysis ENCODE data suggests 'gene' redefinition