Aviv Regev

We are interested in biological networks, gene regulation and evolution. Our work focuses on dissecting complex molecular networks to determine how they function and evolve in the face of genetic and environmental changes, in differentiation, evolution and disease.

We develop experimental and computational approaches to systematically decipher the mechanisms and principles that underlie the rewiring of regulatory networks controlling gene transcription. We study the rewiring of transcriptional networks at different timescales, asking how gene regulation changes when cells adapt to changing growth conditions, when they differentiate, and when species evolve. For linear processes, we study epigenetic rewiring following the response of human cells to pathogens (timescale: hours), and genetic rewiring in forward evolution in yeast and cancer cells under selection (timescale: days to months). In lineages, we characterize the development of novel transcriptional states in the hematopoiesis ontogeny (timescale: days) and the evolution of regulatory networks in the Ascomycota phylogeny (timescale: hundreds of millions of years). These studies provide detailed reconstructions and general principles governing the emergence of novel functions in gene regulation from yeast to humans.

Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A.(2009). Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 326:257-63.

Kim HD, Shay T, O'Shea EK, Regev A. (2009) Transcriptional regulatory circuits: predicting numbers from alphabets. Science. 325:429-432.

D. J Wohlbach*, D. A. Thompson*, A. P Gasch, and A. Regev (2009). From elements to modules: regulatory evolution in Ascomycota fungi. Current Opinions in Genetics and Development. 19:571-8.

S. D. Shapira*, I. Gat-Viks*, B. O.V. Shum, A. Dricot, M. M. de Grace, L. Wu, P. B. Gupta, T. Hao, S. J. Silver, D. E. Root, D. E. Hill, A. Regev*, and N. Hacohen* (2009). A Physical and Regulatory Map of Host-Influenza Interactions Reveals Pathways in H1N1 Infection . Cell 139: 1255-1267.

Yassour M, Kaplan T, Fraser HB, Levin JZ, Pfiffner J, Adiconis X, Schroth G, Luo S, Khrebtukova I, Gnirke A, Nusbaum C, Thompson DA, Friedman N, Regev A. (2009). Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing. Proc Natl Acad Sci U S A. 106:3264-9

Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-7.

G. Chechik, E. Oh, O. Rando, J. Weissman, A. Regev*, and D. Koller*. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network (2008). Nature Biotechnology 26:1251-1219

I. Ben-Porath, M. W. Thomson, V. J. Carey, R. Ge, G. W. Bell, A. Regev, R. A. Weinberg (2008). An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nature Genetics 40: 499-507.

Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir O, Wypij D, Levasseur K, Thomas E, Tamayo P, Dong C, Zhou Y, Lander ES, Ndiaye D, Wirth D, Winzeler EA, Mesirov JP, Regev A. (2007) Distinct physiological states of Plasmodium falciparum in malaria-infected patients. Nature 450:1091-5.

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev (2007) Natural history and evolutionary principles of gene duplication in fungi. Nature. 449: 54-64.

D. Pe'er, A. Tanay and A. Regev (2006) Minreg: A Scalable Algorithm for Learning Parsimonious Regulatory networks in Yeast and Mammals, Journal of Machine Learning Research, 7:167-189.

Tanay*, A. Regev*, and R. Shamir (2005) Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. PNAS. 102:7203-8

E. Segal, N. Friedman, D. Koller, and A. Regev (2004) A module map showing conditional activity of expression modules in cancer. Nature Genetics. 36:1090-1098.