Select Publications

Ram O., Goren A., Amit I., Shoresh N., Yosef N., Ernst J., Kellis M., Gymrek M., Issner R., Coyne M., Durham T., Zhang X., Donaghey J., Epstein C.B., Regev A., Bernstein B.E. (2011) Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells. Cell. 147(7):1628-39.

Chevrier N., Mertins P., Artyomov M.N., Shalek A.K., Iannacone M., Ciaccio M.F., Gat-Viks I., Tonti E., DeGrace M.M., Clauser K.R., Garber M., Eisenhaure T.M., Yosef N., Robinson J., Sutton A., Andersen M.S., Root D.E., von Andrian U., Jones R.B., Park H., Carr S.A., Regev A., Amit I., Hacohen N. (2011) Systematic discovery of TLR signaling components delineates viral-sensing circuits. Cell. 147(4):853-67.

Tsankov A., Yanagisawa Y., Rhind N., Regev A., Rando O.J. (2011) Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization. Genome Res. 21(11):1851-62.

Cabili M.N., Trapnell C., Goff L., Koziol M., Tazon-Vega B., Regev A., Rinn J.L. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25(18):1915-27.

Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N., Regev A. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. 29(7):644-52.

Rabani M., Levin J. Z., Fan L., Adiconis X., Raychowdhury R., Garber M., Gnirke A., Nusbaum C., Hacohen N., Friedman N., Amit I., Regev A. (2011) Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells. Nature Biotechnology. 29(5):436-42.

Novershtern N., Subramanian A., Lawton L. N., Mak R. H., Haining W. N., McConkey M. E., Habib N., Yosef N., Chang C. Y., Shay T., Frampton G. M., Drake A. C., Leskov I., Nilsson B., Preffer F., Dombkowski D., Evans J. W., Liefeld T., Smutko J. S., Chen J., Friedman N., Young R. A., Golub T. R., Regev A., Ebert B. L. (2011) Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell. 144(2):296-309.

Rhind N., Chen Z., Yassour M., Thompson D. A., Haas B. J., Habib N., Wapinski I., Roy S., Lin M. F., Heiman D. I., Young S. K., Furuya K., Guo Y., Pidoux A., Chen H. M., Robbertse B., Goldberg J. M., Aoki K., Bayne E. H., Berlin A. M., Desjardins C. A., Dobbs E., Dukaj L., Fan L., FitzGerald M. G., French C., Gujja S., Hansen K., Keifenheim D., Levin J. Z., Mosher R. A., Müller C. A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P., Sykes S. M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R., Baulcombe D., Birren B. W., Brown W., Ekwall K., Kellis M., Leatherwood J., Levin H., Margalit H., Martienssen R., Nieduszynski C. A., Spatafora J. W., Friedman N., Dalgaard J. Z., Baumann P., Niki H., Regev A., Nusbaum C. (2011) Comparative functional genomics of the fission yeasts. Science. 332(6032):930-6.

Yassour M., Pfiffner J., Levin J. Z., Adiconis X., Gnirke A., Nusbaum C., Thompson D. A., Friedman N., Regev A. (2010) Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species. Genome Biol. 11(8):R87.

Guttman M.*, Garber M.*, Levin J. Z., Donaghey J., Robinson J., Adiconis X., Fan L., Koziol M. J., Gnirke A., Nusbaum C., Rinn J. L., Lander E. S., and Regev A. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology. 28:503 - 510.

Wapinski I., Pfiffner J., French C., Socha A., Thompson D. A. and Regev A. (2010). Gene duplication and the evolution of ribosomal protein gene regulation in yeast. PNAS. 107:5505-5510.

Tsankov A., Thompson D. A., Socha A., Regev A.*, and Rando O. J.* (2010). The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol. 2010 Jul 6;8(7):e1000414.

Smith Z.*, Nachman I.*, Regev A. and Meissner A. (2010). Dynamic single cell imaging of direct reprogramming reveals an early specifying event. Nature Biotechnology. 28:521- 526.

Anderson J. B.*, Funt J.*, Thompson D. A., Prabhu S., Socha A., Sirjusingh C., Dettman J. R., Parreiras L., Guttman D. S., Regev A.*, and Kohn L. M.* (2010). Determinants of divergent adaptation and Dobzhansky-Muller interaction in experimental yeast populations. Current Biology. 20(15):1383-8.

Ozsolak F.*, Goren A.*, Gymrek M.*, Guttman M., Regev A., Bernstein B. E. and Milos P. M. (2010). Digital transcriptome profiling from attomole-level RNA samples. Genome Research. 20:519-25.

Vastenhouw N. L., Zhang Y., Woods I. G., Imam F., Regev A., Liu X. S., Rinn J. and Schier A. F. (2010). Chromatin signature of embryonic pluripotency is established during genome activation. Nature. 464:922-926.

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.

Shapira SD, Gat-Viks I, Shum BO, Dricot A, de Grace MM, Wu L, Gupta PB, Hao T, Silver SJ, Root DE, Hill DE, Regev A, Hacohen N. (2009). A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection. Cell. 139(7):1255-67.

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.

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

Ben-Porath I., Thomson M. W. , 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.

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

Pe'er D., Tanay A., Regev A. (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 A.*, Shamir R. (2005) Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast. Proc Natl Acad Sci U S A. 102:7203-8

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