Selected Cell Circuitry Publications

Genome-scale CRISPR-Cas9 knockout screening in human cells.Shalem, O., Sanjana NE, Hartenian E., Shi X., Scott DA, Mikkelsen TS, Heckl D., Ebert BL, Root DE, Doench JG, and Zhang F. Science (New York, N.Y.), 2014/01/03, Volume 343, Issue 6166, p.84-7, (2014) Read More / View Supplemental Materials
Abstract
Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.Shalek, AK, Satija R., Adiconis X., Gertner RS, Gaublomme JT, Raychowdhury R., Schwartz S., Yosef N., Malboeuf C., Lu D., Trombetta JJ, Gennert D., Gnirke A., Goren A., Hacohen N., Levin JZ, Park H., and Regev A. Nature, 2013/06/13, Volume 498, Issue 7453, p.236-40, (2013) Read More / View Supplemental Materials
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Induction of pathogenic TH17 cells by inducible salt-sensing kinase SGK1.Wu, C., Yosef N., Thalhamer T., Zhu C., Xiao S., Kishi Y., Regev A., and Kuchroo VK Nature, 2013/03/06, (2013) Read More / View Supplemental Materials
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Dynamic regulatory network controlling TH17 cell differentiation.Yosef, N., Shalek AK, Gaublomme JT, Jin H., Lee Y., Awasthi A., Wu C., Karwacz K., Xiao S., Jorgolli M., Gennert D., Satija R., Shakya A., Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M., Tantin D., et al. Nature, 2013/03/06, (2013) Read More / View Supplemental Materials
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A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.Garber, M., Yosef N., Goren A., Raychowdhury R., Thielke A., Guttman M., Robinson J., Minie B., Chevrier N., Itzhaki Z., Blecher-Gonen R., Bornstein C., Amann-Zalcenstein D., Weiner A., Friedrich D., Meldrim J., Ram O., Cheng C., Gnirke A., Fisher S., et al. Molecular cell, 2012/09/14, Volume 47, Issue 5, p.810-22, (2012) Read More / View Supplemental Materials
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A unique regulatory phase of DNA methylation in the early mammalian embryo.Smith, ZD, Chan MM, Mikkelsen TS, Gu H., Gnirke A., Regev A., and Meissner A. Nature, 2012/03/28, Volume 484, Issue 7394, p.339-44, (2012) Read More / View Supplemental Materials
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Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells.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 CB, Regev A., and Bernstein BE Cell, 2011/12/23, Volume 147, Issue 7, p.1628-39, (2011) Read More / View Supplemental Materials
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Strategies to discover regulatory circuits of the mammalian immune system.Amit, I., Regev A., and Hacohen N. Nature reviews. Immunology, 2011/11/18, Volume 11, Issue 12, p.873-80, (2011) Read More / View Supplemental Materials
Abstract
Systematic discovery of TLR signaling components delineates viral-sensing circuits.Chevrier, N., Mertins P., Artyomov MN, Shalek AK, Iannacone M., Ciaccio MF, Gat-Viks I., Tonti E., Degrace MM, Clauser KR, Garber M., Eisenhaure TM, Yosef N., Robinson J., Sutton A., Andersen MS, Root DE, von Andrian U., Jones RB, Park H., et al. Cell, 2011/11/11, Volume 147, Issue 4, p.853-67, (2011) Read More / View Supplemental Materials
Abstract
lincRNAs act in the circuitry controlling pluripotency and differentiation.Guttman, M., Donaghey J., Carey BW, Garber M., Grenier JK, Munson G., Young G., Lucas AB, Ach R., Bruhn L., Yang X., Amit I., Meissner A., Regev A., Rinn JL, Root DE, and Lander E. S. Nature, 2011/08/28, Volume 477, Issue 7364, p.295-300, (2011) Read More / View Supplemental Materials
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Full-length transcriptome assembly from RNA-Seq data without a reference genome.Grabherr, MG, Haas BJ, Yassour M., Levin JZ, Thompson DA, Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., Di Palma F., Birren BW, Nusbaum C., Lindblad-Toh K., Friedman N., et al. Nature biotechnology, 2011/05/15, Volume 29, Issue 7, p.644-52, (2011) Read More / View Supplemental Materials
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Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells.Rabani, M., Levin JZ, Fan L., Adiconis X., Raychowdhury R., Garber M., Gnirke A., Nusbaum C., Hacohen N., Friedman N., Amit I., and Regev A. Nature biotechnology, 2011/05/01, Volume 29, Issue 5, p.436-42, (2011) Read More / View Supplemental Materials
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Densely interconnected transcriptional circuits control cell states in human hematopoiesis.Novershtern, N., Subramanian A., Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N., Yosef N., Chang CY, Shay T., Frampton GM, Drake AC, Leskov I., Nilsson B., Preffer F., Dombkowski D., Evans JW, Liefeld T., Smutko JS, Chen J., et al. Cell, 2011/01/21, Volume 144, Issue 2, p.296-309, (2011) Read More / View Supplemental Materials
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Comprehensive comparative analysis of strand-specific RNA sequencing methods.Levin, JZ, Yassour M., Adiconis X., Nusbaum C., Thompson DA, Friedman N., Gnirke A., and Regev A. Nature methods, 2010/09/01, Volume 7, Issue 9, p.709-15, (2010) Read More / View Supplemental Materials
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A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response.Huarte, M., Guttman M., Feldser D., Garber M., Koziol MJ, Kenzelmann-Broz D., Khalil AM, Zuk O., Amit I., Rabani M., Attardi LD, Regev A., Lander E. S., Jacks T., and Rinn JL Cell, 2010/08/06, Volume 142, Issue 3, p.409-19, (2010) Read More / View Supplemental Materials
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Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs.Guttman, M., Garber M., Levin JZ, Donaghey J., Robinson J., Adiconis X., Fan L., Koziol MJ, Gnirke A., Nusbaum C., Rinn JL, Lander E. S., and Regev A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.503-10, (2010) Read More / View Supplemental Materials
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Dynamic single-cell imaging of direct reprogramming reveals an early specifying event.Smith, ZD, Nachman I., Regev A., and Meissner A. Nature biotechnology, 2010/05/01, Volume 28, Issue 5, p.521-6, (2010) Read More / View Supplemental Materials
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A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection.Shapira, SD, Gat-Viks I., Shum BO, Dricot A., Degrace MM, Wu L., Gupta PB, Hao T., Silver SJ, Root DE, Hill DE, Regev A., and Hacohen N. Cell, 2009/12/24, Volume 139, Issue 7, p.1255-67, (2009) Read More / View Supplemental Materials
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Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.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, et al. Science (New York, N.Y.), 2009/10/09, Volume 326, Issue 5950, p.257-63, (2009) Read More / View Supplemental Materials
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Transcriptional regulatory circuits: predicting numbers from alphabets.Kim, HD, Shay T., O'Shea EK, and Regev A. Science (New York, N.Y.), 2009/07/24, Volume 325, Issue 5939, p.429-32, (2009) Read More / View Supplemental Materials
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Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.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, and Lander E. S. Nature, 2009/03/12, Volume 458, Issue 7235, p.223-7, (2009) Read More / View Supplemental Materials
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