Selected Cell Circuitry Publications

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.Parnas, O., Jovanovic M., Eisenhaure TM, Herbst RH, Dixit A., Ye CJ, Przybylski D., Platt RJ, Tirosh I., Sanjana NE, Shalem O., Satija R., Raychowdhury R., Mertins P., Carr SA, Zhang F., Hacohen N., and Regev A. Cell, 2015/07/30, Volume 162, Issue 3, p.675-86, (2015) Read More / View Supplemental Materials
Abstract
The MicroRNA-132 and MicroRNA-212 Cluster Regulates Hematopoietic Stem Cell Maintenance and Survival with Age by Buffering FOXO3 Expression.Mehta, A., Zhao JL, Sinha N., Marinov GK, Mann M., Kowalczyk MS, Galimidi RP, Du X., Erikci E., Regev A., Chowdhury K., and Baltimore D. Immunity, 2015/06/16, Volume 42, Issue 6, p.1021-32, (2015) Read More / View Supplemental Materials
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.Macosko, EZ, Basu A., Satija R., Nemesh J., Shekhar K., Goldman M., Tirosh I., Bialas AR, Kamitaki N., Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A., and McCarroll SA Cell, 2015/05/21, Volume 161, Issue 5, p.1202-14, (2015) Read More / View Supplemental Materials
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High-throughput functional genomics using CRISPR-Cas9.Shalem, O., Sanjana NE, and Zhang F. Nature reviews. Genetics, 2015/05/01, Volume 16, Issue 5, p.299-311, (2015) Read More / View Supplemental Materials
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In vivo genome editing using Staphylococcus aureus Cas9.Ran, FA, Cong L., Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B., Shalem O., Wu X., Makarova KS, Koonin EV, Sharp PA, and Zhang F. Nature, 2015/04/09, Volume 520, Issue 7546, p.186-91, (2015) Read More / View Supplemental Materials
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Linking traits based on their shared molecular mechanisms.Oren, Y., Nachshon A., Frishberg A., Wilentzik R., and Gat-Viks I. eLife, 2015/03/17, Volume 4, (2015) Read More / View Supplemental Materials
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Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis.Chen, S., Sanjana NE, Zheng K., Shalem O., Lee K., Shi X., Scott DA, Song J., Pan JQ, Weissleder R., Lee H., Zhang F., and Sharp PA Cell, 2015/03/12, Volume 160, Issue 6, p.1246-60, (2015) Read More / View Supplemental Materials
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Immunogenetics. Dynamic profiling of the protein life cycle in response to pathogens.Jovanovic, M., Rooney MS, Mertins P., Przybylski D., Chevrier N., Satija R., Rodriguez EH, Fields AP, Schwartz S., Raychowdhury R., Mumbach MR, Eisenhaure T., Rabani M., Gennert D., Lu D., Delorey T., Weissman JS, Carr SA, Hacohen N., and Regev A. Science (New York, N.Y.), 2015/03/06, Volume 347, Issue 6226, p.1259038, (2015) Read More / View Supplemental Materials
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High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies.Rabani, M., Raychowdhury R., Jovanovic M., Rooney M., Stumpo DJ, Pauli A., Hacohen N., Schier AF, Blackshear PJ, Friedman N., Amit I., and Regev A. Cell, 2014/12/18, Volume 159, Issue 7, p.1698-710, (2014) Read More / View Supplemental Materials
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Deconstructing transcriptional heterogeneity in pluripotent stem cells.Kumar, RM, Cahan P., Shalek AK, Satija R., DaleyKeyser AJ, Li H., Zhang J., Pardee K., Gennert D., Trombetta JJ, Ferrante TC, Regev A., Daley GQ, and Collins JJ Nature, 2014/12/04, Volume 516, Issue 7529, p.56-61, (2014) Read More / View Supplemental Materials
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CRISPR-Cas9 knockin mice for genome editing and cancer modeling.Platt, RJ, Chen S., Zhou Y., Yim MJ, Swiech L., Kempton HR, Dahlman JE, Parnas O., Eisenhaure TM, Jovanovic M., Graham DB, Jhunjhunwala S., Heidenreich M., Xavier RJ, Langer R., Anderson DG, Hacohen N., Regev A., Feng G., Sharp PA, et al. Cell, 2014/10/09, Volume 159, Issue 2, p.440-55, (2014) Read More / View Supplemental Materials
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Improved vectors and genome-wide libraries for CRISPR screening.Sanjana, NE, Shalem O., and Zhang F. Nature methods, 2014/08/01, Volume 11, Issue 8, p.783-4, (2014) Read More / View Supplemental Materials
Preparation of Single-Cell RNA-Seq Libraries for Next Generation Sequencing.Trombetta, JJ, Gennert D., Lu D., Satija R., Shalek AK, and Regev A. Current protocols in molecular biology / edited by Frederick M. Ausubel ... [et al.], 2014/07/01, Volume 107, p.4.22.1-4.22.17, (2014) Read More / View Supplemental Materials
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Generation of mouse models of myeloid malignancy with combinatorial genetic lesions using CRISPR-Cas9 genome editing.Heckl, D., Kowalczyk MS, Yudovich D., Belizaire R., Puram RV, McConkey ME, Thielke A., Aster J. C., Regev A., and Ebert BL Nature biotechnology, 2014/06/22, (2014) Read More / View Supplemental Materials
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Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.Patel, AP, Tirosh I., Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H., Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O., Suvà ML, Regev A., and Bernstein BE Science (New York, N.Y.), 2014/06/20, Volume 344, Issue 6190, p.1396-401, (2014) Read More / View Supplemental Materials
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Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.Shalek, AK, Satija R., Shuga J., Trombetta JJ, Gennert D., Lu D., Chen P., Gertner RS, Gaublomme JT, Yosef N., Schwartz S., Fowler B., Weaver S., Wang J., Wang X., Ding R., Raychowdhury R., Friedman N., Hacohen N., Park H., et al. Nature, 2014/06/19, Volume 509, Issue 7505, p.363-9, (2014) Read More / View Supplemental Materials
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Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.Lohr, JG, Adalsteinsson VA, Cibulskis K., Choudhury AD, Rosenberg M., Cruz-Gordillo P., Francis JM, Zhang CZ, Shalek AK, Satija R., Trombetta JJ, Lu D., Tallapragada N., Tahirova N., Kim S., Blumenstiel B., Sougnez C., Lowe A., Wong B., Auclair D., et al. Nature biotechnology, 2014/05/01, Volume 32, Issue 5, p.479-84, (2014) Read More / View Supplemental Materials
Abstract
Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms.Xiao, S., Yosef N., Yang J., Wang Y., Zhou L., Zhu C., Wu C., Baloglu E., Schmidt D., Ramesh R., Lobera M., Sundrud MS, Tsai PY, Xiang Z., Wang J., Xu Y., Lin X., Kretschmer K., Rahl PB, Young RA, et al. Immunity, 2014/04/17, Volume 40, Issue 4, p.477-89, (2014) Read More / View Supplemental Materials
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Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells.Suvà, ML, Rheinbay E., Gillespie SM, Patel AP, Wakimoto H., Rabkin SD, Riggi N., Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N., Kasif S., Beik S., Kadri S., Tirosh I., Wortman I., Shalek AK, et al. Cell, 2014/04/09, (2014) Read More / View Supplemental Materials
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The treatment-naive microbiome in new-onset Crohn's disease.Gevers, D., Kugathasan S., Denson LA, Vázquez-Baeza Y., Van Treuren W., Ren B., Schwager E., Knights D., Song SJ, Yassour M., Morgan XC, Kostic AD, Luo C., González A., McDonald D., Haberman Y., Walters T., Baker S., Rosh J., Stephens M., et al. Cell host & microbe, 2014/03/12, Volume 15, Issue 3, p.382-92, (2014) Read More / View Supplemental Materials
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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
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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
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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
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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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