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Items: 1 to 20 of 49

1.

Systematic dissection of genomic features determining transcription factor binding and enhancer function.

Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES.

Proc Natl Acad Sci U S A. 2017 Feb 14;114(7):E1291-E1300. doi: 10.1073/pnas.1621150114. Epub 2017 Jan 30.

2.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1567-1568. doi: 10.1093/nar/gkx032. No abstract available.

3.

Massively parallel digital transcriptional profiling of single cells.

Zheng GX, Terry JM, Belgrader P, Ryvkin P, Bent ZW, Wilson R, Ziraldo SB, Wheeler TD, McDermott GP, Zhu J, Gregory MT, Shuga J, Montesclaros L, Underwood JG, Masquelier DA, Nishimura SY, Schnall-Levin M, Wyatt PW, Hindson CM, Bharadwaj R, Wong A, Ness KD, Beppu LW, Deeg HJ, McFarland C, Loeb KR, Valente WJ, Ericson NG, Stevens EA, Radich JP, Mikkelsen TS, Hindson BJ, Bielas JH.

Nat Commun. 2017 Jan 16;8:14049. doi: 10.1038/ncomms14049.

4.

Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration.

Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA.

Nucleic Acids Res. 2017 Feb 17;45(3):1553-1565. doi: 10.1093/nar/gkw1226.

5.

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions.

Ernst J, Melnikov A, Zhang X, Wang L, Rogov P, Mikkelsen TS, Kellis M.

Nat Biotechnol. 2016 Nov;34(11):1180-1190. doi: 10.1038/nbt.3678. Epub 2016 Oct 3.

6.

Phenotypic Characterization of a Comprehensive Set of MAPK1/ERK2 Missense Mutants.

Brenan L, Andreev A, Cohen O, Pantel S, Kamburov A, Cacchiarelli D, Persky NS, Zhu C, Bagul M, Goetz EM, Burgin AB, Garraway LA, Getz G, Mikkelsen TS, Piccioni F, Root DE, Johannessen CM.

Cell Rep. 2016 Oct 18;17(4):1171-1183. doi: 10.1016/j.celrep.2016.09.061.

7.

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.

Ulirsch JC, Nandakumar SK, Wang L, Giani FC, Zhang X, Rogov P, Melnikov A, McDonel P, Do R, Mikkelsen TS, Sankaran VG.

Cell. 2016 Jun 2;165(6):1530-1545. doi: 10.1016/j.cell.2016.04.048.

8.

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay.

Tewhey R, Kotliar D, Park DS, Liu B, Winnicki S, Reilly SK, Andersen KG, Mikkelsen TS, Lander ES, Schaffner SF, Sabeti PC.

Cell. 2016 Jun 2;165(6):1519-1529. doi: 10.1016/j.cell.2016.04.027.

9.

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ.

Cell Syst. 2016 May 25;2(5):323-34. doi: 10.1016/j.cels.2016.04.011. Epub 2016 May 19.

10.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5364-9. doi: 10.1073/pnas.1602886113. Epub 2016 Apr 13.

11.

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.

Cell. 2015 Jul 16;162(2):412-24. doi: 10.1016/j.cell.2015.06.016.

12.

Dissecting neural differentiation regulatory networks through epigenetic footprinting.

Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A.

Nature. 2015 Feb 19;518(7539):355-9. doi: 10.1038/nature13990. Epub 2014 Dec 24.

13.

Altered chromatin occupancy of master regulators underlies evolutionary divergence in the transcriptional landscape of erythroid differentiation.

Ulirsch JC, Lacy JN, An X, Mohandas N, Mikkelsen TS, Sankaran VG.

PLoS Genet. 2014 Dec 18;10(12):e1004890. doi: 10.1371/journal.pgen.1004890. eCollection 2014 Dec.

14.

Identification of nuclear hormone receptor pathways causing insulin resistance by transcriptional and epigenomic analysis.

Kang S, Tsai LT, Zhou Y, Evertts A, Xu S, Griffin MJ, Issner R, Whitton HJ, Garcia BA, Epstein CB, Mikkelsen TS, Rosen ED.

Nat Cell Biol. 2015 Jan;17(1):44-56. doi: 10.1038/ncb3080. Epub 2014 Dec 15.

15.

Enhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples.

Matranga CB, Andersen KG, Winnicki S, Busby M, Gladden AD, Tewhey R, Stremlau M, Berlin A, Gire SK, England E, Moses LM, Mikkelsen TS, Odia I, Ehiane PE, Folarin O, Goba A, Kahn SH, Grant DS, Honko A, Hensley L, Happi C, Garry RF, Malboeuf CM, Birren BW, Gnirke A, Levin JZ, Sabeti PC.

Genome Biol. 2014;15(11):519.

16.

Massively parallel reporter assays in cultured mammalian cells.

Melnikov A, Zhang X, Rogov P, Wang L, Mikkelsen TS.

J Vis Exp. 2014 Aug 17;(90). doi: 10.3791/51719.

17.

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

Schwartz S, Mumbach MR, Jovanovic M, Wang T, Maciag K, Bushkin GG, Mertins P, Ter-Ovanesyan D, Habib N, Cacchiarelli D, Sanjana NE, Freinkman E, Pacold ME, Satija R, Mikkelsen TS, Hacohen N, Zhang F, Carr SA, Lander ES, Regev A.

Cell Rep. 2014 Jul 10;8(1):284-96. doi: 10.1016/j.celrep.2014.05.048. Epub 2014 Jun 26.

18.

Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes.

Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS.

Nucleic Acids Res. 2014 Aug;42(14):e112. doi: 10.1093/nar/gku511. Epub 2014 Jun 9.

19.

Analysis of the effects of five factors relevant to in vitro chondrogenesis of human mesenchymal stem cells using factorial design and high throughput mRNA-profiling.

Jakobsen RB, Østrup E, Zhang X, Mikkelsen TS, Brinchmann JE.

PLoS One. 2014 May 9;9(5):e96615. doi: 10.1371/journal.pone.0096615. eCollection 2014.

20.

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, Younis S, Rubin CJ, Gilbert ER, Sundström E, Ghazal A, Zhang X, Wang L, Mikkelsen TS, Andersson G, Andersson L.

PLoS One. 2014 Apr 8;9(4):e94187. doi: 10.1371/journal.pone.0094187. eCollection 2014.

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