Shibata Y - Search Results

1

Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.

Shibata Y, Sheffield NC, Fedrigo O, Babbitt CC, Wortham M, Tewari AK, London D, Song L, Lee BK, Iyer VR, Parker SC, Margulies EH, Wray GA, Furey TS, Crawford GE. Shibata Y, et al. PLoS Genet. 2012 Jun;8(6):e1002789. doi: 10.1371/journal.pgen.1002789. Epub 2012 Jun 28. PLoS Genet. 2012. PMID: 22761590 Free PMC article.

2

Evidence for nucleosome depletion at active regulatory regions genome-wide.

Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. Lee CK, et al. Among authors: shibata y. Nat Genet. 2004 Aug;36(8):900-5. doi: 10.1038/ng1400. Epub 2004 Jul 11. Nat Genet. 2004. PMID: 15247917

3

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

Shibata Y, Crawford GE. Shibata Y, et al. Methods Mol Biol. 2009;556:177-90. doi: 10.1007/978-1-60327-192-9_13. Methods Mol Biol. 2009. PMID: 19488879

4

Epigenetic instability of cytokine and transcription factor gene loci underlies plasticity of the T helper 17 cell lineage.

Mukasa R, Balasubramani A, Lee YK, Whitley SK, Weaver BT, Shibata Y, Crawford GE, Hatton RD, Weaver CT. Mukasa R, et al. Among authors: shibata y. Immunity. 2010 May 28;32(5):616-27. doi: 10.1016/j.immuni.2010.04.016. Epub 2010 May 13. Immunity. 2010. PMID: 20471290 Free PMC article.

5

Modular utilization of distal cis-regulatory elements controls Ifng gene expression in T cells activated by distinct stimuli.

Balasubramani A, Shibata Y, Crawford GE, Baldwin AS, Hatton RD, Weaver CT. Balasubramani A, et al. Among authors: shibata y. Immunity. 2010 Jul 23;33(1):35-47. doi: 10.1016/j.immuni.2010.07.004. Immunity. 2010. PMID: 20643337 Free PMC article.

6

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium. ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19. PLoS Biol. 2011. PMID: 21526222 Free PMC article.

7

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.

Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, Lee BK, Sheffield NC, Gräf S, Huss M, Keefe D, Liu Z, London D, McDaniell RM, Shibata Y, Showers KA, Simon JM, Vales T, Wang T, Winter D, Zhang Z, Clarke ND, Birney E, Iyer VR, Crawford GE, Lieb JD, Furey TS. Song L, et al. Among authors: shibata y. Genome Res. 2011 Oct;21(10):1757-67. doi: 10.1101/gr.121541.111. Epub 2011 Jul 12. Genome Res. 2011. PMID: 21750106 Free PMC article.

8

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.

Wu W, Cheng Y, Keller CA, Ernst J, Kumar SA, Mishra T, Morrissey C, Dorman CM, Chen KB, Drautz D, Giardine B, Shibata Y, Song L, Pimkin M, Crawford GE, Furey TS, Kellis M, Miller W, Taylor J, Schuster SC, Zhang Y, Chiaromonte F, Blobel GA, Weiss MJ, Hardison RC. Wu W, et al. Among authors: shibata y. Genome Res. 2011 Oct;21(10):1659-71. doi: 10.1101/gr.125088.111. Epub 2011 Jul 27. Genome Res. 2011. PMID: 21795386 Free PMC article.

9

Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.

Tewari AK, Yardimci GG, Shibata Y, Sheffield NC, Song L, Taylor BS, Georgiev SG, Coetzee GA, Ohler U, Furey TS, Crawford GE, Febbo PG. Tewari AK, et al. Among authors: shibata y. Genome Biol. 2012 Oct 3;13(10):R88. doi: 10.1186/gb-2012-13-10-r88. Genome Biol. 2012. PMID: 23034120 Free PMC article.

10

Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription.

Balasubramani A, Winstead CJ, Turner H, Janowski KM, Harbour SN, Shibata Y, Crawford GE, Hatton RD, Weaver CT. Balasubramani A, et al. Among authors: shibata y. PLoS Genet. 2014 Jan;10(1):e1003969. doi: 10.1371/journal.pgen.1003969. Epub 2014 Jan 9. PLoS Genet. 2014. PMID: 24415943 Free PMC article.

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