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Items: 1 to 20 of 107

1.

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z.

Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112.

2.

CTCF-mediated functional chromatin interactome in pluripotent cells.

Handoko L, Xu H, Li G, Ngan CY, Chew E, Schnapp M, Lee CW, Ye C, Ping JL, Mulawadi F, Wong E, Sheng J, Zhang Y, Poh T, Chan CS, Kunarso G, Shahab A, Bourque G, Cacheux-Rataboul V, Sung WK, Ruan Y, Wei CL.

Nat Genet. 2011 Jun 19;43(7):630-8. doi: 10.1038/ng.857. Erratum in: Nat Genet. 2011 Aug;43(8):815.

3.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

Martin D, Pantoja C, Fernández Miñán A, Valdes-Quezada C, Moltó E, Matesanz F, Bogdanović O, de la Calle-Mustienes E, Domínguez O, Taher L, Furlan-Magaril M, Alcina A, Cañón S, Fedetz M, Blasco MA, Pereira PS, Ovcharenko I, Recillas-Targa F, Montoliu L, Manzanares M, Guigó R, Serrano M, Casares F, Gómez-Skarmeta JL.

Nat Struct Mol Biol. 2011 Jun;18(6):708-14. doi: 10.1038/nsmb.2059. Epub 2011 May 22. Erratum in: Nat Struct Mol Biol. 2011 Sep;18(9):1084.

4.

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

ENCODE Project Consortium.

PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19.

5.

Genome-wide analysis of transcription factor E2F1 mutant proteins reveals that N- and C-terminal protein interaction domains do not participate in targeting E2F1 to the human genome.

Cao AR, Rabinovich R, Xu M, Xu X, Jin VX, Farnham PJ.

J Biol Chem. 2011 Apr 8;286(14):11985-96. doi: 10.1074/jbc.M110.217158. Epub 2011 Feb 10.

6.

Transcriptional regulation by GATA1 and GATA2 during erythropoiesis.

Suzuki M, Shimizu R, Yamamoto M.

Int J Hematol. 2011 Feb;93(2):150-5. doi: 10.1007/s12185-011-0770-6. Epub 2011 Feb 1.

PMID:
21279818
7.

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis.

Lee BK, Bhinge AA, Iyer VR.

Nucleic Acids Res. 2011 May;39(9):3558-73. doi: 10.1093/nar/gkq1313. Epub 2011 Jan 18.

8.

Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells.

Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y.

PLoS One. 2010 Jul 26;5(7):e11794. doi: 10.1371/journal.pone.0011794.

9.

Sequence features that drive human promoter function and tissue specificity.

Landolin JM, Johnson DS, Trinklein ND, Aldred SF, Medina C, Shulha H, Weng Z, Myers RM.

Genome Res. 2010 Jul;20(7):890-8. doi: 10.1101/gr.100370.109. Epub 2010 May 25.

10.

GREAT improves functional interpretation of cis-regulatory regions.

McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G.

Nat Biotechnol. 2010 May;28(5):495-501. doi: 10.1038/nbt.1630. Epub 2010 May 2.

11.

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.

Genome Res. 2010 May;20(5):565-77. doi: 10.1101/gr.104471.109. Epub 2010 Apr 2.

12.

Heritable individual-specific and allele-specific chromatin signatures in humans.

McDaniell R, Lee BK, Song L, Liu Z, Boyle AP, Erdos MR, Scott LJ, Morken MA, Kucera KS, Battenhouse A, Keefe D, Collins FS, Willard HF, Lieb JD, Furey TS, Crawford GE, Iyer VR, Birney E.

Science. 2010 Apr 9;328(5975):235-9. doi: 10.1126/science.1184655. Epub 2010 Mar 18.

13.

Variation in transcription factor binding among humans.

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M.

Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar 18.

14.

Critical requirement of GABPalpha for normal T cell development.

Yu S, Zhao DM, Jothi R, Xue HH.

J Biol Chem. 2010 Apr 2;285(14):10179-88. doi: 10.1074/jbc.M109.088740. Epub 2010 Feb 5.

15.

ENCODE whole-genome data in the UCSC Genome Browser.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. doi: 10.1093/nar/gkp961. Epub 2009 Nov 17.

16.

CTCF: master weaver of the genome.

Phillips JE, Corces VG.

Cell. 2009 Jun 26;137(7):1194-211. doi: 10.1016/j.cell.2009.06.001. Review.

17.

Assessing phylogenetic motif models for predicting transcription factor binding sites.

Hawkins J, Grant C, Noble WS, Bailey TL.

Bioinformatics. 2009 Jun 15;25(12):i339-47. doi: 10.1093/bioinformatics/btp201.

18.

Statistical detection of cooperative transcription factors with similarity adjustment.

Pape UJ, Klein H, Vingron M.

Bioinformatics. 2009 Aug 15;25(16):2103-9. doi: 10.1093/bioinformatics/btp143. Epub 2009 Mar 13.

19.

E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites.

Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ.

Genome Res. 2008 Nov;18(11):1763-77. doi: 10.1101/gr.080622.108. Epub 2008 Oct 3.

20.

Model-based analysis of ChIP-Seq (MACS).

Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS.

Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.

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