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Items: 1 to 20 of 79

1.

Relaxed selection against accidental binding of transcription factors with conserved chromatin contexts.

Babbitt GA.

Gene. 2010 Oct 15;466(1-2):43-8. doi: 10.1016/j.gene.2010.07.002. Epub 2010 Jul 15.

PMID:
20637845
2.

Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local.

Goh WS, Orlov Y, Li J, Clarke ND.

PLoS Comput Biol. 2010 Jan 22;6(1):e1000649. doi: 10.1371/journal.pcbi.1000649.

3.

Ceres: software for the integrated analysis of transcription factor binding sites and nucleosome positions in Saccharomyces cerevisiae.

Morris RT, O'Connor TR, Wyrick JJ.

Bioinformatics. 2010 Jan 15;26(2):168-74. doi: 10.1093/bioinformatics/btp657. Epub 2009 Dec 2.

PMID:
19959498
4.
5.

Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation.

Westholm JO, Xu F, Ronne H, Komorowski J.

BMC Bioinformatics. 2008 Nov 17;9:484. doi: 10.1186/1471-2105-9-484.

6.

Insights into distinct regulatory modes of nucleosome positioning.

Dai Z, Dai X, Xiang Q, Feng J, Deng Y, Wang J.

BMC Genomics. 2009 Dec 14;10:602. doi: 10.1186/1471-2164-10-602.

7.

Genome-scale identification of nucleosome positions in S. cerevisiae.

Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ.

Science. 2005 Jul 22;309(5734):626-30. Epub 2005 Jun 16.

8.

The effects of selection against spurious transcription factor binding sites.

Hahn MW, Stajich JE, Wray GA.

Mol Biol Evol. 2003 Jun;20(6):901-6. Epub 2003 Apr 25.

PMID:
12716998
9.

Activator control of nucleosome occupancy in activation and repression of transcription.

Bryant GO, Prabhu V, Floer M, Wang X, Spagna D, Schreiber D, Ptashne M.

PLoS Biol. 2008 Dec 23;6(12):2928-39. doi: 10.1371/journal.pbio.0060317.

10.

Chromatin remodelling at promoters suppresses antisense transcription.

Whitehouse I, Rando OJ, Delrow J, Tsukiyama T.

Nature. 2007 Dec 13;450(7172):1031-5.

PMID:
18075583
11.

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals.

Halder K, Halder R, Chowdhury S.

Mol Biosyst. 2009 Dec;5(12):1703-12. doi: 10.1039/b905132e. Epub 2009 May 29.

PMID:
19587895
12.

Distinguishing direct versus indirect transcription factor-DNA interactions.

Gordân R, Hartemink AJ, Bulyk ML.

Genome Res. 2009 Nov;19(11):2090-100. doi: 10.1101/gr.094144.109. Epub 2009 Aug 3.

13.

Cbf1p is required for chromatin remodeling at promoter-proximal CACGTG motifs in yeast.

Kent NA, Eibert SM, Mellor J.

J Biol Chem. 2004 Jun 25;279(26):27116-23. Epub 2004 Apr 24.

14.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

Genome Inform. 2005;16(1):83-94.

PMID:
16362910
15.
16.

New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome.

Feng J, Dai X, Xiang Q, Dai Z, Wang J, Deng Y, He C.

BMC Genomics. 2010 Jan 15;11:33. doi: 10.1186/1471-2164-11-33.

17.
18.

Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.

He X, Chatterjee R, John S, Bravo H, Sathyanarayana BK, Biddie SC, FitzGerald PC, Stamatoyannopoulos JA, Hager GL, Vinson C.

BMC Genomics. 2013 Jun 28;14:428. doi: 10.1186/1471-2164-14-428.

19.

Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation.

Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR.

PLoS Biol. 2008 Mar 18;6(3):e65. doi: 10.1371/journal.pbio.0060065.

20.

Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective.

Dong D, Shao X, Zhang Z.

Bioinformatics. 2011 Jan 15;27(2):147-52. doi: 10.1093/bioinformatics/btq637. Epub 2010 Nov 11.

PMID:
21075748

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