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Items: 1 to 20 of 28

1.

Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.

Zhou X, O'Shea EK.

Mol Cell. 2011 Jun 24;42(6):826-36. doi: 10.1016/j.molcel.2011.05.025.

2.

Incorporating nucleosomes into thermodynamic models of transcription regulation.

Raveh-Sadka T, Levo M, Segal E.

Genome Res. 2009 Aug;19(8):1480-96. doi: 10.1101/gr.088260.108. Epub 2009 May 18.

3.

Diversity and complexity in DNA recognition by transcription factors.

Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, Kuznetsov H, Wang CF, Coburn D, Newburger DE, Morris Q, Hughes TR, Bulyk ML.

Science. 2009 Jun 26;324(5935):1720-3. doi: 10.1126/science.1162327. Epub 2009 May 14.

4.

Inferring transcription factor targets from gene expression changes and predicted promoter occupancy.

Yeo ZX, Yeo HC, Yeo JK, Yeo AL, Li Y, Clarke ND.

J Comput Biol. 2009 Feb;16(2):357-68. doi: 10.1089/cmb.2008.19TT.

PMID:
19193152
5.

High-resolution DNA-binding specificity analysis of yeast transcription factors.

Zhu C, Byers KJ, McCord RP, Shi Z, Berger MF, Newburger DE, Saulrieta K, Smith Z, Shah MV, Radhakrishnan M, Philippakis AA, Hu Y, De Masi F, Pacek M, Rolfs A, Murthy T, Labaer J, Bulyk ML.

Genome Res. 2009 Apr;19(4):556-66. doi: 10.1101/gr.090233.108. Epub 2009 Jan 21.

6.

A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters.

Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, Gebbia M, Talukder S, Yang A, Mnaimneh S, Terterov D, Coburn D, Li Yeo A, Yeo ZX, Clarke ND, Lieb JD, Ansari AZ, Nislow C, Hughes TR.

Mol Cell. 2008 Dec 26;32(6):878-87. doi: 10.1016/j.molcel.2008.11.020.

7.

A quantitative model of transcription factor-activated gene expression.

Kim HD, O'Shea EK.

Nat Struct Mol Biol. 2008 Nov;15(11):1192-8. doi: 10.1038/nsmb.1500. Epub 2008 Oct 12.

8.

Nhp6p and Med3p regulate gene expression by controlling the local subunit composition of RNA polymerase II.

Xue X, Lehming N.

J Mol Biol. 2008 May 30;379(2):212-30. doi: 10.1016/j.jmb.2008.03.069. Epub 2008 Apr 7.

PMID:
18448120
9.

Chromatin decouples promoter threshold from dynamic range.

Lam FH, Steger DJ, O'Shea EK.

Nature. 2008 May 8;453(7192):246-50. doi: 10.1038/nature06867. Epub 2008 Apr 16.

10.
11.

An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

BMC Bioinformatics. 2006 Mar 7;7:113.

12.

Explicit equilibrium modeling of transcription-factor binding and gene regulation.

Granek JA, Clarke ND.

Genome Biol. 2005;6(10):R87. Epub 2005 Sep 30.

13.

Inference of combinatorial regulation in yeast transcriptional networks: a case study of sporulation.

Wang W, Cherry JM, Nochomovitz Y, Jolly E, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2005 Feb 8;102(6):1998-2003. Epub 2005 Jan 31.

14.

Transcriptional regulatory code of a eukaryotic genome.

Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, Jennings EG, Zeitlinger J, Pokholok DK, Kellis M, Rolfe PA, Takusagawa KT, Lander ES, Gifford DK, Fraenkel E, Young RA.

Nature. 2004 Sep 2;431(7004):99-104.

15.

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.

16.

Partially phosphorylated Pho4 activates transcription of a subset of phosphate-responsive genes.

Springer M, Wykoff DD, Miller N, O'Shea EK.

PLoS Biol. 2003 Nov;1(2):E28. Epub 2003 Nov 17.

17.

Global analysis of protein expression in yeast.

Ghaemmaghami S, Huh WK, Bower K, Howson RW, Belle A, Dephoure N, O'Shea EK, Weissman JS.

Nature. 2003 Oct 16;425(6959):737-41.

18.

Sum1 and Ndt80 proteins compete for binding to middle sporulation element sequences that control meiotic gene expression.

Pierce M, Benjamin KR, Montano SP, Georgiadis MM, Winter E, Vershon AK.

Mol Cell Biol. 2003 Jul;23(14):4814-25.

19.

Regulated displacement of TBP from the PHO8 promoter in vivo requires Cbf1 and the Isw1 chromatin remodeling complex.

Moreau JL, Lee M, Mahachi N, Vary J, Mellor J, Tsukiyama T, Goding CR.

Mol Cell. 2003 Jun;11(6):1609-20.

20.

A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae.

Wang W, Cherry JM, Botstein D, Li H.

Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16893-8. Epub 2002 Dec 13.

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