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Results: 1 to 20 of 128

1.

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.

PMID:
19158363
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights.

Gordân R, Murphy KF, McCord RP, Zhu C, Vedenko A, Bulyk ML.

Genome Biol. 2011 Dec 21;12(12):R125. doi: 10.1186/gb-2011-12-12-r125.

PMID:
22189060
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Identifying combinatorial regulation of transcription factors and binding motifs.

Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ.

Genome Biol. 2004;5(8):R56. Epub 2004 Jul 28.

PMID:
15287978
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
19652015
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Genome-wide expression profiling, in vivo DNA binding analysis, and probabilistic motif prediction reveal novel Abf1 target genes during fermentation, respiration, and sporulation in yeast.

Schlecht U, Erb I, Demougin P, Robine N, Borde V, van Nimwegen E, Nicolas A, Primig M.

Mol Biol Cell. 2008 May;19(5):2193-207. doi: 10.1091/mbc.E07-12-1242. Epub 2008 Feb 27.

PMID:
18305101
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Integrating genomic data to predict transcription factor binding.

Holloway DT, Kon M, DeLisi C.

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

PMID:
16362910
[PubMed - indexed for MEDLINE]
7.

Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification.

Haverty PM, Hansen U, Weng Z.

Nucleic Acids Res. 2004 Jan 2;32(1):179-88. Print 2004.

PMID:
14704355
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.

Liu XS, Brutlag DL, Liu JS.

Nat Biotechnol. 2002 Aug;20(8):835-9. Epub 2002 Jul 8.

PMID:
12101404
[PubMed - indexed for MEDLINE]
9.

Mapping functional transcription factor networks from gene expression data.

Haynes BC, Maier EJ, Kramer MH, Wang PI, Brown H, Brent MR.

Genome Res. 2013 Aug;23(8):1319-28. doi: 10.1101/gr.150904.112. Epub 2013 May 1.

PMID:
23636944
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Identification of transcription factor targets by phenotypic activation and microarray expression profiling in yeast.

Chua G.

Methods Mol Biol. 2009;548:19-35. doi: 10.1007/978-1-59745-540-4_2.

PMID:
19521817
[PubMed - indexed for MEDLINE]
11.

Differences in local genomic context of bound and unbound motifs.

Hansen L, Mariño-Ramírez L, Landsman D.

Gene. 2012 Sep 10;506(1):125-34. doi: 10.1016/j.gene.2012.06.005. Epub 2012 Jun 10.

PMID:
22692006
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.

de Boer CG, Hughes TR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D169-79. doi: 10.1093/nar/gkr993. Epub 2011 Nov 18.

PMID:
22102575
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

High-resolution mapping of transcription factor binding sites on native chromatin.

Kasinathan S, Orsi GA, Zentner GE, Ahmad K, Henikoff S.

Nat Methods. 2014 Feb;11(2):203-9. doi: 10.1038/nmeth.2766. Epub 2013 Dec 15.

PMID:
24336359
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Computational identification of combinatorial regulation and transcription factor binding sites.

Ryu T, Kim Y, Kim DW, Lee D.

Biotechnol Bioeng. 2007 Aug 15;97(6):1594-602.

PMID:
17252601
[PubMed - indexed for MEDLINE]
15.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data.

He X, Chen CC, Hong F, Fang F, Sinha S, Ng HH, Zhong S.

PLoS One. 2009 Dec 1;4(12):e8155. doi: 10.1371/journal.pone.0008155.

PMID:
19956545
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Functional characterization of variations on regulatory motifs.

Lapidot M, Mizrahi-Man O, Pilpel Y.

PLoS Genet. 2008 Mar 7;4(3):e1000018. doi: 10.1371/journal.pgen.1000018. Erratum in: PLoS Genet. 2008 Jun;4(6). doi: 10.1371/annotation/99662172-8f18-4bfb-ad0f-79ed1d69fffd. Michal, Lapidot [corrected to Lapidot, Michal].

PMID:
18369443
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Transcriptional regulatory networks in Saccharomyces cerevisiae.

Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA.

Science. 2002 Oct 25;298(5594):799-804.

PMID:
12399584
[PubMed - indexed for MEDLINE]
Free Article
18.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

PMID:
16477324
[PubMed - indexed for MEDLINE]
Free PMC Article
19.
20.

Nucleosome free regions in yeast promoters result from competitive binding of transcription factors that interact with chromatin modifiers.

Ozonov EA, van Nimwegen E.

PLoS Comput Biol. 2013;9(8):e1003181. doi: 10.1371/journal.pcbi.1003181. Epub 2013 Aug 22.

PMID:
23990766
[PubMed - indexed for MEDLINE]
Free PMC Article

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