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Results: 1 to 20 of 368

1.

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
2.

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
3.

Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape.

Gordân R, Shen N, Dror I, Zhou T, Horton J, Rohs R, Bulyk ML.

Cell Rep. 2013 Apr 25;3(4):1093-104. doi: 10.1016/j.celrep.2013.03.014. Epub 2013 Apr 4.

PMID:
23562153
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses.

Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL.

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3084-93. doi: 10.1073/pnas.1212457109. Epub 2012 Oct 10.

PMID:
23054834
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
6.

Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex.

Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML.

Mol Syst Biol. 2011 Dec 6;7:555. doi: 10.1038/msb.2011.89.

PMID:
22146299
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

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
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.

De novo motif discovery facilitates identification of interactions between transcription factors in Saccharomyces cerevisiae.

Chen MJ, Chou LC, Hsieh TT, Lee DD, Liu KW, Yu CY, Oyang YJ, Tsai HK, Chen CY.

Bioinformatics. 2012 Mar 1;28(5):701-8. doi: 10.1093/bioinformatics/bts002. Epub 2012 Jan 11.

PMID:
22238267
[PubMed - indexed for MEDLINE]
Free Article
11.

A basic helix-loop-helix-leucine zipper transcription complex in yeast functions in a signaling pathway from mitochondria to the nucleus.

Jia Y, Rothermel B, Thornton J, Butow RA.

Mol Cell Biol. 1997 Mar;17(3):1110-7.

PMID:
9032238
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The GCN4 bZIP can bind to noncognate gene regulatory sequences.

Fedorova AV, Chan IS, Shin JA.

Biochim Biophys Acta. 2006 Jul;1764(7):1252-9. Epub 2006 May 4.

PMID:
16784907
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions.

Agius P, Arvey A, Chang W, Noble WS, Leslie C.

PLoS Comput Biol. 2010 Sep 9;6(9). pii: e1000916. doi: 10.1371/journal.pcbi.1000916.

PMID:
20838582
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
15.

Improved protein-binding microarrays for the identification of DNA-binding specificities of transcription factors.

Godoy M, Franco-Zorrilla JM, Pérez-Pérez J, Oliveros JC, Lorenzo O, Solano R.

Plant J. 2011 May;66(4):700-11. doi: 10.1111/j.1365-313X.2011.04519.x. Epub 2011 Mar 9.

PMID:
21284757
[PubMed - indexed for MEDLINE]
16.

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]
17.

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
18.

DNA binding site of the yeast heteromeric Ino2p/Ino4p basic helix-loop-helix transcription factor: structural requirements as defined by saturation mutagenesis.

Schüller HJ, Richter K, Hoffmann B, Ebbert R, Schweizer E.

FEBS Lett. 1995 Aug 14;370(1-2):149-52.

PMID:
7649294
[PubMed - indexed for MEDLINE]
Free Article
19.

Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets.

Reimand J, Vaquerizas JM, Todd AE, Vilo J, Luscombe NM.

Nucleic Acids Res. 2010 Aug;38(14):4768-77. doi: 10.1093/nar/gkq232. Epub 2010 Apr 12.

PMID:
20385592
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Graphical analysis and experimental evaluation of Saccharomyces cerevisiae PTRK1|2 and PBMH1|2 promoter region.

Gerber S, Hasenbrink G, Hendriksen W, Van Heusden P, Ludwig J, Klipp E, Lichtenberg-Fraté H.

Genome Inform. 2010 Jan;22:11-20.

PMID:
20238415
[PubMed - indexed for MEDLINE]

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