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Items: 1 to 20 of 73

1.

One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data.

Dümcke S, Seizl M, Etzold S, Pirkl N, Martin DE, Cramer P, Tresch A.

Nucleic Acids Res. 2012 Oct;40(18):8883-92. doi: 10.1093/nar/gks695. Epub 2012 Jul 25.

2.

Genome-wide inference of transcription factor-DNA binding specificity in cell regeneration using a combination strategy.

Wang X, Zhang A, Ren W, Chen C, Dong J.

Chem Biol Drug Des. 2012 Nov;80(5):734-44. doi: 10.1111/cbdd.12013. Epub 2012 Sep 10.

PMID:
22863142
3.
4.

Genome-wide prediction and characterization of interactions between transcription factors in Saccharomyces cerevisiae.

Yu X, Lin J, Masuda T, Esumi N, Zack DJ, Qian J.

Nucleic Acids Res. 2006 Feb 6;34(3):917-27. Print 2006.

5.
6.

Identification of context-specific gene regulatory networks with GEMULA--gene expression modeling using LAsso.

Geeven G, van Kesteren RE, Smit AB, de Gunst MC.

Bioinformatics. 2012 Jan 15;28(2):214-21. doi: 10.1093/bioinformatics/btr641. Epub 2011 Nov 21.

PMID:
22106333
7.

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.

8.

Transcriptome network component analysis with limited microarray data.

Galbraith SJ, Tran LM, Liao JC.

Bioinformatics. 2006 Aug 1;22(15):1886-94. Epub 2006 Jun 9.

PMID:
16766556
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
11.

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.

12.

RIP: the regulatory interaction predictor--a machine learning-based approach for predicting target genes of transcription factors.

Bauer T, Eils R, König R.

Bioinformatics. 2011 Aug 15;27(16):2239-47. doi: 10.1093/bioinformatics/btr366. Epub 2011 Jun 20.

PMID:
21690103
13.

Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.

Moxley JF, Jewett MC, Antoniewicz MR, Villas-Boas SG, Alper H, Wheeler RT, Tong L, Hinnebusch AG, Ideker T, Nielsen J, Stephanopoulos G.

Proc Natl Acad Sci U S A. 2009 Apr 21;106(16):6477-82. doi: 10.1073/pnas.0811091106. Epub 2009 Apr 3.

14.

Modelling the network of cell cycle transcription factors in the yeast Saccharomyces cerevisiae.

Cokus S, Rose S, Haynor D, Grønbech-Jensen N, Pellegrini M.

BMC Bioinformatics. 2006 Aug 16;7:381.

15.

Mcm1p binding sites in the ARG1 promoter positively regulate ARG1 transcription and S. cerevisiae growth in the absence of arginine and Gcn4p.

Hong S, Yoon S.

Amino Acids. 2011 Feb;40(2):623-31. doi: 10.1007/s00726-010-0687-z. Epub 2010 Jul 13.

PMID:
20625780
16.

Genome-wide analysis of the cis-regulatory modules of divergent gene pairs in yeast.

Su CH, Shih CH, Chang TH, Tsai HK.

Genomics. 2010 Dec;96(6):352-61. doi: 10.1016/j.ygeno.2010.08.008. Epub 2010 Sep 6.

17.

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.

18.

An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors.

Yang HT, Hsu CP, Hwang MJ.

J Biochem. 2007 Aug;142(2):135-44. Epub 2007 Jul 25.

PMID:
17652330
19.

Gcn4p-mediated transcriptional repression of ribosomal protein genes under amino-acid starvation.

Joo YJ, Kim JH, Kang UB, Yu MH, Kim J.

EMBO J. 2011 Mar 2;30(5):859-72. doi: 10.1038/emboj.2010.332. Epub 2010 Dec 24.

20.

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.

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