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Items: 1 to 20 of 90

1.

Inferring condition-specific transcription factor function from DNA binding and gene expression data.

McCord RP, Berger MF, Philippakis AA, Bulyk ML.

Mol Syst Biol. 2007;3:100. Epub 2007 Apr 17. Erratum in: Mol Syst Biol. 2010;6:362.

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.

3.
4.

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.

5.

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast.

Tsai ZT, Shiu SH, Tsai HK.

PLoS Comput Biol. 2015 Aug 20;11(8):e1004418. doi: 10.1371/journal.pcbi.1004418. eCollection 2015 Aug.

6.

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.

7.

Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression.

Boorsma A, Lu XJ, Zakrzewska A, Klis FM, Bussemaker HJ.

PLoS One. 2008 Sep 3;3(9):e3112. doi: 10.1371/journal.pone.0003112.

8.

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
9.

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.

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
12.

The YEASTRACT database: an upgraded information system for the analysis of gene and genomic transcription regulation in Saccharomyces cerevisiae.

Teixeira MC, Monteiro PT, Guerreiro JF, Gonçalves JP, Mira NP, dos Santos SC, Cabrito TR, Palma M, Costa C, Francisco AP, Madeira SC, Oliveira AL, Freitas AT, Sá-Correia I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D161-6. doi: 10.1093/nar/gkt1015. Epub 2013 Oct 28.

13.

Uncovering transcriptional interactions via an adaptive fuzzy logic approach.

Chuang CL, Hung K, Chen CM, Shieh GS.

BMC Bioinformatics. 2009 Dec 6;10:400. doi: 10.1186/1471-2105-10-400.

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.

The transcriptional network activated by Cln3 cyclin at the G1-to-S transition of the yeast cell cycle.

Ferrezuelo F, Colomina N, Futcher B, Aldea M.

Genome Biol. 2010;11(6):R67. doi: 10.1186/gb-2010-11-6-r67. Epub 2010 Jun 23.

16.
17.

Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets.

Roy S, Heinrich K, Phan V, Berry MW, Homayouni R.

BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S19. doi: 10.1186/1471-2105-12-S10-S19.

18.
19.

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.

20.

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.

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