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Inferring activity changes of transcription factors by binding association with sorted expression profiles.

Cheng C, Yan X, Sun F, Li LM.

BMC Bioinformatics. 2007 Nov 16;8:452.PMID: 18021409 [PubMed - indexed for MEDLINE]Related articlesFree article

Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data.

Li H, Zhan M.

Bioinformatics. 2008 Sep 1;24(17):1874-80. Epub 2008 Jun 27.PMID: 18586698 [PubMed - indexed for MEDLINE]Related articlesFree article

Systematic identification of cell cycle regulated transcription factors from microarray time series data.

Cheng C, Li LM.

BMC Genomics. 2008 Mar 3;9:116.PMID: 18315882 [PubMed - indexed for MEDLINE]Related articlesFree article

Learning position weight matrices from sequence and expression data.

Chen X, Guo L, Fan Z, Jiang T.

Comput Syst Bioinformatics Conf. 2007;6:249-60.PMID: 17951829 [PubMed - indexed for MEDLINE]Related articlesFree article

Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.

Huber BR, Bulyk ML.

BMC Bioinformatics. 2006 Apr 27;7:229.PMID: 16643658 [PubMed - indexed for MEDLINE]Related articlesFree article

Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data.

Zhang Y, Xuan J, de los Reyes BG, Clarke R, Ressom HW.

BMC Bioinformatics. 2008 Apr 21;9:203.PMID: 18426580 [PubMed - indexed for MEDLINE]Related articlesFree article

Factor analysis for gene regulatory networks and transcription factor activity profiles.

Pournara I, Wernisch L.

BMC Bioinformatics. 2007 Feb 23;8:61.PMID: 17319944 [PubMed - indexed for MEDLINE]Related articlesFree article

DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies.

Mahony S, Auron PE, Benos PV.

PLoS Comput Biol. 2007 Mar 30;3(3):e61. Epub 2007 Feb 15.PMID: 17397256 [PubMed - indexed for MEDLINE]Related articlesFree article

Motif-directed network component analysis for regulatory network inference.

Wang C, Xuan J, Chen L, Zhao P, Wang Y, Clarke R, Hoffman E.

BMC Bioinformatics. 2008;9 Suppl 1:S21.PMID: 18315853 [PubMed - indexed for MEDLINE]Related articlesFree article

Identifying regulatory targets of cell cycle transcription factors using gene expression and ChIP-chip data.

Wu WS, Li WH, Chen BS.

BMC Bioinformatics. 2007 Jun 8;8:188.PMID: 17559637 [PubMed - indexed for MEDLINE]Related articlesFree article

Bayesian variable selection for gene expression modeling with regulatory motif binding sites in neuroinflammatory events.

Liu KY, Zhou X, Kan K, Wong ST.

Neuroinformatics. 2006 Winter;4(1):95-117.PMID: 16595861 [PubMed - indexed for MEDLINE]Related articles

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP-chip data.

Liu X, Jessen WJ, Sivaganesan S, Aronow BJ, Medvedovic M.

BMC Bioinformatics. 2007 Aug 3;8:283.PMID: 17683565 [PubMed - indexed for MEDLINE]Related articlesFree article

Sequence features of DNA binding sites reveal structural class of associated transcription factor.

Narlikar L, Hartemink AJ.

Bioinformatics. 2006 Jan 15;22(2):157-63. Epub 2005 Nov 2.PMID: 16267080 [PubMed - indexed for MEDLINE]Related articlesFree article

Knowledge-guided multi-scale independent component analysis for biomarker identification.

Chen L, Xuan J, Wang C, Shih IeM, Wang Y, Zhang Z, Hoffman E, Clarke R.

BMC Bioinformatics. 2008 Oct 6;9:416.PMID: 18837990 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory.

Sayyed-Ahmad A, Tuncay K, Ortoleva PJ.

BMC Bioinformatics. 2007 Jan 23;8:20.PMID: 17244365 [PubMed - indexed for MEDLINE]Related articlesFree article

Transcription factor target prediction using multiple short expression time series from Arabidopsis thaliana.

Redestig H, Weicht D, Selbig J, Hannah MA.

BMC Bioinformatics. 2007 Nov 18;8:454.PMID: 18021423 [PubMed - indexed for MEDLINE]Related articlesFree article

A boosting approach for motif modeling using ChIP-chip data.

Hong P, Liu XS, Zhou Q, Lu X, Liu JS, Wong WH.

Bioinformatics. 2005 Jun 1;21(11):2636-43. Epub 2005 Apr 7.PMID: 15817698 [PubMed - indexed for MEDLINE]Related articlesFree article

Clustering and re-clustering for pattern discovery in gene expression data.

Ma PC, Chan KC, Chiu DK.

J Bioinform Comput Biol. 2005 Apr;3(2):281-301.PMID: 15852506 [PubMed - indexed for MEDLINE]Related articles

Method for identifying transcription factor binding sites in yeast.

Tsai HK, Huang GT, Chou MY, Lu HH, Li WH.

Bioinformatics. 2006 Jul 15;22(14):1675-81. Epub 2006 Apr 27.PMID: 16644789 [PubMed - indexed for MEDLINE]Related articlesFree article

Inferring biological functions and associated transcriptional regulators using gene set expression coherence analysis.

Kim TM, Chung YJ, Rhyu MG, Jung MH.

BMC Bioinformatics. 2007 Nov 17;8:453.PMID: 18021416 [PubMed - indexed for MEDLINE]Related articlesFree article