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    Results: 1 to 20 of 173

    1.

    Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules.

    Boeva V, Clément J, Régnier M, Roytberg MA, Makeev VJ.

    Algorithms Mol Biol. 2007 Oct 10;2:13.PMID: 17927813 [PubMed]Related articlesFree article

    2.

    Searching for statistically significant regulatory modules.

    Bailey TL, Noble WS.

    Bioinformatics. 2003 Oct;19 Suppl 2:ii16-25.PMID: 14534166 [PubMed - indexed for MEDLINE]Related articlesFree article

    3.

    MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs.

    Hu J, Hu H, Li X.

    Nucleic Acids Res. 2008 Aug;36(13):4488-97. Epub 2008 Jul 7.PMID: 18606616 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    Statistical significance of cis-regulatory modules.

    Schones DE, Smith AD, Zhang MQ.

    BMC Bioinformatics. 2007 Jan 22;8:19.PMID: 17241466 [PubMed - indexed for MEDLINE]Related articlesFree article

    5.

    On counting position weight matrix matches in a sequence, with application to discriminative motif finding.

    Sinha S.

    Bioinformatics. 2006 Jul 15;22(14):e454-63.PMID: 16873507 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    Computational methods for the detection of cis-regulatory modules.

    Van Loo P, Marynen P.

    Brief Bioinform. 2009 Sep;10(5):509-24. Epub 2009 Jun 4. Review.PMID: 19498042 [PubMed - indexed for MEDLINE]Related articles

    7.

    Statistical detection of cooperative transcription factors with similarity adjustment.

    Pape UJ, Klein H, Vingron M.

    Bioinformatics. 2009 Aug 15;25(16):2103-9. Epub 2009 Mar 13.PMID: 19286833 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

    Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

    BMC Bioinformatics. 2009 Jul 7;10:208.PMID: 19583839 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    Identifying cis-regulatory modules by combining comparative and compositional analysis of DNA.

    Pierstorff N, Bergman CM, Wiehe T.

    Bioinformatics. 2006 Dec 1;22(23):2858-64. Epub 2006 Oct 10.PMID: 17032682 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    Prediction of cis-regulatory elements: from high-information content analysis to motif identification.

    Li G, Lu J, Olman V, Xu Y.

    J Bioinform Comput Biol. 2007 Aug;5(4):817-38.PMID: 17787058 [PubMed - indexed for MEDLINE]Related articles

    11.

    Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression.

    Blanchette M, Bataille AR, Chen X, Poitras C, Laganière J, Lefèbvre C, Deblois G, Giguère V, Ferretti V, Bergeron D, Coulombe B, Robert F.

    Genome Res. 2006 May;16(5):656-68. Epub 2006 Apr 10.PMID: 16606704 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.

    Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ.

    Bioinformatics. 2005 May 15;21(10):2240-5. Epub 2005 Feb 22.PMID: 15728117 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome.

    Berman BP, Nibu Y, Pfeiffer BD, Tomancak P, Celniker SE, Levine M, Rubin GM, Eisen MB.

    Proc Natl Acad Sci U S A. 2002 Jan 22;99(2):757-62.PMID: 11805330 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    MATLIGN: a motif clustering, comparison and matching tool.

    Kankainen M, Löytynoja A.

    BMC Bioinformatics. 2007 Jun 8;8:189.PMID: 17559640 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the Drosophila genome: the fluffy-tail test.

    Abnizova I, te Boekhorst R, Walter K, Gilks WR.

    BMC Bioinformatics. 2005 Apr 27;6:109.PMID: 15857505 [PubMed - indexed for MEDLINE]Related articlesFree article

    16.

    Cross-species de novo identification of cis-regulatory modules with GibbsModule: application to gene regulation in embryonic stem cells.

    Xie D, Cai J, Chia NY, Ng HH, Zhong S.

    Genome Res. 2008 Aug;18(8):1325-35. Epub 2008 May 15.PMID: 18490265 [PubMed - indexed for MEDLINE]Related articlesFree article

    17.

    Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs.

    Wilczynski B, Dojer N, Patelak M, Tiuryn J.

    BMC Bioinformatics. 2009 Mar 10;10:82.PMID: 19284541 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    CompMoby: comparative MobyDick for detection of cis-regulatory motifs.

    Chaivorapol C, Melton C, Wei G, Yeh RF, Ramalho-Santos M, Blelloch R, Li H.

    BMC Bioinformatics. 2008 Oct 27;9:455.PMID: 18950538 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors.

    Yu X, Lin J, Zack DJ, Qian J.

    BMC Bioinformatics. 2007 Nov 9;8:437.PMID: 17996093 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Efficient representation and P-value computation for high-order Markov motifs.

    da Fonseca PG, Guimarães KS, Sagot MF.

    Bioinformatics. 2008 Aug 15;24(16):i160-6.PMID: 18689819 [PubMed - indexed for MEDLINE]Related articlesFree article

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