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    Results: 1 to 20 of 133

    1.

    Detecting DNA regulatory motifs by incorporating positional trends in information content.

    Kechris KJ, van Zwet E, Bickel PJ, Eisen MB.

    Genome Biol. 2004;5(7):R50. Epub 2004 Jun 24.

    PMID:
    15239835
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Discovering novel cis-regulatory motifs using functional networks.

    Ettwiller LM, Rung J, Birney E.

    Genome Res. 2003 May;13(5):883-95.

    PMID:
    12727907
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    RSIR: regularized sliced inverse regression for motif discovery.

    Zhong W, Zeng P, Ma P, Liu JS, Zhu Y.

    Bioinformatics. 2005 Nov 15;21(22):4169-75. Epub 2005 Sep 15.

    PMID:
    16166098
    [PubMed - indexed for MEDLINE]
    Free Article
    4.

    PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences.

    Sinha S, Blanchette M, Tompa M.

    BMC Bioinformatics. 2004 Oct 28;5:170.

    PMID:
    15511292
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    Context specific transcription factor prediction.

    Yang E, Simcha D, Almon RR, Dubois DC, Jusko WJ, Androulakis IP.

    Ann Biomed Eng. 2007 Jun;35(6):1053-67. Epub 2007 Mar 22.

    PMID:
    17377845
    [PubMed - indexed for MEDLINE]
    6.

    Computational identification of transcription factor binding sites by functional analysis of sets of genes sharing overrepresented upstream motifs.

    CorĂ  D, Di Cunto F, Provero P, Silengo L, Caselle M.

    BMC Bioinformatics. 2004 May 11;5:57.

    PMID:
    15137914
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Characterization of binding sites of eukaryotic transcription factors.

    Qian J, Lin J, Zack DJ.

    Genomics Proteomics Bioinformatics. 2006 May;4(2):67-79.

    PMID:
    16970547
    [PubMed - indexed for MEDLINE]
    8.

    DNA motif representation with nucleotide dependency.

    Chin F, Leung HC.

    IEEE/ACM Trans Comput Biol Bioinform. 2008 Jan-Mar;5(1):110-9.

    PMID:
    18245880
    [PubMed - indexed for MEDLINE]
    9.

    Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis.

    Cliften PF, Hillier LW, Fulton L, Graves T, Miner T, Gish WR, Waterston RH, Johnston M.

    Genome Res. 2001 Jul;11(7):1175-86.

    PMID:
    11435399
    [PubMed - indexed for MEDLINE]
    Free Article
    10.

    Whole-genome discovery of transcription factor binding sites by network-level conservation.

    Pritsker M, Liu YC, Beer MA, Tavazoie S.

    Genome Res. 2004 Jan;14(1):99-108. Epub 2003 Dec 12.

    PMID:
    14672978
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Nucleotide variation of regulatory motifs may lead to distinct expression patterns.

    Segal L, Lapidot M, Solan Z, Ruppin E, Pilpel Y, Horn D.

    Bioinformatics. 2007 Jul 1;23(13):i440-9.

    PMID:
    17646329
    [PubMed - indexed for MEDLINE]
    Free Article
    12.

    A transdimensional Bayesian model for pattern recognition in DNA sequences.

    Li SM, Wakefield J, Self S.

    Biostatistics. 2008 Oct;9(4):668-85. Epub 2008 Mar 18.

    PMID:
    18349034
    [PubMed - indexed for MEDLINE]
    Free Article
    13.

    Correlating overrepresented upstream motifs to gene expression: a computational approach to regulatory element discovery in eukaryotes.

    Caselle M, Di Cunto F, Provero P.

    BMC Bioinformatics. 2002;3:7. Epub 2002 Feb 14.

    PMID:
    11876822
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

    Siddharthan R, Siggia ED, van Nimwegen E.

    PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

    PMID:
    16477324
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Regulatory motif discovery using a population clustering evolutionary algorithm.

    Lones MA, Tyrrell AM.

    IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):403-14.

    PMID:
    17666760
    [PubMed - indexed for MEDLINE]
    16.

    An improved map of conserved regulatory sites for Saccharomyces cerevisiae.

    MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD, Fraenkel E.

    BMC Bioinformatics. 2006 Mar 7;7:113.

    PMID:
    16522208
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    Supervised detection of regulatory motifs in DNA sequences.

    Keles S, van der Laan MJ, Dudoit S, Xing B, Eisen MB.

    Stat Appl Genet Mol Biol. 2003;2:Article5. Epub 2003 Aug 25.

    PMID:
    16646783
    [PubMed]
    Free Article
    18.

    rMotifGen: random motif generator for DNA and protein sequences.

    Rouchka EC, Hardin CT.

    BMC Bioinformatics. 2007 Aug 7;8:292.

    PMID:
    17683637
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    19.

    Phylogenetic motif detection by expectation-maximization on evolutionary mixtures.

    Moses AM, Chiang DY, Eisen MB.

    Pac Symp Biocomput. 2004:324-35.

    PMID:
    14992514
    [PubMed - indexed for MEDLINE]
    Free Article
    20.

    Discovering motifs in ranked lists of DNA sequences.

    Eden E, Lipson D, Yogev S, Yakhini Z.

    PLoS Comput Biol. 2007 Mar 23;3(3):e39.

    PMID:
    17381235
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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