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    Results: 1 to 20 of 174

    1.

    BIPAD: a web server for modeling bipartite sequence elements.

    Bi C, Rogan PK.

    BMC Bioinformatics. 2006 Feb 17;7:76.PMID: 16503993 [PubMed - indexed for MEDLINE]Related articlesFree article

    2.

    Bipartite pattern discovery by entropy minimization-based multiple local alignment.

    Bi C, Rogan PK.

    Nucleic Acids Res. 2004 Sep 23;32(17):4979-91. Print 2004. Erratum in: Nucleic Acids Res. 2004;32(17):5320. PMID: 15388800 [PubMed - indexed for MEDLINE]Related articlesFree article

    3.

    Bounded search for de novo identification of degenerate cis-regulatory elements.

    Carlson JM, Chakravarty A, Khetani RS, Gross RH.

    BMC Bioinformatics. 2006 May 15;7:254.PMID: 16700920 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    SCOPE: a web server for practical de novo motif discovery.

    Carlson JM, Chakravarty A, DeZiel CE, Gross RH.

    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W259-64. Epub 2007 May 7.PMID: 17485471 [PubMed - indexed for MEDLINE]Related articlesFree article

    5.

    Improved benchmarks for computational motif discovery.

    Sandve GK, Abul O, Walseng V, Drabløs F.

    BMC Bioinformatics. 2007 Jun 8;8:193.PMID: 17559676 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    TFBScluster: a resource for the characterization of transcriptional regulatory networks.

    Donaldson IJ, Chapman M, Göttgens B.

    Bioinformatics. 2005 Jul 1;21(13):3058-9. Epub 2005 Apr 26.PMID: 15855248 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    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

    8.

    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

    9.

    ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors.

    Papatsenko D.

    Bioinformatics. 2007 Apr 15;23(8):1032-4. Epub 2007 Feb 18.PMID: 17308342 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    Using TESS to predict transcription factor binding sites in DNA sequence.

    Schug J.

    Curr Protoc Bioinformatics. 2008 Mar;Chapter 2:Unit 2.6.PMID: 18428685 [PubMed - indexed for MEDLINE]Related articles

    11.

    Context-specific independence mixture modeling for positional weight matrices.

    Georgi B, Schliep A.

    Bioinformatics. 2006 Jul 15;22(14):e166-73.PMID: 16873468 [PubMed - indexed for MEDLINE]Related articlesFree article

    12.

    MotifCut: regulatory motifs finding with maximum density subgraphs.

    Fratkin E, Naughton BT, Brutlag DL, Batzoglou S.

    Bioinformatics. 2006 Jul 15;22(14):e150-7.PMID: 16873465 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Deltarho-web, an online tool to assess composition similarity of individual nucleic acid sequences.

    van Passel MW, Luyf AC, van Kampen AH, Bart A, van der Ende A.

    Bioinformatics. 2005 Jul 1;21(13):3053-5. Epub 2005 Apr 26.PMID: 15855249 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

    Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

    BMC Bioinformatics. 2008 Mar 26;9:170.PMID: 18366802 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    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]Related articles

    16.

    CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

    Berezikov E, Guryev V, Plasterk RH, Cuppen E.

    Genome Res. 2004 Jan;14(1):170-8. Epub 2003 Dec 12.PMID: 14672977 [PubMed - indexed for MEDLINE]Related articlesFree article

    17.

    Predicting transcription factor binding sites using local over-representation and comparative genomics.

    Defrance M, Touzet H.

    BMC Bioinformatics. 2006 Aug 31;7:396.PMID: 16945132 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences.

    Pavesi G, Zambelli F, Pesole G.

    BMC Bioinformatics. 2007 Feb 7;8:46.PMID: 17286865 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    SMASHing regulatory sites in DNA by human-mouse sequence comparisons.

    Zavolan M, Socci ND, Rajewsky N, Gaasterlamd T.

    Proc IEEE Comput Soc Bioinform Conf. 2003;2:277-86.PMID: 16452803 [PubMed - indexed for MEDLINE]Related articles

    20.

    Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements.

    Doh ST, Zhang Y, Temple MH, Cai L.

    BMC Bioinformatics. 2007 Mar 15;8:94.PMID: 17362514 [PubMed - indexed for MEDLINE]Related articlesFree article

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