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    Results: 1 to 20 of 89

    1.

    PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.

    Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, Ticoll A, Snoddy J, Wasserman WW.

    Genome Biol. 2007;8(10):R207.

    PMID:
    17916232
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences.

    Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, McCallum A, Kirov S, Wasserman WW.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D54-60. Epub 2008 Oct 29.

    PMID:
    18971253
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation.

    Montgomery SB, Griffith OL, Sleumer MC, Bergman CM, Bilenky M, Pleasance ED, Prychyna Y, Zhang X, Jones SJ.

    Bioinformatics. 2006 Mar 1;22(5):637-40. Epub 2006 Jan 5.

    PMID:
    16397004
    [PubMed - indexed for MEDLINE]
    Free Article
    4.

    Osiris: an integrated promoter database for Oryza sativa L.

    Morris RT, O'Connor TR, Wyrick JJ.

    Bioinformatics. 2008 Dec 15;24(24):2915-7. Epub 2008 Oct 15.

    PMID:
    18922805
    [PubMed - indexed for MEDLINE]
    Free Article
    5.

    ORegAnno: an open-access community-driven resource for regulatory annotation.

    Griffith OL, Montgomery SB, Bernier B, Chu B, Kasaian K, Aerts S, Mahony S, Sleumer MC, Bilenky M, Haeussler M, Griffith M, Gallo SM, Giardine B, Hooghe B, Van Loo P, Blanco E, Ticoll A, Lithwick S, Portales-Casamar E, Donaldson IJ, Robertson G, Wadelius C, De Bleser P, Vlieghe D, Halfon MS, Wasserman W, Hardison R, Bergman CM, Jones SJ; Open Regulatory Annotation Consortium.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D107-13. Epub 2007 Nov 15.

    PMID:
    18006570
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    6.

    A new generation of JASPAR, the open-access repository for transcription factor binding site profiles.

    Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B.

    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D95-7.

    PMID:
    16381983
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    TFBS: Computational framework for transcription factor binding site analysis.

    Lenhard B, Wasserman WW.

    Bioinformatics. 2002 Aug;18(8):1135-6.

    PMID:
    12176838
    [PubMed - indexed for MEDLINE]
    Free Article
    8.

    Version VI of the ESTree db: an improved tool for peach transcriptome analysis.

    Lazzari B, Caprera A, Vecchietti A, Merelli I, Barale F, Milanesi L, Stella A, Pozzi C.

    BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S9.

    PMID:
    18387211
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    ppdb: a plant promoter database.

    Yamamoto YY, Obokata J.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D977-81. Epub 2007 Oct 18.

    PMID:
    17947329
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.

    Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D102-6. Epub 2007 Nov 15.

    PMID:
    18006571
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila.

    Halfon MS, Gallo SM, Bergman CM.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D594-8. Epub 2007 Nov 26.

    PMID:
    18039705
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    TOBFAC: the database of tobacco transcription factors.

    Rushton PJ, Bokowiec MT, Laudeman TW, Brannock JF, Chen X, Timko MP.

    BMC Bioinformatics. 2008 Jan 25;9:53.

    PMID:
    18221524
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    The Innate Immune Database (IIDB).

    Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy KA, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H.

    BMC Immunol. 2008 Mar 5;9:7.

    PMID:
    18321385
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes.

    Grote A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D, Münch R.

    Nucleic Acids Res. 2009 Jan;37(Database issue):D61-5. Epub 2008 Oct 30.

    PMID:
    18974177
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    EST processing: from trace to sequence.

    Schmid R, Blaxter M.

    Methods Mol Biol. 2009;533:189-220.

    PMID:
    19277557
    [PubMed - indexed for MEDLINE]
    16.

    EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration.

    Forment J, Gilabert F, Robles A, Conejero V, Nuez F, Blanca JM.

    BMC Bioinformatics. 2008 Jan 7;9:5.

    PMID:
    18179701
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    17.

    myGRN: a database and visualisation system for the storage and analysis of developmental genetic regulatory networks.

    Bacha J, Brodie JS, Loose MW.

    BMC Dev Biol. 2009 Jun 6;9:33.

    PMID:
    19500400
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    [Bio-database literacy and its application with cis-regulatory modules to find novel drug target proteins].

    Miyazaki S.

    Yakugaku Zasshi. 2008 Nov;128(11):1525-35. Review. Japanese.

    PMID:
    18981686
    [PubMed - indexed for MEDLINE]
    Free Article
    19.

    ChIPCodis: mining complex regulatory systems in yeast by concurrent enrichment analysis of chip-on-chip data.

    Abascal F, Carmona-Saez P, Carazo JM, Pascual-Montano A.

    Bioinformatics. 2008 May 1;24(9):1208-9. Epub 2008 Mar 12.

    PMID:
    18339638
    [PubMed - indexed for MEDLINE]
    Free Article
    20.

    ISOL@: an Italian SOLAnaceae genomics resource.

    Chiusano ML, D'Agostino N, Traini A, Licciardello C, Raimondo E, Aversano M, Frusciante L, Monti L.

    BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S7.

    PMID:
    18387209
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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