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    Results: 1 to 20 of 118

    1.

    Text-mining assisted regulatory annotation.

    Aerts S, Haeussler M, van Vooren S, Griffith OL, Hulpiau P, Jones SJ, Montgomery SB, Bergman CM; Open Regulatory Annotation Consortium.

    Genome Biol. 2008;9(2):R31. Epub 2008 Feb 13.

    PMID:
    18271954
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    Computational identification of transcriptional regulatory elements in DNA sequence.

    GuhaThakurta D.

    Nucleic Acids Res. 2006 Jul 19;34(12):3585-98. Print 2006. Review.

    PMID:
    16855295
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    3.

    Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?

    Winnenburg R, Wächter T, Plake C, Doms A, Schroeder M.

    Brief Bioinform. 2008 Nov;9(6):466-78. Epub 2008 Dec 6. Review.

    PMID:
    19060303
    [PubMed - indexed for MEDLINE]
    Free Article
    4.

    Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements.

    Janky R, Helden J, Babu MM.

    Methods. 2009 Jul;48(3):277-86. Epub 2009 May 18.

    PMID:
    19450688
    [PubMed - indexed for MEDLINE]
    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.

    MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

    Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

    Genome Biol. 2008;9 Suppl 2:S5. Epub 2008 Sep 1.

    PMID:
    18834496
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    A systems biology approach to understanding cis-regulatory module function.

    Jeziorska DM, Jordan KW, Vance KW.

    Semin Cell Dev Biol. 2009 Sep;20(7):856-62. Epub 2009 Aug 4. Review.

    PMID:
    19660565
    [PubMed - indexed for MEDLINE]
    8.

    [Identification and mapping of cis-regulatory elements within long genomic sequences].

    Akopov SB, Chernov IP, Vetchinova AS, Bulanenkova SS, Nikolaev LG.

    Mol Biol (Mosk). 2007 Sep-Oct;41(5):787-92. Review. Russian.

    PMID:
    18240562
    [PubMed - indexed for MEDLINE]
    9.

    Computational approaches to study transcriptional regulation.

    Babu MM.

    Biochem Soc Trans. 2008 Aug;36(Pt 4):758-65. Review.

    PMID:
    18631154
    [PubMed - indexed for MEDLINE]
    10.

    Integrative mining of traditional Chinese medicine literature and MEDLINE for functional gene networks.

    Zhou X, Liu B, Wu Z, Feng Y.

    Artif Intell Med. 2007 Oct;41(2):87-104. Epub 2007 Sep 5.

    PMID:
    17804209
    [PubMed - indexed for MEDLINE]
    11.

    Annotating the regulatory genome.

    Montgomery SB, Kasaian K, Jones SJ, Griffith OL.

    Methods Mol Biol. 2010;674:313-49. Review.

    PMID:
    20827601
    [PubMed - indexed for MEDLINE]
    12.

    Genome-wide analysis of protein-DNA interactions.

    Kim TH, Ren B.

    Annu Rev Genomics Hum Genet. 2006;7:81-102. Review.

    PMID:
    16722805
    [PubMed - indexed for MEDLINE]
    13.

    CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.

    Neuweger H, Baumbach J, Albaum S, Bekel T, Dondrup M, Hüser AT, Kalinowski J, Oehm S, Pühler A, Rahmann S, Weile J, Goesmann A.

    BMC Syst Biol. 2007 Nov 22;1:55.

    PMID:
    18034885
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge.

    Krallinger M, Morgan A, Smith L, Leitner F, Tanabe L, Wilbur J, Hirschman L, Valencia A.

    Genome Biol. 2008;9 Suppl 2:S1. Epub 2008 Sep 1.

    PMID:
    18834487
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Functional genomics of the chicken--a model organism.

    Cogburn LA, Porter TE, Duclos MJ, Simon J, Burgess SC, Zhu JJ, Cheng HH, Dodgson JB, Burnside J.

    Poult Sci. 2007 Oct;86(10):2059-94. Review.

    PMID:
    17878436
    [PubMed - indexed for MEDLINE]
    Free Article
    16.

    Genomic strategies to identify mammalian regulatory sequences.

    Pennacchio LA, Rubin EM.

    Nat Rev Genet. 2001 Feb;2(2):100-9. Review.

    PMID:
    11253049
    [PubMed - indexed for MEDLINE]
    17.

    Strategies for characterising cis-regulatory elements in Xenopus.

    Khokha MK, Loots GG.

    Brief Funct Genomic Proteomic. 2005 May;4(1):58-68. Review.

    PMID:
    15975265
    [PubMed - indexed for MEDLINE]
    Free Article
    18.

    Effect of mutations on the detection of translational signals based on a communications theory approach.

    Bataineh MA, Alonso M, Huang L, Atkin GE, Menhart N.

    Conf Proc IEEE Eng Med Biol Soc. 2009;2009:3853-6.

    PMID:
    19963598
    [PubMed - indexed for MEDLINE]
    19.

    ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome.

    Hon G, Ren B, Wang W.

    PLoS Comput Biol. 2008 Oct;4(10):e1000201. Epub 2008 Oct 17.

    PMID:
    18927605
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    Charting gene regulatory networks: strategies, challenges and perspectives.

    Wei GH, Liu DP, Liang CC.

    Biochem J. 2004 Jul 1;381(Pt 1):1-12. Review.

    PMID:
    15080794
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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