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    Results: 1 to 20 of 135

    1.

    DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli.

    Lemmens K, De Bie T, Dhollander T, De Keersmaecker SC, Thijs IM, Schoofs G, De Weerdt A, De Moor B, Vanderleyden J, Collado-Vides J, Engelen K, Marchal K.

    Genome Biol. 2009;10(3):R27. Epub 2009 Mar 6.

    PMID:
    19265557
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    2.

    The condition-dependent transcriptional network in Escherichia coli.

    Lemmens K, De Bie T, Dhollander T, Monsieurs P, De Moor B, Collado-Vides J, Engelen K, Marchal K.

    Ann N Y Acad Sci. 2009 Mar;1158:29-35.

    PMID:
    19348629
    [PubMed - indexed for MEDLINE]
    3.

    Reconstruction of Escherichia coli transcriptional regulatory networks via regulon-based associations.

    Zare H, Sangurdekar D, Srivastava P, Kaveh M, Khodursky A.

    BMC Syst Biol. 2009 Apr 14;3:39.

    PMID:
    19366454
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    4.

    RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

    Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J.

    Nucleic Acids Res. 2008 Jan;36(Database issue):D120-4. Epub 2007 Dec 23.

    PMID:
    18158297
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    5.

    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]
    6.

    A comparative genomics approach to prediction of new members of regulons.

    Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo GD.

    Genome Res. 2001 Apr;11(4):566-84.

    PMID:
    11282972
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    7.

    Clustering of genes into regulons using integrated modeling-COGRIM.

    Chen G, Jensen ST, Stoeckert CJ Jr.

    Genome Biol. 2007;8(1):R4.

    PMID:
    17204163
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    8.

    RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.

    Salgado H, Gama-Castro S, Peralta-Gil M, Díaz-Peredo E, Sánchez-Solano F, Santos-Zavaleta A, Martínez-Flores I, Jiménez-Jacinto V, Bonavides-Martínez C, Segura-Salazar J, Martínez-Antonio A, Collado-Vides J.

    Nucleic Acids Res. 2006 Jan 1;34(Database issue):D394-7.

    PMID:
    16381895
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    9.

    RegulonDB (version 2.0): a database on transcriptional regulation in Escherichia coli.

    Salgado H, Santos A, Garza-Ramos U, van Helden J, Díaz E, Collado-Vides J.

    Nucleic Acids Res. 1999 Jan 1;27(1):59-60.

    PMID:
    9847141
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    10.

    Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

    Marr C, Theis FJ, Liebovitch LS, Hütt MT.

    PLoS Comput Biol. 2010 Jul 1;6:e1000836.

    PMID:
    20617198
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    11.

    Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus.

    Alkema WB, Lenhard B, Wasserman WW.

    Genome Res. 2004 Jul;14(7):1362-73.

    PMID:
    15231752
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    12.

    Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.

    Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS.

    PLoS Biol. 2007 Jan;5(1):e8.

    PMID:
    17214507
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    13.

    RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.

    Salgado H, Santos-Zavaleta A, Gama-Castro S, Millán-Zárate D, Díaz-Peredo E, Sánchez-Solano F, Pérez-Rueda E, Bonavides-Martínez C, Collado-Vides J.

    Nucleic Acids Res. 2001 Jan 1;29(1):72-4.

    PMID:
    11125053
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    14.

    RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12.

    Salgado H, Gama-Castro S, Martínez-Antonio A, Díaz-Peredo E, Sánchez-Solano F, Peralta-Gil M, Garcia-Alonso D, Jiménez-Jacinto V, Santos-Zavaleta A, Bonavides-Martínez C, Collado-Vides J.

    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D303-6.

    PMID:
    14681419
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    15.

    Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.

    Baumbach J, Wittkop T, Kleindt CK, Tauch A.

    Nat Protoc. 2009;4(6):992-1005.

    PMID:
    19498379
    [PubMed - indexed for MEDLINE]
    16.

    Web-based visualisation of the transcriptional control network of Escherichia coli.

    Sosa N, Kremling A, Ratsch E, Rojas I.

    In Silico Biol. 2004;4(4):507-15.

    PMID:
    15506999
    [PubMed - indexed for MEDLINE]
    Free Article
    17.

    Identifying promoter features of co-regulated genes with similar network motifs.

    Harari O, del Val C, Romero-Zaliz R, Shin D, Huang H, Groisman EA, Zwir I.

    BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S1.

    PMID:
    19426448
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    18.

    Inference of active transcriptional networks by integration of gene expression kinetics modeling and multisource data.

    Vu TT, Vohradsky J.

    Genomics. 2009 May;93(5):426-33. Epub 2009 Feb 5.

    PMID:
    19442636
    [PubMed - indexed for MEDLINE]
    19.

    Linking Cytoscape and the corynebacterial reference database CoryneRegNet.

    Baumbach J, Apeltsin L.

    BMC Genomics. 2008 Apr 21;9:184.

    PMID:
    18426593
    [PubMed - indexed for MEDLINE]
    Free PMC Article
    20.

    Modeling post-transcriptional regulation activity of small non-coding RNAs in Escherichia coli.

    Wang RS, Jin G, Zhang XS, Chen L.

    BMC Bioinformatics. 2009 Apr 29;10 Suppl 4:S6.

    PMID:
    19426454
    [PubMed - indexed for MEDLINE]
    Free PMC Article

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