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The comprehensive updated regulatory network of Escherichia coli K-12.

Salgado H, Santos-Zavaleta A, Gama-Castro S, Peralta-Gil M, Peñaloza-Spínola MI, Martínez-Antonio A, Karp PD, Collado-Vides J.

BMC Bioinformatics. 2006 Jan 6;7:5.PMID: 16398937 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

EcoCyc: a comprehensive database resource for Escherichia coli.

Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD.

Nucleic Acids Res. 2005 Jan 1;33(Database issue):D334-7.PMID: 15608210 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Automatic reconstruction of a bacterial regulatory network using Natural Language Processing.

Rodríguez-Penagos C, Salgado H, Martínez-Flores I, Collado-Vides J.

BMC Bioinformatics. 2007 Aug 7;8:293.PMID: 17683642 [PubMed - indexed for MEDLINE]Related articlesFree article

Multidimensional annotation of the Escherichia coli K-12 genome.

Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J.

Nucleic Acids Res. 2007;35(22):7577-90. Epub 2007 Oct 16.PMID: 17940092 [PubMed - indexed for MEDLINE]Related articlesFree article

EcoCyc: a comprehensive view of Escherichia coli biology.

Keseler IM, Bonavides-Martínez C, Collado-Vides J, Gama-Castro S, Gunsalus RP, Johnson DA, Krummenacker M, Nolan LM, Paley S, Paulsen IT, Peralta-Gil M, Santos-Zavaleta A, Shearer AG, Karp PD.

Nucleic Acids Res. 2009 Jan;37(Database issue):D464-70. Epub 2008 Oct 30.PMID: 18974181 [PubMed - indexed for MEDLINE]Related articlesFree article

CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.

Baumbach J.

BMC Bioinformatics. 2007 Nov 6;8:429.PMID: 17986320 [PubMed - indexed for MEDLINE]Related articlesFree article

A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli.

Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z.

PLoS Comput Biol. 2008 Mar 28;4(3):e1000044.PMID: 18369434 [PubMed - indexed for MEDLINE]Related articlesFree article

RegulonDB (version 3.0): transcriptional regulation and operon organization in Escherichia coli K-12.

Salgado H, Santos-Zavaleta A, Gama-Castro S, Millán-Zárate D, Blattner FR, Collado-Vides J.

Nucleic Acids Res. 2000 Jan 1;28(1):65-7.PMID: 10592182 [PubMed - indexed for MEDLINE]Related articlesFree article

Predicting protein linkages in bacteria: which method is best depends on task.

Karimpour-Fard A, Leach SM, Gill RT, Hunter LE.

BMC Bioinformatics. 2008 Sep 24;9:397.PMID: 18816389 [PubMed - indexed for MEDLINE]Related articlesFree article

Discovering functional gene expression patterns in the metabolic network of Escherichia coli with wavelets transforms.

König R, Schramm G, Oswald M, Seitz H, Sager S, Zapatka M, Reinelt G, Eils R.

BMC Bioinformatics. 2006 Mar 8;7:119.PMID: 16524469 [PubMed - indexed for MEDLINE]Related articlesFree article

An extended transcriptional regulatory network of Escherichia coli and analysis of its hierarchical structure and network motifs.

Ma HW, Kumar B, Ditges U, Gunzer F, Buer J, Zeng AP.

Nucleic Acids Res. 2004 Dec 16;32(22):6643-9. Print 2004.PMID: 15604458 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

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]Related articlesFree article

EcID. A database for the inference of functional interactions in E. coli.

Andres Leon E, Ezkurdia I, García B, Valencia A, Juan D.

Nucleic Acids Res. 2009 Jan;37(Database issue):D629-35. Epub 2008 Nov 12.PMID: 19004873 [PubMed - indexed for MEDLINE]Related articlesFree article

Interplay between network structures, regulatory modes and sensing mechanisms of transcription factors in the transcriptional regulatory network of E. coli.

Balaji S, Babu MM, Aravind L.

J Mol Biol. 2007 Sep 28;372(4):1108-22. Epub 2007 Jul 3.PMID: 17706247 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

Phenotype prediction in regulated metabolic networks.

Kaleta C, Centler F, di Fenizio PS, Dittrich P.

BMC Syst Biol. 2008 Apr 25;2:37.PMID: 18439260 [PubMed - indexed for MEDLINE]Related articlesFree article

The Modular Organization of Protein Interactions in Escherichia coli.

Peregrín-Alvarez JM, Xiong X, Su C, Parkinson J.

PLoS Comput Biol. 2009 Oct;5(10):e1000523. Epub 2009 Oct 2.PMID: 19798435 [PubMed - indexed for MEDLINE]Related articlesFree article