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Results: 1 to 20 of 182

1.

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
2.

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
3.

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
4.

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E.

PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526.

PMID:
19838305
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more.

Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J.

Nucleic Acids Res. 2013 Jan;41(Database issue):D203-13. doi: 10.1093/nar/gks1201. Epub 2012 Nov 29.

PMID:
23203884
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units).

Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Ríos J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J.

Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105. doi: 10.1093/nar/gkq1110. Epub 2010 Nov 4.

PMID:
21051347
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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
8.

Evidence classification of high-throughput protocols and confidence integration in RegulonDB.

Weiss V, Medina-Rivera A, Huerta AM, Santos-Zavaleta A, Salgado H, Morett E, Collado-Vides J.

Database (Oxford). 2013 Jan 17;2013:bas059. doi: 10.1093/database/bas059. Print 2013.

PMID:
23327937
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Extracting regulatory networks of Escherichia coli from RegulonDB.

Salgado H, Martínez-Flores I, López-Fuentes A, García-Sotelo JS, Porrón-Sotelo L, Solano H, Muñiz-Rascado L, Collado-Vides J.

Methods Mol Biol. 2012;804:179-95. doi: 10.1007/978-1-61779-361-5_10.

PMID:
22144154
[PubMed - indexed for MEDLINE]
10.

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
11.

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]
Free PMC Article
12.

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]
Free PMC Article
13.

Linking Cytoscape and the corynebacterial reference database CoryneRegNet.

Baumbach J, Apeltsin L.

BMC Genomics. 2008 Apr 21;9:184. doi: 10.1186/1471-2164-9-184.

PMID:
18426593
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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. doi: 10.1186/1752-0509-3-39.

PMID:
19366454
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

RegulonDB: a database on transcriptional regulation in Escherichia coli.

Huerta AM, Salgado H, Thieffry D, Collado-Vides J.

Nucleic Acids Res. 1998 Jan 1;26(1):55-9.

PMID:
9399800
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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. doi: 10.1093/nar/gkn837. Epub 2008 Oct 30.

PMID:
18974177
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Environmental conditions and transcriptional regulation in Escherichia coli: a physiological integrative approach.

Martínez-Antonio A, Salgado H, Gama-Castro S, Gutiérrez-Ríos RM, Jiménez-Jacinto V, Collado-Vides J.

Biotechnol Bioeng. 2003 Dec 30;84(7):743-9.

PMID:
14708114
[PubMed - indexed for MEDLINE]
18.

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.

Thieffry D, Salgado H, Huerta AM, Collado-Vides J.

Bioinformatics. 1998 Jun;14(5):391-400.

PMID:
9682052
[PubMed - indexed for MEDLINE]
Free Article
19.

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. doi: 10.1186/gb-2009-10-3-r27. Epub 2009 Mar 6.

PMID:
19265557
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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]
Free PMC Article

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