PubMed

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

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

CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.

Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A.

BMC Genomics. 2006 Feb 14;7:24.PMID: 16478536 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articles

CoryneRegNet 3.0--an interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli.

Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A.

J Biotechnol. 2007 Apr 30;129(2):279-89. Epub 2006 Dec 20.PMID: 17229482 [PubMed - indexed for MEDLINE]Related articles

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.

Baumbach J, Tauch A, Rahmann S.

Brief Bioinform. 2009 Jan;10(1):75-83. Epub 2008 Dec 12.PMID: 19074493 [PubMed - indexed for MEDLINE]Related articles

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

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]Related articlesFree article

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.

Guziolowski C, Bourdé A, Moreews F, Siegel A.

BMC Genomics. 2009 May 26;10:244.PMID: 19470162 [PubMed - indexed for MEDLINE]Related articlesFree article

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. Review.PMID: 19381531 [PubMed - indexed for MEDLINE]Related articles

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures.

Koehler J, Rawlings C, Verrier P, Mitchell R, Skusa A, Ruegg A, Philippi S.

In Silico Biol. 2005;5(1):33-44.PMID: 15972003 [PubMed - indexed for MEDLINE]Related articlesFree article

A database and tool, IM Browser, for exploring and integrating emerging gene and protein interaction data for Drosophila.

Pacifico S, Liu G, Guest S, Parrish JR, Fotouhi F, Finley RL Jr.

BMC Bioinformatics. 2006 Apr 7;7:195.PMID: 16603075 [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

ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining.

Huan T, Sivachenko AY, Harrison SH, Chen JY.

BMC Bioinformatics. 2008 Aug 12;9 Suppl 9:S5.PMID: 18793469 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articles

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 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

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Genome Res. 2003 Nov;13(11):2498-504.PMID: 14597658 [PubMed - indexed for MEDLINE]Related articlesFree article

Exploring biological networks with Cytoscape software.

Yeung N, Cline MS, Kuchinsky A, Smoot ME, Bader GD.

Curr Protoc Bioinformatics. 2008 Sep;Chapter 8:Unit 8.13.PMID: 18819078 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article