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 (2007)
In: Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY, 129(2). ELSEVIER SCIENCE BV: 279-289.

Konferenzbeitrag | Veröffentlicht | Englisch
 
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DOI
Autor*in
Baumbach, Jan; Wittkop, Tobias; Rademacher, Katrin; Rahmann, Sven; Brinkrolf, KarinaUniBi; Tauch, AndreasUniBi
Einrichtung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe A. Tauch
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Institut für Bioinformatik
Stichworte
Corynebacterium glutamicum; SOS response; systems biology; regulatory network; regulation; Escherichia coli; transcriptional
Erscheinungsjahr
2007
Titel des Konferenzbandes
Journal of Biotechnology
Serien- oder Zeitschriftentitel
JOURNAL OF BIOTECHNOLOGY
Band
129
Ausgabe
2
Seite(n)
279-289
ISSN
0168-1656
Page URI
https://pub.uni-bielefeld.de/record/1594020

Zitieren

Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A. CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. In: Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. Vol 129. ELSEVIER SCIENCE BV; 2007: 279-289.
Baumbach, J., Wittkop, T., Rademacher, K., Rahmann, S., Brinkrolf, K., & Tauch, A. (2007). CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. Journal of Biotechnology, JOURNAL OF BIOTECHNOLOGY, 129, 279-289. ELSEVIER SCIENCE BV. https://doi.org/10.1016/j.jbiotec.2006.12.012
Baumbach, Jan, Wittkop, Tobias, Rademacher, Katrin, Rahmann, Sven, Brinkrolf, Karina, and Tauch, Andreas. 2007. “CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli”. In Journal of Biotechnology, 129:279-289. JOURNAL OF BIOTECHNOLOGY. ELSEVIER SCIENCE BV.
Baumbach, J., Wittkop, T., Rademacher, K., Rahmann, S., Brinkrolf, K., and Tauch, A. (2007). “CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli” in Journal of Biotechnology JOURNAL OF BIOTECHNOLOGY, vol. 129, (ELSEVIER SCIENCE BV), 279-289.
Baumbach, J., et al., 2007. CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. In Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. no.129 ELSEVIER SCIENCE BV, pp. 279-289.
J. Baumbach, et al., “CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli”, Journal of Biotechnology, JOURNAL OF BIOTECHNOLOGY, vol. 129, ELSEVIER SCIENCE BV, 2007, pp.279-289.
Baumbach, J., Wittkop, T., Rademacher, K., Rahmann, S., Brinkrolf, K., Tauch, A.: CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli. Journal of Biotechnology. JOURNAL OF BIOTECHNOLOGY. 129, p. 279-289. ELSEVIER SCIENCE BV (2007).
Baumbach, Jan, Wittkop, Tobias, Rademacher, Katrin, Rahmann, Sven, Brinkrolf, Karina, and Tauch, Andreas. “CoryneRegNet 3.0 - An interactive systems biology platform for the analysis of gene regulatory networks in corynebacteria and Escherichia coli”. Journal of Biotechnology. ELSEVIER SCIENCE BV, 2007.Vol. 129. JOURNAL OF BIOTECHNOLOGY. 279-289.

20 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Regulons of global transcription factors in Corynebacterium glutamicum.
Toyoda K, Inui M., Appl Microbiol Biotechnol 100(1), 2016
PMID: 26496920
Advantages of mixing bioinformatics and visualization approaches for analyzing sRNA-mediated regulatory bacterial networks.
Thébault P, Bourqui R, Benchimol W, Gaspin C, Sirand-Pugnet P, Uricaru R, Dutour I., Brief Bioinform 16(5), 2015
PMID: 25477348
CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R., BMC Genomics 16(), 2015
PMID: 26062809
Transcriptional control of the F0F1-ATP synthase operon of Corynebacterium glutamicum: SigmaH factor binds to its promoter and regulates its expression at different pH values.
Barriuso-Iglesias M, Barreiro C, Sola-Landa A, Martín JF., Microb Biotechnol 6(2), 2013
PMID: 23298179
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res 40(database issue), 2012
PMID: 22080556
Prokaryotic genome regulation: a revolutionary paradigm.
Ishihama A., Proc Jpn Acad Ser B Phys Biol Sci 88(9), 2012
PMID: 23138451
Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks.
Ishihama A., FEMS Microbiol Rev 34(5), 2010
PMID: 20491932
On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.
Baumbach J., Nucleic Acids Res 38(22), 2010
PMID: 20699275
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Baumbach J, Tauch A, Rahmann S., Brief Bioinform 10(1), 2009
PMID: 19074493
Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.
Baumbach J, Wittkop T, Kleindt CK, Tauch A., Nat Protoc 4(6), 2009
PMID: 19498379
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
Baumbach J, Rahmann S, Tauch A., BMC Syst Biol 3(), 2009
PMID: 19146695
Regulation of ldh expression during biotin-limited growth of Corynebacterium glutamicum.
Dietrich C, Nato A, Bost B, Le Maréchal P, Guyonvarch A., Microbiology 155(pt 4), 2009
PMID: 19332837
Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays.
Jochmann N, Kurze AK, Czaja LF, Brinkrolf K, Brune I, Hüser AT, Hansmeier N, Pühler A, Borovok I, Tauch A., Microbiology 155(pt 5), 2009
PMID: 19372162
Investigating transcriptional regulation: from analysis of complex networks to discovery of cis-regulatory elements.
Janky R, Helden Jv, Babu MM., Methods 48(3), 2009
PMID: 19450688
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
Systems biology of cyanobacterial secondary metabolite production and its role in drug discovery.
Wase NV, Wright PC., Expert Opin Drug Discov 3(8), 2008
PMID: 23484967
The dual transcriptional regulator CysR in Corynebacterium glutamicum ATCC 13032 controls a subset of genes of the McbR regulon in response to the availability of sulphide acceptor molecules.
Rückert C, Milse J, Albersmeier A, Koch DJ, Pühler A, Kalinowski J., BMC Genomics 9(), 2008
PMID: 18854009
Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.
Wittkop T, Baumbach J, Lobo FP, Rahmann S., BMC Bioinformatics 8(), 2007
PMID: 17941985
CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks.
Baumbach J., BMC Bioinformatics 8(), 2007
PMID: 17986320
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 1(), 2007
PMID: 18034885

28 References

Daten bereitgestellt von Europe PubMed Central.

Systems biology: its practice and challenges.
Aderem A., Cell 121(4), 2005
PMID: 15907465
Genetic improvement of processes yielding microbial products.
Adrio JL, Demain AL., FEMS Microbiol. Rev. 30(2), 2006
PMID: 16472304
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 7(), 2006
PMID: 16478536
CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes
Baumbach, J. Integr. Bioinform. 3(), 2006
Fast index based algorithms and software for matching position specific scoring matrices.
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
The complete genome sequence of Escherichia coli K-12.
Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y., Science 277(5331), 1997
PMID: 9278503
Integrating high-throughput and computational data elucidates bacterial networks.
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO., Nature 429(6987), 2004
PMID: 15129285
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
From natural products discovery to commercialization: a success story.
Demain AL., J. Ind. Microbiol. Biotechnol. 33(7), 2006
PMID: 16402247
In silico analysis reveals substantial variability in the gene contents of the gamma proteobacteria LexA-regulon.
Erill I, Escribano M, Campoy S, Barbe J., Bioinformatics 19(17), 2003
PMID: 14630651
Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics.
Erill I, Jara M, Salvador N, Escribano M, Campoy S, Barbe J., Nucleic Acids Res. 32(22), 2004
PMID: 15604457
Reconstruction of microbial transcriptional regulatory networks.
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
RegulonDB: a database on transcriptional regulation in Escherichia coli.
Huerta AM, Salgado H, Thieffry D, Collado-Vides J., Nucleic Acids Res. 26(1), 1998
PMID: 9399800
A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient L-lysine production.
Ikeda M, Ohnishi J, Hayashi M, Mitsuhashi S., J. Ind. Microbiol. Biotechnol. 33(7), 2006
PMID: 16506038
Graph-based analysis and visualization of experimental results with ONDEX.
Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S., Bioinformatics 22(11), 2006
PMID: 16533819
Biotechnological production of amino acids and derivatives: current status and prospects.
Leuchtenberger W, Huthmacher K, Drauz K., Appl. Microbiol. Biotechnol. 69(1), 2005
PMID: 16195792
Reconstruction of the evolutionary history of the LexA-binding sequence.
Mazon G, Erill I, Campoy S, Cortes P, Forano E, Barbe J., Microbiology (Reading, Engl.) 150(Pt 11), 2004
PMID: 15528664
BLAST: at the core of a powerful and diverse set of sequence analysis tools.
McGinnis S, Madden TL., Nucleic Acids Res. 32(Web Server issue), 2004
PMID: 15215342
From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli.
Mori H., J. Biochem. Mol. Biol. 37(1), 2004
PMID: 14761306
A novel method for accurate operon predictions in all sequenced prokaryotes.
Price MN, Huang KH, Alm EJ, Arkin AP., Nucleic Acids Res. 33(3), 2005
PMID: 15701760
Thirteen years of building constraint-based in silico models of Escherichia coli.
Reed JL, Palsson BO., J. Bacteriol. 185(9), 2003
PMID: 12700248
A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome.
Robison K, McGuire AM, Church GM., J. Mol. Biol. 284(2), 1998
PMID: 9813115
RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12.
Salgado H, Santos-Zavaleta A, Gama-Castro S, Millan-Zarate D, Diaz-Peredo E, Sanchez-Solano F, Perez-Rueda E, Bonavides-Martinez C, Collado-Vides J., Nucleic Acids Res. 29(1), 2001
PMID: 11125053
RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions.
Salgado H, Gama-Castro S, Peralta-Gil M, Diaz-Peredo E, Sanchez-Solano F, Santos-Zavaleta A, Martinez-Flores I, Jimenez-Jacinto V, Bonavides-Martinez C, Segura-Salazar J, Martinez-Antonio A, Collado-Vides J., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381895
Sequence logos: a new way to display consensus sequences.
Schneider TD, Stephens RM., Nucleic Acids Res. 18(20), 1990
PMID: 2172928
HMM Logos for visualization of protein families.
Schuster-Bockler B, Schultz J, Rahmann S., BMC Bioinformatics 5(), 2004
PMID: 14736340
DNA binding sites: representation and discovery.
Stormo GD., Bioinformatics 16(1), 2000
PMID: 10812473
Database resources of the National Center for Biotechnology Information.
Wheeler DL, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Geer LY, Helmberg W, Kapustin Y, Kenton DL, Khovayko O, Lipman DJ, Madden TL, Maglott DR, Ostell J, Pruitt KD, Schuler GD, Schriml LM, Sequeira E, Sherry ST, Sirotkin K, Souvorov A, Starchenko G, Suzek TO, Tatusov R, Tatusova TA, Wagner L, Yaschenko E., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381840
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