CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks
Baumbach J (2007)
BMC Bioinformatics 8(1): 429.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Autor*in
Baumbach, Jan
Einrichtung
Abstract / Bemerkung
Background: Detailed information on DNA-binding transcription factors (the key players in the regulation of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. The large-scale reconstruction of these networks allows the in silico analysis of cell behavior in response to changing environmental conditions. We previously published CoryneRegNet, an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Results: Now we introduce CoryneRegNet release 4.0, which integrates data on the gene regulatory networks of 4 corynebacteria, 2 mycobacteria and the model organism Escherichia coli K12. As the previous versions, CoryneRegNet provides a web-based user interface to access the database content, to allow various queries, and to support the reconstruction, analysis and visualization of regulatory networks at different hierarchical levels. In this article, we present the further improved database content of CoryneRegNet along with novel analysis features. The network visualization feature GraphVis now allows the inter-species comparisons of reconstructed gene regulatory networks and the projection of gene expression levels onto that networks. Therefore, we added stimulon data directly into the database, but also provide Web Service access to the DNA microarray analysis platform EMMA. Additionally, CoryneRegNet now provides a SOAP based Web Service server, which can easily be consumed by other bioinformatics software systems. Stimulons (imported from the database, or uploaded by the user) can be analyzed in the context of known transcriptional regulatory networks to predict putative contradictions or further gene regulatory interactions. Furthermore, it integrates protein clusters by means of heuristically solving the weighted graph cluster editing problem. In addition, it provides Web Service based access to up to date gene annotation data from GenDB. Conclusion: The release 4.0 of CoryneRegNet is a comprehensive system for the integrated analysis of procaryotic gene regulatory networks. It is a versatile systems biology platform to support the efficient and large-scale analysis of transcriptional regulation of gene expression in microorganisms. It is publicly available at http://www.CoryneRegNet.DE.
Erscheinungsjahr
2007
Zeitschriftentitel
BMC Bioinformatics
Band
8
Ausgabe
1
Art.-Nr.
429
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1783743
Zitieren
Baumbach J. CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics. 2007;8(1): 429.
Baumbach, J. (2007). CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1), 429. https://doi.org/10.1186/1471-2105-8-429
Baumbach, Jan. 2007. “CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks”. BMC Bioinformatics 8 (1): 429.
Baumbach, J. (2007). CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 8:429.
Baumbach, J., 2007. CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics, 8(1): 429.
J. Baumbach, “CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks”, BMC Bioinformatics, vol. 8, 2007, : 429.
Baumbach, J.: CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks. BMC Bioinformatics. 8, : 429 (2007).
Baumbach, Jan. “CoryneRegNet 4.0: a reference database for corynebacterial gene regulatory networks”. BMC Bioinformatics 8.1 (2007): 429.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level

Zuletzt Hochgeladen
2019-09-06T08:48:52Z
MD5 Prüfsumme
450a3cd696ef9cb55496d85a463f586d
Daten bereitgestellt von European Bioinformatics Institute (EBI)
39 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Biotypes analysis of Corynebacterium glutamicum growing in dicarboxylic acids demonstrates the existence of industrially-relevant intra-species variations.
Pérez-García F, Vasco-Cárdenas MF, Barreiro C., J Proteomics 146(), 2016
PMID: 27371347
Pérez-García F, Vasco-Cárdenas MF, Barreiro C., J Proteomics 146(), 2016
PMID: 27371347
Rho and RNase play a central role in FMN riboswitch regulation in Corynebacterium glutamicum.
Takemoto N, Tanaka Y, Inui M., Nucleic Acids Res 43(1), 2015
PMID: 25477389
Takemoto N, Tanaka Y, Inui M., Nucleic Acids Res 43(1), 2015
PMID: 25477389
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
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Röttger R., BMC Genomics 16(), 2015
PMID: 26062809
Recent progress in development of synthetic biology platforms and metabolic engineering of Corynebacterium glutamicum.
Woo HM, Park JB., J Biotechnol 180(), 2014
PMID: 24632177
Woo HM, Park JB., J Biotechnol 180(), 2014
PMID: 24632177
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I., BMC Genomics 14(), 2013
PMID: 23547897
Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I., BMC Genomics 14(), 2013
PMID: 23547897
Increments and duplication events of enzymes and transcription factors influence metabolic and regulatory diversity in prokaryotes.
Martínez-Núñez MA, Poot-Hernandez AC, Rodríguez-Vázquez K, Perez-Rueda E., PLoS One 8(7), 2013
PMID: 23922780
Martínez-Núñez MA, Poot-Hernandez AC, Rodríguez-Vázquez K, Perez-Rueda E., PLoS One 8(7), 2013
PMID: 23922780
RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.
Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA., BMC Genomics 14(), 2013
PMID: 24175918
Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA., BMC Genomics 14(), 2013
PMID: 24175918
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
Pauling J, Röttger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res 40(database issue), 2012
PMID: 22080556
Phylogenetic footprinting: a boost for microbial regulatory genomics.
Katara P, Grover A, Sharma V., Protoplasma 249(4), 2012
PMID: 22113593
Katara P, Grover A, Sharma V., Protoplasma 249(4), 2012
PMID: 22113593
Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.
McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J., BMC Genomics 13(), 2012
PMID: 22452820
McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J., BMC Genomics 13(), 2012
PMID: 22452820
Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum.
Chen X, Kohl TA, Rückert C, Rodionov DA, Li LH, Ding JY, Kalinowski J, Liu SJ., Appl Environ Microbiol 78(16), 2012
PMID: 22685150
Chen X, Kohl TA, Rückert C, Rodionov DA, Li LH, Ding JY, Kalinowski J, Liu SJ., Appl Environ Microbiol 78(16), 2012
PMID: 22685150
RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.
Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 40(web server issue), 2012
PMID: 22700702
Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 40(web server issue), 2012
PMID: 22700702
Regulatory network operations in the Pathway Tools software.
Paley SM, Latendresse M, Karp PD., BMC Bioinformatics 13(), 2012
PMID: 22998532
Paley SM, Latendresse M, Karp PD., BMC Bioinformatics 13(), 2012
PMID: 22998532
Diversity and distribution of transcription factors: their partner domains play an important role in regulatory plasticity in bacteria.
Rivera-Gómez N, Segovia L, Pérez-Rueda E., Microbiology 157(pt 8), 2011
PMID: 21636649
Rivera-Gómez N, Segovia L, Pérez-Rueda E., Microbiology 157(pt 8), 2011
PMID: 21636649
Genome-wide identification of in vivo binding sites of GlxR, a cyclic AMP receptor protein-type regulator in Corynebacterium glutamicum.
Toyoda K, Teramoto H, Inui M, Yukawa H., J Bacteriol 193(16), 2011
PMID: 21665967
Toyoda K, Teramoto H, Inui M, Yukawa H., J Bacteriol 193(16), 2011
PMID: 21665967
phiGENOME: an integrative navigation throughout bacteriophage genomes.
Stano M, Klucar L., Genomics 98(5), 2011
PMID: 21824513
Stano M, Klucar L., Genomics 98(5), 2011
PMID: 21824513
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 38(database issue), 2010
PMID: 19884135
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res 38(database issue), 2010
PMID: 19884135
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R., Brief Bioinform 11(1), 2010
PMID: 19955237
Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R., Brief Bioinform 11(1), 2010
PMID: 19955237
Network inference and network response identification: moving genome-scale data to the next level of biological discovery.
Veiga DF, Dutta B, Balázsi G., Mol Biosyst 6(3), 2010
PMID: 20174676
Veiga DF, Dutta B, Balázsi G., Mol Biosyst 6(3), 2010
PMID: 20174676
Systems biology approaches to understanding mycobacterial survival mechanisms.
Boshoff HI, Lun DS., Drug Discov Today Dis Mech 7(1), 2010
PMID: 21072257
Boshoff HI, Lun DS., Drug Discov Today Dis Mech 7(1), 2010
PMID: 21072257
PcaO positively regulates pcaHG of the beta-ketoadipate pathway in Corynebacterium glutamicum.
Zhao KX, Huang Y, Chen X, Wang NX, Liu SJ., J Bacteriol 192(6), 2010
PMID: 20081038
Zhao KX, Huang Y, Chen X, Wang NX, Liu SJ., J Bacteriol 192(6), 2010
PMID: 20081038
Transcriptional regulation of gene expression in Corynebacterium glutamicum: the role of global, master and local regulators in the modular and hierarchical gene regulatory network.
Schröder J, Tauch A., FEMS Microbiol Rev 34(5), 2010
PMID: 20491930
Schröder J, Tauch A., FEMS Microbiol Rev 34(5), 2010
PMID: 20491930
Semantic integration of data on transcriptional regulation.
Baitaluk M, Ponomarenko J., Bioinformatics 26(13), 2010
PMID: 20427517
Baitaluk M, Ponomarenko J., Bioinformatics 26(13), 2010
PMID: 20427517
Monotonicity, frustration, and ordered response: an analysis of the energy landscape of perturbed large-scale biological networks.
Iacono G, Altafini C., BMC Syst Biol 4(), 2010
PMID: 20537143
Iacono G, Altafini C., BMC Syst Biol 4(), 2010
PMID: 20537143
RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I., Nucleic Acids Res 38(web server issue), 2010
PMID: 20542910
Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I., Nucleic Acids Res 38(web server issue), 2010
PMID: 20542910
Corynebacterium glutamicum exhibits a membrane-related response to a small ferrocene-conjugated antimicrobial peptide.
Fränzel B, Frese C, Penkova M, Metzler-Nolte N, Bandow JE, Wolters DA., J Biol Inorg Chem 15(8), 2010
PMID: 20658302
Fränzel B, Frese C, Penkova M, Metzler-Nolte N, Bandow JE, Wolters DA., J Biol Inorg Chem 15(8), 2010
PMID: 20658302
Genomic repertoires of DNA-binding transcription factors across the tree of life.
Charoensawan V, Wilson D, Teichmann SA., Nucleic Acids Res 38(21), 2010
PMID: 20675356
Charoensawan V, Wilson D, Teichmann SA., Nucleic Acids Res 38(21), 2010
PMID: 20675356
On the power and limits of evolutionary conservation--unraveling bacterial gene regulatory networks.
Baumbach J., Nucleic Acids Res 38(22), 2010
PMID: 20699275
Baumbach J., Nucleic Acids Res 38(22), 2010
PMID: 20699275
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 37(database issue), 2009
PMID: 18974177
Grote A, Klein J, Retter I, Haddad I, Behling S, Bunk B, Biegler I, Yarmolinetz S, Jahn D, Münch R., Nucleic Acids Res 37(database issue), 2009
PMID: 18974177
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
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
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
Baumbach J, Rahmann S, Tauch A., BMC Syst Biol 3(), 2009
PMID: 19146695
The two-phase partitioning system--a powerful technique to purify integral membrane proteins of Corynebacterium glutamicum for quantitative shotgun analysis.
Fränzel B, Fischer F, Trötschel C, Poetsch A, Wolters D., Proteomics 9(8), 2009
PMID: 19322788
Fränzel B, Fischer F, Trötschel C, Poetsch A, Wolters D., Proteomics 9(8), 2009
PMID: 19322788
From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.
Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J., Nucleic Acids Res 37(14), 2009
PMID: 19494184
Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J., Nucleic Acids Res 37(14), 2009
PMID: 19494184
Physiological adaptation of Corynebacterium glutamicum to benzoate as alternative carbon source - a membrane proteome-centric view.
Haussmann U, Qi SW, Wolters D, Rögner M, Liu SJ, Poetsch A., Proteomics 9(14), 2009
PMID: 19639586
Haussmann U, Qi SW, Wolters D, Rögner M, Liu SJ, Poetsch A., Proteomics 9(14), 2009
PMID: 19639586
Mechanisms and evolution of control logic in prokaryotic transcriptional regulation.
van Hijum SA, Medema MH, Kuipers OP., Microbiol Mol Biol Rev 73(3), 2009
PMID: 19721087
van Hijum SA, Medema MH, Kuipers OP., Microbiol Mol Biol Rev 73(3), 2009
PMID: 19721087
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
Baumbach J, Apeltsin L., BMC Genomics 9(), 2008
PMID: 18426593
The GlxR regulon of the amino acid producer Corynebacterium glutamicum: in silico and in vitro detection of DNA binding sites of a global transcription regulator.
Kohl TA, Baumbach J, Jungwirth B, Pühler A, Tauch A., J Biotechnol 135(4), 2008
PMID: 18573287
Kohl TA, Baumbach J, Jungwirth B, Pühler A, Tauch A., J Biotechnol 135(4), 2008
PMID: 18573287
Nitrogen control in Mycobacterium smegmatis: nitrogen-dependent expression of ammonium transport and assimilation proteins depends on the OmpR-type regulator GlnR.
Amon J, Bräu T, Grimrath A, Hänssler E, Hasselt K, Höller M, Jessberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A., J Bacteriol 190(21), 2008
PMID: 18689485
Amon J, Bräu T, Grimrath A, Hänssler E, Hasselt K, Höller M, Jessberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A., J Bacteriol 190(21), 2008
PMID: 18689485
45 References
Daten bereitgestellt von Europe PubMed Central.
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651856
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
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO., Nature 429(6987), 2004
PMID: 15129285
Reconstruction of microbial transcriptional regulatory networks.
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
Herrgard MJ, Covert MW, Palsson BO., Curr. Opin. Biotechnol. 15(1), 2004
PMID: 15102470
Thirteen years of building constraint-based in silico models of Escherichia coli.
Reed JL, Palsson BO., J. Bacteriol. 185(9), 2003
PMID: 12700248
Reed JL, Palsson BO., J. Bacteriol. 185(9), 2003
PMID: 12700248
Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.
Martinez-Antonio A, Janga SC, Salgado H, Collado-Vides J., Trends Microbiol. 14(1), 2005
PMID: 16311037
Martinez-Antonio A, Janga SC, Salgado H, Collado-Vides J., Trends Microbiol. 14(1), 2005
PMID: 16311037
From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli.
Mori H., J. Biochem. Mol. Biol. 37(1), 2004
PMID: 14761306
Mori H., J. Biochem. Mol. Biol. 37(1), 2004
PMID: 14761306
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
Baumbach J, Brinkrolf K, Czaja LF, Rahmann S, Tauch A., BMC Genomics 7(), 2006
PMID: 16478536
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. 129(2), 2006
PMID: 17229482
Baumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A., J. Biotechnol. 129(2), 2006
PMID: 17229482
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
Beckstette M, Homann R, Giegerich R, Kurtz S., BMC Bioinformatics 7(), 2006
PMID: 16930469
Structure and evolution of transcriptional regulatory networks.
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193307
Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA., Curr. Opin. Struct. Biol. 14(3), 2004
PMID: 15193307
Evolutionary dynamics of prokaryotic transcriptional regulatory networks.
Madan Babu M, Teichmann SA, Aravind L., J. Mol. Biol. 358(2), 2006
PMID: 16530225
Madan Babu M, Teichmann SA, Aravind L., J. Mol. Biol. 358(2), 2006
PMID: 16530225
Bacterial regulatory networks are extremely flexible in evolution.
Lozada-Chavez I, Janga SC, Collado-Vides J., Nucleic Acids Res. 34(12), 2006
PMID: 16840530
Lozada-Chavez I, Janga SC, Collado-Vides J., Nucleic Acids Res. 34(12), 2006
PMID: 16840530
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
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
PRODORIC: prokaryotic database of gene regulation.
Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D., Nucleic Acids Res. 31(1), 2003
PMID: 12519998
Munch R, Hiller K, Barg H, Heldt D, Linz S, Wingender E, Jahn D., Nucleic Acids Res. 31(1), 2003
PMID: 12519998
Addressing the problems with life-science databases for traditional uses and systems biology.
Philippi S, Kohler J., Nat. Rev. Genet. 7(6), 2006
PMID: 16682980
Philippi S, Kohler J., Nat. Rev. Genet. 7(6), 2006
PMID: 16682980
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980569
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980569
SOAP-based services provided by the European Bioinformatics Institute.
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980463
Pillai S, Silventoinen V, Kallio K, Senger M, Sobhany S, Tate J, Velankar S, Golovin A, Henrick K, Rice P, Stoehr P, Lopez R., Nucleic Acids Res. 33(Web Server issue), 2005
PMID: 15980463
BRENDA, AMENDA and FRENDA: the enzyme information system in 2007.
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202167
Barthelmes J, Ebeling C, Chang A, Schomburg I, Schomburg D., Nucleic Acids Res. 35(Database issue), 2007
PMID: 17202167
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
Kohler J, Baumbach J, Taubert J, Specht M, Skusa A, Ruegg A, Rawlings C, Verrier P, Philippi S., Bioinformatics 22(11), 2006
PMID: 16533819
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. (Gedrukt) 5(1), 2005
PMID: 15972003
Koehler J, Rawlings C, Verrier P, Mitchell R, Skusa A, Ruegg A, Philippi S., In Silico Biol. (Gedrukt) 5(1), 2005
PMID: 15972003
MySQL
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Apache HTTP server
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
PHP
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
Java
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
SOAPlite library
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
NuSOAP
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
From genomics to chemical genomics: new developments in KEGG.
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381885
Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M., Nucleic Acids Res. 34(Database issue), 2006
PMID: 16381885
Unraveling the Web Services Web: An Introduction to SOAP, WSDL, and UDDI
Curbera F, Duftler M, Khalaf R, Nagy W, Mukhi N, Weerawarana S., 2002
Curbera F, Duftler M, Khalaf R, Nagy W, Mukhi N, Weerawarana S., 2002
BioMOBY: an open source biological web services proposal.
Wilkinson MD, Links M., Brief. Bioinformatics 3(4), 2002
PMID: 12511062
Wilkinson MD, Links M., Brief. Bioinformatics 3(4), 2002
PMID: 12511062
Exact and Heuristic Algorithms for Weighted Cluster Editing
Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S., 2007
Rahmann S, Wittkop T, Baumbach J, Martin M, Truss A, Boecker S., 2007
Graph drawing by force-directed placement
Fruchterman TMJ, Reingold EM., 1991
Fruchterman TMJ, Reingold EM., 1991
Protein complex prediction via cost-based clustering.
King AD, Przulj N, Jurisica I., Bioinformatics 20(17), 2004
PMID: 15180928
King AD, Przulj N, Jurisica I., Bioinformatics 20(17), 2004
PMID: 15180928
FORCE
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum.
Brune I, Werner H, Huser AT, Kalinowski J, Puhler A, Tauch A., BMC Genomics 7(), 2006
PMID: 16469103
Brune I, Werner H, Huser AT, Kalinowski J, Puhler A, Tauch A., BMC Genomics 7(), 2006
PMID: 16469103
The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum.
Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A., J. Bacteriol. 189(7), 2007
PMID: 17259312
Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A., J. Bacteriol. 189(7), 2007
PMID: 17259312
The McbR repressor modulated by the effector substance S-adenosylhomocysteine controls directly the transcription of a regulon involved in sulphur metabolism of Corynebacterium glutamicum ATCC 13032.
Rey DA, Nentwich SS, Koch DJ, Ruckert C, Puhler A, Tauch A, Kalinowski J., Mol. Microbiol. 56(4), 2005
PMID: 15853877
Rey DA, Nentwich SS, Koch DJ, Ruckert C, Puhler A, Tauch A, Kalinowski J., Mol. Microbiol. 56(4), 2005
PMID: 15853877
The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes.
Nakunst D, Larisch C, Huser AT, Tauch A, Puhler A, Kalinowski J., J. Bacteriol. 189(13), 2007
PMID: 17483229
Nakunst D, Larisch C, Huser AT, Tauch A, Puhler A, Kalinowski J., J. Bacteriol. 189(13), 2007
PMID: 17483229
The transcriptional regulator SsuR activates expression of the Corynebacterium glutamicum sulphonate utilization genes in the absence of sulphate.
Koch DJ, Ruckert C, Albersmeier A, Huser AT, Tauch A, Puhler A, Kalinowski J., Mol. Microbiol. 58(2), 2005
PMID: 16194234
Koch DJ, Ruckert C, Albersmeier A, Huser AT, Tauch A, Puhler A, Kalinowski J., Mol. Microbiol. 58(2), 2005
PMID: 16194234
Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.
Huser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Puhler A, Wiegrabe I, Tauch A., J. Biotechnol. 106(2-3), 2003
PMID: 14651867
Huser AT, Becker A, Brune I, Dondrup M, Kalinowski J, Plassmeier J, Puhler A, Wiegrabe I, Tauch A., J. Biotechnol. 106(2-3), 2003
PMID: 14651867
The alternative sigma factor SigB of Corynebacterium glutamicum modulates global gene expression during transition from exponential growth to stationary phase.
Larisch C, Nakunst D, Huser AT, Tauch A, Kalinowski J., BMC Genomics 8(), 2007
PMID: 17204139
Larisch C, Nakunst D, Huser AT, Tauch A, Kalinowski J., BMC Genomics 8(), 2007
PMID: 17204139
Under the influence of the active deodorant ingredient 4-hydroxy-3-methoxybenzyl alcohol, the skin bacterium Corynebacterium jeikeium moderately responds with differential gene expression.
Brune I, Becker A, Paarmann D, Albersmeier A, Kalinowski J, Puhler A, Tauch A., J. Biotechnol. 127(1), 2006
PMID: 16890319
Brune I, Becker A, Paarmann D, Albersmeier A, Kalinowski J, Puhler A, Tauch A., J. Biotechnol. 127(1), 2006
PMID: 16890319
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 17986320
PubMed | Europe PMC
Suchen in