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Volumn 129, Issue 2, 2007, Pages 279-289

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

Author keywords

Corynebacterium glutamicum; Escherichia coli; Regulatory network; SOS response; Systems biology; Transcriptional regulation

Indexed keywords

DATA WAREHOUSES; ESCHERICHIA COLI; GENES; ONTOLOGY;

EID: 34047170261     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2006.12.012     Document Type: Article
Times cited : (25)

References (28)
  • 1
    • 19344372271 scopus 로고    scopus 로고
    • Systems biology: its practice and challenges
    • Aderem A. Systems biology: its practice and challenges. Cell 121 (2005) 511-513
    • (2005) Cell , vol.121 , pp. 511-513
    • Aderem, A.1
  • 2
    • 33644942482 scopus 로고    scopus 로고
    • Genetic improvement of processes yielding microbial products
    • Adrio J.L., and Demain A.L. Genetic improvement of processes yielding microbial products. FEMS Microbiol. Rev. 30 (2006) 187-214
    • (2006) FEMS Microbiol. Rev. , vol.30 , pp. 187-214
    • Adrio, J.L.1    Demain, A.L.2
  • 3
    • 33644604851 scopus 로고    scopus 로고
    • CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks
    • Baumbach J., Brinkrolf K., Czaja L.F., Rahmann S., and Tauch A. CoryneRegNet: an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. BMC Genomics 7 (2006) 24
    • (2006) BMC Genomics , vol.7 , pp. 24
    • Baumbach, J.1    Brinkrolf, K.2    Czaja, L.F.3    Rahmann, S.4    Tauch, A.5
  • 4
    • 34047189243 scopus 로고    scopus 로고
    • CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes
    • Baumbach J., Brinkrolf K., Wittkop T., Tauch A., and Rahmann S. CoryneRegNet 2: an integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes. J. Integr. Bioinform. 3 (2006) 24
    • (2006) J. Integr. Bioinform. , vol.3 , pp. 24
    • Baumbach, J.1    Brinkrolf, K.2    Wittkop, T.3    Tauch, A.4    Rahmann, S.5
  • 5
    • 33750959240 scopus 로고    scopus 로고
    • Fast index based algorithms and software for matching position specific scoring matrices
    • Beckstette M., Homann R., Giegerich R., and Kurtz S. Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinform. 7 (2006) 389
    • (2006) BMC Bioinform. , vol.7 , pp. 389
    • Beckstette, M.1    Homann, R.2    Giegerich, R.3    Kurtz, S.4
  • 7
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert M.W., Knight E.M., Reed J.L., Herrgard M.J., and Palsson B.O. Integrating high-throughput and computational data elucidates bacterial networks. Nature 429 (2004) 92-96
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 9
    • 33745024719 scopus 로고    scopus 로고
    • From natural products discovery to commercialization: a success story
    • Demain A.L. From natural products discovery to commercialization: a success story. J. Ind. Microbiol. Biotechnol. 33 (2006) 486-495
    • (2006) J. Ind. Microbiol. Biotechnol. , vol.33 , pp. 486-495
    • Demain, A.L.1
  • 10
    • 0344464768 scopus 로고    scopus 로고
    • In silico analysis reveals substantial variability in the gene contents of the gamma Proteobacteria LexA-regulon
    • Erill I., Escribano M., Campoy S., and Barbé J. In silico analysis reveals substantial variability in the gene contents of the gamma Proteobacteria LexA-regulon. Bioinformatics 19 (2003) 2225-2236
    • (2003) Bioinformatics , vol.19 , pp. 2225-2236
    • Erill, I.1    Escribano, M.2    Campoy, S.3    Barbé, J.4
  • 11
    • 13544260858 scopus 로고    scopus 로고
    • Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics
    • Erill I., Jara M., Salvador N., Escribano M., Campoy S., and Barbé J. Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics. Nucleic Acids Res. 32 (2004) 6617-6626
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6617-6626
    • Erill, I.1    Jara, M.2    Salvador, N.3    Escribano, M.4    Campoy, S.5    Barbé, J.6
  • 12
    • 1242328740 scopus 로고    scopus 로고
    • Reconstruction of microbial transcriptional regulatory networks
    • Herrgård M.J., Covert M.W., and Palsson B.O. Reconstruction of microbial transcriptional regulatory networks. Curr. Opin. Biotechnol. 15 (2004) 70-77
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 70-77
    • Herrgård, M.J.1    Covert, M.W.2    Palsson, B.O.3
  • 13
  • 14
    • 33745013345 scopus 로고    scopus 로고
    • A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient l-lysine production
    • Ikeda M., Ohnishi J., Hayashi M., and Mitsuhashi S. A genome-based approach to create a minimally mutated Corynebacterium glutamicum strain for efficient l-lysine production. J. Ind. Microbiol. Biotechnol. 33 (2006) 610-615
    • (2006) J. Ind. Microbiol. Biotechnol. , vol.33 , pp. 610-615
    • Ikeda, M.1    Ohnishi, J.2    Hayashi, M.3    Mitsuhashi, S.4
  • 16
    • 28344455644 scopus 로고    scopus 로고
    • Biotechnological production of amino acids and derivatives: current status and prospects
    • Leuchtenberger W., Huthmacher K., and Drauz K. Biotechnological production of amino acids and derivatives: current status and prospects. Appl. Microbiol. Biotechnol. 69 (2005) 1-8
    • (2005) Appl. Microbiol. Biotechnol. , vol.69 , pp. 1-8
    • Leuchtenberger, W.1    Huthmacher, K.2    Drauz, K.3
  • 17
    • 9144266449 scopus 로고    scopus 로고
    • Reconstruction of the evolutionary history of the LexA-binding sequence
    • Mazón G., Erill I., Campoy S., Cortés P., Forano E., and Barbé J. Reconstruction of the evolutionary history of the LexA-binding sequence. Microbiology 150 (2004) 3783-3795
    • (2004) Microbiology , vol.150 , pp. 3783-3795
    • Mazón, G.1    Erill, I.2    Campoy, S.3    Cortés, P.4    Forano, E.5    Barbé, J.6
  • 18
    • 3242876311 scopus 로고    scopus 로고
    • BLAST: at the core of a powerful and diverse set of sequence analysis tools
    • McGinnis S., and Madden T.L. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 32 (2004) W20-W25
    • (2004) Nucleic Acids Res. , vol.32
    • McGinnis, S.1    Madden, T.L.2
  • 19
    • 1642446957 scopus 로고    scopus 로고
    • From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli
    • Mori H. From the sequence to cell modeling: comprehensive functional genomics in Escherichia coli. J. Biochem. Mol. Biol. 37 (2004) 83-92
    • (2004) J. Biochem. Mol. Biol. , vol.37 , pp. 83-92
    • Mori, H.1
  • 20
    • 13944268797 scopus 로고    scopus 로고
    • A novel method for accurate operon predictions in all sequenced prokaryotes
    • Price M.N., Huang K.H., Alm E.J., and Arkin A.P. A novel method for accurate operon predictions in all sequenced prokaryotes. Nucleic Acids Res. 33 (2005) 880-892
    • (2005) Nucleic Acids Res. , vol.33 , pp. 880-892
    • Price, M.N.1    Huang, K.H.2    Alm, E.J.3    Arkin, A.P.4
  • 21
    • 0037406843 scopus 로고    scopus 로고
    • Thirteen years of building constraint-based in silico models of Escherichia coli
    • Reed J.L., and Palsson B.O. Thirteen years of building constraint-based in silico models of Escherichia coli. J. Bacteriol. 185 (2003) 2692-2699
    • (2003) J. Bacteriol. , vol.185 , pp. 2692-2699
    • Reed, J.L.1    Palsson, B.O.2
  • 22
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    • Robison K., McGuire A.M., and Church G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284 (1998) 241-254
    • (1998) J. Mol. Biol. , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 25
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider T.D., and Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18 (1990) 6097-6100
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 27
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 16 (2000) 16-23
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.