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Volumn 54, Issue 3, 2011, Pages 200-206

CADLIVE Converter for constructing a biochemical network map

Author keywords

Bioinformatics; Design; Integration; Network; Simulator; Software; Systems biotechnology

Indexed keywords

BIOCHEMICAL NETWORK; COMPLEX NETWORKS; COMPUTATIONAL TOOLS; DATA FORMAT; DYNAMIC BEHAVIORS; DYNAMIC MODELING; INTUITIVE UNDERSTANDING; METABOLIC PATHWAY ANALYSIS; METABOLIC PATHWAYS; NETWORK; NETWORK DATA; PROTEIN-PROTEIN INTERACTIONS; PUBLIC DATABASE; SOFTWARE; SYSTEMS BIOTECHNOLOGY; TOPOLOGICAL FEATURES;

EID: 79953796685     PISSN: 1369703X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bej.2011.02.022     Document Type: Article
Times cited : (3)

References (37)
  • 1
    • 66149172363 scopus 로고    scopus 로고
    • Diversity-based, model-guided construction of synthetic gene networks with predicted functions
    • Ellis T., Wang X., Collins J.J. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 2009, 27:465-471.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 465-471
    • Ellis, T.1    Wang, X.2    Collins, J.J.3
  • 2
    • 38349066180 scopus 로고    scopus 로고
    • Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
    • Nishio Y., Usuda Y., Matsui K., Kurata H. Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol. Syst. Biol. 2008, 4:160.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 160
    • Nishio, Y.1    Usuda, Y.2    Matsui, K.3    Kurata, H.4
  • 3
    • 28544440364 scopus 로고    scopus 로고
    • Reconstruction of genetic circuits
    • Sprinzak D., Elowitz M.B. Reconstruction of genetic circuits. Nature 2005, 438:443-448.
    • (2005) Nature , vol.438 , pp. 443-448
    • Sprinzak, D.1    Elowitz, M.B.2
  • 4
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabasi A.L., Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 2004, 5:101-113.
    • (2004) Nat. Rev. Genet. , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 7
    • 23444439817 scopus 로고    scopus 로고
    • Using process diagrams for the graphical representation of biological networks
    • Kitano H., Funahashi A., Matsuoka Y., Oda K. Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol. 2005, 23:961-966.
    • (2005) Nat. Biotechnol. , vol.23 , pp. 961-966
    • Kitano, H.1    Funahashi, A.2    Matsuoka, Y.3    Oda, K.4
  • 8
    • 2642527148 scopus 로고    scopus 로고
    • Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension
    • Doi A., Nagasaki M., Fujita S., Matsuno H., Miyano S. Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl. Bioinformatics 2003, 2:185-188.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 185-188
    • Doi, A.1    Nagasaki, M.2    Fujita, S.3    Matsuno, H.4    Miyano, S.5
  • 9
    • 2642533799 scopus 로고    scopus 로고
    • Genomic Object Net: I. A platform for modelling and simulating biopathways
    • Nagasaki M., Doi A., Matsuno H., Miyano S. Genomic Object Net: I. A platform for modelling and simulating biopathways. Appl. Bioinformatics 2003, 2:181-184.
    • (2003) Appl. Bioinformatics , vol.2 , pp. 181-184
    • Nagasaki, M.1    Doi, A.2    Matsuno, H.3    Miyano, S.4
  • 10
    • 36749043657 scopus 로고    scopus 로고
    • Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis
    • Kurata H., Inoue K., Maeda K., Masaki K., Shimokawa Y., Zhao Q. Extended CADLIVE: a novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res. 2007, 35:e134.
    • (2007) Nucleic Acids Res. , vol.35
    • Kurata, H.1    Inoue, K.2    Maeda, K.3    Masaki, K.4    Shimokawa, Y.5    Zhao, Q.6
  • 11
    • 17844397967 scopus 로고    scopus 로고
    • CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models
    • Kurata H., Masaki K., Sumida Y., Iwasaki R. CADLIVE dynamic simulator: direct link of biochemical networks to dynamic models. Genome Res. 2005, 15:590-600.
    • (2005) Genome Res. , vol.15 , pp. 590-600
    • Kurata, H.1    Masaki, K.2    Sumida, Y.3    Iwasaki, R.4
  • 12
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • Kurata H., Matoba N., Shimizu N. CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res. 2003, 31:4071-4084.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 4071-4084
    • Kurata, H.1    Matoba, N.2    Shimizu, N.3
  • 13
    • 0036326896 scopus 로고    scopus 로고
    • PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
    • Demir E., Babur O., Dogrusoz U., Gursoy A., Nisanci G., Cetin-Atalay R., Ozturk M. PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinformatics 2002, 18:996-1003.
    • (2002) Bioinformatics , vol.18 , pp. 996-1003
    • Demir, E.1    Babur, O.2    Dogrusoz, U.3    Gursoy, A.4    Nisanci, G.5    Cetin-Atalay, R.6    Ozturk, M.7
  • 15
    • 79953775804 scopus 로고    scopus 로고
    • BioPAX-Biological Pathways Exchange Language Level 2, Version 1.0 Documentation
    • G. Bader, M. Cary, BioPAX-Biological Pathways Exchange Language Level 2, Version 1.0 Documentation, 2005.
    • (2005)
    • Bader, G.1    Cary, M.2
  • 16
    • 18744387729 scopus 로고    scopus 로고
    • A grid layout algorithm for automatic drawing of biochemical networks
    • Li W., Kurata H. A grid layout algorithm for automatic drawing of biochemical networks. Bioinformatics 2005, 21:2036-2042.
    • (2005) Bioinformatics , vol.21 , pp. 2036-2042
    • Li, W.1    Kurata, H.2
  • 18
    • 0037245913 scopus 로고    scopus 로고
    • BIND: the biomolecular interaction network database
    • Bader G.D., Betel D., Hogue C.W. BIND: the biomolecular interaction network database. Nucleic Acids Res. 2003, 31:248-250.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 248-250
    • Bader, G.D.1    Betel, D.2    Hogue, C.W.3
  • 23
    • 46049087782 scopus 로고    scopus 로고
    • The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    • Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinformatics 2008, 9:326-332.
    • (2008) Brief Bioinformatics , vol.9 , pp. 326-332
    • Wingender, E.1
  • 24
    • 38549162091 scopus 로고    scopus 로고
    • DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information
    • Sierro N., Makita Y., de Hoon M., Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res. 2008, 36:D93-96.
    • (2008) Nucleic Acids Res. , vol.36
    • Sierro, N.1    Makita, Y.2    de Hoon, M.3    Nakai, K.4
  • 26
    • 58149185126 scopus 로고    scopus 로고
    • BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009
    • Chang A., Scheer M., Grote A., Schomburg I., Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res. 2009, 37:D588-592.
    • (2009) Nucleic Acids Res. , vol.37
    • Chang, A.1    Scheer, M.2    Grote, A.3    Schomburg, I.4    Schomburg, D.5
  • 27
    • 70449515104 scopus 로고    scopus 로고
    • KEGGconverter: a tool for the in silico modelling of metabolic networks of the KEGG Pathways database
    • Moutselos K., Kanaris I., Chatziioannou A., Maglogiannis I., Kolisis F.N. KEGGconverter: a tool for the in silico modelling of metabolic networks of the KEGG Pathways database. BMC Bioinformatics 2009, 10:324.
    • (2009) BMC Bioinformatics , vol.10 , pp. 324
    • Moutselos, K.1    Kanaris, I.2    Chatziioannou, A.3    Maglogiannis, I.4    Kolisis, F.N.5
  • 28
    • 40749087306 scopus 로고    scopus 로고
    • BiNoM: a cytoscape plugin for manipulating and analyzing biological networks
    • Zinovyev A., Viara E., Calzone L., Barillot E. BiNoM: a cytoscape plugin for manipulating and analyzing biological networks. Bioinformatics 2008, 24:876-877.
    • (2008) Bioinformatics , vol.24 , pp. 876-877
    • Zinovyev, A.1    Viara, E.2    Calzone, L.3    Barillot, E.4
  • 29
    • 58149279036 scopus 로고    scopus 로고
    • Maximum entropy decomposition of flux distribution at steady state to elementary modes
    • Zhao Q., Kurata H. Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng. 2009, 107:84-89.
    • (2009) J. Biosci. Bioeng. , vol.107 , pp. 84-89
    • Zhao, Q.1    Kurata, H.2
  • 30
    • 67649218402 scopus 로고    scopus 로고
    • Genetic modification of flux for flux prediction of mutants
    • Zhao Q., Kurata H. Genetic modification of flux for flux prediction of mutants. Bioinformatics 2009, 25:1702-1708.
    • (2009) Bioinformatics , vol.25 , pp. 1702-1708
    • Zhao, Q.1    Kurata, H.2
  • 31
    • 77954313563 scopus 로고    scopus 로고
    • Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis
    • Zhao Q., Kurata H. Use of maximum entropy principle with Lagrange multipliers extends the feasibility of elementary mode analysis. J. Biosci. Bioeng. 2010, 110:254-261.
    • (2010) J. Biosci. Bioeng. , vol.110 , pp. 254-261
    • Zhao, Q.1    Kurata, H.2
  • 32
    • 0032776303 scopus 로고    scopus 로고
    • Molecular interaction map of the mammalian cell cycle control and DNA repair systems
    • Kohn K.W. Molecular interaction map of the mammalian cell cycle control and DNA repair systems. Mol. Biol. Cell 1999, 10:2703-2734.
    • (1999) Mol. Biol. Cell , vol.10 , pp. 2703-2734
    • Kohn, K.W.1
  • 34
    • 77349107936 scopus 로고    scopus 로고
    • LucidDraw: efficiently visualizing complex biochemical networks within MATLAB
    • He S., Mei J., Shi G., Wang Z., Li W. LucidDraw: efficiently visualizing complex biochemical networks within MATLAB. BMC Bioinformatics 2010, 11:31.
    • (2010) BMC Bioinformatics , vol.11 , pp. 31
    • He, S.1    Mei, J.2    Shi, G.3    Wang, Z.4    Li, W.5
  • 36
  • 37
    • 67849110019 scopus 로고    scopus 로고
    • Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases
    • Imanishi T., Nakaoka H. Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases. Nucleic Acids Res. 2009, 37:W17-22.
    • (2009) Nucleic Acids Res. , vol.37
    • Imanishi, T.1    Nakaoka, H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.