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Volumn 15, Issue 1, 2014, Pages 123-135

Reconciliation of metabolites and biochemical reactions for metabolic networks

Author keywords

Cheminformatics; Data integration; Data interoperability; Metabolic networks; Metabolic resources

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CHEMICAL STRUCTURE; CHEMINFORMATICS; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA INTEGRATION; DATA INTEROPERABILITY; FACTUAL DATABASE; GENETICS; GENOMICS; METABOLIC NETWORKS; METABOLIC RESOURCES; METABOLISM; STATISTICS;

EID: 84892989181     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbs058     Document Type: Article
Times cited : (51)

References (36)
  • 1
    • 31144435316 scopus 로고    scopus 로고
    • Towards multidimensional genome annotation
    • Reed JL, Famili I, Thiele I, et al. Towards multidimensional genome annotation. Nat Rev Genet 2006;7:130-41.
    • (2006) Nat Rev Genet , vol.7 , pp. 130-141
    • Reed, J.L.1    Famili, I.2    Thiele, I.3
  • 2
    • 80555156100 scopus 로고    scopus 로고
    • Genome-scale metabolic models: reconstruction and analysis
    • Baart GJE, Martens DE. Genome-scale metabolic models: reconstruction and analysis. Methods Mol Biol 2012;799: 107-26.
    • (2012) Methods Mol Biol , vol.799 , pp. 107-126
    • Baart, G.J.E.1    Martens, D.E.2
  • 5
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling J, Klamt S, Bettenbrock K, etal. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002;420:190-3.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1    Klamt, S.2    Bettenbrock, K.3
  • 6
    • 62449140981 scopus 로고    scopus 로고
    • Identifying essential genes in Escherichia coli from a metabolic optimization principle
    • Martelli C, De Martino A, Marinari E, et al. Identifying essential genes in Escherichia coli from a metabolic optimization principle. Proc Natl Acad Sci USA 2009;106: 2607-11.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 2607-2611
    • Martelli, C.1    De Martino, A.2    Marinari, E.3
  • 7
    • 70449647110 scopus 로고    scopus 로고
    • How to identify essential genes from molecular networks
    • del Rio G, Koschutzki D, Coello G. How to identify essential genes from molecular networks? BMCSystBiol 2009; 3:102.
    • (2009) BMCSystBiol , vol.3 , pp. 102
    • del Rio, G.1    Koschutzki, D.2    Coello, G.3
  • 8
    • 84555178661 scopus 로고    scopus 로고
    • Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets
    • Navid A. Applications of system-level models of metabolism for analysis of bacterial physiology and identification of new drug targets. Brief Funct Genomics 2011;10:354-64.
    • (2011) Brief Funct Genomics , vol.10 , pp. 354-364
    • Navid, A.1
  • 9
    • 1242283921 scopus 로고    scopus 로고
    • Use of genome-scale microbial models for metabolic engineering
    • Patil KR, Akesson M, Nielsen J. Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 2004;15:64-9.
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 64-69
    • Patil, K.R.1    Akesson, M.2    Nielsen, J.3
  • 10
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson Bø. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 2010;5:93-121.
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.ø.2
  • 11
    • 77951612556 scopus 로고    scopus 로고
    • BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger J, Park JO, Conrad TM, et al. BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 2010;11:213.
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3
  • 12
    • 77956696072 scopus 로고    scopus 로고
    • High-throughput generation, optimization and analysis of genome-scale metabolic models
    • Henry CS, DeJongh M, Best AA, et al. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 2010;28:977-82.
    • (2010) Nat Biotechnol , vol.28 , pp. 977-982
    • Henry, C.S.1    DeJongh, M.2    Best, A.A.3
  • 13
    • 77955534569 scopus 로고    scopus 로고
    • Integration of metabolic databases for the reconstruction of genome-scale metabolic networks
    • Radrich K, Tsuruoka Y, Dobson P, et al. Integration of metabolic databases for the reconstruction of genome-scale metabolic networks. BMCSyst Biol 2010;4:114.
    • (2010) BMCSyst Biol , vol.4 , pp. 114
    • Radrich, K.1    Tsuruoka, Y.2    Dobson, P.3
  • 14
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism- 2011
    • Orth JD, Conrad TM, Na J, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism- 2011. Mol Syst Biol 2011;7:535.
    • (2011) Mol Syst Biol , vol.7 , pp. 535
    • Orth, J.D.1    Conrad, T.M.2    Na, J.3
  • 15
    • 84856314687 scopus 로고    scopus 로고
    • MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis
    • Chindelevitch L, Stanley S, Hung D, et al. MetaMerge: scaling up genome-scale metabolic reconstructions, with application to Mycobacterium tuberculosis. Genome Biol 2012;13:R6.
    • (2012) Genome Biol , vol.13
    • Chindelevitch, L.1    Stanley, S.2    Hung, D.3
  • 16
    • 79953649492 scopus 로고    scopus 로고
    • Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis
    • Oberhardt MA, Puchalka J, Martins dos Santos VAP, et al. Reconciliation of genome-scale metabolic reconstructions for comparative systems analysis. PLoS Comput Biol 2011;7: e1001116.
    • (2011) PLoS Comput Biol , vol.7
    • Oberhardt, M.A.1    Puchalka, J.2    Martins dos Santos, V.A.P.3
  • 17
    • 79953144460 scopus 로고    scopus 로고
    • Challenges in integrating Escherichia coli molecular biology data
    • Lourenço A, Carneiro S, Rocha M, et al. Challenges in integrating Escherichia coli molecular biology data. Brief Bioinform 2011;12:91-103.
    • (2011) Brief Bioinform , vol.12 , pp. 91-103
    • Lourenço, A.1    Carneiro, S.2    Rocha, M.3
  • 18
    • 79961121106 scopus 로고    scopus 로고
    • BKM-react, an integrated biochemical reaction database
    • Lang M, Stelzer M, Schomburg D. BKM-react, an integrated biochemical reaction database. BMC Biochem 2011; 12:42.
    • (2011) BMC Biochem , vol.12 , pp. 42
    • Lang, M.1    Stelzer, M.2    Schomburg, D.3
  • 19
    • 84855499408 scopus 로고    scopus 로고
    • MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
    • Kumar A, Suthers P, Maranas C. MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinform 2012;13:6.
    • (2012) BMC Bioinform , vol.13 , pp. 6
    • Kumar, A.1    Suthers, P.2    Maranas, C.3
  • 20
    • 38549127678 scopus 로고    scopus 로고
    • ChEBI: a database and ontology for chemical entities of biological interest
    • Degtyarenko K, de Matos P, Ennis M, et al. ChEBI: a database and ontology for chemical entities of biological interest. Nucleic Acids Res 2007;36:D344-50.
    • (2007) Nucleic Acids Res , vol.36
    • Degtyarenko, K.1    de Matos, P.2    Ennis, M.3
  • 21
    • 84862220951 scopus 로고    scopus 로고
    • Rhea-a manually curated resource of biochemical reactions
    • Alcantara R, Axelsen KB, Morgat A, etal. Rhea-a manually curated resource of biochemical reactions. Nucleic Acids Res 2011;40:D754-60.
    • (2011) Nucleic Acids Res , vol.40
    • Alcantara, R.1    Axelsen, K.B.2    Morgat, A.3
  • 22
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: kyoto encyclopedia of genes and genomes
    • Kanehisa M, Goto S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000;28:27-30.
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 23
    • 33644877904 scopus 로고    scopus 로고
    • MetaCyc: a multiorganism database of metabolic pathways and enzymes
    • Caspi R. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 2006;34:D511-6.
    • (2006) Nucleic Acids Res , vol.34
    • Caspi, R.1
  • 24
    • 78651330012 scopus 로고    scopus 로고
    • BRENDA, the enzyme information system in 2011
    • Scheer M, Grote A, Chang A, et al. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2010;39: D670-6.
    • (2010) Nucleic Acids Res , vol.39
    • Scheer, M.1    Grote, A.2    Chang, A.3
  • 25
    • 33846088138 scopus 로고    scopus 로고
    • HMDB: the human metabolome database
    • Wishart DS. HMDB: the human metabolome database. Nucleic Acids Res 2007;35:D521-6.
    • (2007) Nucleic Acids Res , vol.35
    • Wishart, D.S.1
  • 26
    • 84859821563 scopus 로고    scopus 로고
    • UniPathway: a resource for the exploration and annotation of metabolic pathways
    • Morgat A, Coissac E, Coudert E, et al. UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res 2011;40:D761-9.
    • (2011) Nucleic Acids Res , vol.40
    • Morgat, A.1    Coissac, E.2    Coudert, E.3
  • 27
    • 84893009049 scopus 로고    scopus 로고
    • BioPath: Database on Biochemical Pathways
    • (1 March 2012, date last accessed).
    • BioPath: Database on Biochemical Pathways. www.molecularnetworks. com/biopath3/ (1 March 2012, date last accessed).
  • 28
    • 33846058198 scopus 로고    scopus 로고
    • LMSD: LIPID MAPS structure database
    • Sud M. LMSD: LIPID MAPS structure database. Nucleic Acids Res 2007;35:D527-32.
    • (2007) Nucleic Acids Res , vol.35
    • Sud, M.1
  • 30
    • 34249874435 scopus 로고    scopus 로고
    • The IUPAC international chemical identifier: InChl - a new standard for molecular informatics
    • McNaught A. The IUPAC international chemical identifier: InChl - a new standard for molecular informatics. Chem Int 2006;28:12-5.
    • (2006) Chem Int , vol.28 , pp. 12-15
    • McNaught, A.1
  • 31
    • 0026113011 scopus 로고
    • Very broad Markush claims; a solution or a problem? Proceedings of a round-table discussion held on 29 August 1990
    • Milne GW. Very broad Markush claims; a solution or a problem? Proceedings of a round-table discussion held on 29 August 1990. JChem Inf Comput Sci 1991;31:930.
    • (1991) JChem Inf Comput Sci , vol.31 , pp. 930
    • Milne, G.W.1
  • 32
    • 84892986239 scopus 로고    scopus 로고
    • ChemAxon: Cheminformatics Platforms and Desktop Applications
    • (15 January 2012, date last accessed).
    • ChemAxon: Cheminformatics Platforms and Desktop Applications. www.chemaxon.com (15 January 2012, date last accessed).
  • 33
    • 84890996840 scopus 로고
    • International Union of Pure and Applied Chemistry
    • (eds).Commission on the Nomenclature of Organic Chemistry. A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993). Oxford: Blackwell Scientific Publications
    • Panico R, Powell WH, Richer J-C, (eds). International Union of Pure and Applied Chemistry. Commission on the Nomenclature of Organic Chemistry. A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993). Oxford: Blackwell Scientific Publications http://en.wikipedia.org/wiki/Blackwell_ Science, 1993.
    • (1993)
    • Panico, R.1    Powell, W.H.2    Richer, J.-C.3
  • 34
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information
    • Feist AM, Henry CS, Reed JL, et al. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007;3:121-138.
    • (2007) Mol Syst Biol , vol.3 , pp. 121-138
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3
  • 35
    • 0003410183 scopus 로고
    • Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes
    • San Diego: Academic Press
    • Webb EC. Enzyme Nomenclature 1992: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. San Diego: Academic Press, 1992.
    • (1992)
    • Webb, E.C.1
  • 36
    • 78651275182 scopus 로고    scopus 로고
    • Reactome: a database of reactions, pathways and biological processes
    • Croft D, O'Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011;39:D691-7.
    • (2011) Nucleic Acids Res , vol.39
    • Croft, D.1    O'Kelly, G.2    Wu, G.3


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