메뉴 건너뛰기




Volumn 30, Issue 14, 2014, Pages 2043-2050

Optimal metabolic route search based on atom mappings

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; GENETICS; GENOME; METABOLIC ENGINEERING; METABOLISM; METHODOLOGY;

EID: 84903954626     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu150     Document Type: Article
Times cited : (43)

References (27)
  • 1
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi, S. et al. (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature, 451, 86-89.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1
  • 2
    • 74149094503 scopus 로고    scopus 로고
    • Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes
    • Atsumi, S. et al. (2010) Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl. Microbiol. Biotechnol., 85, 651-657.
    • (2010) Appl. Microbiol. Biotechnol , vol.85 , pp. 651-657
    • Atsumi, S.1
  • 3
    • 0002610737 scopus 로고
    • On a routing problem
    • Bellman, R. (1958) On a routing problem. Q. App. Math., 16, 87-90.
    • (1958) Q. App. Math. , vol.16 , pp. 87-90
    • Bellman, R.1
  • 4
    • 51749088153 scopus 로고    scopus 로고
    • Meta route: Fast search for relevant metabolic routes for interactive network navigation and visualization
    • Blum, T. and Kohlbacher, O. (2008a) Meta Route: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics, 24, 2108-2109.
    • (2008) Bioinformatics , vol.24 , pp. 2108-2109
    • Blum, T.1    Kohlbacher, O.2
  • 5
    • 47549099578 scopus 로고    scopus 로고
    • Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks
    • Blum, T. and Kohlbacher, O. (2008b) Using atom mapping rules for an improved detection of relevant routes in weighted metabolic networks. J. Comput. Biol., 15, 565-576.
    • (2008) J. Comput. Biol. , vol.15 , pp. 565-576
    • Blum, T.1    Kohlbacher, O.2
  • 6
    • 84860490976 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Caspi, R. et al. (2012) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res., 40, D742-D753.
    • (2012) Nucleic Acids Res. , vol.40
    • Caspi, R.1
  • 7
    • 52649153633 scopus 로고    scopus 로고
    • Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol
    • Connor, M.R. and Liao, J.C. (2008) Engineering of an Escherichia coli strain for the production of 3-methyl-1-butanol. Appl. Environ. Microbiol., 74, 5769-5775.
    • (2008) Appl. Environ. Microbiol , vol.74 , pp. 5769-5775
    • Connor, M.R.1    Liao, J.C.2
  • 8
    • 23144466440 scopus 로고    scopus 로고
    • Metabolic path finding: Inferring relevant pathways in biochemical networks
    • Croes, D. et al. (2005) Metabolic Path Finding: inferring relevant pathways in biochemical networks. Nucleic Acids Res., 33 (Suppl. 2), W326-W330.
    • (2005) Nucleic Acids Res. , vol.33 , Issue.SUPPL. 2
    • Croes, D.1
  • 9
    • 0032108018 scopus 로고    scopus 로고
    • Finding the k shortest paths
    • Eppstein, D. (1998) Finding the k shortest paths. SIAM J. Comput., 28, 652-673.
    • (1998) SIAM J. Comput. , vol.28 , pp. 652-673
    • Eppstein, D.1
  • 10
    • 0003870959 scopus 로고
    • Rand Corporation. Santa Monica, CA, USA
    • Ford, L. (1956) Network Flow Theory. Rand Corporation. Santa Monica, CA, USA.
    • (1956) Network Flow Theory
    • Ford, L.1
  • 11
    • 77954188312 scopus 로고    scopus 로고
    • Finding metabolic pathways using atom tracking
    • Heath, A.P. et al. (2010) Finding metabolic pathways using atom tracking. Bioinformatics, 26, 1548-1555.
    • (2010) Bioinformatics , vol.26 , pp. 1548-1555
    • Heath, A.P.1
  • 13
    • 84858983547 scopus 로고    scopus 로고
    • KEGG for integration and interpretation of large-scale molecular data sets
    • Kanehisa, M. et al. (2012) KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res., 40, D109-D114.
    • (2012) Nucleic Acids Res. , vol.40
    • Kanehisa, M.1
  • 14
    • 75849133666 scopus 로고    scopus 로고
    • Pathway tools version 13.0: Integrated software for pathway/genome informatics and systems biology
    • Karp, P. et al. (2010) Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform., 11, 40-79.
    • (2010) Brief. Bioinform , vol.11 , pp. 40-79
    • Karp, P.1
  • 15
    • 84879916305 scopus 로고    scopus 로고
    • Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
    • Kotera, M. et al. (2013) Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics, 29, i135-i144.
    • (2013) Bioinformatics , vol.29
    • Kotera, M.1
  • 16
    • 84870051910 scopus 로고    scopus 로고
    • Accurate atom-mapping computation for biochemical reactions
    • Latendresse, M. et al. (2012) Accurate atom-mapping computation for biochemical reactions. J. Chem. Inf. Model., 52, 2970-2982.
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2970-2982
    • Latendresse, M.1
  • 17
    • 84876694741 scopus 로고    scopus 로고
    • Biosynthesis of ethylene glycol in Escherichia coli
    • Liu, H. et al. (2013) Biosynthesis of ethylene glycol in Escherichia coli. Appl. Microbiol. Biotechnol., 97, 3409-3417.
    • (2013) Appl. Microbiol. Biotechnol , vol.97 , pp. 3409-3417
    • Liu, H.1
  • 18
    • 0141850380 scopus 로고    scopus 로고
    • PathMiner: Predicting metabolic pathways by heuristic search
    • McShan, D. et al. (2003) PathMiner: predicting metabolic pathways by heuristic search. Bioinformatics, 19, 1692-1698.
    • (2003) Bioinformatics , vol.19 , pp. 1692-1698
    • McShan, D.1
  • 19
    • 77954268488 scopus 로고    scopus 로고
    • PathPred: An enzyme-catalyzed metabolic pathway prediction server
    • Moriya, Y. et al. (2010) PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res., 38, W138-W143.
    • (2010) Nucleic Acids Res. , vol.38
    • Moriya, Y.1
  • 20
    • 0142027026 scopus 로고    scopus 로고
    • Metabolic engineering for the microbial production of 1,3-propanediol
    • Nakamura, C.E. and Whited, G.M. (2003) Metabolic engineering for the microbial production of 1,3-propanediol. Curr. Opin. Biotechnol., 14, 454-459.
    • (2003) Curr. Opin. Biotechnol , vol.14 , pp. 454-459
    • Nakamura, C.E.1    Whited, G.M.2
  • 21
    • 70749083404 scopus 로고    scopus 로고
    • Inferring branching pathways in genome-scale metabolic networks
    • Pitkänen, E. et al. (2009) Inferring branching pathways in genome-scale metabolic networks. BMC Syst. Biol., 3, 1-22.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 1-22
    • Pitkänen, E.1
  • 22
    • 16344376028 scopus 로고    scopus 로고
    • Metabolic pathway analysis web service (Pathway Hunter tool at cubic)
    • Rahman, S.A. et al. (2005) Metabolic pathway analysis web service (Pathway Hunter tool at cubic). Bioinformatics, 21, 1189-1193.
    • (2005) Bioinformatics , vol.21 , pp. 1189-1193
    • Rahman, S.A.1
  • 23
    • 79958715193 scopus 로고    scopus 로고
    • Optimization of a heterologous pathway for the production of flavonoids from glucose
    • Santos, C.N. et al. (2011) Optimization of a heterologous pathway for the production of flavonoids from glucose. Metab. Eng., 13, 392-400.
    • (2011) Metab. Eng. , vol.13 , pp. 392-400
    • Santos, C.N.1
  • 24
    • 80052445503 scopus 로고    scopus 로고
    • Use of the valine biosynthetic pathway to convert glucose into isobutanol
    • Savrasova, E.A. et al. (2011) Use of the valine biosynthetic pathway to convert glucose into isobutanol. J. Ind. Microbiol. Biotechnol., 38, 1287-1294.
    • (2011) J. Ind. Microbiol. Biotechnol , vol.38 , pp. 1287-1294
    • Savrasova, E.A.1
  • 25
    • 0035815724 scopus 로고    scopus 로고
    • Fructose-6-phosphate aldolase is a novel class I aldolase from Escherichia coli and is related to a novel group of bacterial transaldolases
    • Schurmann, M. and Sprenger, G.A. (2001) Fructose-6-phosphate aldolase is a novel class I aldolase from Escherichia coli and is related to a novel group of bacterial transaldolases. J. Biol. Chem., 276, 11055-11061.
    • (2001) J. Biol. Chem. , vol.276 , pp. 11055-11061
    • Schurmann, M.1    Sprenger, G.A.2
  • 26
    • 33847252518 scopus 로고    scopus 로고
    • Production of p-hydroxycinnamic acid from glucose in Saccharomyces cerevisiae and Escherichia coli by expression of heterologous genes from plants and fungi
    • Vannelli, T. et al. (2007) Production of p-hydroxycinnamic acid from glucose in Saccharomyces cerevisiae and Escherichia coli by expression of heterologous genes from plants and fungi. Metab. Eng., 9, 142-151.
    • (2007) Metab. Eng. , vol.9 , pp. 142-151
    • Vannelli, T.1
  • 27
    • 84859561004 scopus 로고    scopus 로고
    • A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. Exhibits p-coumaroyl CoA 2′-hydroxylase activity (C2'H): A missing step in the synthesis of umbelliferone in plants
    • Vialart, G. et al. (2012) A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2′-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants. Plant J., 70, 460-470.
    • (2012) Plant J. , vol.70 , pp. 460-470
    • Vialart, G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.