메뉴 건너뛰기




Volumn 28, Issue 5, 2003, Pages 250-258

Metabolic pathways in the post-genome era

Author keywords

[No Author keywords available]

Indexed keywords

BIOENGINEERING; GENOME; GENOME ANALYSIS; GROWTH RATE; METABOLISM; PREDICTION; PRIORITY JOURNAL; REVIEW; STOICHIOMETRY;

EID: 0037727678     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0968-0004(03)00064-1     Document Type: Review
Times cited : (275)

References (55)
  • 1
    • 0035281870 scopus 로고    scopus 로고
    • Metabolic modeling of microbial strains in silico
    • Covert M.W., et al. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26:2001;179-186.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 179-186
    • Covert, M.W.1
  • 2
    • 0036001069 scopus 로고    scopus 로고
    • Metabolic modelling of microbes: The flux-balance approach
    • Edwards J.S., et al. Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4:2002;133-140.
    • (2002) Environ. Microbiol. , vol.4 , pp. 133-140
    • Edwards, J.S.1
  • 3
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling J., et al. Metabolic network structure determines key aspects of functionality and regulation. Nature. 420:2002;190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1
  • 5
    • 0033168258 scopus 로고    scopus 로고
    • Integrated pathway-genome databases and their role in drug discovery
    • Karp P.D., et al. Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol. 17:1999;275-281.
    • (1999) Trends Biotechnol. , vol.17 , pp. 275-281
    • Karp, P.D.1
  • 6
    • 0035860545 scopus 로고    scopus 로고
    • Pathway databases: A case study in computational symbolic theories
    • Karp P.D. Pathway databases: a case study in computational symbolic theories. Science. 293:2001;2040-2044.
    • (2001) Science , vol.293 , pp. 2040-2044
    • Karp, P.D.1
  • 7
    • 0034020583 scopus 로고    scopus 로고
    • Global properties of the metabolic map of Escherichia coli
    • Ouzounis C.A., Karp P.D. Global properties of the metabolic map of Escherichia coli. Genome Res. 10:2000;568-576.
    • (2000) Genome Res. , vol.10 , pp. 568-576
    • Ouzounis, C.A.1    Karp, P.D.2
  • 8
    • 0035169963 scopus 로고    scopus 로고
    • An algebraic-combinatorial model for the identification and mapping of biochemical pathways
    • Oliveira J.S., et al. An algebraic-combinatorial model for the identification and mapping of biochemical pathways. Bull. Math. Biol. 63:2001;1163-1196.
    • (2001) Bull. Math. Biol. , vol.63 , pp. 1163-1196
    • Oliveira, J.S.1
  • 9
    • 0023995387 scopus 로고
    • MPS: An artificially intelligent software system for the analysis and synthesis of metabolic pathways
    • Seressiotis A., Bailey J.E. MPS: an artificially intelligent software system for the analysis and synthesis of metabolic pathways. Biotechnol. Bioeng. 31:1988;587-602.
    • (1988) Biotechnol. Bioeng. , vol.31 , pp. 587-602
    • Seressiotis, A.1    Bailey, J.E.2
  • 10
    • 0025647585 scopus 로고
    • Computer-aided synthesis of biochemical pathways
    • Mavrovouniotis M.L., et al. Computer-aided synthesis of biochemical pathways. Biotechnol. Bioeng. 36:1990;1119-1132.
    • (1990) Biotechnol. Bioeng. , vol.36 , pp. 1119-1132
    • Mavrovouniotis, M.L.1
  • 11
    • 0000029295 scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Schuster S., Hilgetag C. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. 2:1994;165-182.
    • (1994) J. Biol. Syst. , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 12
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S., et al. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18:2000;326-332.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 326-332
    • Schuster, S.1
  • 13
    • 0033136109 scopus 로고    scopus 로고
    • Metabolic pathway analysis: Basic concepts and scientific applications in the post-genomic era
    • Schilling C.H., et al. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15:1999;296-303.
    • (1999) Biotechnol. Prog. , vol.15 , pp. 296-303
    • Schilling, C.H.1
  • 14
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Schilling C.H., et al. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203:2000;229-248.
    • (2000) J. Theor. Biol. , vol.203 , pp. 229-248
    • Schilling, C.H.1
  • 15
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of Helicobacterpylori 26695
    • Schilling C.H., et al. Genome-scale metabolic model of Helicobacterpylori 26695. J. Bacteriol. 184:2002;4582-4593.
    • (2002) J. Bacteriol. , vol.184 , pp. 4582-4593
    • Schilling, C.H.1
  • 16
    • 0034615788 scopus 로고    scopus 로고
    • Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
    • Schilling C.H., Palsson B.O. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J. Theor. Biol. 203:2000;249-283.
    • (2000) J. Theor. Biol. , vol.203 , pp. 249-283
    • Schilling, C.H.1    Palsson, B.O.2
  • 17
    • 0036350955 scopus 로고    scopus 로고
    • The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy
    • Papin J.A., et al. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy. J. Theor. Biol. 215:2002;67-82.
    • (2002) J. Theor. Biol. , vol.215 , pp. 67-82
    • Papin, J.A.1
  • 18
    • 0036100243 scopus 로고    scopus 로고
    • Determination of redundancy and systems properties of Helicobacterpylori's metabolic network using genome-scale extreme pathway analysis
    • Price N.D., et al. Determination of redundancy and systems properties of Helicobacterpylori's metabolic network using genome-scale extreme pathway analysis. Genome Res. 12:2002;760-769.
    • (2002) Genome Res. , vol.12 , pp. 760-769
    • Price, N.D.1
  • 19
    • 0026802334 scopus 로고
    • Metabolic control analysis: A survey of its theoretical and experimental development
    • Fell D.A. Metabolic control analysis: a survey of its theoretical and experimental development. Biochem. J. 286:1992;313-330.
    • (1992) Biochem. J. , vol.286 , pp. 313-330
    • Fell, D.A.1
  • 20
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • Reder C. Metabolic control theory: a structural approach. J. Theor. Biol. 135:1988;175-201.
    • (1988) J. Theor. Biol. , vol.135 , pp. 175-201
    • Reder, C.1
  • 21
    • 0017754837 scopus 로고
    • Metabolic regulation and mathematical models
    • Heinrich R., et al. Metabolic regulation and mathematical models. Prog. Biophys. Mol. Biol. 32:1977;1-82.
    • (1977) Prog. Biophys. Mol. Biol. , vol.32 , pp. 1-82
    • Heinrich, R.1
  • 25
    • 0023714694 scopus 로고
    • Stoichiometric network analysis
    • Clarke B.L. Stoichiometric network analysis. Cell Biophys. 12:1988;237-253.
    • (1988) Cell Biophys. , vol.12 , pp. 237-253
    • Clarke, B.L.1
  • 26
    • 0002013127 scopus 로고
    • Stability of complex reaction networks
    • I.P.A.S.A. Rice. New York: John Wiley
    • Clarke B.L. Stability of complex reaction networks. Rice I.P.A.S.A. Advances in Chemical Physics. 1980;1-215 John Wiley, New York.
    • (1980) Advances in Chemical Physics , pp. 1-215
    • Clarke, B.L.1
  • 28
    • 0037197159 scopus 로고    scopus 로고
    • Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria
    • Klamt S. Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol. Bioeng. 77:2002;734-751.
    • (2002) Biotechnol. Bioeng. , vol.77 , pp. 734-751
    • Klamt, S.1
  • 29
    • 0038335203 scopus 로고    scopus 로고
    • Elementary mode analysis illustrated with human red cell metabolism
    • D. et al. Larsson. Chalmers
    • Schuster S., et al. Elementary mode analysis illustrated with human red cell metabolism. Larsson D., et al. BioThermoKinetics in the Post Genomic Era. 1998;332-339 Chalmers.
    • (1998) BioThermoKinetics in the Post Genomic Era , pp. 332-339
    • Schuster, S.1
  • 30
    • 0035997009 scopus 로고    scopus 로고
    • Extreme pathway analysis of human red blood cell metabolism
    • Wiback S.J., Palsson B.O. Extreme pathway analysis of human red blood cell metabolism. Biophys. J. 83:2002;808-818.
    • (2002) Biophys. J. , vol.83 , pp. 808-818
    • Wiback, S.J.1    Palsson, B.O.2
  • 31
    • 0030571222 scopus 로고    scopus 로고
    • Pathway analysis, engineering and physiological considerations for redirecting central metabolism
    • Liao J.C., et al. Pathway analysis, engineering and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52:1996;129-140.
    • (1996) Biotechnol. Bioeng. , vol.52 , pp. 129-140
    • Liao, J.C.1
  • 32
    • 0034447725 scopus 로고    scopus 로고
    • Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
    • Schilling C.H., et al. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71:2000;286-306.
    • (2000) Biotechnol. Bioeng. , vol.71 , pp. 286-306
    • Schilling, C.H.1
  • 33
    • 0037023907 scopus 로고    scopus 로고
    • Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism
    • Van Dien S.J., Lidstrom M.E. Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol. Bioeng. 78:2002;296-312.
    • (2002) Biotechnol. Bioeng. , vol.78 , pp. 296-312
    • Van Dien, S.J.1    Lidstrom, M.E.2
  • 34
    • 0037200931 scopus 로고    scopus 로고
    • A functional genomics approach using metabolomics and in silico pathway analysis
    • Forster J., et al. A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioeng. 79:2002;703-712.
    • (2002) Biotechnol. Bioeng. , vol.79 , pp. 703-712
    • Forster, J.1
  • 35
    • 0037142769 scopus 로고    scopus 로고
    • Metabolic pathway analysis of a recombinant yeast for rational strain development
    • Carlson R., et al. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79:2002;121-134.
    • (2002) Biotechnol. Bioeng. , vol.79 , pp. 121-134
    • Carlson, R.1
  • 36
    • 0033215210 scopus 로고    scopus 로고
    • Pathway alignment: Application to the comparative analysis of glycolytic enzymes
    • Dandekar T., et al. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem. J. 343:1999;115-124.
    • (1999) Biochem. J. , vol.343 , pp. 115-124
    • Dandekar, T.1
  • 37
    • 0036526245 scopus 로고    scopus 로고
    • Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy
    • Flores S., et al. Analysis of carbon metabolism in Escherichia coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy. Metab. Eng. 4:2002;124-137.
    • (2002) Metab. Eng. , vol.4 , pp. 124-137
    • Flores, S.1
  • 38
    • 0344052685 scopus 로고    scopus 로고
    • METATOOL: For studying metabolic networks
    • Pfeiffer T., et al. METATOOL: for studying metabolic networks. Bioinformatics. 15:1999;251-257.
    • (1999) Bioinformatics , vol.15 , pp. 251-257
    • Pfeiffer, T.1
  • 39
    • 0036916269 scopus 로고    scopus 로고
    • Extreme pathway lengths and reaction participation in genome-scale metabolic networks
    • Papin J.A., et al. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res. 12:2002;1889-1900.
    • (2002) Genome Res. , vol.12 , pp. 1889-1900
    • Papin, J.A.1
  • 40
    • 0035725112 scopus 로고    scopus 로고
    • Use of network analysis of metaoblic systems in bioengineering
    • Schuster S., et al. Use of network analysis of metaoblic systems in bioengineering. Bioprocess Biosyst. Eng. 24:2002;363-372.
    • (2002) Bioprocess Biosyst. Eng. , vol.24 , pp. 363-372
    • Schuster, S.1
  • 41
    • 0037424661 scopus 로고    scopus 로고
    • Constraints-based models: Regulation of gene expression reduces the steady-state solution space
    • Covert M.W., Palsson B.O. Constraints-based models: regulation of gene expression reduces the steady-state solution space. J. Theor. Biol. 221:2003;309-325.
    • (2003) J. Theor. Biol. , vol.221 , pp. 309-325
    • Covert, M.W.1    Palsson, B.O.2
  • 42
    • 0035071155 scopus 로고    scopus 로고
    • Dynamic simulation of the human red blood cell metabolic network
    • Jamshidi N., et al. Dynamic simulation of the human red blood cell metabolic network. Bioinformatics. 17:2001;286-287.
    • (2001) Bioinformatics , vol.17 , pp. 286-287
    • Jamshidi, N.1
  • 43
    • 0024842144 scopus 로고
    • Metabolic dynamics in the human red cell. Part I-A comprehensive kinetic model
    • Joshi A., Palsson B.O. Metabolic dynamics in the human red cell. Part I-A comprehensive kinetic model. J. Theor. Biol. 141:1989;515-528.
    • (1989) J. Theor. Biol. , vol.141 , pp. 515-528
    • Joshi, A.1    Palsson, B.O.2
  • 44
    • 0033567930 scopus 로고    scopus 로고
    • Model of 2-3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed kinetic equations: Computer simulation and metabolic control analysis
    • Mulquiney P.J., Kuchel P.W. Model of 2-3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed kinetic equations: computer simulation and metabolic control analysis. Biochem. J. 342:1999;597-604.
    • (1999) Biochem. J. , vol.342 , pp. 597-604
    • Mulquiney, P.J.1    Kuchel, P.W.2
  • 45
    • 0016524924 scopus 로고
    • Mathematical analysis of multienzyme systems. I: Modelling of glycolysis of human erythrocytes
    • Rapoport T.A., Heinrich R. Mathematical analysis of multienzyme systems. I: modelling of glycolysis of human erythrocytes. Biosystems. 7:1975;120-129.
    • (1975) Biosystems , vol.7 , pp. 120-129
    • Rapoport, T.A.1    Heinrich, R.2
  • 46
    • 0034995375 scopus 로고    scopus 로고
    • Complex biology with no parameters
    • Bailey J.E. Complex biology with no parameters. Nat. Biotechnol. 19:2001;503-504.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 503-504
    • Bailey, J.E.1
  • 47
    • 0001827017 scopus 로고    scopus 로고
    • Metabolic flux balance analysis
    • S.Y. Lee, & E.T. et al. Papoutsakis. Marcel Deker
    • Edwards J.S., et al. Metabolic flux balance analysis. Lee S.Y., Papoutsakis E.T., et al. Metabolic Engineering. 1999;Marcel Deker.
    • (1999) Metabolic Engineering
    • Edwards, J.S.1
  • 48
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster S., et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol. 17:1999;53-60.
    • (1999) Trends Biotechnol. , vol.17 , pp. 53-60
    • Schuster, S.1
  • 51
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
    • Schuster S., et al. Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics. 18:2002;351-361.
    • (2002) Bioinformatics , vol.18 , pp. 351-361
    • Schuster, S.1
  • 52
    • 0036840340 scopus 로고    scopus 로고
    • Extreme pathways and Kirchhoff's second law
    • Price N.D., et al. Extreme pathways and Kirchhoff's second law. Biophys. J. 83:2002;2879-2882.
    • (2002) Biophys. J. , vol.83 , pp. 2879-2882
    • Price, N.D.1
  • 53
    • 0033764285 scopus 로고    scopus 로고
    • The challenges of in silico biology
    • Palsson B.O. The challenges of in silico biology. Nat. Biotechnol. 18:2000;1147-1150.
    • (2000) Nat. Biotechnol. , vol.18 , pp. 1147-1150
    • Palsson, B.O.1
  • 55
    • 0037304679 scopus 로고    scopus 로고
    • Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices
    • (2003) Biophys. J. , vol.84 , pp. 794-804
    • Price, N.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.