메뉴 건너뛰기




Volumn 9, Issue 5, 2008, Pages 422-436

A critical examination of stoichiometric and path-finding approaches to metabolic pathways

Author keywords

Elementary flux modes; Extreme pathways; Metabolic pathways; Path finding; Shortest path; Systems biology

Indexed keywords

BIOENGINEERING; BIOTECHNOLOGY; COMPUTER PROGRAM; ENZYME KINETICS; ENZYME METABOLISM; GENE REGULATORY NETWORK; GENETIC ALGORITHM; GENOMICS; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; METABOLIC ENGINEERING; NETWORK LEARNING; NONHUMAN; REACTION ANALYSIS; REVIEW; SIGNAL TRANSDUCTION; STOICHIOMETRY;

EID: 49949089557     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbn018     Document Type: Review
Times cited : (47)

References (78)
  • 2
    • 23144466440 scopus 로고    scopus 로고
    • Metabolic PathFinding: Inferring relevant pathways in biochemical networks
    • Croes D, Couche F, Wodak SJ, et al. Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 2005;33:W326-30.
    • (2005) Nucleic Acids Res , vol.33
    • Croes, D.1    Couche, F.2    Wodak, S.J.3
  • 3
    • 30344456708 scopus 로고    scopus 로고
    • Inferring meaningful pathways in weighted metabolic networks
    • Croes D, Couche F, Wodak SJ, et al. Inferring meaningful pathways in weighted metabolic networks. J Mol Biol 2006; 356:222-36.
    • (2006) J Mol Biol , vol.356 , pp. 222-236
    • Croes, D.1    Couche, F.2    Wodak, S.J.3
  • 4
    • 0037881782 scopus 로고    scopus 로고
    • Metabolic reconstruction using shortest paths
    • Arita M. Metabolic reconstruction using shortest paths. Simulat Pract Theory 2000;8:109-25.
    • (2000) Simulat Pract Theory , vol.8 , pp. 109-125
    • Arita, M.1
  • 5
    • 33845877959 scopus 로고    scopus 로고
    • Recovering metabolic pathways via optimization
    • Beasley JE, Planes FJ. Recovering metabolic pathways via optimization. Bioinformatics 2007;23:92-8.
    • (2007) Bioinformatics , vol.23 , pp. 92-98
    • Beasley, J.E.1    Planes, F.J.2
  • 6
    • 49949118584 scopus 로고    scopus 로고
    • Path finding approaches and metabolic pathways
    • in press
    • Planes FJ, Beasley JE. Path finding approaches and metabolic pathways. Discrete Appl Math 2007 (in press).
    • (2007) Discrete Appl Math
    • Planes, F.J.1    Beasley, J.E.2
  • 8
    • 0033168258 scopus 로고    scopus 로고
    • Integrated pathway-genome databases and their role in drug discovery
    • Karp PD, Krummenacker M, Paley S, et al. Integrated pathway-genome databases and their role in drug discovery. Trends Biotechnol 1999;17:275-81.
    • (1999) Trends Biotechnol , vol.17 , pp. 275-281
    • Karp, P.D.1    Krummenacker, M.2    Paley, S.3
  • 9
    • 0032919364 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopaedia of Genes and Genomes
    • Ogata H, Goto S, Saco K, et al. KEGG: Kyoto Encyclopaedia of Genes and Genomes. Nucleic Acids Res 1999;27:29-34.
    • (1999) Nucleic Acids Res , vol.27 , pp. 29-34
    • Ogata, H.1    Goto, S.2    Saco, K.3
  • 10
    • 0033977576 scopus 로고    scopus 로고
    • WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction
    • Overbeek R, Larsen N, Pusch GD, et al. WIT: Integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res 2000;28:123-5.
    • (2000) Nucleic Acids Res , vol.28 , pp. 123-125
    • Overbeek, R.1    Larsen, N.2    Pusch, G.D.3
  • 11
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed JL, Vo TD, Schilling CH, et al. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003;4:R54.
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3
  • 12
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of Helicobaccer pylori 26695
    • Schilling CH, Covert MW, Famili I, et al. Genome-scale metabolic model of Helicobaccer pylori 26695. J Bacteriol 2002;184 4582-4593.
    • (2002) J Bacteriol , vol.184 , pp. 4582-4593
    • Schilling, C.H.1    Covert, M.W.2    Famili, I.3
  • 13
    • 0347506655 scopus 로고    scopus 로고
    • An overview of data models for the analysis of biochemical pathways
    • Deville Y, Gilbert D, van Helden J, et al. An overview of data models for the analysis of biochemical pathways. Brief Bioinform 2003;4:246-59.
    • (2003) Brief Bioinform , vol.4 , pp. 246-259
    • Deville, Y.1    Gilbert, D.2    van Helden, J.3
  • 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 CH, Letscher D, Palsson BO. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 2000;203 229-48.
    • (2000) J Theor Biol , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 15
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnol 2000;18:326-32.
    • (2000) Nature Biotechnol , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 16
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • Klamt S, Stelfing J. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep 2002;29:233-6.
    • (2002) Mol Biol Rep , vol.29 , pp. 233-236
    • Klamt, S.1    Stelfing, J.2
  • 17
    • 0022971582 scopus 로고
    • An algorithm and data base for metabolic pathway synthesis
    • Seressiotis A, Bailey JE. MPS: An algorithm and data base for metabolic pathway synthesis. Biotechnol Lett 1986;8: 837-42.
    • (1986) Biotechnol Lett , vol.8 , pp. 837-842
    • Seressiotis, A.1    Bailey, J.M.2
  • 18
    • 0023995387 scopus 로고
    • MPS - an artificially intelligent software system for the analysis and synthesis of metabolic pathways
    • Seressiotis A, Bailey JE. MPS - an artificially intelligent software system for the analysis and synthesis of metabolic pathways. Biotechnol Bioeng 1988;31:587-602.
    • (1988) Biotechnol Bioeng , vol.31 , pp. 587-602
    • Seressiotis, A.1    Bailey, J.E.2
  • 19
    • 0026898402 scopus 로고
    • Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 2. Formalization and analysis of the synthesis algorithm
    • Mavrovouniotis ML. Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 2. Formalization and analysis of the synthesis algorithm. Ind Eng Chem Res 1992;31:1637-53.
    • (1992) Ind Eng Chem Res , vol.31 , pp. 1637-1653
    • Mavrovouniotis, M.L.1
  • 20
    • 2042440312 scopus 로고
    • Identification of qualitatively feasible metabolic pathways
    • Hunter I, ed, Menlo Park, CA: AAAI Press/MIT Press
    • Mavrovouniotis ML. Identification of qualitatively feasible metabolic pathways. In: Hunter I. (ed). Artificial Intelligence and Molecular Biology. Menlo Park, CA: AAAI Press/MIT Press, 1993;325-64.
    • (1993) Artificial Intelligence and Molecular Biology , pp. 325-364
    • Mavrovouniotis, M.L.1
  • 21
    • 0026898481 scopus 로고
    • Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 1. A synthesis approach in the context of simple examples
    • Mavrovouniotis ML, Stephanopoulos G. Synthesis of reaction mechanisms consisting of reversible and irreversible steps. 1. A synthesis approach in the context of simple examples. Ind Eng Chem Res 1992;31 1625-37.
    • (1992) Ind Eng Chem Res , vol.31 , pp. 1625-1637
    • Mavrovouniotis, M.L.1    Stephanopoulos, G.2
  • 22
    • 0002013127 scopus 로고
    • Stability of complex reaction networks
    • Prigogine I, Rice SA eds, New York: John Wiley & Sons
    • Clarke BL. Stability of complex reaction networks. In: Prigogine I, Rice SA (eds). Advances in Chemical Physics; Vol. 43. New York: John Wiley & Sons, 1980:1-215.
    • (1980) Advances in Chemical Physics , vol.43 , pp. 1-215
    • Clarke, B.L.1
  • 23
    • 0020089561 scopus 로고
    • Multiple reaction mechanisms in catalysis
    • Happel J, Sellers PH. Multiple reaction mechanisms in catalysis. Ind Eng Chem Fund 1982;21:67-76.
    • (1982) Ind Eng Chem Fund , vol.21 , pp. 67-76
    • Happel, J.1    Sellers, P.H.2
  • 24
    • 0001780266 scopus 로고
    • The characterization of complex systems of chemical reactions
    • Happel J, Sellers PH. The characterization of complex systems of chemical reactions. Chem Eng Commun 1989;83: 221-40.
    • (1989) Chem Eng Commun , vol.83 , pp. 221-240
    • Happel, J.1    Sellers, P.H.2
  • 25
    • 0001229632 scopus 로고
    • The possible mechanisms of complex reactions involving consecutive steps
    • Milner PC. The possible mechanisms of complex reactions involving consecutive steps. J Electrochem Soc 1964;111:228-32.
    • (1964) J Electrochem Soc , vol.111 , pp. 228-232
    • Milner, P.C.1
  • 26
    • 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 1994; 2:165-82.
    • (1994) J Biol Syst , vol.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 27
    • 25444515956 scopus 로고    scopus 로고
    • YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities
    • Schwarz R, Musch P, von Kamp A, et al. YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities. BMC Bioinformatics 2005;6:135.
    • (2005) BMC Bioinformatics , vol.6 , pp. 135
    • Schwarz, R.1    Musch, P.2    von Kamp, A.3
  • 28
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: Fast and flexible elementary mode analysis
    • von Kamp A, Schuster S. Metatool 5.0: Fast and flexible elementary mode analysis. Bioinformatics 2006;22: 1930-1.
    • (2006) Bioinformatics , vol.22 , pp. 1930-1931
    • von Kamp, A.1    Schuster, S.2
  • 29
    • 0042662951 scopus 로고    scopus 로고
    • A method for classifying metabolites in topological pathway analyses based on minimization of pathway number
    • Dandekar T, Moldenhauer F, Bulik S, et al. A method for classifying metabolites in topological pathway analyses based on minimization of pathway number. Biosystems 2003;70: 255-70.
    • (2003) Biosystems , vol.70 , pp. 255-270
    • Dandekar, T.1    Moldenhauer, F.2    Bulik, S.3
  • 30
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae
    • Schuster S, Pfeiffer T, Moldenhauer F, et al. Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae. Bioinformatics 2002;18 351-61.
    • (2002) Bioinformatics , vol.18 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3
  • 31
    • 33846015888 scopus 로고    scopus 로고
    • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
    • Teusink B, Wiersma A, Molenaar D, et al. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 2006;281:40041-8.
    • (2006) J Biol Chem , vol.281 , pp. 40041-40048
    • Teusink, B.1    Wiersma, A.2    Molenaar, D.3
  • 32
    • 0030571222 scopus 로고    scopus 로고
    • Pathway analysis, engineering, and physiological considerations for redirecting central metabolism
    • Liao JC, Hou SY, Chao YP. Pathway analysis, engineering, and physiological considerations for redirecting central metabolism. Biotechnol Bioeng 1996;52:129-40.
    • (1996) Biotechnol Bioeng , vol.52 , pp. 129-140
    • Liao, J.C.1    Hou, S.Y.2    Chao, Y.P.3
  • 33
    • 0033215210 scopus 로고    scopus 로고
    • Pathway alignment: Application to the comparative analysis of glycolytic enzymes
    • Dandekar T, Schuster S, Snel B, et al. Pathway alignment: application to the comparative analysis of glycolytic enzymes. Biochem J 1999;343:115-24.
    • (1999) Biochem J , vol.343 , pp. 115-124
    • Dandekar, T.1    Schuster, S.2    Snel, B.3
  • 34
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Förster J, Famili I, Fu P, et al. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003;13:244-53.
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3
  • 35
    • 0037317848 scopus 로고    scopus 로고
    • Elementary modes analysis of photosynthate metabolism in the chloroplast stroma
    • Poolman MG, Fell DA, Raines CA. Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur J Biochem 2003;270:430-9.
    • (2003) Eur J Biochem , vol.270 , pp. 430-439
    • Poolman, M.G.1    Fell, D.A.2    Raines, C.A.3
  • 36
    • 0347761259 scopus 로고    scopus 로고
    • Fundamental Escherichia coli biochemical pathways for biomass and energy production: Identification of reactions
    • Carlson R, Srienc F. Fundamental Escherichia coli biochemical pathways for biomass and energy production: Identification of reactions. Biotechnol Bioeng 2004;85:1-19.
    • (2004) Biotechnol Bioeng , vol.85 , pp. 1-19
    • Carlson, R.1    Srienc, F.2
  • 37
    • 8844231118 scopus 로고    scopus 로고
    • Metabolic pathway analysis of enzyme-deficient human red blood cells
    • Çakir T, Tacer CS, Ülgen KÖ. Metabolic pathway analysis of enzyme-deficient human red blood cells. BioSystems 2004;78 49-67.
    • (2004) BioSystems , vol.78 , pp. 49-67
    • Çakir, T.1    Tacer, C.S.2    Ülgen, K.O.D.I.E.3
  • 38
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya C. Petri net modelling of biological networks. Brief Bioinform 2007;8:210-9.
    • (2007) Brief Bioinform , vol.8 , pp. 210-219
    • Chaouiya, C.1
  • 39
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • Koch I, Junker BH, Heiner M. Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 2005;21: 1219-26.
    • (2005) Bioinformatics , vol.21 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 40
    • 0345602990 scopus 로고    scopus 로고
    • Topological analysis of metabolic networks based on Petri net theory
    • 0029, 28 February, date last accessed
    • Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on Petri net theory. In: Silico Biol, Vol. 3. 2003, 0029. http://www.bioinfo.de/isb/2003/03/0029/ (28 February 2008, date last accessed).
    • (2003) Silico Biol , vol.3
    • Zevedei-Oancea, I.1    Schuster, S.2
  • 41
    • 0001896749 scopus 로고
    • Convex geometry and semiflows in P/T nets. A comparative study of algorithms for computation of minimal P-semiflows
    • Colom JM, Silva M. Convex geometry and semiflows in P/T nets. A comparative study of algorithms for computation of minimal P-semiflows. Lect Notes Comput Sci 1991; 483:79-112.
    • (1991) Lect Notes Comput Sci , vol.483 , pp. 79-112
    • Colom, J.M.1    Silva, M.2
  • 42
    • 17544366029 scopus 로고    scopus 로고
    • Expa: A program for calculating extreme pathways in biochemical reaction networks
    • Bell SL, Palsson BO. Expa: A program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 2005;21 1739-40.
    • (2005) Bioinformatics , vol.21 , pp. 1739-1740
    • Bell, S.L.1    Palsson, B.O.2
  • 43
    • 0037406237 scopus 로고    scopus 로고
    • Development of network-based pathway definitions: The need to analyze real metabolic networks
    • Palsson BO, Price ND, Papin JA. Development of network-based pathway definitions: The need to analyze real metabolic networks. Trends Biotechnol 2003;21: 195-8.
    • (2003) Trends Biotechnol , vol.21 , pp. 195-198
    • Palsson, B.O.1    Price, N.D.2    Papin, J.A.3
  • 44
    • 3342925846 scopus 로고    scopus 로고
    • Comparison of network-based pathway analysis methods
    • Papin JA, Stelling J, Price ND, et al. Comparison of network-based pathway analysis methods. Trends Biotechnol 2004;22:400-5.
    • (2004) Trends Biotechnol , vol.22 , pp. 400-405
    • Papin, J.A.1    Stelling, J.2    Price, N.D.3
  • 45
    • 36348959154 scopus 로고    scopus 로고
    • Estimation of the number of extreme pathways for metabolic networks
    • Yeung M, Thiele I, Palsson BO. Estimation of the number of extreme pathways for metabolic networks. BMC Bioinformatics 2007;8 363.
    • (2007) BMC Bioinformatics , vol.8 , pp. 363
    • Yeung, M.1    Thiele, I.2    Palsson, B.O.3
  • 46
    • 0034615788 scopus 로고    scopus 로고
    • Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis
    • Schilling CH, Palsson BO. Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 2000;203: 249-83.
    • (2000) J Theor Biol , vol.203 , pp. 249-283
    • Schilling, C.H.1    Palsson, B.O.2
  • 47
    • 0036916269 scopus 로고    scopus 로고
    • Extreme pathway lengths and reaction participation in genome-scale metabolic networks
    • Papin JA, Price ND, Palsson BO. Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res 2002;12:1889-900.
    • (2002) Genome Res , vol.12 , pp. 1889-1900
    • Papin, J.A.1    Price, N.D.2    Palsson, B.O.3
  • 48
    • 0036100243 scopus 로고    scopus 로고
    • Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis
    • Price ND, Papin JA, Palsson BO. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res 2002;12 760-9.
    • (2002) Genome Res , vol.12 , pp. 760-769
    • Price, N.D.1    Papin, J.A.2    Palsson, B.O.3
  • 50
    • 0037424661 scopus 로고    scopus 로고
    • Constraints-based models: Regulation of gene expression reduces the steady-state solution space
    • Covert MW, Palsson BO. Constraints-based models: Regulation of gene expression reduces the steady-state solution space. J Theor Biol 2003;221:309-25.
    • (2003) J Theor Biol , vol.221 , pp. 309-325
    • Covert, M.W.1    Palsson, B.O.2
  • 52
    • 0035997009 scopus 로고    scopus 로고
    • Extreme pathway analysis of human red blood cell metabolism
    • Wiback SJ, Palsson BO. Extreme pathway analysis of human red blood cell metabolism. Biophys J 2002;83: 808-18.
    • (2002) Biophys J , vol.83 , pp. 808-818
    • Wiback, S.J.1    Palsson, B.O.2
  • 53
    • 0034973362 scopus 로고    scopus 로고
    • Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems
    • Ebenhöh O, Heinrich R. Evolutionary optimization of metabolic pathways. Theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bull Math Biol 2001;63:21-55.
    • (2001) Bull Math Biol , vol.63 , pp. 21-55
    • Ebenhöh, O.1    Heinrich, R.2
  • 54
    • 0031030714 scopus 로고    scopus 로고
    • Theoretical approaches to the evolutionary optimization of glycolysis. Thermodynamic and kinetic constraints
    • Heinrich R, Montero F, Klipp E, et al. Theoretical approaches to the evolutionary optimization of glycolysis. Thermodynamic and kinetic constraints. Eur J Biochem 1997; 243:191-201.
    • (1997) Eur J Biochem , vol.243 , pp. 191-201
    • Heinrich, R.1    Montero, F.2    Klipp, E.3
  • 55
    • 0029837737 scopus 로고    scopus 로고
    • The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution
    • Meléndez-Hevia E, Waddell TG, Casante M. The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution. J Mol Evol 1996;43:293-303.
    • (1996) J Mol Evol , vol.43 , pp. 293-303
    • Meléndez-Hevia, E.1    Waddell, T.G.2    Casante, M.3
  • 56
    • 0031058143 scopus 로고    scopus 로고
    • Theoretical approaches to the evolutionary optimization of glycolysis. Chemical analysis
    • Meléndez-Hevia E, Waddell TG, Heinrich R, et al. Theoretical approaches to the evolutionary optimization of glycolysis. Chemical analysis. Eur J Biochem 1997;244:527-43.
    • (1997) Eur J Biochem , vol.244 , pp. 527-543
    • Meléndez-Hevia, E.1    Waddell, T.G.2    Heinrich, R.3
  • 57
    • 0032079021 scopus 로고    scopus 로고
    • Kinetic and thermodynamic principles determining the structural design of ATP-producing systems
    • Stephani A, Heinrich R. Kinetic and thermodynamic principles determining the structural design of ATP-producing systems. Bull Math Biol 1998;60:505-43.
    • (1998) Bull Math Biol , vol.60 , pp. 505-543
    • Stephani, A.1    Heinrich, R.2
  • 58
    • 0033532830 scopus 로고    scopus 로고
    • Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm
    • Stephani A, Nuno JC, Heinrich R. Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm. J Theor Biol 1999;199:45-61.
    • (1999) J Theor Biol , vol.199 , pp. 45-61
    • Stephani, A.1    Nuno, J.C.2    Heinrich, R.3
  • 59
    • 0037342134 scopus 로고    scopus 로고
    • Stoichiometric design of metabolic networks: Multifunctionality, clusters, optimization, weak and strong robustness
    • Ebenhöh O, Heinrich R. Stoichiometric design of metabolic networks: multifunctionality, clusters, optimization, weak and strong robustness. Bull Math Biol 2003;65: 323-57.
    • (2003) Bull Math Biol , vol.65 , pp. 323-357
    • Ebenhöh, O.1    Heinrich, R.2
  • 60
    • 0025607185 scopus 로고
    • The game of the penrose phosphate cycle - a mathematical approach to study the optimization in design of metabolic pathways during evolution
    • Meléndez-Hevia E. The game of the penrose phosphate cycle - a mathematical approach to study the optimization in design of metabolic pathways during evolution. Biomedica Biochimica Acta 1990;49 903-16.
    • (1990) Biomedica Biochimica Acta , vol.49 , pp. 903-916
    • Meléndez-Hevia, E.1
  • 61
    • 0022350091 scopus 로고
    • The game of the penrose phosphate cycle
    • Meléndez-Hevia E, Isidoro A. The game of the penrose phosphate cycle. J Theor Biol 1985;117:251-63.
    • (1985) J Theor Biol , vol.117 , pp. 251-263
    • Meléndez-Hevia, E.1    Isidoro, A.2
  • 62
    • 0024280618 scopus 로고
    • Economy of design in metabolic pathways - further remarks on the game of the penrose phosphate cycle
    • Meléndez-Hevia E, Torres NV. Economy of design in metabolic pathways - further remarks on the game of the penrose phosphate cycle. J Theor Biol 1988;132:97-111.
    • (1988) J Theor Biol , vol.132 , pp. 97-111
    • Meléndez-Hevia, E.1    Torres, N.V.2
  • 63
    • 0028223931 scopus 로고
    • Optimization of metabolism: The evolution of metabolic pathways toward simplicity through the game of the penrose phosphate cycle
    • Meléndez-Hevia E, Waddell TG, Montero F. Optimization of metabolism: the evolution of metabolic pathways toward simplicity through the game of the penrose phosphate cycle. J Theor Biol 1994;166:201-20.
    • (1994) J Theor Biol , vol.166 , pp. 201-220
    • Meléndez-Hevia, E.1    Waddell, T.G.2    Montero, F.3
  • 64
    • 0032170434 scopus 로고    scopus 로고
    • Designing metabolism: Alternative connectivities for the penrose phosphate pathway
    • Mittenthal JE, Yuan A, Clarke B, et al. Designing metabolism: Alternative connectivities for the penrose phosphate pathway. Bull Math Biol 1998;60:815-56.
    • (1998) Bull Math Biol , vol.60 , pp. 815-856
    • Mittenthal, J.E.1    Yuan, A.2    Clarke, B.3
  • 67
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004;2:886-97.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 68
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display (DMD)
    • Küffner R, Zimmer R, Lengauer T. Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 2000;16:825-36.
    • (2000) Bioinformatics , vol.16 , pp. 825-836
    • Küffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 69
    • 0141850380 scopus 로고    scopus 로고
    • PathMiner: Predicting metabolic pathways by heuristic search
    • McShan DC, Rao S, Shah I. PathMiner: Predicting metabolic pathways by heuristic search. Bioinformatics 2003;19:1692-8.
    • (2003) Bioinformatics , vol.19 , pp. 1692-1698
    • McShan, D.C.1    Rao, S.2    Shah, I.3
  • 71
    • 16344376028 scopus 로고    scopus 로고
    • Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
    • Rahman SA, Advani P, Schunk R, et al. Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC). Bioinformatics 2005; 21:1189-93.
    • (2005) Bioinformatics , vol.21 , pp. 1189-1193
    • Rahman, S.A.1    Advani, P.2    Schunk, R.3
  • 72
  • 73
    • 33645983211 scopus 로고    scopus 로고
    • Efficient algorithms for detecting signaling pathways in protein interaction networks
    • Scott J, Ideker T, Karp RM, et al. Efficient algorithms for detecting signaling pathways in protein interaction networks. J Comput Biol 2006;13:133-44.
    • (2006) J Comput Biol , vol.13 , pp. 133-144
    • Scott, J.1    Ideker, T.2    Karp, R.M.3
  • 74
    • 33646347364 scopus 로고    scopus 로고
    • QPath: A method for querying pathways in a protein-protein interaction network
    • Shlomi T, Segal D, Ruppin E, et al. QPath: A method for querying pathways in a protein-protein interaction network. BMC Bioinformatics 2006;7:199.
    • (2006) BMC Bioinformatics , vol.7 , pp. 199
    • Shlomi, T.1    Segal, D.2    Ruppin, E.3
  • 75
    • 0003009091 scopus 로고    scopus 로고
    • Automated modelling of signal transduction networks
    • Steffen M, Petti A, Aach J, et al. Automated modelling of signal transduction networks. BMC Bioinformatics 2002;3: 34.
    • (2002) BMC Bioinformatics , vol.3 , pp. 34
    • Steffen, M.1    Petti, A.2    Aach, J.3
  • 76
    • 33748798478 scopus 로고    scopus 로고
    • Graph-based methods for analysing networks in cell biology
    • Aittokallio T, Schwikowski B. Graph-based methods for analysing networks in cell biology. Brief Bioinform 2006;7: 243-55.
    • (2006) Brief Bioinform , vol.7 , pp. 243-255
    • Aittokallio, T.1    Schwikowski, B.2
  • 77
    • 36849004088 scopus 로고    scopus 로고
    • PathFinder: Mining signal transduction pathway segments from protein-protein interaction networks
    • Bebek G, Yang J. PathFinder: Mining signal transduction pathway segments from protein-protein interaction networks. BMC Bioinformatics 2007;8:335.
    • (2007) BMC Bioinformatics , vol.8 , pp. 335
    • Bebek, G.1    Yang, J.2
  • 78
    • 0141593601 scopus 로고    scopus 로고
    • Conserved pathways within bacteria and yeast as revealed by global protein network alignment
    • Kelley BP, Sharan R, Karp RM, et al. Conserved pathways within bacteria and yeast as revealed by global protein network alignment. Proc Natl Acad Sci 2003;100:11394-9.
    • (2003) Proc Natl Acad Sci , vol.100 , pp. 11394-11399
    • Kelley, B.P.1    Sharan, R.2    Karp, R.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.