메뉴 건너뛰기




Volumn 10, Issue 5, 2011, Pages 266-279

Systems approaches to modelling pathways and networks

Author keywords

Constraint based modelling; Dynamic systems; Genome scale networks; Mathematicalmodel; Metabolism; Systems biology

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; GENE REGULATORY NETWORK; GENOME ANALYSIS; LARGE SCALE PRODUCTION; MATHEMATICAL MODEL; STATISTICAL MODEL; THEORETICAL MODEL; THERMODYNAMICS;

EID: 80054983940     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/elr022     Document Type: Article
Times cited : (21)

References (81)
  • 1
    • 67650747333 scopus 로고    scopus 로고
    • A review on molecular topology: applying graph theory to drug discovery and design
    • Amigó JM, Glvez J, Villar VM. A review on molecular topology: applying graph theory to drug discovery and design. Naturwissenschaften 2009;96(7):749-61.
    • (2009) Naturwissenschaften , vol.96 , Issue.7 , pp. 749-761
    • Amigó, J.M.1    Glvez, J.2    Villar, V.M.3
  • 2
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem 1977;81(25):2340-61.
    • (1977) J Phys Chem , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 4
    • 0001119103 scopus 로고
    • Notice sur la loi que la population poursuit dans son accroissement
    • Verhulst PF. Notice sur la loi que la population poursuit dans son accroissement. Correspondance mathmatique et physique 1838;10:113-21.
    • (1838) Correspondance mathmatique et physique , vol.10 , pp. 113-121
    • Verhulst, P.F.1
  • 6
    • 77957930021 scopus 로고    scopus 로고
    • A mechanistic model of PCR for accurate quantification of quantitative PCR data
    • Boggy GJ, Woolf PJ. A mechanistic model of PCR for accurate quantification of quantitative PCR data. PLoS ONE 2010;5(8):e12355.
    • (2010) PLoS ONE , vol.5 , Issue.8
    • Boggy, G.J.1    Woolf, P.J.2
  • 7
    • 0001620238 scopus 로고
    • Analytical note on certain rhythmic relations in organic systems
    • Lotka AJ. Analytical note on certain rhythmic relations in organic systems. Proc Natl Acad SciUSA 1920;6(7):410-5.
    • (1920) Proc Natl Acad SciUSA , vol.6 , Issue.7 , pp. 410-415
    • Lotka, A.J.1
  • 8
    • 0002604954 scopus 로고
    • Variazioni e fluttuazioni del numero dindividui in specie animali conviventi
    • Volterra V. Variazioni e fluttuazioni del numero dindividui in specie animali conviventi. Mem Acad Lincei Roma 1926;2: 31-113.
    • (1926) Mem Acad Lincei Roma , vol.2 , pp. 31-113
    • Volterra, V.1
  • 9
    • 0027075622 scopus 로고
    • The origin and evolutoin of predator-prey theory
    • Berryman AA. The origin and evolutoin of predator-prey theory. Ecology 1992;73:1530-5.
    • (1992) Ecology , vol.73 , pp. 1530-1535
    • Berryman, A.A.1
  • 11
    • 0000870544 scopus 로고
    • Kinetik der Invertinwirkung
    • Michaelis L, Menten M. Kinetik der Invertinwirkung. Biochem. Z 1913;49:333-369.
    • (1913) Biochem. Z , vol.49 , pp. 333-369
    • Michaelis, L.1    Menten, M.2
  • 12
    • 0001736256 scopus 로고
    • Metabolic control mechanisms. VII. A detailed computer model of the glycolytic pathway in Ascites cells
    • Garfinkel D, Hess B. Metabolic control mechanisms. VII.A detailed computer model of the glycolytic pathway in Ascites cells. J Biol Chem 1964;239:971-83.
    • (1964) J Biol Chem , vol.239 , pp. 971-983
    • Garfinkel, D.1    Hess, B.2
  • 13
    • 33846050368 scopus 로고    scopus 로고
    • Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana
    • Locke JCW, Kozma-Bognr L, Gould PD, et al. Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol 2006;2:59.
    • (2006) Mol Syst Biol , vol.2 , pp. 59
    • Locke, J.C.W.1    Kozma-Bognr, L.2    Gould, P.D.3
  • 14
    • 0017306757 scopus 로고
    • The regulatory principles of glycolysis in erythrocytes in vivo and in vitro
    • Rapoport TA, Heinrich R, Rapoport SM. The regulatory principles of glycolysis in erythrocytes in vivo and in vitro. Biochem J 1976;154(2):449-69.
    • (1976) Biochem J , vol.154 , Issue.2 , pp. 449-469
    • Rapoport, T.A.1    Heinrich, R.2    Rapoport, S.M.3
  • 15
    • 0014258550 scopus 로고
    • Self-oscillations in glycolysis. 1. A simple kinetic mode
    • Sel'kov EE. Self-oscillations in glycolysis. 1. A simple kinetic model. EurJ Biochem 1968;4(1):79-86.
    • (1968) EurJ Biochem , vol.4 , Issue.1 , pp. 79-86
    • Sel'kov, E.E.1
  • 16
    • 0013823048 scopus 로고
    • Oscillatory behavior in enzymatic control processes
    • Goodwin BC. Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 1965;3:425-38.
    • (1965) Adv Enzyme Regul , vol.3 , pp. 425-438
    • Goodwin, B.C.1
  • 18
    • 0015989446 scopus 로고
    • A linear steady-state treatment of enzymatic chains. General properties, control and effector strengt
    • Heinrich R, Rapoport TA. A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. EurJ Biochem 1974;42(1):89-95.
    • (1974) EurJ Biochem , vol.42 , Issue.1 , pp. 89-95
    • Heinrich, R.1    Rapoport, T.A.2
  • 20
    • 0015949374 scopus 로고
    • A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector
    • Heinrich R, Rapoport TA. A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. EurJ Biochem 1974b;42(1):97-105.
    • (1974) EurJ Biochem , vol.42 , Issue.1 , pp. 97-105
    • Heinrich, R.1    Rapoport, T.A.2
  • 21
    • 0000068994 scopus 로고
    • Determining all extreme semi-positive conservation relations in chemical reaction systems: a test criterion for conservativity
    • Schuster S, Höfer T. Determining all extreme semi-positive conservation relations in chemical reaction systems: a test criterion for conservativity. J. Chem. Soc., Faraday Trans 1991;87:2561-6.
    • (1991) J. Chem. Soc., Faraday Trans , vol.87 , pp. 2561-2566
    • Schuster, S.1    Höfer, T.2
  • 23
    • 36248982110 scopus 로고    scopus 로고
    • Modular decomposition of metabolic systems via null-space analysis
    • Poolman MG, Sebu C, Pidcock MK, etal. Modular decomposition of metabolic systems via null-space analysis. J Theor Biol 2007;249(4):691-705.
    • (2007) J Theor Biol , vol.249 , Issue.4 , pp. 691-705
    • Poolman, M.G.1    Sebu, C.2    Pidcock, M.K.3
  • 24
    • 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(2):165-82.
    • (1994) J Biol Syst , vol.2 , Issue.2 , pp. 165-182
    • Schuster, S.1    Hilgetag, C.2
  • 25
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering
    • Schuster S, Dandekar T, Fell DA. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 1999;17(2):53-60.
    • (1999) Trends Biotechnol , vol.17 , Issue.2 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 26
    • 58049211936 scopus 로고    scopus 로고
    • Can sugars be produced from fatty acids? A test case for pathway analysis tools
    • de Figueiredo LF, Schuster S, Kaleta C, et al. Can sugars be produced from fatty acids? A test case for pathway analysis tools. Bioinformatics 2009a;25(1):152-8.
    • (2009) Bioinformatics , vol.25 , Issue.1 , pp. 152-158
    • de Figueiredo, L.F.1    Schuster, S.2    Kaleta, C.3
  • 27
    • 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(3):229-8.
    • (2000) J Theor Biol , vol.203 , Issue.3 , pp. 229-238
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 28
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of Helicobacter pylori 26695
    • Schilling CH, Covert MW, Famili I, et al. Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 2002;184(16):4582-93.
    • (2002) J Bacteriol , vol.184 , Issue.16 , pp. 4582-4593
    • Schilling, C.H.1    Covert, M.W.2    Famili, I.3
  • 29
    • 77249147418 scopus 로고    scopus 로고
    • On algebraic properties of extreme pathways in metabolic networks
    • Jevremovic D, Trinh CT, Srienc F, et al. On algebraic properties of extreme pathways in metabolic networks. J Comput Biol 2010;17(2):107-19.
    • (2010) J Comput Biol , vol.17 , Issue.2 , pp. 107-119
    • Jevremovic, D.1    Trinh, C.T.2    Srienc, F.3
  • 30
    • 1042269472 scopus 로고    scopus 로고
    • Minimal cut sets in biochemical reaction networks
    • Klamt S, Gilles ED. Minimal cut sets in biochemical reaction networks. Bioinformatics 2004;20(2):226-34.
    • (2004) Bioinformatics , vol.20 , Issue.2 , pp. 226-234
    • Klamt, S.1    Gilles, E.D.2
  • 31
    • 32144453095 scopus 로고    scopus 로고
    • Generalized concept of minimal cut sets in biochemical networks
    • Klamt S. Generalized concept of minimal cut sets in biochemical networks. Biosystems 2006;83(2-3):233-47.
    • (2006) Biosystems , vol.83 , Issue.2-3 , pp. 233-247
    • Klamt, S.1
  • 32
    • 0036039060 scopus 로고    scopus 로고
    • Combinatorial complexity of pathway analysis in metabolic networks
    • Klamt S, Stelling J. Combinatorial complexity of pathway analysis in metabolic networks. Mol Biol Rep 2002; 29(1-2):233-6.
    • (2002) Mol Biol Rep , vol.29 , Issue.1-2 , pp. 233-236
    • Klamt, S.1    Stelling, J.2
  • 33
    • 0027537642 scopus 로고
    • Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed
    • Schuster R, Schuster S. Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed. Comput Appl Biosci 1993; 9(1):79-85.
    • (1993) Comput Appl Biosci , vol.9 , Issue.1 , pp. 79-85
    • Schuster, R.1    Schuster, S.2
  • 34
    • 75849164426 scopus 로고    scopus 로고
    • Computing the shortest elementary flux modes in genome-scale metabolic networks
    • de Figueiredo LF, Podhorski A, Rubio A, et al. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics 2009b;25(23):3158-65.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3158-3165
    • de Figueiredo, L.F.1    Podhorski, A.2    Rubio, A.3
  • 36
    • 77956649528 scopus 로고    scopus 로고
    • Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
    • Ruppin E, Papin JA, de Figueiredo LF, et al. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol 2010;21(4):502-10.
    • (2010) Curr Opin Biotechnol , vol.21 , Issue.4 , pp. 502-510
    • Ruppin, E.1    Papin, J.A.2    de Figueiredo, L.F.3
  • 38
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities
    • Edwards JS, Palsson BO. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000; 97(10):5528-33.
    • (2000) Proc Natl Acad Sci USA , vol.97 , Issue.10 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 39
    • 77952886804 scopus 로고    scopus 로고
    • The biomass objective function
    • Feist AM, Palsson BO. The biomass objective function. Curr OpinMicrobiol 2010;13(3):344-9.
    • (2010) Curr OpinMicrobiol , vol.13 , Issue.3 , pp. 344-349
    • Feist, A.M.1    Palsson, B.O.2
  • 40
    • 0035017810 scopus 로고    scopus 로고
    • Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints
    • Ramakrishna R, Edwards JS, McCulloch A, et al. Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints. Am J Physiol Regul Integr Comp Physiol 2001;280(3):R695- R704.
    • (2001) Am J Physiol Regul Integr Comp Physiol , vol.280 , Issue.3
    • Ramakrishna, R.1    Edwards, J.S.2    McCulloch, A.3
  • 41
    • 0034844144 scopus 로고    scopus 로고
    • Stoichiometric growth model for riboflavin-producing Bacillus subtilis
    • Dauner M, Sauer U. Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol Bioeng 2001;76(2):132-43.
    • (2001) Biotechnol Bioeng , vol.76 , Issue.2 , pp. 132-143
    • Dauner, M.1    Sauer, U.2
  • 42
    • 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(1):21-55.
    • (2001) Bull Math Biol , vol.63 , Issue.1 , pp. 21-55
    • Ebenhöh, O.1    Heinrich, R.2
  • 43
    • 70350676551 scopus 로고    scopus 로고
    • A genome-scale metabolic model of Arabidopsis and some of its properties
    • Poolman MG, Miguet L, Sweetlove LJ, et al. A genome-scale metabolic model of Arabidopsis and some of its properties. Plant Physiol 2009;151(3):1570-81.
    • (2009) Plant Physiol , vol.151 , Issue.3 , pp. 1570-1581
    • Poolman, M.G.1    Miguet, L.2    Sweetlove, L.J.3
  • 44
    • 25444467580 scopus 로고    scopus 로고
    • Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
    • Blank LM, Kuepfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 2005; 6(6):R49.
    • (2005) Genome Biol , vol.6 , Issue.6
    • Blank, L.M.1    Kuepfer, L.2    Sauer, U.3
  • 45
    • 77956703554 scopus 로고    scopus 로고
    • A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions
    • Williams TCR, Poolman MG, Howden AJM, et al. A genome-scale metabolic model accurately predicts fluxes in central carbon metabolism under stress conditions. Plant Physiol 2010;154(1):311-23.
    • (2010) Plant Physiol , vol.154 , Issue.1 , pp. 311-323
    • Williams, T.C.R.1    Poolman, M.G.2    Howden, A.J.M.3
  • 47
    • 0034661295 scopus 로고    scopus 로고
    • Recursive MILP model for finding all the alternate optima in LP models for metabolic networks
    • Lee S, Phalakornkule C, Domach MM, et al. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput Chem Eng 2000; 24(2-7):711-6.
    • (2000) Comput Chem Eng , vol.24 , Issue.2-7 , pp. 711-716
    • Lee, S.1    Phalakornkule, C.2    Domach, M.M.3
  • 48
    • 69449096938 scopus 로고    scopus 로고
    • Capturing the essence of a metabolic network: a flux balance analysis approach
    • Murabito E, Simeonidis E, Smallbone K, et al. Capturing the essence of a metabolic network: a flux balance analysis approach. J Theor Biol 2009;260(3):445-52.
    • (2009) J Theor Biol , vol.260 , Issue.3 , pp. 445-452
    • Murabito, E.1    Simeonidis, E.2    Smallbone, K.3
  • 49
    • 63749088241 scopus 로고    scopus 로고
    • Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds
    • Kruse K, Ebenhöh O. Comparing flux balance analysis to network expansion: producibility, sustainability and the scope of compounds. Genome Inform 2008;20:91-101.
    • (2008) Genome Inform , vol.20 , pp. 91-101
    • Kruse, K.1    Ebenhöh, O.2
  • 50
    • 77950786776 scopus 로고    scopus 로고
    • Flux balance analysis accounting for metabolite dilution
    • Benyamini T, Folger O, Ruppin E, et al. Flux balance analysis accounting for metabolite dilution. Genome Biol 2010; 11(4):R43.
    • (2010) Genome Biol , vol.11 , Issue.4
    • Benyamini, T.1    Folger, O.2    Ruppin, E.3
  • 51
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. ProcNatAcad Sci USA 2002;99(23):15112-7.
    • (2002) ProcNatAcad Sci USA , vol.99 , Issue.23 , pp. 15112-15117
    • Segrè, D.1    Vitkup, D.2    Church, G.M.3
  • 52
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • Shlomi T, Berkman O, Ruppin E. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. ProcNatl Acad SciUSA 2005;102(21):7695-700.
    • (2005) ProcNatl Acad SciUSA , vol.102 , Issue.21 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 53
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard AP, Pharkya P, Maranas CD. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003;84(6):647-57.
    • (2003) Biotechnol Bioeng , vol.84 , Issue.6 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 54
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways
    • Tepper N, Shlomi T. Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 2010;26(4):536-43.
    • (2010) Bioinformatics , vol.26 , Issue.4 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 55
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • Beard DA, dan Liang S, Qian H. Energy balance for analysis of complex metabolic networks. Biophys J 2002;83(1):79-86.
    • (2002) Biophys J , vol.83 , Issue.1 , pp. 79-86
    • Beard, D.A.1    dan Liang, S.2    Qian, H.3
  • 56
    • 33847797256 scopus 로고    scopus 로고
    • Thermodynamics-based metabolic flux analysis
    • Henry CS, Broadbelt LJ, Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys J 2007;92(5):1792-805.
    • (2007) Biophys J , vol.92 , Issue.5 , pp. 1792-1805
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 57
    • 36248990302 scopus 로고    scopus 로고
    • Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks
    • Hoppe A, Hoffmann S, Holzhütter HG. Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks. BMCSyst Biol 2007;1:23.
    • (2007) BMCSyst Biol , vol.1 , pp. 23
    • Hoppe, A.1    Hoffmann, S.2    Holzhütter, H.G.3
  • 58
    • 77952643400 scopus 로고    scopus 로고
    • Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
    • Fleming RMT, Thiele I, Provan G, et al. Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. J Theor Biol 2010;264:683-92.
    • (2010) J Theor Biol , vol.264 , pp. 683-692
    • Fleming, R.M.T.1    Thiele, I.2    Provan, G.3
  • 59
    • 77954197778 scopus 로고    scopus 로고
    • Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model
    • Yizhak K, Benyamini T, Liebermeister W, et al. Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model. Bioinformatics 2010;26(12):i255-60.
    • (2010) Bioinformatics , vol.26 , Issue.12
    • Yizhak, K.1    Benyamini, T.2    Liebermeister, W.3
  • 60
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism
    • Jerby L, Shlomi T, Ruppin E. Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 2010;6:401.
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 61
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using escherichia coli
    • Feist AM, Palsson BO. The growing scope of applications of genome-scale metabolic reconstructions using escherichia coli. Nat Biotechnol 2008;26(6):659-7.
    • (2008) Nat Biotechnol , vol.26 , Issue.6 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 62
    • 77957272033 scopus 로고    scopus 로고
    • Building and analysing genome-scale metabolic models
    • Fell DA, Poolman MG, Gevorgyan A. Building and analysing genome-scale metabolic models. Biochem SocTrans 2010; 38(5):1197-201.
    • (2010) Biochem SocTrans , vol.38 , Issue.5 , pp. 1197-1201
    • Fell, D.A.1    Poolman, M.G.2    Gevorgyan, A.3
  • 63
    • 75549086416 scopus 로고    scopus 로고
    • The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata
    • Database issue
    • Liolios K, Chen IMA, Mavromatis K, et al. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010;38(Database issue):D346-54.
    • (2010) Nucleic Acids Res , vol.38
    • Liolios, K.1    Chen, I.M.A.2    Mavromatis, K.3
  • 64
    • 18244404606 scopus 로고    scopus 로고
    • Structural analysis of expanding metabolic networks
    • Ebenhöh O, Handorf T, Heinrich R. Structural analysis of expanding metabolic networks. Genome Inform 2004; 15(1):35-45.
    • (2004) Genome Inform , vol.15 , Issue.1 , pp. 35-45
    • Ebenhöh, O.1    Handorf, T.2    Heinrich, R.3
  • 65
    • 26244437466 scopus 로고    scopus 로고
    • Expanding metabolic networks: scopes of compounds, robustness, and evolution
    • Handorf T, Ebenhöh O, Heinrich R. Expanding metabolic networks: scopes of compounds, robustness, and evolution. J Mol Evol 2005;61(4):498-512.
    • (2005) J Mol Evol , vol.61 , Issue.4 , pp. 498-512
    • Handorf, T.1    Ebenhöh, O.2    Heinrich, R.3
  • 66
    • 75549090213 scopus 로고    scopus 로고
    • KEGG for representation and analysis of molecular networks involving diseases and drugs
    • Database issue
    • Kanehisa M, Goto S, Furumichi M, et al. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010;38(Database issue):D355-60.
    • (2010) Nucleic Acids Res , vol.38
    • Kanehisa, M.1    Goto, S.2    Furumichi, M.3
  • 67
    • 75549090505 scopus 로고    scopus 로고
    • The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
    • Database issue
    • Caspi R, Altman T, Dale JM, et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2010; 38(Database issue):D473-9.
    • (2010) Nucleic Acids Res , vol.38
    • Caspi, R.1    Altman, T.2    Dale, J.M.3
  • 68
    • 34547609127 scopus 로고    scopus 로고
    • Meta Path Online: a web server implementation of the network expansion algorithm
    • Database issue
    • Handorf T, Ebenhöh O. Meta Path Online: a web server implementation of the network expansion algorithm. Nucleic Acids Res 2007;35(Database issue):W613-W8.
    • (2007) Nucleic Acids Res , vol.35
    • Handorf, T.1    Ebenhöh, O.2
  • 69
    • 63749102445 scopus 로고    scopus 로고
    • Functional classification of genome-scale metabolic networks
    • Ebenhöh O, Handorf T. Functional classification of genome-scale metabolic networks. EURASIP J Bioinform Syst Biol 2009, 570456.
    • (2009) EURASIP J Bioinform Syst Biol , pp. 570456
    • Ebenhöh, O.1    Handorf, T.2
  • 70
    • 43649084234 scopus 로고    scopus 로고
    • An environmental perspective on metabolism
    • Handorf T, Christian N, Ebenhöh O, etal. An environmental perspective on metabolism. J Theor Biol 2008; 252(3):530-7.
    • (2008) J Theor Biol , vol.252 , Issue.3 , pp. 530-537
    • Handorf, T.1    Christian, N.2    Ebenhöh, O.3
  • 71
    • 72949099680 scopus 로고    scopus 로고
    • An integrative approach towards completing genome-scale metabolic networks
    • Christian N, May P, Kempa S, etal. An integrative approach towards completing genome-scale metabolic networks. Mol Biosyst 2009;5(12):1889-903.
    • (2009) Mol Biosyst , vol.5 , Issue.12 , pp. 1889-1903
    • Christian, N.1    May, P.2    Kempa, S.3
  • 72
    • 52049100420 scopus 로고    scopus 로고
    • Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii
    • May P, Wienkoop S, Kempa S, et al. Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics 2008;179(1):157-66.
    • (2008) Genetics , vol.179 , Issue.1 , pp. 157-166
    • May, P.1    Wienkoop, S.2    Kempa, S.3
  • 73
    • 33751226921 scopus 로고    scopus 로고
    • Systems approach to refining genome annotation
    • Reed JL, Patel TR, Chen KH, et al. Systems approach to refining genome annotation. Proc Natl Acad Sci USA 2006; 103(46):17480-4.
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.46 , pp. 17480-17484
    • Reed, J.L.1    Patel, T.R.2    Chen, K.H.3
  • 74
    • 33645211903 scopus 로고    scopus 로고
    • The effect of oxygen on biochemical networks and the evolution of complex life
    • Raymond J, Segrè D. The effect of oxygen on biochemical networks and the evolution of complex life. Science 2006; 311(5768):1764-7.
    • (2006) Science , vol.311 , Issue.5768 , pp. 1764-1767
    • Raymond, J.1    Segrè, D.2
  • 75
    • 78650716528 scopus 로고    scopus 로고
    • Modeling the complex dynamics of enzyme-pathway coevolution
    • Schütte M, Skupin A, Segrè D, et al. Modeling the complex dynamics of enzyme-pathway coevolution. Chaos 2010; 20(4):045115.
    • (2010) Chaos , vol.20 , Issue.4 , pp. 045115
    • Schütte, M.1    Skupin, A.2    Segrè, D.3
  • 77
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro HM, et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003;19(4):524-31.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3
  • 78
    • 28644433993 scopus 로고    scopus 로고
    • Minimum information requested in the annotation of biochemical models (miriam)
    • Novère NL, Finney A, Hucka M, et al. Minimum information requested in the annotation of biochemical models (miriam). Nat Biotechnol 2005;23(12):1509-15.
    • (2005) Nat Biotechnol , vol.23 , Issue.12 , pp. 1509-1515
    • Novère, N.L.1    Finney, A.2    Hucka, M.3
  • 79
    • 77955499190 scopus 로고    scopus 로고
    • The carbon assimilation network in escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes
    • Baldazzi V, Ropers D, Markowicz Y, et al. The carbon assimilation network in escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. PLoS Comput Biol 2010;6(6):e1000812.
    • (2010) PLoS Comput Biol , vol.6 , Issue.6
    • Baldazzi, V.1    Ropers, D.2    Markowicz, Y.3
  • 80
    • 42449164727 scopus 로고    scopus 로고
    • The regulatory network of E. coli metabolism as a boolean dynamical system exhibits both homeostasis and flexibility of response
    • Samal A, Jain S. The regulatory network of E. coli metabolism as a boolean dynamical system exhibits both homeostasis and flexibility of response. BMCSyst Biol 2008;2:21.
    • (2008) BMCSyst Biol , vol.2 , pp. 21
    • Samal, A.1    Jain, S.2
  • 81
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran S, Price ND. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad SciUSA 2010;107(41):17845-50.
    • (2010) Proc Natl Acad SciUSA , vol.107 , Issue.41 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.