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Volumn 7, Issue 9, 2012, Pages

Identifying the Preferred Subset of Enzymatic Profiles in Nonlinear Kinetic Metabolic Models via Multiobjective Global Optimization and Pareto Filters

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; CONCEPTUAL FRAMEWORK; ENZYME ANALYSIS; ENZYME KINETICS; FERMENTATION; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; METABOLIC ENGINEERING; NONHUMAN; PROCESS OPTIMIZATION; SACCHAROMYCES CEREVISIAE; STOICHIOMETRY;

EID: 84866726930     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0043487     Document Type: Article
Times cited : (12)

References (47)
  • 1
    • 84857058761 scopus 로고    scopus 로고
    • A systems-level approach for metabolic engineering of yeast cell factories
    • Kim IK, Roldao A, Siewers V, Nielsen J, (2012) A systems-level approach for metabolic engineering of yeast cell factories. FEMS yeast research 12 (2):: 228-248.
    • (2012) FEMS Yeast Research , vol.12 , Issue.2 , pp. 228-248
    • Kim, I.K.1    Roldao, A.2    Siewers, V.3    Nielsen, J.4
  • 2
    • 80052037221 scopus 로고    scopus 로고
    • Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant saccharomyces cere- visiae
    • Parachin NS, Bergdahl B, van Niel EW, Gorwa-Grauslund MF, (2011) Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant saccharomyces cere- visiae. Metabolic engineering 13: 508-517.
    • (2011) Metabolic Engineering , vol.13 , pp. 508-517
    • Parachin, N.S.1    Bergdahl, B.2    van Niel, E.W.3    Gorwa-Grauslund, M.F.4
  • 3
    • 79959189547 scopus 로고    scopus 로고
    • An improved kinetic model for the acetone-butanol-ethanol pathway of clostridium acetobutylicum and model-based perturbation analysis
    • Li RD, Li YY, Lu LY, Ren C, Li YX, et al. (2011) An improved kinetic model for the acetone-butanol-ethanol pathway of clostridium acetobutylicum and model-based perturbation analysis. BMC systems biology 5 Suppl 1: S12.
    • (2011) BMC Systems Biology , vol.5 , Issue.SUPPL.
    • Li, R.D.1    Li, Y.Y.2    Lu, L.Y.3    Ren, C.4    Li, Y.X.5
  • 4
    • 0026911028 scopus 로고
    • Optimization in integrated biochemical systems
    • Voit EO, (1992) Optimization in integrated biochemical systems. Biotechnol Bioeng 40: 572-82.
    • (1992) Biotechnol Bioeng , vol.40 , pp. 572-582
    • Voit, E.O.1
  • 6
    • 0034610099 scopus 로고    scopus 로고
    • Metabolism of citric acid production by aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate
    • Alvarez-Vasquez F, González-Alcón C, Torres NV, (2000) Metabolism of citric acid production by aspergillus niger: model definition, steady-state analysis and constrained optimization of citric acid production rate. Biotechnol Bioeng 70: 82-108.
    • (2000) Biotechnol Bioeng , vol.70 , pp. 82-108
    • Alvarez-Vasquez, F.1    González-Alcón, C.2    Torres, N.V.3
  • 7
    • 0037696059 scopus 로고    scopus 로고
    • Optimization of biochemical systems by linear programming and general mass action model representations
    • Marín-Sanguino A, Torres NV, (2003) Optimization of biochemical systems by linear programming and general mass action model representations. Math Biosci 184: 187-200.
    • (2003) Math Biosci , vol.184 , pp. 187-200
    • Marín-Sanguino, A.1    Torres, N.V.2
  • 8
    • 41249087796 scopus 로고    scopus 로고
    • Yield optimization of regulated metabolic systems using deterministic branch-and-reduce methods
    • Polisetty P, Gatzke E, Voit E, (2008) Yield optimization of regulated metabolic systems using deterministic branch-and-reduce methods. Biotechnology and Bioengineering 99 (5):: 1154-1169.
    • (2008) Biotechnology and Bioengineering , vol.99 , Issue.5 , pp. 1154-1169
    • Polisetty, P.1    Gatzke, E.2    Voit, E.3
  • 11
    • 0037366966 scopus 로고    scopus 로고
    • Design principles and operating principles: the yin and yang of optimal functioning
    • Voit E, (2003) Design principles and operating principles: the yin and yang of optimal functioning. Math Bioscience 182: 81-92.
    • (2003) Math Bioscience , vol.182 , pp. 81-92
    • Voit, E.1
  • 12
    • 74049099516 scopus 로고    scopus 로고
    • Identifying quantitaive operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses
    • Guillén-Gosálbez G, Sorribas A, (2009) Identifying quantitaive operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses. BMC Bioinformatics 10 (386).
    • (2009) BMC Bioinformatics , vol.10 , Issue.386
    • Guillén-Gosálbez, G.1    Sorribas, A.2
  • 13
    • 80052023331 scopus 로고    scopus 로고
    • Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models
    • 137-0509-5-137
    • Pozo C, Marín-Sanguino A, Alves R, Guillén-Gosálbez G, Jiménez L, et al. (2011) Steady-state global optimization of metabolic non-linear dynamic models through recasting into power-law canonical models. BMC systems biology 5: 137-0509-5-137.
    • (2011) BMC Systems Biology , vol.5
    • Pozo, C.1    Marín-Sanguino, A.2    Alves, R.3    Guillén-Gosálbez, G.4    Jiménez, L.5
  • 15
    • 77956011197 scopus 로고    scopus 로고
    • Optimization and evolution in metabolic pathways: Global optimization techniques in generalized mass action models
    • Sorribas A, Pozo C, Vilaprinyo E, Guillén-Gosálbez G, Jiménez L, et al. (2010) Optimization and evolution in metabolic pathways: Global optimization techniques in generalized mass action models. Journal of Biotechnology 149 (3):: 141-153.
    • (2010) Journal of Biotechnology , vol.149 , Issue.3 , pp. 141-153
    • Sorribas, A.1    Pozo, C.2    Vilaprinyo, E.3    Guillén-Gosálbez, G.4    Jiménez, L.5
  • 16
    • 0025935927 scopus 로고
    • Minimization of intermediate concentrations as a sug-gested optimality principle for biochemical networks. ii. time hierarchy, enzymatic rate laws, and erythrocyte metabolism
    • Schuster S, Schuster R, Heinrich R, (1991) Minimization of intermediate concentrations as a sug-gested optimality principle for biochemical networks. ii. time hierarchy, enzymatic rate laws, and erythrocyte metabolism. J Math Biol 29 (5):: 443-455.
    • (1991) J Math Biol , vol.29 , Issue.5 , pp. 443-455
    • Schuster, S.1    Schuster, R.2    Heinrich, R.3
  • 18
    • 77953296954 scopus 로고    scopus 로고
    • Multi-objective mixed integer strategy for the optimization of biological networks
    • Sendín J, Exler O, Banga J, (2010) Multi-objective mixed integer strategy for the optimization of biological networks. IET Systems Biology 4 (3):: 236-248.
    • (2010) IET Systems Biology , vol.4 , Issue.3 , pp. 236-248
    • Sendín, J.1    Exler, O.2    Banga, J.3
  • 19
    • 0037899231 scopus 로고    scopus 로고
    • Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by saccharomyces cerevisiae
    • Vera J, de Atauri P, Cascante M, Torres NV, (2003) Multicriteria optimization of biochemical systems by linear programming: application to production of ethanol by saccharomyces cerevisiae. Biotechnol Bioeng 83: 335-43.
    • (2003) Biotechnol Bioeng , vol.83 , pp. 335-343
    • Vera, J.1    de Atauri, P.2    Cascante, M.3    Torres, N.V.4
  • 20
    • 41949109225 scopus 로고    scopus 로고
    • Inference of biochemical network models in s-system using multiobjective optimization approach
    • Liu PK, Wang FS, (2008) Inference of biochemical network models in s-system using multiobjective optimization approach. Bioinformatics 24: 1085-92.
    • (2008) Bioinformatics , vol.24 , pp. 1085-1092
    • Liu, P.K.1    Wang, F.S.2
  • 21
    • 80052826612 scopus 로고    scopus 로고
    • Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects
    • 145-0509-1455-145
    • Wu WH, Wang FS, Chang MS, (2011) Multi-objective optimization of enzyme manipulations in metabolic networks considering resilience effects. BMC systems biology 5: 145-0509-5-145.
    • (2011) BMC Systems Biology , vol.5
    • Wu, W.H.1    Wang, F.S.2    Chang, M.S.3
  • 22
    • 34248385237 scopus 로고    scopus 로고
    • Multiobjective optimization in bioinformatics and computational biology
    • Handl J, Kell D, Knowles J, (2007) Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Trans Comput Biol Bioinf 4 (2):: 279-291.
    • (2007) IEEE/ACM Trans Comput Biol Bioinf , vol.4 , Issue.2 , pp. 279-291
    • Handl, J.1    Kell, D.2    Knowles, J.3
  • 24
    • 24344437114 scopus 로고    scopus 로고
    • Multi-objective evolutionary algorithms: Introducing bias among pareto-optimal solutions
    • In: Ghosh A, Tsutsui S, editors, London: Springer-Verlag
    • Deb K (2003) Multi-objective evolutionary algorithms: Introducing bias among pareto-optimal solutions. In: Ghosh A, Tsutsui S, editors. Advances in Evolutionary Computing: Theory and Applications. London: Springer-Verlag. pp. 263-292.
    • (2003) Advances in Evolutionary Computing: Theory and Applications , pp. 263-292
    • Deb, K.1
  • 25
    • 33750268348 scopus 로고    scopus 로고
    • Integrating user preferences into evolutionary multi-objective optimization
    • Branke J, Deb K, (2004) Integrating user preferences into evolutionary multi-objective optimization. Knowledge Incorporation in Evolutionary Computation pp. 461-477.
    • (2004) Knowledge Incorporation in Evolutionary Computation , pp. 461-477
    • Branke, J.1    Deb, K.2
  • 29
    • 0037596462 scopus 로고    scopus 로고
    • Concept selection using s-pareto frontiers
    • Mattson C, Messac A, (2003) Concept selection using s-pareto frontiers. AIAA Journal 41 (6):: 1190-1198.
    • (2003) AIAA Journal , vol.41 , Issue.6 , pp. 1190-1198
    • Mattson, C.1    Messac, A.2
  • 31
    • 0025505855 scopus 로고
    • A decomposition strategy for multicriteria optimization with application to machine tool design
    • Montusiewicz J, Osyczka A, (1990) A decomposition strategy for multicriteria optimization with application to machine tool design. Engineering Costs and Production Economics 20: 191-202.
    • (1990) Engineering Costs and Production Economics , vol.20 , pp. 191-202
    • Montusiewicz, J.1    Osyczka, A.2
  • 33
    • 11644257573 scopus 로고    scopus 로고
    • Genetic algorithm development for multiobjective optimization of struc-tures
    • Cheng FY, Li D, (1998) Genetic algorithm development for multiobjective optimization of struc-tures. AIAA Journal 36 (6):: 1105-1112.
    • (1998) AIAA Journal , vol.36 , Issue.6 , pp. 1105-1112
    • Cheng, F.Y.1    Li, D.2
  • 35
    • 33746828943 scopus 로고    scopus 로고
    • Model-based optimization of biochemical systems using multiple objectives: a comparison of several solution strategies
    • Sendín J, Vera J, Torres N, Banga J, (2006) Model-based optimization of biochemical systems using multiple objectives: a comparison of several solution strategies. Math Comput Model Dyn Syst 12 (5):: 469-487.
    • (2006) Math Comput Model Dyn Syst , vol.12 , Issue.5 , pp. 469-487
    • Sendín, J.1    Vera, J.2    Torres, N.3    Banga, J.4
  • 37
  • 38
    • 0014649230 scopus 로고
    • Biochemical systems analysis. i. some mathematical properties of the rate law for the component enzymatic reactions
    • Savageau M, (1969) Biochemical systems analysis. i. some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 25: 365-369.
    • (1969) J Theor Biol , vol.25 , pp. 365-369
    • Savageau, M.1
  • 39
    • 0014658880 scopus 로고
    • Biochemical systems analysis. ii. the steady-state solutions for an n-pool system using a power-law approximation
    • Savageau M, (1969) Biochemical systems analysis. ii. the steady-state solutions for an n-pool system using a power-law approximation. J Theor Biol 25: 370-379.
    • (1969) J Theor Biol , vol.25 , pp. 370-379
    • Savageau, M.1
  • 41
    • 0032348480 scopus 로고    scopus 로고
    • Normal-boundary intersection: A new method for generating the pareto surface in nonlinear multicriteria optimization problems
    • Das I, Dennis J, (1998) Normal-boundary intersection: A new method for generating the pareto surface in nonlinear multicriteria optimization problems. SIAM Journal on Optimization 8 (3):: 631-657.
    • (1998) SIAM Journal on Optimization , vol.8 , Issue.3 , pp. 631-657
    • Das, I.1    Dennis, J.2
  • 42
    • 7044260540 scopus 로고    scopus 로고
    • Normal constraint method with guarantee of even representation of complete pareto frontier
    • Messac A, Mattson C, (2004) Normal constraint method with guarantee of even representation of complete pareto frontier. AIAA Journal 42 (10):: 2101-2111.
    • (2004) AIAA Journal , vol.42 , Issue.10 , pp. 2101-2111
    • Messac, A.1    Mattson, C.2
  • 43
    • 24144473642 scopus 로고    scopus 로고
    • Logic-based outer approximation for globally optimal synthesis of process networks
    • Bergamini M, Aguirre P, Grossmann I, (2005) Logic-based outer approximation for globally optimal synthesis of process networks. Computers and Chemical Engineering 29: 1914-1933.
    • (2005) Computers and Chemical Engineering , vol.29 , pp. 1914-1933
    • Bergamini, M.1    Aguirre, P.2    Grossmann, I.3
  • 46
    • 6344235466 scopus 로고    scopus 로고
    • Smart pareto filter: obtaining a minimal representation of multiobjective design space
    • Mattson C, Mullur A, Messac A, (2004) Smart pareto filter: obtaining a minimal representation of multiobjective design space. Engineering Optimization 36 (6):: 721-740.
    • (2004) Engineering Optimization , vol.36 , Issue.6 , pp. 721-740
    • Mattson, C.1    Mullur, A.2    Messac, A.3
  • 47
    • 0033169395 scopus 로고    scopus 로고
    • A preference ordering among various pareto optimal alternatives
    • Das I, (1999) A preference ordering among various pareto optimal alternatives. Structural Opti-mization 18: 30-35.
    • (1999) Structural Opti-Mization , vol.18 , pp. 30-35
    • Das, I.1


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