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Volumn 72, Issue , 2015, Pages 325-333

Gobal optimization of hybrid kinetic/FBA models via outer-approximation

Author keywords

FBA; Global optimization; GMA; Kinetic models; Metabolic engineering

Indexed keywords

METABOLIC ENGINEERING;

EID: 84908393613     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compchemeng.2014.06.011     Document Type: Article
Times cited : (18)

References (30)
  • 1
    • 56249085943 scopus 로고    scopus 로고
    • Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways
    • Alves R., Vilaprinyo E., Hernandez-Bermejo B., Sorribas A. Mathematical formalisms based on approximated kinetic representations for modeling genetic and metabolic pathways. Biotechnol Genet Eng Rev 2008, 25:1-40.
    • (2008) Biotechnol Genet Eng Rev , vol.25 , pp. 1-40
    • Alves, R.1    Vilaprinyo, E.2    Hernandez-Bermejo, B.3    Sorribas, A.4
  • 2
    • 70449623601 scopus 로고    scopus 로고
    • Integrating bioinformatics and computational biology: perspectives and possibilities for in silico network reconstruction in molecular systems biology
    • Alves R., Vilaprinyo E., Sorribas A. Integrating bioinformatics and computational biology: perspectives and possibilities for in silico network reconstruction in molecular systems biology. Curr Bioinform 2008, 3:98-129.
    • (2008) Curr Bioinform , vol.3 , pp. 98-129
    • Alves, R.1    Vilaprinyo, E.2    Sorribas, A.3
  • 3
    • 83055194714 scopus 로고    scopus 로고
    • Flux balance analysis of mixed anaerobic microbial communities: effects of linoleic acid (LA) and pH on biohydrogen production
    • Chaganti S.R., Kim D.H., Lalman J.A. Flux balance analysis of mixed anaerobic microbial communities: effects of linoleic acid (LA) and pH on biohydrogen production. Int J Hydrogen Energy 2011, 36:14141-14152.
    • (2011) Int J Hydrogen Energy , vol.36 , pp. 14141-14152
    • Chaganti, S.R.1    Kim, D.H.2    Lalman, J.A.3
  • 4
    • 78049255973 scopus 로고    scopus 로고
    • Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
    • Chandrasekaran S., Price N.D. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2010, 107(41):17845-17850.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.41 , pp. 17845-17850
    • Chandrasekaran, S.1    Price, N.D.2
  • 5
    • 84873053978 scopus 로고    scopus 로고
    • Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models
    • Cotten C., Reed J.L. Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models. BMC Bioinform 2013, 14:32.
    • (2013) BMC Bioinform , vol.14 , pp. 32
    • Cotten, C.1    Reed, J.L.2
  • 6
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high throughput and computational data elucidates bacterial networks
    • Covert M.W., Knight E.M., Reed J.L., Herrgard M.J., Palsson B.O. Integrating high throughput and computational data elucidates bacterial networks. Nature 2004, 429(6987):92-96.
    • (2004) Nature , vol.429 , Issue.6987 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3    Herrgard, M.J.4    Palsson, B.O.5
  • 8
    • 0036001069 scopus 로고    scopus 로고
    • Metabolic modelling of microbes: the flux-balance approach
    • Edwards J.S., Covert M., Palsson B. Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 2002, 4(3):133-140.
    • (2002) Environ Microbiol , vol.4 , Issue.3 , pp. 133-140
    • Edwards, J.S.1    Covert, M.2    Palsson, B.3
  • 9
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities
    • Edwards J.S., Palsson B.O. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 2000, 97:5528-5533.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson, B.O.2
  • 11
    • 77957687260 scopus 로고    scopus 로고
    • Mathematical modeling of monolignol biosynthesis in Populus xylem
    • Lee Y., Voit E.O. Mathematical modeling of monolignol biosynthesis in Populus xylem. Math Biosci 2010, 228(1):78-89.
    • (2010) Math Biosci , vol.228 , Issue.1 , pp. 78-89
    • Lee, Y.1    Voit, E.O.2
  • 12
    • 84870469140 scopus 로고    scopus 로고
    • Global optimization of mixed-integer quadratically-constrained quadratic programs (MIQCQP) through piecewise linear and edge-concave relaxations
    • Misener R., Floudas C.A. Global optimization of mixed-integer quadratically-constrained quadratic programs (MIQCQP) through piecewise linear and edge-concave relaxations. Math Progr 2012, 136(1):155-182.
    • (2012) Math Progr , vol.136 , Issue.1 , pp. 155-182
    • Misener, R.1    Floudas, C.A.2
  • 13
  • 14
    • 0033764285 scopus 로고    scopus 로고
    • The challenges of in silico biology
    • Palsson B. The challenges of in silico biology. Nat Biotechnol 2000, 18:1147-1150.
    • (2000) Nat Biotechnol , vol.18 , pp. 1147-1150
    • Palsson, B.1
  • 15
    • 0021383728 scopus 로고
    • Equations and calculations for fermentations of butyric acid bacteria
    • Papoutsakis E.T. Equations and calculations for fermentations of butyric acid bacteria. Biotechnol Bioeng 1984, 26:174-187.
    • (1984) Biotechnol Bioeng , vol.26 , pp. 174-187
    • Papoutsakis, E.T.1
  • 16
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems
    • Pharkya P., Maranas C.D. An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 2006, 8:1-13.
    • (2006) Metab Eng , vol.8 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 17
    • 70350676551 scopus 로고    scopus 로고
    • A genomescale metabolic model of Arabidopsis and some of its properties
    • Poolman M.G., Miguet L., Sweetlove L.J., Fell D.A. A genomescale metabolic model of Arabidopsis and some of its properties. Plant Physiol 2009, 151:1570-1581.
    • (2009) Plant Physiol , vol.151 , pp. 1570-1581
    • Poolman, M.G.1    Miguet, L.2    Sweetlove, L.J.3    Fell, D.A.4
  • 18
    • 77956181582 scopus 로고    scopus 로고
    • Outer approximation-based algorithm for biotechnology studies in systems biology
    • Pozo C., Guillén-Gosélbez G., Sorribas A., Jiménez L. Outer approximation-based algorithm for biotechnology studies in systems biology. Comp Chem Eng 2010, 34(10):1719-1730.
    • (2010) Comp Chem Eng , vol.34 , Issue.10 , pp. 1719-1730
    • Pozo, C.1    Guillén-Gosélbez, G.2    Sorribas, A.3    Jiménez, L.4
  • 19
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price N.D., Reed J.L., Palsson B.O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2(11):886-897.
    • (2004) Nat Rev Microbiol , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 20
    • 0037385718 scopus 로고    scopus 로고
    • Genomescale microbial in silico models: the constraints-based approach
    • Price N.D., Papin J.A., Schilling C.H., Palsson B.O. Genomescale microbial in silico models: the constraints-based approach. Trends Biotechnol 2003, 21:162-169.
    • (2003) Trends Biotechnol , vol.21 , pp. 162-169
    • Price, N.D.1    Papin, J.A.2    Schilling, C.H.3    Palsson, B.O.4
  • 21
    • 0033136116 scopus 로고    scopus 로고
    • Toward metabolic phenomics: analysis of genomic data using flux balances
    • Schilling C.H., Edwards J.S., Palsson B.O. Toward metabolic phenomics: analysis of genomic data using flux balances. Biotechnol Progr 1999, 15:288-295.
    • (1999) Biotechnol Progr , vol.15 , pp. 288-295
    • Schilling, C.H.1    Edwards, J.S.2    Palsson, B.O.3
  • 22
    • 0034447725 scopus 로고    scopus 로고
    • Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems
    • Schilling C.H., Edwards J.S., Letscher D., Palsson B.O. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol Bioeng 2000, 71:286-306.
    • (2000) Biotechnol Bioeng , vol.71 , pp. 286-306
    • Schilling, C.H.1    Edwards, J.S.2    Letscher, D.3    Palsson, B.O.4
  • 23
    • 34247183123 scopus 로고    scopus 로고
    • A genome-scale computational study of the interplay between transcriptional regulation and metabolism
    • Shlomi T., Eisenberg Y., Sharan R., Ruppin E. A genome-scale computational study of the interplay between transcriptional regulation and metabolism. Mol Syst Biol 2007, 3:101.
    • (2007) Mol Syst Biol , vol.3 , pp. 101
    • Shlomi, T.1    Eisenberg, Y.2    Sharan, R.3    Ruppin, E.4
  • 24
    • 84876716313 scopus 로고    scopus 로고
    • Comparing methods for metabolic network analysis and an application to metabolic engineering
    • Tomar N., De R.K. Comparing methods for metabolic network analysis and an application to metabolic engineering. Gene 2013, 521:1-14.
    • (2013) Gene , vol.521 , pp. 1-14
    • Tomar, N.1    De, R.K.2
  • 25
    • 0031554875 scopus 로고    scopus 로고
    • An indirect optimization method for biochemical systems: Description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae
    • Torres N.V., Voit E.O., Glez-Alcón C., Rodríguez F. An indirect optimization method for biochemical systems: Description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae. Biotechnol Bioeng 1997, 55(5):758-772.
    • (1997) Biotechnol Bioeng , vol.55 , Issue.5 , pp. 758-772
    • Torres, N.V.1    Voit, E.O.2    Glez-Alcón, C.3    Rodríguez, F.4
  • 26
    • 0028108519 scopus 로고
    • Metabolic flux balancing-basic concepts, scientific and practical use
    • Varma A., Palsson B.O. Metabolic flux balancing-basic concepts, scientific and practical use. Nat Biotechnol 1994, 12(10):994-998.
    • (1994) Nat Biotechnol , vol.12 , Issue.10 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 27
    • 0028146781 scopus 로고
    • Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli
    • Varma A., Palsson B.O. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli. Appl Environ Microbiol 1994, 60:3724-3731.
    • (1994) Appl Environ Microbiol , vol.60 , pp. 3724-3731
    • Varma, A.1    Palsson, B.O.2
  • 28
    • 0037443768 scopus 로고    scopus 로고
    • Modeling of discrete/continuous optimization problems: characterization and formulation of disjunctions and their relaxations
    • Vecchietti A., Sangbum L., Grossmann I. Modeling of discrete/continuous optimization problems: characterization and formulation of disjunctions and their relaxations. Comput Chem Eng 2003, 27:433-448.
    • (2003) Comput Chem Eng , vol.27 , pp. 433-448
    • Vecchietti, A.1    Sangbum, L.2    Grossmann, I.3
  • 29
    • 33746736869 scopus 로고    scopus 로고
    • Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock
    • Vilaprinyo E., Alves R., Sorribas A. Use of physiological constraints to identify quantitative design principles for gene expression in yeast adaptation to heat shock. BMC Bioinform 2006, 7:184.
    • (2006) BMC Bioinform , vol.7 , pp. 184
    • Vilaprinyo, E.1    Alves, R.2    Sorribas, A.3
  • 30
    • 84890401782 scopus 로고    scopus 로고
    • Global optimization of general non-convex problems with intermediate bilinear substructures
    • Zorn K., Sahinidis N.V. Global optimization of general non-convex problems with intermediate bilinear substructures. Optim Methods Softw 2014, 29(3):442-462.
    • (2014) Optim Methods Softw , vol.29 , Issue.3 , pp. 442-462
    • Zorn, K.1    Sahinidis, N.V.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.