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Volumn 8, Issue 11, 2013, Pages

Systematic construction of kinetic models from genome-scale metabolic networks

Author keywords

[No Author keywords available]

Indexed keywords

GENOME; KINETICS; METABOLIC NETWORKS AND PATHWAYS; THERMODYNAMICS;

EID: 84893707475     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0079195     Document Type: Article
Times cited : (85)

References (47)
  • 1
    • 77953934646 scopus 로고    scopus 로고
    • BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    • Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, et al. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4: 92.
    • (2010) BMC Systems Biology , vol.4 , pp. 92
    • Li, C.1    Donizelli, M.2    Rodriguez, N.3    Dharuri, H.4    Endler, L.5
  • 2
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26: 1155-60.
    • (2008) Nature Biotechnology , vol.26 , pp. 1155-1160
    • Herrgård, M.J.1    Swainston, N.2    Dobson, P.3    Dunn, W.B.4    Arga, K.Y.5
  • 4
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster S (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends in Biotechnology 17: 53-60.
    • (1999) Trends in Biotechnology , vol.17 , pp. 53-60
    • Schuster, S.1
  • 7
    • 10044224601 scopus 로고    scopus 로고
    • Metabolic control analysis under uncertainty: Framework development and case studies
    • Wang L, Birol I, Hatzimanikatis V (2004) Metabolic control analysis under uncertainty: framework development and case studies. Biophysical Journal 87: 3750.
    • (2004) Biophysical Journal , vol.87 , pp. 3750
    • Wang, L.1    Birol, I.2    Hatzimanikatis, V.3
  • 8
    • 33644820781 scopus 로고    scopus 로고
    • Metabolic engineering under uncertainty. I: Framework development
    • Wang L, Hatzimanikatis V (2006) Metabolic engineering under uncertainty. I: framework development. Metabolic Engineering 8: 133.
    • (2006) Metabolic Engineering , vol.8 , pp. 133
    • Wang, L.1    Hatzimanikatis, V.2
  • 9
    • 77955058605 scopus 로고    scopus 로고
    • Production of biofuels and biochemicals: In need of an oracle
    • Miskovic L, Hatzimanikatis V (2010) Production of biofuels and biochemicals: in need of an oracle. Trends in Biotechnology 28: 391-397.
    • (2010) Trends in Biotechnology , vol.28 , pp. 391-397
    • Miskovic, L.1    Hatzimanikatis, V.2
  • 10
    • 84857052437 scopus 로고    scopus 로고
    • From network models to network responses: Integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks
    • Soh K, Miskovic L, Hatzimanikatis V (2012) From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks. FEMS Yeast Research.
    • (2012) FEMS Yeast Research
    • Soh, K.1    Miskovic, L.2    Hatzimanikatis, V.3
  • 13
    • 36248952170 scopus 로고    scopus 로고
    • The stability and robustness of metabolic states: Identifying stabilizing sites in metabolic networks
    • Grimbs S, Selbig J, Bulik S, Holzhütter HG, Steuer R (2007) The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Molecular Systems Biology 3: 146.
    • (2007) Molecular Systems Biology , vol.3 , pp. 146
    • Grimbs, S.1    Selbig, J.2    Bulik, S.3    Holzhütter, H.G.4    Steuer, R.5
  • 14
    • 84880812703 scopus 로고    scopus 로고
    • Kinetic modeling of metabolic pathways: Application to serine biosynthesis
    • Humana Press.
    • Smallbone K, Stanford NJ (2013) Kinetic modeling of metabolic pathways: Application to serine biosynthesis. In: Systems Metabolic Engineering, Humana Press. pp. 113-121.
    • (2013) Systems Metabolic Engineering , pp. 113-121
    • Smallbone, K.1    Stanford, N.J.2
  • 17
    • 25144492110 scopus 로고    scopus 로고
    • Approximative kinetic formats used in metabolic network modeling
    • Heijnen JJ (2005) Approximative kinetic formats used in metabolic network modeling. Biotechnology and Bioengineering 91: 534-45.
    • (2005) Biotechnology and Bioengineering , vol.91 , pp. 534-545
    • Heijnen, J.J.1
  • 18
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
    • Liebermeister W, Klipp E (2006) Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 3: 41.
    • (2006) Theor Biol Med Model , vol.3 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 19
    • 33947677189 scopus 로고    scopus 로고
    • Thermodynamically feasible kinetic models of reaction networks
    • DOI 10.1529/biophysj.106.094094
    • Ederer M, Gilles ED (2007) Thermodynamically feasible kinetic models of reaction networks. Biophysical Journal 92: 1846-57. (Pubitemid 46495251)
    • (2007) Biophysical Journal , vol.92 , Issue.6 , pp. 1846-1857
    • Ederer, M.1    Gilles, E.D.2
  • 20
    • 77954196484 scopus 로고    scopus 로고
    • Modular rate laws for enzymatic reactions: Thermodynamics, elasticities, and implementation
    • Liebermeister W, Uhlendorf J, Klipp E (2010) Modular rate laws for enzymatic reactions: thermodynamics, elasticities, and implementation. Bioinformatics 26: 1528-1534.
    • (2010) Bioinformatics , vol.26 , pp. 1528-1534
    • Liebermeister, W.1    Uhlendorf, J.2    Klipp, E.3
  • 22
    • 35448974147 scopus 로고    scopus 로고
    • Something from nothing - Bridging the gap between constraint-based and kinetic modelling
    • DOI 10.1111/j.1742-4658.2007.06076.x
    • Smallbone K, Simeonidis E, Broomhead DS, Kell DB (2007) Something from nothing: bridging the gap between constraint-based and kinetic modelling. The FEBS Journal 274: 5576-85. (Pubitemid 47628580)
    • (2007) FEBS Journal , vol.274 , Issue.21 , pp. 5576-5585
    • Smallbone, K.1    Simeonidis, E.2    Broomhead, D.S.3    Kell, D.B.4
  • 23
    • 77956333400 scopus 로고    scopus 로고
    • Systematic integration of experimental data and models in systems biology
    • Li P, Dada JO, Jameson D, Spasic I, Swainston N, et al. (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11: 582.
    • (2010) BMC Bioinformatics , vol.11 , pp. 582
    • Li, P.1    Dada, J.O.2    Jameson, D.3    Spasic, I.4    Swainston, N.5
  • 25
    • 78650082315 scopus 로고    scopus 로고
    • Parameter balancing for kinetic models of cell metabolism
    • Lubitz T, Schulz M, Klipp E, Liebermeister W (2010) Parameter balancing for kinetic models of cell metabolism. J Phys Chem B 114: 16298-16303.
    • (2010) J Phys Chem B , vol.114 , pp. 16298-16303
    • Lubitz, T.1    Schulz, M.2    Klipp, E.3    Liebermeister, W.4
  • 28
    • 0010633955 scopus 로고
    • Über simultane Gleichgewichte und die Beziehungen zwischen Thermodynamik und Reactionskinetik homogener Systeme
    • Wegscheider R (1902) Über simultane Gleichgewichte und die Beziehungen zwischen Thermodynamik und Reactionskinetik homogener Systeme. Z Phys Chem 39: 257-303.
    • (1902) Z Phys Chem , vol.39 , pp. 257-303
    • Wegscheider, R.1
  • 29
    • 0004214524 scopus 로고
    • Longmans, Green and Co., London. (republished in 1965 by MIT Press, Cambridge, MA).
    • Haldane J (1930) Enzymes. Longmans, Green and Co., London. (republished in 1965 by MIT Press, Cambridge, MA).
    • (1930) Enzymes
    • Haldane, J.1
  • 33
    • 0032534832 scopus 로고    scopus 로고
    • A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite-concentration regulation
    • DOI 10.1046/j.1432-1327.1998.2580956.x
    • Thomas S, Fell DA (1998) A control analysis exploration of the role of ATP utilisation in glycolytic-flux control and glycolytic-metabolite- concentration regulation. European Journal of Biochemistry 258: 956-67. (Pubitemid 29013533)
    • (1998) European Journal of Biochemistry , vol.258 , Issue.3 , pp. 956-967
    • Thomas, S.1    Fell, D.A.2
  • 34
    • 0028102217 scopus 로고
    • Decrease in glycolytic flux in Saccharomyces cerevisiae cdc35-1 cells at restrictive temperature correlates with a decrease in glucose transport
    • Oehlen LJWM, Scholte ME, de Koning W, van Dam K (1994) Decrease in glycolytic flux in Saccharomyces cerevisiae cdc35-1 cells at restrictive temperature correlates with a decrease in glucose transport. Microbiology 140: 1891-1898. (Pubitemid 24259022)
    • (1994) Microbiology , vol.140 , Issue.8 , pp. 1891-1898
    • Oehlen, L.J.W.M.1    Scholte, M.E.2    De Koning, W.3    Van Dam, K.4
  • 35
    • 0033977087 scopus 로고    scopus 로고
    • Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs
    • DOI 10.1016/S0166-6851(99)00197-8, PII S0166685199001978
    • Bakker BM, Westerhoff HV, Opperdoes FR, Michels PA (2000) Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Molecular and Biochemical Parasitology 106: 1-10. (Pubitemid 30089205)
    • (2000) Molecular and Biochemical Parasitology , vol.106 , Issue.1 , pp. 1-10
    • Bakker, B.M.1    Westerhoff, H.V.2    Opperdoes, F.R.3    Michels, P.A.M.4
  • 37
    • 0032520988 scopus 로고    scopus 로고
    • Regulation of ATP supply during muscle contraction: Theoretical studies
    • Korzeniewski B (1998) Regulation of ATP supply during muscle contraction: theoretical studies. Biochemical Journal 330 (Pt 3: 1189-95.
    • (1998) Biochemical Journal , vol.330 , Issue.PART 3 , pp. 1189-1195
    • Korzeniewski, B.1
  • 42
    • 0033397980 scopus 로고    scopus 로고
    • Python: A programming language for software integration and development
    • Sanner M (1999) Python: a programming language for software integration and development. J Mol Graph Model 17: 57-61.
    • (1999) J Mol Graph Model , vol.17 , pp. 57-61
    • Sanner, M.1
  • 43
    • 0035846723 scopus 로고    scopus 로고
    • Full-scale model of glycolysis in Saccharomyces cerevisiae
    • DOI 10.1016/S0301-4622(01)00229-0, PII S0301462201002290
    • Hynne F, Dan S, Srensen P (2001) Full-scale model of glycolysis in saccharomyces cerevisiae. Biophysical Chemistry 94: 121-163. (Pubitemid 34015989)
    • (2001) Biophysical Chemistry , vol.94 , Issue.1-2 , pp. 121-163
    • Hynne, F.1    Dano, S.2    Sorensen, P.G.3
  • 45
    • 0036038886 scopus 로고    scopus 로고
    • Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis
    • DOI 10.1046/j.1432-1033.2002.03055.x
    • Pritchard L, Kell DB (2002) Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. European Journal of Biochemistry 269: 3894-3904. (Pubitemid 34994884)
    • (2002) European Journal of Biochemistry , vol.269 , Issue.16 , pp. 3894-3904
    • Pritchard, L.1    Kell, D.B.2
  • 46
    • 34547611439 scopus 로고    scopus 로고
    • Increased glycolytic flux as an outcome of wholegenome duplication in yeast
    • Conant GC, Wolfe KH (2007) Increased glycolytic flux as an outcome of wholegenome duplication in yeast. Molecular Systems Biology 3: 129.
    • (2007) Molecular Systems Biology , vol.3 , pp. 129
    • Conant, G.C.1    Wolfe, K.H.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.