메뉴 건너뛰기




Volumn 9, Issue 4, 2013, Pages 179-184

Large-scale metabolic models: From reconstruction to differential equations

Author keywords

[No Author keywords available]

Indexed keywords

CONCENTRATION DATA; DETAILED MODELS; EXPERIMENTAL DATUM; GENOME-SCALE MODEL; INDUSTRIAL BIOTECHNOLOGY; KINETIC CONSTANT; METABOLIC MODELS; RATIONAL DESIGN;

EID: 84881518999     PISSN: 15509087     EISSN: None     Source Type: Journal    
DOI: 10.1089/ind.2013.0003     Document Type: Review
Times cited : (55)

References (29)
  • 1
    • 0347762745 scopus 로고    scopus 로고
    • Identifying Constraints that Govern Cell Behavior: A Key to Converting Conceptual to Computational Models in Biology?
    • DOI 10.1002/bit.10849
    • Covert MW, Famili I, Palsson BO. Identifying constraints that govern cell behavior: A key to converting conceptual to computational models in biology? Biotechnol Bioeng 2003;84:763-772. (Pubitemid 38089692)
    • (2003) Biotechnology and Bioengineering , vol.84 , Issue.7 , pp. 763-772
    • Covert, M.W.1    Famili, I.2    Palsson, B.O.3
  • 2
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • DOI 10.1038/nrmicro1023
    • Price ND, Reed JL, Palsson BO. Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2004;2:886-897. (Pubitemid 39567269)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 3
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network obtained from a community approach to systems biology
    • Herrgard MJ, Swainston N, Dobson P, et al. A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol 2008;26:1155-1160.
    • (2008) Nature Biotechnol , vol.26 , pp. 1155-1160
    • Herrgard, M.J.1    Swainston, N.2    Dobson, P.3
  • 4
    • 77958597036 scopus 로고    scopus 로고
    • Further developments towards a genome-scale metabolic model of yeast
    • Dobson PD, Jameson D, Simeonidis E, et al. Further developments towards a genome-scale metabolic model of yeast. BMC Syst Biol 2010;4:145.
    • (2010) BMC Syst Biol , vol.4 , pp. 145
    • Dobson, P.D.1    Jameson, D.2    Simeonidis, E.3
  • 5
    • 84861744439 scopus 로고    scopus 로고
    • Yeast 5 - An expanded reconstruction of the Saccharomyces cerevisiae metabolic network
    • Heavner BD, Smallbone K, Barker B, et al. Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 2012;6:55.
    • (2012) BMC Syst Biol , vol.6 , pp. 55
    • Heavner, B.D.1    Smallbone, K.2    Barker, B.3
  • 7
    • 77953934646 scopus 로고    scopus 로고
    • BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    • Li C, Donizelli M, Rodriguez N, et al. BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010;4:92.
    • (2010) BMC Syst Biol , vol.4 , pp. 92
    • Li, C.1    Donizelli, M.2    Rodriguez, N.3
  • 8
    • 0033857139 scopus 로고    scopus 로고
    • Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
    • Teusink B, Passarge J, Reijenga CA, et al. Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 2000;267:53113-5329.
    • (2000) Eur J Biochem , vol.267 , pp. 53113-55329
    • Teusink, B.1    Passarge, J.2    Reijenga, C.A.3
  • 9
    • 47149095277 scopus 로고    scopus 로고
    • Towards Kinetic Modeling of Global Metabolic Networks: Methylobacterium extorquens AM1 Growth as Validation
    • DOI 10.1016/S1872-2075(08)60046-1, PII S1872207508600461
    • Ao P, Lee LW, Lidstrom M, et al. Towards kinetic modeling of global metabolic networks: Methylobacterium extorquens AM1 growth as validation. Chinese J Biotechnol 2008;24:980-994. (Pubitemid 351978317)
    • (2008) Chinese Journal of Biotechnology , vol.24 , Issue.6 , pp. 980-994
    • Ao, P.1    Lee, L.W.2    Lidstrom, M.E.3    Yin, L.4    Zhu, X.5
  • 12
    • 0141684666 scopus 로고    scopus 로고
    • Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics
    • DOI 10.1016/S1096-7176(03)00025-9
    • Visser D, Heijnen JJ. Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metab Eng 2003;5:164-176. (Pubitemid 37124115)
    • (2003) Metabolic Engineering , vol.5 , Issue.3 , pp. 164-176
    • Visser, D.1    Heijnen, J.J.2
  • 13
    • 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. Something from nothing: Bridging the gap between constraint-based and kinetic modelling. FEBS J 2007;274:5576-5585. (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
  • 14
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
    • Liebermeister W, Klipp E. Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006;3:1-11.
    • (2006) Theor Biol Med Model , vol.3 , pp. 1-11
    • Liebermeister, W.1    Klipp, E.2
  • 16
    • 77954196484 scopus 로고    scopus 로고
    • Modular rate laws for enzymatic reactions: Thermodynamics, elasticities and Implementation
    • Liebermeister W, Uhlendorf J, Klipp E. Modular rate laws for enzymatic reactions: Thermodynamics, elasticities and Implementation. Bioinformatics 2010;26:1528-1534.
    • (2010) Bioinformatics , vol.26 , pp. 1528-1534
    • Liebermeister, W.1    Uhlendorf, J.2    Klipp, E.3
  • 17
    • 78650082315 scopus 로고    scopus 로고
    • Parameter balancing in kinetic models of cell metabolism
    • Lubitz T, Schulz M, Klipp E, Liebermeister W. Parameter balancing in kinetic models of cell metabolism. J Phys Chem B 2010;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
  • 19
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011
    • Orth JD, Conrad TM, Na J, et al. A comprehensive genome-scale reconstruction of Escherichia coli metabolism - 2011. Mol Syst Biol 2011;7:535.
    • (2011) Mol Syst Biol , vol.7 , pp. 535
    • Orth, J.D.1    Conrad, T.M.2    Na, J.3
  • 20
    • 67349218872 scopus 로고    scopus 로고
    • Flux balance analysis: A geometric perspective
    • Smallbone K, Simeonidis E. flux balance analysis: A geometric perspective. J Theor Biol 2009;258:311-315.
    • (2009) J Theor Biol , vol.258 , pp. 311-315
    • Smallbone, K.1    Simeonidis, E.2
  • 21
    • 84876148784 scopus 로고    scopus 로고
    • HMDB 3.0 - The human metabolome database in 2013
    • Wishart DS, Jewison T, Guo AC, et al. HMDB 3.0 - The Human Metabolome Database in 2013. Nucleic Acids Res 2013;41:D801-D807.
    • (2013) Nucleic Acids Res , vol.41
    • Wishart, D.S.1    Jewison, T.2    Guo, A.C.3
  • 22
    • 84862214722 scopus 로고    scopus 로고
    • SABIO-RK - Database for biochemical reaction kinetics
    • Wittig U, Kania R, Golebiewski M, et al. SABIO-RK - database for biochemical reaction kinetics. Nucleic Acids Res 2012;40:D790-D796.
    • (2012) Nucleic Acids Res , vol.40
    • Wittig, U.1    Kania, R.2    Golebiewski, M.3
  • 23
    • 78651330012 scopus 로고    scopus 로고
    • BRENDA, the enzyme information system in 2011
    • Scheer M, Grote A, Chang A, et al. BRENDA, the enzyme information system in 2011. Nucleic Acids Res 2011;39:D670-D676.
    • (2011) Nucleic Acids Res , vol.39
    • Scheer, M.1    Grote, A.2    Chang, A.3
  • 24
    • 8844259501 scopus 로고    scopus 로고
    • Thermodynamics of enzyme-catalyzed reactions - A database for quantitative biochemistry
    • DOI 10.1093/bioinformatics/bth314
    • Goldberg RN, Tewari YB, Bhat TN. Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. Bioinformatics 2004;20:2874-2877. (Pubitemid 39530187)
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2874-2877
    • Goldberg, R.N.1    Tewari, Y.B.2    Bhat, T.N.3
  • 25
    • 40749162829 scopus 로고    scopus 로고
    • LibSBML: An API library for SBML
    • DOI 10.1093/bioinformatics/btn051
    • Bornstein BJ, Keating SM Jouraku A, Hucka M. LibSBML: An API library for SBML. Bioinformatics 2008;24:880-881. (Pubitemid 351386935)
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 880-881
    • Bornstein, B.J.1    Keating, S.M.2    Jouraku, A.3    Hucka, M.4
  • 26
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox v2.0
    • Schellenberger J, Que R, fleming RM, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 Nat Protoc 2011;6:1290-1307.
    • (2011) Nat Protoc , vol.6 , pp. 1290-1307
    • Schellenberger, J.1    Que Rfleming, R.M.2
  • 27
    • 33845368513 scopus 로고    scopus 로고
    • COPASI: A complex PA the way SI mulator
    • Hoops S, Sahle S, Gauges R, et al. COPASI: a COmplex PAthway SImulator. Bioinformatics 2006;22:3067-3074.
    • (2006) Bioinformatics , vol.22 , pp. 3067-3074
    • Hoops, S.1    Sahle, S.2    Gauges, R.3
  • 28
    • 0014198718 scopus 로고
    • Adenosine triphosphate conservation in metabolic regulation. Rat liver citrate cleavage enzyme
    • Atkinson DE, Walton GM. Adenosine triphosphate conservation in metabolic regulation. Rat liver citrate cleavage enzyme. J Biol Chem 1967;242:3239-3241.
    • (1967) J Biol Chem , vol.242 , pp. 3239-3241
    • Atkinson, D.E.1    Walton, G.M.2
  • 29
    • 0036038886 scopus 로고    scopus 로고
    • Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis
    • Pritchard L, Kell DB. Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. Eur J Biochem 2001;269:3894-3904.
    • (2001) Eur J Biochem , vol.269 , pp. 3894-3904
    • Pritchard, L.1    Kell, D.B.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.