메뉴 건너뛰기




Volumn 3, Issue , 2006, Pages

Bringing metabolic networks to life: Integration of kinetic, metabolic, and proteomic data

Author keywords

[No Author keywords available]

Indexed keywords

THREONINE; ENZYME;

EID: 33846647495     PISSN: None     EISSN: 17424682     Source Type: Journal    
DOI: 10.1186/1742-4682-3-42     Document Type: Article
Times cited : (62)

References (37)
  • 1
    • 0004234375 scopus 로고    scopus 로고
    • G Michal (Ed), Heidelberg: Spektrum Akademischer Verlag
    • G Michal (Ed), Biochemical Pathways Heidelberg: Spektrum Akademischer Verlag 1999
    • (1999) Biochemical Pathways
  • 2
    • 0036081062 scopus 로고    scopus 로고
    • The KEGG databases at GenomeNet
    • 11752249. 10.1093/nar/30.1.42
    • The KEGG databases at GenomeNet. M Kanehisa S Goto SK S A Nakaya, Nucleic Acids Res 2002 30 42 46 11752249 10.1093/nar/30.1.42
    • (2002) Nucleic Acids Res , vol.30 , pp. 42-46
    • Kanehisa, M.1    Goto, S.2    K, S.S.3    Nakaya, A.4
  • 4
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • 12952533. 10.1186/gb-2003-4-9
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). J Reed T Vo C Schilling B Palsson, Genome Biol 2003 4 9 R54 12952533 10.1186/gb-2003-4-9-r54
    • (2003) Genome Biol , vol.4 , Issue.9-54 , pp. 54
    • Reed, J.1    Vo, T.2    Schilling, C.3    Palsson, B.4
  • 5
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • 12566402. 10.1101/gr.234503
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. J Förster I Famili P Fu B Palsson J Nielsen, Genome Research 2003 13 2 244 253 12566402 10.1101/gr.234503
    • (2003) Genome Research , vol.13 , Issue.2 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3    Palsson, B.4    Nielsen, J.5
  • 6
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • 16204195. 10.1101/gr.3992505
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae. L Küpfer U Sauer LM Blank, Genome Research 2005 15 1421 1430 16204195 10.1101/gr.3992505
    • (2005) Genome Research , vol.15 , pp. 1421-1430
    • Küpfer, L.1    Sauer, U.2    Blank, L.M.3
  • 7
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific and practical use
    • 10.1038/nbt1094
    • Metabolic flux balancing: basic concepts, scientific and practical use. A Varma BO Palsson, Biotechnology 1994 12 994 998 10.1038/nbt1094-994
    • (1994) Biotechnology , vol.12 , Issue.10 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 8
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • 10.1016/S0167-7799(98)01290. 10087604
    • Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. S Schuster T Dandekar DA Fell, Trends Biotechnol 1999 17 2 53 60 10.1016/S0167-7799(98)01290-6 10087604
    • (1999) Trends Biotechnol , vol.17 , Issue.2-6 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 9
    • 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
    • 10.1006/jtbi.2000.1073. 10716907
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. CH Schilling D Letscher BO Palsson, J Theor Biol 2000 203 229 248 10.1006/jtbi.2000.1073 10716907
    • (2000) J Theor Biol , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 10
    • 0036286631 scopus 로고    scopus 로고
    • Energy balance for analysis of complex metabolic networks
    • 12080101
    • Energy balance for analysis of complex metabolic networks. DA Beard S Liang H Qian, Biophys J 2002 83 79 86 12080101
    • (2002) Biophys J , vol.83 , pp. 79-86
    • Beard, D.A.1    Liang, S.2    Qian, H.3
  • 11
    • 0015824267 scopus 로고
    • The control of flux
    • 4148886
    • The control of flux. H Kacser J Burns, Symp Soc Exp Biol 1973 27 65 104 4148886
    • (1973) Symp Soc Exp Biol , vol.27 , pp. 65-104
    • Kacser, H.1    Burns, J.2
  • 12
    • 0026802334 scopus 로고
    • Metabolic control analysis: A survey of its theoretical and experimental development
    • 1530563
    • Metabolic control analysis: a survey of its theoretical and experimental development. DA Fell, Biochem J 1992 286 313 330 1530563
    • (1992) Biochem J , vol.286 , pp. 313-330
    • Fell, D.A.1
  • 14
    • 42749109054 scopus 로고    scopus 로고
    • Statistical mechanical approaches to models with many poorly known parameters
    • 10.1103/PhysRevE.68.021904. 14525003
    • Statistical mechanical approaches to models with many poorly known parameters. KS Brown JP Sethna, Phys Rev E Stat Nonlin Soft Matter Phys 2003 68 021904 10.1103/PhysRevE.68.021904 14525003
    • (2003) Phys Rev e Stat Nonlin Soft Matter Phys , vol.68 , pp. 021904
    • Brown, K.S.1    Sethna, J.P.2
  • 15
    • 27244440301 scopus 로고    scopus 로고
    • Biochemical networks with uncertain parameters
    • 10.1049/ip. 16986274
    • Biochemical networks with uncertain parameters. W Liebermeister E Klipp, Syst Biol (Stevenage) 2005 152 3 97 107 10.1049/ip-syb:20045033 16986274
    • (2005) Syst Biol (Stevenage) , vol.152 , Issue.3 , pp. 97-107
    • Liebermeister, W.1    Klipp, E.2
  • 16
    • 33747061013 scopus 로고    scopus 로고
    • Structural kinetic modeling of metabolic networks
    • 16880395. 10.1073/pnas.0600013103
    • Structural kinetic modeling of metabolic networks. R Steuer T Gross J Selbig B Blasius, Proc Natl Acad Sci USA 2006 103 32 11868 11873 16880395 10.1073/pnas.0600013103
    • (2006) Proc Natl Acad Sci USA , vol.103 , Issue.32 , pp. 11868-11873
    • Steuer, R.1    Gross, T.2    Selbig, J.3    Blasius, B.4
  • 17
    • 33746083686 scopus 로고    scopus 로고
    • Quantitative element are mode analysis of metabolic pathways: The example of yeast glycolysis
    • 10.1186/1471-2105-7. 16584566
    • Quantitative element are mode analysis of metabolic pathways: the example of yeast glycolysis. JM Schwartz M Kanehisa, BMC Bioinformatics 2006 7 186 10.1186/1471-2105-7-186 16584566
    • (2006) BMC Bioinformatics , vol.7-186 , pp. 186
    • Schwartz, J.M.1    Kanehisa, M.2
  • 19
    • 8844259501 scopus 로고    scopus 로고
    • Thermodynamics of enzyme-catalyzed reactions - A database for quantitative biochemistry
    • 10.1093/bioinformatics/bth314. 15145806
    • Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. RN Goldberg YB Tewari TN Bhat, Bioinformatics 2004 20 2874 7 10.1093/bioinformatics/bth314 15145806
    • (2004) Bioinformatics , vol.20 , pp. 2874-7
    • Goldberg, R.N.1    Tewari, Y.B.2    Bhat, T.N.3
  • 21
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modelling using JWS Online
    • 10.1093/bioinformatics/bth200. 15072998
    • Web-based kinetic modelling using JWS Online. B Olivier J Snoep, Bioinformatics 2004 20 13 2143 2144 10.1093/bioinformatics/bth200 15072998
    • (2004) Bioinformatics , vol.20 , Issue.13 , pp. 2143-2144
    • Olivier, B.1    Snoep, J.2
  • 22
    • 33846605217 scopus 로고    scopus 로고
    • http://www.ebi.ac.uk/biomodels
    • http://www.ebi.ac.uk/biomodels
  • 23
    • 0025701406 scopus 로고
    • Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution
    • 10.1002/bit.260361013
    • Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution. M Mavrovouniotis, Biotechnology and Bioengineering 1990 36 1070 1082 10.1002/bit.260361013
    • (1990) Biotechnology and Bioengineering , vol.36 , pp. 1070-1082
    • Mavrovouniotis, M.1
  • 24
    • 0025276048 scopus 로고
    • Cellular concentrations of enzymes and their substrates
    • 10.1016/S0022-5193(05)80266. 2200929
    • Cellular concentrations of enzymes and their substrates. KR Albe MH Butler BE Wright, J Theor Biol 1990 143 163 195 10.1016/S0022-5193(05)80266-8 2200929
    • (1990) J Theor Biol , vol.143 , Issue.8 , pp. 163-195
    • Albe, K.R.1    Butler, M.H.2    Wright, B.E.3
  • 25
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • 14559783. 10.1101/gr.1262503
    • Parameter estimation in biochemical pathways: a comparison of global optimization methods. C Moles P Mendes J Banga, Genome Research 2003 13 11 2467 2474 14559783 10.1101/gr.1262503
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2467-2474
    • Moles, C.1    Mendes, P.2    Banga, J.3
  • 26
    • 32044474451 scopus 로고    scopus 로고
    • A hybrid approach for efficient and robust parameter estimation in biochemical pathways
    • 10.1016/j.biosystems.2005.06.016. 16236429
    • A hybrid approach for efficient and robust parameter estimation in biochemical pathways. M Rodriguez-Fernandeza P Mendes J Banga, Biosystems 2006 83 2-3 248 265 10.1016/j.biosystems.2005.06.016 16236429
    • (2006) Biosystems , vol.83 , Issue.2-3 , pp. 248-265
    • Rodriguez-Fernandeza, M.1    Mendes, P.2    Banga, J.3
  • 27
    • 33750415038 scopus 로고    scopus 로고
    • SBML-PET: A Systems Biology Markup Language-based parameter estimation tool
    • 10.1093/bioinformatics/btl443. 16926221
    • SBML-PET: a Systems Biology Markup Language-based parameter estimation tool. Z Zi E Klipp, Bioinformatics 2006 22 21 2704 2705 10.1093/bioinformatics/ btl443 16926221
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2704-2705
    • Zi, Z.1    Klipp, E.2
  • 28
    • 33646364037 scopus 로고    scopus 로고
    • Identification of metabolic system parameters using global optimization methods
    • 16441881. 10.1186/1742-4682-3
    • Identification of metabolic system parameters using global optimization methods. P Polisetty E Voit E Gatzke, Theor Biol Med Model 2006 3 4 16441881 10.1186/1742-4682-3-4
    • (2006) Theor Biol Med Model , vol.3-4 , pp. 4
    • Polisetty, P.1    Voit, E.2    Gatzke, E.3
  • 29
    • 33747876155 scopus 로고    scopus 로고
    • A decompositional approach to parameter estimation in pathway modeling: A case study of the Akt and MAPK pathways and their crosstalk
    • 10.1093/bioinformatics/btl264. 16873482
    • A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk. G Koh H Teong M Clement D Hsu P Thiagarajan, Bioinformatics 2006 22 14 e271 e280 10.1093/bioinformatics/btl264 16873482
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Koh, G.1    Teong, H.2    Clement, M.3    Hsu, D.4    Thiagarajan, P.5
  • 30
    • 18244406832 scopus 로고    scopus 로고
    • Inferring dynamic properties of biochemical reaction networks from structural knowledge
    • 15712116
    • Inferring dynamic properties of biochemical reaction networks from structural knowledge. E Klipp W Liebermeister C Wierling, Genome Informatics 2004 15 125 137 15712116
    • (2004) Genome Informatics , vol.15 , pp. 125-137
    • Klipp, E.1    Liebermeister, W.2    Wierling, C.3
  • 31
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: Convenience rate law and thermodynamic constraints
    • 10.1186/1742-4682-3. 17173669
    • Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. W Liebermeister E Klipp, Theor Biol Med Model 2006 3 41 10.1186/1742-4682-3-41 17173669
    • (2006) Theor Biol Med Model , vol.3-41 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 32
    • 0025302537 scopus 로고
    • Metabolic control analysis. Sensitivity of control coefficients to elasticities
    • 10.1111/j.1432. 2384089
    • Metabolic control analysis. Sensitivity of control coefficients to elasticities. JR Small D Fell, Eur J Biochem 1990 191 413 420 10.1111/j.1432-1033.1990.tb19137.x 2384089
    • (1990) Eur J Biochem , vol.191 , pp. 413-420
    • Small, J.R.1    Fell, D.2
  • 33
    • 0035365847 scopus 로고    scopus 로고
    • An integrated study of threonine-pathway enzyme kinetics in Escherichia coli
    • 11368768. 10.1042/0264
    • An integrated study of threonine-pathway enzyme kinetics in Escherichia coli. C Chassagnole B Ras E Quentin DA Fell J Mazat, Biochem J 2001 356 415 423 11368768 10.1042/0264-6021:3560415
    • (2001) Biochem J , vol.356 , pp. 415-423
    • Chassagnole, C.1    Ras, B.2    Quentin, E.3    Fell, D.A.4    Mazat, J.5
  • 34
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • 10.1016/S0022-5193(88)80073. 3267767
    • Metabolic control theory: a structural approach. C Reder, J Theor Biol 1988 135 175 201 10.1016/S0022-5193(88)80073-0 3267767
    • (1988) J Theor Biol , vol.135 , pp. 175-201
    • Reder, C.1
  • 36
    • 0037466509 scopus 로고    scopus 로고
    • Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories
    • 10.1016/S0022-5193(03)00011. 12699732
    • Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. BP Ingalls HM Sauro, J Theor Biol 2003 222 23 36 10.1016/S0022-5193(03)00011-0 12699732
    • (2003) J Theor Biol , vol.222 , pp. 23-36
    • Ingalls, B.P.1    Sauro, H.M.2
  • 37
    • 33645015786 scopus 로고    scopus 로고
    • Predicting physiological concentrations of metabolites from their molecular structure
    • 10.1089/cmb.2005.12.1307
    • Predicting physiological concentrations of metabolites from their molecular structure. W Liebermeister, J Comp Biol 2005 12 10 1307 1315 10.1089/cmb.2005.12.1307
    • (2005) J Comp Biol , vol.12 , Issue.10 , pp. 1307-1315
    • Liebermeister, W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.