메뉴 건너뛰기




Volumn 83, Issue 2-3 SPEC. ISS., 2006, Pages 207-216

Towards building the silicon cell: A modular approach

Author keywords

Detailed kinetic model; JWS online; Model repository; Systems biology

Indexed keywords

SILICON;

EID: 32044435851     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2005.07.006     Document Type: Conference Paper
Times cited : (89)

References (46)
  • 1
    • 0037974422 scopus 로고    scopus 로고
    • Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design
    • S. Bhartiya, S. Rawool, and K.V. Venkatesh Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design Eur. J. Biochem. 270 2003 2644 2651
    • (2003) Eur. J. Biochem. , vol.270 , pp. 2644-2651
    • Bhartiya, S.1    Rawool, S.2    Venkatesh, K.V.3
  • 3
    • 0003381877 scopus 로고
    • Metabolic Control Mechanisms V. a solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells
    • B. Chance, D. Garfinkel, J. Higgins, and B. Hess Metabolic Control Mechanisms V. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells J. Biol. Chem. 235 1960 2426 2439
    • (1960) J. Biol. Chem. , vol.235 , pp. 2426-2439
    • Chance, B.1    Garfinkel, D.2    Higgins, J.3    Hess, B.4
  • 4
    • 0035367217 scopus 로고    scopus 로고
    • Control of the threonine-synthesis pathway in Escherichia coli: A theoretical and experimental approach
    • C. Chassagnole, D.A. Fell, B. Rais, B. Kudla, and J.-P. Mazat Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach Biochem. J. 356 2001 433 444
    • (2001) Biochem. J. , vol.356 , pp. 433-444
    • Chassagnole, C.1    Fell, D.A.2    Rais, B.3    Kudla, B.4    Mazat, J.-P.5
  • 6
    • 0036304317 scopus 로고    scopus 로고
    • The role of stoichiometric analysis in studies of metabolism: An example
    • A. Cornish-Bowden, and J.H.S. Hofmeyr The role of stoichiometric analysis in studies of metabolism: an example J. Theor. Biol. 216 2 2002 179 191
    • (2002) J. Theor. Biol. , vol.216 , Issue.2 , pp. 179-191
    • Cornish-Bowden, A.1    Hofmeyr, J.H.S.2
  • 7
    • 0036713452 scopus 로고    scopus 로고
    • Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae
    • G.R. Cronwright, J.M. Rohwer, and B.A. Prior Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae Appl. Environ. Microbiol. 68 2003 4448 4456
    • (2003) Appl. Environ. Microbiol. , vol.68 , pp. 4448-4456
    • Cronwright, G.R.1    Rohwer, J.M.2    Prior, B.A.3
  • 8
    • 0345688035 scopus 로고    scopus 로고
    • A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana
    • G. Curien, S. Ravanel, and R. Dumas A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana Eur. J. Biochem. 270 2003 1 13
    • (2003) Eur. J. Biochem. , vol.270 , pp. 1-13
    • Curien, G.1    Ravanel, S.2    Dumas, R.3
  • 9
    • 0029023952 scopus 로고
    • Control of metabolic pathways by time-scale separation
    • J. Delgado, and J.C. Liao Control of metabolic pathways by time-scale separation Biosystems 36 1 1995 55 70
    • (1995) Biosystems , vol.36 , Issue.1 , pp. 55-70
    • Delgado, J.1    Liao, J.C.2
  • 10
    • 11444266042 scopus 로고    scopus 로고
    • Kinetics of intra- and intermolecular zymogen activation with formation of an enzyme-zymogen complex
    • M.E. Fuentes, R. Varon, M. Garcia-Moreno, and E. Valero Kinetics of intra- and intermolecular zymogen activation with formation of an enzyme-zymogen complex FEBS J. 272 2005 85 96
    • (2005) FEBS J. , vol.272 , pp. 85-96
    • Fuentes, M.E.1    Varon, R.2    Garcia-Moreno, M.3    Valero, E.4
  • 11
    • 0025400371 scopus 로고
    • Fermentation pathway kinetics and metabolic flux control in suspended and immobilized saccharomyces cerevisiae
    • J.L. Galazzo, and J.E. Bailey Fermentation pathway kinetics and metabolic flux control in suspended and immobilized saccharomyces cerevisiae Enz. Microb. Technol. 12 1990 162 172
    • (1990) Enz. Microb. Technol. , vol.12 , pp. 162-172
    • Galazzo, J.L.1    Bailey, J.E.2
  • 14
    • 0035397515 scopus 로고    scopus 로고
    • Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei
    • S. Helfert, A.M. Estevez, B.M. Bakker, P. Michels, and C. Clayton Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei Biochem. J. 357 2001 117 125
    • (2001) Biochem. J. , vol.357 , pp. 117-125
    • Helfert, S.1    Estevez, A.M.2    Bakker, B.M.3    Michels, P.4    Clayton, C.5
  • 16
    • 0036037732 scopus 로고    scopus 로고
    • Time dependent responses of glycolytic intermediates in a detailed glycolytic model of Lactococcus lactis during glucose run-out experiments
    • M.H.N. Hoefnagel, A. Van Der Burgt, D.E. Martens, J. Hugenholtz, and J.L. Snoep Time dependent responses of glycolytic intermediates in a detailed glycolytic model of Lactococcus lactis during glucose run-out experiments Mol. Biol. Rep. 29 2002 157 161
    • (2002) Mol. Biol. Rep. , vol.29 , pp. 157-161
    • Hoefnagel, M.H.N.1    Van Der Burgt, A.2    Martens, D.E.3    Hugenholtz, J.4    Snoep, J.L.5
  • 17
    • 3242795003 scopus 로고    scopus 로고
    • The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks
    • H.-G. Holzhutter The principle of flux minimization and its application to estimate stationary fluxes in metabolic networks Eur. J. Biochem. 271 2004 2905 2922
    • (2004) Eur. J. Biochem. , vol.271 , pp. 2905-2922
    • Holzhutter, H.-G.1
  • 19
    • 0035846723 scopus 로고    scopus 로고
    • Full-scale model of glycolysis in Saccharomyces cerevisiae
    • F. Hynne, S. Dano, and P.G. Sorensen Full-scale model of glycolysis in Saccharomyces cerevisiae Biophys. Chem. 94 2001 121 163
    • (2001) Biophys. Chem. , vol.94 , pp. 121-163
    • Hynne, F.1    Dano, S.2    Sorensen, P.G.3
  • 20
    • 0037466509 scopus 로고    scopus 로고
    • Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories
    • B.P. Ingalls, and H.M. Sauro Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories J. Theor. Biol. 222 1 2003 23 36
    • (2003) J. Theor. Biol. , vol.222 , Issue.1 , pp. 23-36
    • Ingalls, B.P.1    Sauro, H.M.2
  • 21
    • 4444272353 scopus 로고    scopus 로고
    • Modelling the dynamics of the yeast pheromone pathway
    • B. Kofahl, and E. Klipp Modelling the dynamics of the yeast pheromone pathway Yeast 21 2004 831 850
    • (2004) Yeast , vol.21 , pp. 831-850
    • Kofahl, B.1    Klipp, E.2
  • 22
    • 0033570090 scopus 로고    scopus 로고
    • Quantification of short term signaling by the epidermal growth factor receptor
    • B.N. Kholodenko, O.V. Demin, G. Moehren, and J.B. Hoek Quantification of short term signaling by the epidermal growth factor receptor J. Biol. Chem. 274 1999 30169 30181
    • (1999) J. Biol. Chem. , vol.274 , pp. 30169-30181
    • Kholodenko, B.N.1    Demin, O.V.2    Moehren, G.3    Hoek, J.B.4
  • 23
    • 0020827805 scopus 로고
    • Simplifying principles for chemical and enzyme reaction kinetics
    • W. Klonowski Simplifying principles for chemical and enzyme reaction kinetics Biophys. Chem. 18 1983 73 87
    • (1983) Biophys. Chem. , vol.18 , pp. 73-87
    • Klonowski, W.1
  • 24
    • 0023738065 scopus 로고
    • Kinetics of histone gene expression during early development of Xenopus laevis
    • J.G. Koster, O.H.J. Destree, and H.V. Westerhoff Kinetics of histone gene expression during early development of Xenopus laevis J. Theor. Biol. 135 1988 139 167
    • (1988) J. Theor. Biol. , vol.135 , pp. 139-167
    • Koster, J.G.1    Destree, O.H.J.2    Westerhoff, H.V.3
  • 25
    • 0035982810 scopus 로고    scopus 로고
    • A computational model for glucogenolysis in skeletal muscle
    • M.J. Lambeth, and M.J. Kushmerick A computational model for glucogenolysis in skeletal muscle Ann. Biomed. Eng. 30 2002 808 827
    • (2002) Ann. Biomed. Eng. , vol.30 , pp. 808-827
    • Lambeth, M.J.1    Kushmerick, M.J.2
  • 26
    • 0141815496 scopus 로고    scopus 로고
    • Mathematical modeling of the urea cycle: A numerical investigation into substrate channelling
    • A.D. Maher, P.W. Kuchel, F. Ortega, P. de Atauri, J. Centelles, and M. Cascante Mathematical modeling of the urea cycle: a numerical investigation into substrate channelling Eur. J. Biochem. 270 2003 3953 3961
    • (2003) Eur. J. Biochem. , vol.270 , pp. 3953-3961
    • Maher, A.D.1    Kuchel, P.W.2    Ortega, F.3    De Atauri, P.4    Centelles, J.5    Cascante, M.6
  • 27
    • 0034828640 scopus 로고    scopus 로고
    • In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae
    • A.M. Martins, P. Mendes, C. Cordeiro, and A.P. Freire In situ kinetic analysis of glyoxalase I and glyoxalase II in Saccharomyces cerevisiae Eur. J. Biochem. 268 2001 3930 3936
    • (2001) Eur. J. Biochem. , vol.268 , pp. 3930-3936
    • Martins, A.M.1    Mendes, P.2    Cordeiro, C.3    Freire, A.P.4
  • 28
    • 0033568448 scopus 로고    scopus 로고
    • Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: Equations and parameter refinement
    • P.J. Mulquiney, and P.W. Kuchel Model of 2,3-bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement Biochem. J. 342 1999 581 596
    • (1999) Biochem. J. , vol.342 , pp. 581-596
    • Mulquiney, P.J.1    Kuchel, P.W.2
  • 29
    • 0032485816 scopus 로고    scopus 로고
    • Sustained oscillations in glycolysis: An experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations
    • K. Nielsen, P.G. Sorensen, F. Hynne, and H.-G. Busse Sustained oscillations in glycolysis: an experimental and theoretical study of chaotic and complex periodic behavior and of quenching of simple oscillations Biophys. Chem. 72 1998 49 62
    • (1998) Biophys. Chem. , vol.72 , pp. 49-62
    • Nielsen, K.1    Sorensen, P.G.2    Hynne, F.3    Busse, H.-G.4
  • 30
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modeling using JWS online
    • B.G. Olivier, and J.L. Snoep Web-based kinetic modeling using JWS online Bioinformatics 20 2004 2143 2144
    • (2004) Bioinformatics , vol.20 , pp. 2143-2144
    • Olivier, B.G.1    Snoep, J.L.2
  • 31
    • 0037707891 scopus 로고    scopus 로고
    • Mechanism of protection of peroxidase activity by oscillatory dynamics
    • L.F. Olsen, M.J.B. Hauser, and U. Kummer Mechanism of protection of peroxidase activity by oscillatory dynamics Eur. J. Biochem. 270 2003 2796 2804
    • (2003) Eur. J. Biochem. , vol.270 , pp. 2796-2804
    • Olsen, L.F.1    Hauser, M.J.B.2    Kummer, U.3
  • 32
    • 0037385718 scopus 로고    scopus 로고
    • Genome-scale microbial in silico models: The constraints-based approach
    • N.D. Price, J.A. Papin, C.H. Schilling, and B.O. Palsson Genome-scale microbial in silico models: the constraints-based approach Trends Biotechnol. 21 2003 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
  • 33
    • 0033975578 scopus 로고    scopus 로고
    • Modeling photosynthesis and its control
    • M.G. Poolman, D.A. Fell, and S. Thomas Modeling photosynthesis and its control J. Exp. Bot. 51 2000 319 328
    • (2000) J. Exp. Bot. , vol.51 , pp. 319-328
    • Poolman, M.G.1    Fell, D.A.2    Thomas, S.3
  • 34
    • 0023709196 scopus 로고
    • Metabolic control theory: A structural approach
    • C. Reder Metabolic control theory: a structural approach J. Theor. Biol. 135 2 1988 175 201
    • (1988) J. Theor. Biol. , vol.135 , Issue.2 , pp. 175-201
    • Reder, C.1
  • 35
    • 0034634571 scopus 로고    scopus 로고
    • Understanding glucose transport by the bacterial phosphoenolpyruvate: Glucose phosphotransferase system on the basis of kinetic measurements in vitro
    • J.M. Rohwer, N.D. Meadow, S. Roseman, H.V. Westerhoff, and P.W. Postma Understanding glucose transport by the bacterial phosphoenolpyruvate: glucose phosphotransferase system on the basis of kinetic measurements in vitro J. Biol. Chem. 275 2001 34909 34921
    • (2001) J. Biol. Chem. , vol.275 , pp. 34909-34921
    • Rohwer, J.M.1    Meadow, N.D.2    Roseman, S.3    Westerhoff, H.V.4    Postma, P.W.5
  • 36
    • 0035448427 scopus 로고    scopus 로고
    • Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data
    • J.M. Rohwer, and F.C. Botha Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data Biochem. J. 358 2001 437 445
    • (2001) Biochem. J. , vol.358 , pp. 437-445
    • Rohwer, J.M.1    Botha, F.C.2
  • 37
    • 1842474510 scopus 로고    scopus 로고
    • Conservation analysis in biochemical networks: Computational issues for software writers
    • H.M. Sauro, and B. Ingalls Conservation analysis in biochemical networks: computational issues for software writers Biophys. Chem. 109 1 2004 1 15
    • (2004) Biophys. Chem. , vol.109 , Issue.1 , pp. 1-15
    • Sauro, H.M.1    Ingalls, B.2
  • 38
    • 32044435066 scopus 로고
    • Relationships between modal analysis and rapid-equilibrium approximation in the modeling of biochemical networks
    • R. Schuster, and S. Schuster Relationships between modal analysis and rapid-equilibrium approximation in the modeling of biochemical networks Syst. Anal. Modell. Simul. 8 8 1991 623 633
    • (1991) Syst. Anal. Modell. Simul. , vol.8 , Issue.8 , pp. 623-633
    • Schuster, R.1    Schuster, S.2
  • 39
    • 0015413883 scopus 로고
    • Simplification and scaling
    • L.A. Segel Simplification and scaling SIAM Rev. 14 4 1972 547 571
    • (1972) SIAM Rev. , vol.14 , Issue.4 , pp. 547-571
    • Segel, L.A.1
  • 42
    • 0035926571 scopus 로고    scopus 로고
    • Regulation of the eukaryotic cell cycle: Molecular antagonism, hysteresis, and irreversible transitions
    • J.J. Tyson, and B. Novak Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions J. Theor. Biol. 210 2001 249 263
    • (2001) J. Theor. Biol. , vol.210 , pp. 249-263
    • Tyson, J.J.1    Novak, B.2
  • 43
    • 0028108519 scopus 로고
    • Metabolic flux balancing: Basic concepts, scientific and practical use
    • A. Varma, and B.O. Palsson Metabolic flux balancing: basic concepts, scientific and practical use Biotechnology 12 1994 994 998
    • (1994) Biotechnology , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 44
    • 0034741983 scopus 로고    scopus 로고
    • 13C metabolic flux analysis
    • 13C metabolic flux analysis Metab. Eng. 3 2001 195 206
    • (2001) Metab. Eng. , vol.3 , pp. 195-206
    • Wiechert, W.1
  • 45
    • 5044227742 scopus 로고    scopus 로고
    • The evolution of molecular biology into systems biology
    • H.V. Westerhoff, and B.O. Palsson The evolution of molecular biology into systems biology Nat. Biotechnol. 22 2004 1249 1252
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1249-1252
    • Westerhoff, H.V.1    Palsson, B.O.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.