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Volumn , Issue , 2011, Pages 31-51

Modeling Approaches in Systems Biology, Including Silicon Cell Models

Author keywords

Bottom up; Emergence; Middle out; Silicon cell model; Systems biology; Top down

Indexed keywords


EID: 84866547997     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9780470963012.ch2     Document Type: Chapter
Times cited : (7)

References (42)
  • 1
    • 32044452595 scopus 로고    scopus 로고
    • Systems biology: definitions and perspectives
    • In: Topics in Current Genetics,(Ed. S. Hohmann). Springer, Berlin
    • Alberghina, L. & Westerhoff, H.V. (2005) Systems biology: definitions and perspectives. In: Topics in Current Genetics, Vol. 13, (Ed. S. Hohmann). Springer, Berlin.
    • (2005) , vol.13
    • Alberghina, L.1    Westerhoff, H.V.2
  • 3
    • 0031021873 scopus 로고    scopus 로고
    • Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes
    • Bakker, B.M., Michels, P.A.M., Opperdoes, F.R., et al. (1997) Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. Journal of Biological Chemistry 272, 3207-3215.
    • (1997) Journal of Biological Chemistry , vol.272 , pp. 3207-3215
    • Bakker, B.M.1    Michels, P.A.M.2    Opperdoes, F.R.3
  • 4
    • 0033977087 scopus 로고    scopus 로고
    • Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs
    • Bakker, B.M., Westerhoff, H.V., Opperdoes, F.R., et al. (2000b) Metabolic control analysis of glycolysis in trypanosomes as an approach to improve selectivity and effectiveness of drugs. Molecular and Biochemical Parasitology 106, 1-10.
    • (2000) Molecular and Biochemical Parasitology , vol.106 , pp. 1-10
    • Bakker, B.M.1    Westerhoff, H.V.2    Opperdoes, F.R.3
  • 9
    • 33645079892 scopus 로고    scopus 로고
    • An integrated biological approach to nuclear receptor signaling in physiological control and disease
    • Carlberg, C. & Dunlop, T.W. (2006) An integrated biological approach to nuclear receptor signaling in physiological control and disease. Critical Reviews in Eukaryotic Gene Expression 16, 1-22.
    • (2006) Critical Reviews in Eukaryotic Gene Expression , vol.16 , pp. 1-22
    • Carlberg, C.1    Dunlop, T.W.2
  • 10
    • 15944375811 scopus 로고    scopus 로고
    • Modular kinetic analysis of the adenine nucleotide translocator-mediated effects of palmitoyl-CoA on the oxidative phosphorylation in isolated rat liver mitochondria
    • Ciapaite, J., Van Eikenhorst, G., Bakker, B.M., et al. (2005) Modular kinetic analysis of the adenine nucleotide translocator-mediated effects of palmitoyl-CoA on the oxidative phosphorylation in isolated rat liver mitochondria. Diabetes 54, 944-951.
    • (2005) Diabetes , vol.54 , pp. 944-951
    • Ciapaite, J.1    Van Eikenhorst, G.2    Bakker, B.M.3
  • 11
    • 33644895955 scopus 로고    scopus 로고
    • Vitamin D signaling is modulated on multiple levels in health and disease
    • Ebert, R., Schutze, N., Adamski, J., et al. (2006) Vitamin D signaling is modulated on multiple levels in health and disease. Molecular and Cellular Endocrinology 248, 149-159.
    • (2006) Molecular and Cellular Endocrinology 2 , vol.48 , pp. 149-159
    • Ebert, R.1    Schutze, N.2    Adamski, J.3
  • 12
    • 0036707623 scopus 로고    scopus 로고
    • Glucocorticoid-mediated induction of CYP3A4 is decreased by disruption of a protein:DNAinteraction distinct from the pregnane X receptor response element
    • El-Sankary,W., Bombail, V., Gibson, G.G., et al. (2002) Glucocorticoid-mediated induction of CYP3A4 is decreased by disruption of a protein:DNAinteraction distinct from the pregnane X receptor response element. Drug Metabolism and Disposition 30, 1029-1034.
    • (2002) Drug Metabolism and Disposition , vol.30 , pp. 1029-1034
    • El-Sankary, W.1    Bombail, V.2    Gibson, G.G.3
  • 13
    • 0033764169 scopus 로고    scopus 로고
    • The small world of metabolism
    • Fell, D.A. & Wagner, A. (2000) The small world of metabolism. Nature Biotechnology 18, 1121-1122.
    • (2000) Nature Biotechnology , vol.18 , pp. 1121-1122
    • Fell, D.A.1    Wagner, A.2
  • 15
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgard, M. J., Swainston, N., Dobson, P., et al. (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. NatureBiotechnology 26, 1155-1160.
    • (2008) NatureBiotechnology , vol.26 , pp. 1155-1160
    • Herrgard, M.J.1    Swainston, N.2    Dobson, P.3
  • 17
    • 73949094856 scopus 로고    scopus 로고
    • Metabolic engineering of escherichia coli for the production of polylactic acid and its copolymers
    • Jung, Y.K., Kim, T.Y., Park, S.J., et al. (2010) Metabolic engineering of escherichia coli for the production of polylactic acid and its copolymers. Biotechnology and Bioengineering 105, 161-171.
    • (2010) Biotechnology and Bioengineering 1 , vol.5 , pp. 161-171
    • Jung, Y.K.1    Kim, T.Y.2    Park, S.J.3
  • 18
    • 58149159905 scopus 로고    scopus 로고
    • Network modeling of signal transduction: establishing the global view
    • Kestler, H.A., Wawra, C., Kracher, B., et al. (2008). Network modeling of signal transduction: establishing the global view. Bioessays 30, 1110-1125.
    • (2008) Bioessays , vol.30 , pp. 1110-1125
    • Kestler, H.A.1    Wawra, C.2    Kracher, B.3
  • 19
    • 68749116325 scopus 로고    scopus 로고
    • Systems biology and the virtual physiological human
    • doi:10.1038/msb.2009.51
    • Kohl, P. & Noble, D. (2009) Systems biology and the virtual physiological human. Molecular Systems Biology 5, 292. doi:10.1038/msb.2009.51.
    • (2009) Molecular Systems Biology , vol.5 , pp. 292
    • Kohl, P.1    Noble, D.2
  • 21
    • 33644877164 scopus 로고    scopus 로고
    • BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
    • Le Novere, N., Bornstein, B., Broicher, A., et al. (2006) BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34, D689-D691.
    • (2006) Nucleic Acids Research , vol.34 , pp. 689-691
    • Le Novere, N.1    Bornstein, B.2    Broicher, A.3
  • 25
    • 4544344218 scopus 로고    scopus 로고
    • Web-based kinetic modelling using JWS Online
    • B.G. & Snoep, J.L. (2004) Web-based kinetic modelling using JWS Online. Bioinformatics 20, 2143-2144.
    • (2004) Bioinformatics , vol.20 , pp. 2143-2144
    • Olivier, B.G.1    Snoep, J.L.2
  • 26
    • 14544299215 scopus 로고    scopus 로고
    • Mechanisms of receptor-mediated nuclear import and nuclear export
    • Pemberton, L.F.&Paschal, B.M. (2005) Mechanisms of receptor-mediated nuclear import and nuclear export. Traffic 6, 187-198.
    • (2005) Traffic , vol.6 , pp. 187-198
    • Pemberton, L.F.1    Paschal, B.M.2
  • 27
    • 71149103484 scopus 로고    scopus 로고
    • Modularity and design principles in the sea urchin embryo gene regulatory network
    • Peter, I.S. & Davidson, E.H. (2009) Modularity and design principles in the sea urchin embryo gene regulatory network. FEBS Letters 583, 3948-3958.
    • (2009) FEBS Letters , vol.583 , pp. 3948-3958
    • Peter, I.S.1    Davidson, E.H.2
  • 28
    • 65649105134 scopus 로고    scopus 로고
    • Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction
    • doi:10.1186/1752-0509-3-38
    • Raghunathan, A., Reed, J., Shin, S., et al. (2009) Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction. BMC Systems Biology 3, 38. doi:10.1186/1752-0509-3-38.
    • (2009) BMC Systems Biology , vol.3 , Issue.38
    • Raghunathan, A.1    Reed, J.2    Shin, S.3
  • 29
    • 9744248681 scopus 로고    scopus 로고
    • Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength
    • Reijenga, K.A., Van Megen, Y., Kooi, B.W., et al. (2005) Yeast glycolytic oscillations that are not controlled by a single oscillophore: a new definition of oscillophore strength. Journal of Theoretical Biology 232, 385-398.
    • (2005) Journal of Theoretical Biology , vol.232 , pp. 385-398
    • Reijenga, K.A.1    Van Megen, Y.2    Kooi, B.W.3
  • 30
    • 0034634571 scopus 로고    scopus 로고
    • Understanding glucose transport by the bacterial phosphoenolpyruvate: glycose phosphotransferase system on the basis of kinetic measurements in vitro
    • Rohwer, J.M., Meadow, N.D., Roseman, S., et al. (2000) Understanding glucose transport by the bacterial phosphoenolpyruvate: glycose phosphotransferase system on the basis of kinetic measurements in vitro. Journal of Biological Chemistry 275, 34909-34921.
    • (2000) Journal of Biological Chemistry 2 , vol.75 , pp. 34909-34921
    • Rohwer, J.M.1    Meadow, N.D.2    Roseman, S.3
  • 31
    • 0036036934 scopus 로고    scopus 로고
    • Java Web Simulation (JWS); a web based database of kinetic models
    • Snoep, J.L.&Olivier, B.G. (2002) Java Web Simulation (JWS); a web based database of kinetic models. Molecular Biology Reports 29, 259-263.
    • (2002) Molecular Biology Reports , vol.29 , pp. 259-263
    • Snoep, J.L.1    Olivier, B.G.2
  • 32
    • 33748291535 scopus 로고    scopus 로고
    • The dual role of 'emergence' in the philosophy of mind and in cognitive science
    • Stephan, A. (2006) The dual role of 'emergence' in the philosophy of mind and in cognitive science. Synthese 151, 485-498.
    • (2006) Synthese , vol.151 , pp. 485-498
    • Stephan, A.1
  • 34
    • 0030661628 scopus 로고    scopus 로고
    • Internal regulation of a modular system: the different faces of internal control
    • Van Der Gugten, A.A. &Westerhoff, H.V. (1997) Internal regulation of a modular system: the different faces of internal control. Biosystems 44, 79-106.
    • (1997) Biosystems , vol.44 , pp. 79-106
    • Van Der Gugten, A.A.1    Westerhoff, H.V.2
  • 35
    • 76749130738 scopus 로고    scopus 로고
    • For more protein, filet of cricket
    • Vogel, G. (2010) For more protein, filet of cricket. Science 327, 811.
    • (2010) Science , vol.327 , pp. 811
    • Vogel, G.1
  • 39
    • 0023385129 scopus 로고
    • Matrix-method for determining stepsmost rate-limiting to metabolic fluxes in biotechnological processes
    • Westerhoff, H.V.&Kell, D.B. (1987) Matrix-method for determining stepsmost rate-limiting to metabolic fluxes in biotechnological processes. Biotechnology and Bioengineering 30, 101-107.
    • (1987) Biotechnology and Bioengineering , vol.30 , pp. 101-107
    • Westerhoff, H.V.1    Kell, D.B.2
  • 40
    • 62049085905 scopus 로고    scopus 로고
    • Systems biology towards life in silico: mathematics of the control of living cells
    • Westerhoff, H.V., Kolodkin, A., Conradie, R., et al. (2009) Systems biology towards life in silico: mathematics of the control of living cells. Journal of Mathematical Biology 58, 7-34.
    • (2009) Journal of Mathematical Biology , vol.58 , pp. 7-34
    • Westerhoff, H.V.1    Kolodkin, A.2    Conradie, R.3
  • 41
    • 5044227742 scopus 로고    scopus 로고
    • The evolution of molecular biology into systems biology
    • Westerhoff, H.V. & Palsson, B.O. (2004) The evolution of molecular biology into systems biology. Nature Biotechnology 22, 1249-1252.
    • (2004) Nature Biotechnology , vol.22 , pp. 1249-1252
    • Westerhoff, H.V.1    Palsson, B.O.2
  • 42
    • 34249660479 scopus 로고    scopus 로고
    • Design explanation: determining the constraints on what can be alive
    • Wouters, A.G. (2007) Design explanation: determining the constraints on what can be alive. Erkenntnis 67, 65-80.
    • (2007) Erkenntnis , vol.67 , pp. 65-80
    • Wouters, A.G.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.