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Volumn 255, Issue 3, 2008, Pages 269-277

The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model

Author keywords

Boolean networks; Cell cycle; Computer simulations; Differential equations; Fission yeast; Gene regulatory networks

Indexed keywords

COMPUTER SIMULATION; CYTOLOGY; ECOLOGICAL MODELING; EQUATION; LIFE CYCLE; NUMERICAL METHOD; YEAST;

EID: 55549143637     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.07.020     Document Type: Article
Times cited : (90)

References (31)
  • 1
    • 33748846734 scopus 로고    scopus 로고
    • Aguda, D.B., 2006. Modeling the Cell Division Cycle, Lecture Notes in Mathematics, vol. 1872, Springer, Berlin, pp. 1-22.
    • Aguda, D.B., 2006. Modeling the Cell Division Cycle, Lecture Notes in Mathematics, vol. 1872, Springer, Berlin, pp. 1-22.
  • 2
    • 0037686112 scopus 로고    scopus 로고
    • The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes
    • 10.1016/S0022-5193(03)00035-3
    • Albert R., and Othmer H.G. The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes. J. Theor. Biol. 223 (2003) 1-18 10.1016/S0022-5193(03)00035-3
    • (2003) J. Theor. Biol. , vol.223 , pp. 1-18
    • Albert, R.1    Othmer, H.G.2
  • 3
    • 27144450537 scopus 로고    scopus 로고
    • Systems biology: less is more in modeling large genetic networks
    • Bornholdt S. Systems biology: less is more in modeling large genetic networks. Science 310 5747 (2005) 449-451
    • (2005) Science , vol.310 , Issue.5747 , pp. 449-451
    • Bornholdt, S.1
  • 4
    • 33947361606 scopus 로고    scopus 로고
    • Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity
    • 10.1016/j.jtbi.2006.11.012
    • Braunewell S., and Bornholdt S. Superstability of the yeast cell-cycle dynamics: ensuring causality in the presence of biochemical stochasticity. J. Theor. Biol. 245 4 (2006) 638-643 10.1016/j.jtbi.2006.11.012
    • (2006) J. Theor. Biol. , vol.245 , Issue.4 , pp. 638-643
    • Braunewell, S.1    Bornholdt, S.2
  • 6
    • 45849093636 scopus 로고    scopus 로고
    • Boolean network model predicts cell cycle sequence of fission yeast
    • Davidich M., and Bornholdt S. Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3 2 (2008) e1672
    • (2008) PLoS ONE , vol.3 , Issue.2
    • Davidich, M.1    Bornholdt, S.2
  • 7
    • 16644389406 scopus 로고    scopus 로고
    • A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles
    • Espinosa-Soto C., Padilla-Longoria P., and Alvarez-Buylla E.R. A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell 16 (2004) 2923-2939
    • (2004) Plant Cell , vol.16 , pp. 2923-2939
    • Espinosa-Soto, C.1    Padilla-Longoria, P.2    Alvarez-Buylla, E.R.3
  • 8
    • 33747874092 scopus 로고    scopus 로고
    • Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
    • Faure A., Naldi A., Chaouiya C., and Thieffry D. Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics 22 14 (2006) e124-e131
    • (2006) Bioinformatics , vol.22 , Issue.14
    • Faure, A.1    Naldi, A.2    Chaouiya, C.3    Thieffry, D.4
  • 9
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie D.T. A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comp. Phys. 22 (1976) 403-434
    • (1976) J. Comp. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 10
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340-2361
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 11
    • 0032520557 scopus 로고    scopus 로고
    • Ordered and disordered dynamics in random networks
    • Glass L., and Hill C. Ordered and disordered dynamics in random networks. Europhys. Lett. 41 6 (1998) 599-604
    • (1998) Europhys. Lett. , vol.41 , Issue.6 , pp. 599-604
    • Glass, L.1    Hill, C.2
  • 12
    • 0015609281 scopus 로고
    • The logical analysis of continuous, nonlinear biochemical control networks
    • 10.1016/0022-5193(73)90208-7
    • Glass L., and Kauffman S.A. The logical analysis of continuous, nonlinear biochemical control networks. J. Theor. Biol. 39 (1973) 103-129 10.1016/0022-5193(73)90208-7
    • (1973) J. Theor. Biol. , vol.39 , pp. 103-129
    • Glass, L.1    Kauffman, S.A.2
  • 13
    • 0001424903 scopus 로고
    • An amplified sensitivity arising from covalent modification in biological systems
    • Goldbeter A., and Koshland D.E. An amplified sensitivity arising from covalent modification in biological systems. Proc. Natl. Acad. Sci. USA 78 (1981) 6840-6844
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 6840-6844
    • Goldbeter, A.1    Koshland, D.E.2
  • 14
    • 23844494458 scopus 로고    scopus 로고
    • Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis
    • Gunsalus K.C., Ge H., Schetter A.J., Goldberg D.S., Han J.-D.J., et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436 11 (2005) 861-865
    • (2005) Nature , vol.436 , Issue.11 , pp. 861-865
    • Gunsalus, K.C.1    Ge, H.2    Schetter, A.J.3    Goldberg, D.S.4    Han, J.-D.J.5
  • 15
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • 10.1016/0022-5193(69)90015-0
    • Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22 (1969) 437-467 10.1016/0022-5193(69)90015-0
    • (1969) J. Theor. Biol. , vol.22 , pp. 437-467
    • Kauffman, S.A.1
  • 16
    • 1842687878 scopus 로고    scopus 로고
    • The yeast cell-cycle network is robustly designed
    • Li F., Long T., Lu Y., Quyang Q., and Tang C. The yeast cell-cycle network is robustly designed. Proc. Natl. Acad. Sci. USA 101 14 (2004) 4781-4786
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.14 , pp. 4781-4786
    • Li, F.1    Long, T.2    Lu, Y.3    Quyang, Q.4    Tang, C.5
  • 17
    • 0032879544 scopus 로고    scopus 로고
    • Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis
    • Mendoza L., Thieffry D., and Alvarez-Buylla E.R. Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics 15 (1999) 593-606
    • (1999) Bioinformatics , vol.15 , pp. 593-606
    • Mendoza, L.1    Thieffry, D.2    Alvarez-Buylla, E.R.3
  • 18
    • 0027716813 scopus 로고
    • Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos
    • Novak B., and Tyson J.J. Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos. J. Cell Sci. 106 (1993) 1153-1168
    • (1993) J. Cell Sci. , vol.106 , pp. 1153-1168
    • Novak, B.1    Tyson, J.J.2
  • 19
    • 0030787863 scopus 로고    scopus 로고
    • Modeling the control of DNA replication in fission yeast. Cell biology
    • Novak B., and Tyson J.J. Modeling the control of DNA replication in fission yeast. Cell biology. Proc. Natl. Acad. Sci. USA 94 (1997) 9147-9152
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 9147-9152
    • Novak, B.1    Tyson, J.J.2
  • 20
    • 4444349425 scopus 로고    scopus 로고
    • A model for restriction point control of the mammalian cell cycle
    • 10.1016/j.jtbi.2004.04.039
    • Novak B., and Tyson J.J. A model for restriction point control of the mammalian cell cycle. J. Theor. Biol. 230 (2004) 563-579 10.1016/j.jtbi.2004.04.039
    • (2004) J. Theor. Biol. , vol.230 , pp. 563-579
    • Novak, B.1    Tyson, J.J.2
  • 21
    • 0035579883 scopus 로고    scopus 로고
    • Mathematical model of the cell division cycle of fission yeast
    • Novak B., Pataki Z., Ciliberto A., and Tyson J.J. Mathematical model of the cell division cycle of fission yeast. Chaos 11 1 (2001) 277-286
    • (2001) Chaos , vol.11 , Issue.1 , pp. 277-286
    • Novak, B.1    Pataki, Z.2    Ciliberto, A.3    Tyson, J.J.4
  • 22
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
    • Riel N.A.W. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Briefings Bioinformatics 7 4 (2006) 364-374
    • (2006) Briefings Bioinformatics , vol.7 , Issue.4 , pp. 364-374
    • Riel, N.A.W.1
  • 23
    • 0035928464 scopus 로고    scopus 로고
    • A logical analysis of the drosophila gap-gene system
    • 10.1006/jtbi.2001.2335
    • Sanchez L., and Thieffry D. A logical analysis of the drosophila gap-gene system. J. Theor. Biol. 211 (2001) 115-141 10.1006/jtbi.2001.2335
    • (2001) J. Theor. Biol. , vol.211 , pp. 115-141
    • Sanchez, L.1    Thieffry, D.2
  • 24
    • 0031583031 scopus 로고    scopus 로고
    • Establishement of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: a logical analysis
    • 10.1006/jtbi.1997.0523
    • Sanchez L., van Helden J., and Thieffry D. Establishement of the dorso-ventral pattern during embryonic development of Drosophila melanogaster: a logical analysis. J. Theor. Biol. 189 4 (1997) 377-389 10.1006/jtbi.1997.0523
    • (1997) J. Theor. Biol. , vol.189 , Issue.4 , pp. 377-389
    • Sanchez, L.1    van Helden, J.2    Thieffry, D.3
  • 25
    • 0034608810 scopus 로고    scopus 로고
    • Modeling the fission yeast cell cycle: quantized cycle times in wee1-cdc25 mutant cells
    • Sveiczer A., Csikasz-Nagy A., Gyorffy B., Tyson J.J., and Novak B. Modeling the fission yeast cell cycle: quantized cycle times in wee1-cdc25 mutant cells. Proc. Natl. Acad. Sci. USA 97 14 (2000) 7865-7870
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , Issue.14 , pp. 7865-7870
    • Sveiczer, A.1    Csikasz-Nagy, A.2    Gyorffy, B.3    Tyson, J.J.4    Novak, B.5
  • 26
    • 0015823097 scopus 로고
    • Boolean formalization of genetic control circuits
    • 10.1016/0022-5193(73)90247-6
    • Thomas R. Boolean formalization of genetic control circuits. J. Theor. Biol. 42 (1973) 563-585 10.1016/0022-5193(73)90247-6
    • (1973) J. Theor. Biol. , vol.42 , pp. 563-585
    • Thomas, R.1
  • 27
    • 0029267491 scopus 로고
    • Dynamical behaviour of biological regulatory networks. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
    • Thomas R., Thieffry D., and Kaufmann M. Dynamical behaviour of biological regulatory networks. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol. 57 2 (1995) 247-276
    • (1995) Bull. Math. Biol. , vol.57 , Issue.2 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufmann, M.3
  • 28
    • 0038460054 scopus 로고    scopus 로고
    • Light- and carbon-signaling pathways. Modeling circuits of interactions
    • Thum K.E., Shasha D.E., Lejay L.V., and Coruzzi G.M. Light- and carbon-signaling pathways. Modeling circuits of interactions. Plant Physiol. 132 (2003) 440-452
    • (2003) Plant Physiol. , vol.132 , pp. 440-452
    • Thum, K.E.1    Shasha, D.E.2    Lejay, L.V.3    Coruzzi, G.M.4
  • 30
    • 0036905483 scopus 로고    scopus 로고
    • The dynamics of the cell-cycle regulation
    • Tyson J.J., Csikasz-Nagy A., and Novak B. The dynamics of the cell-cycle regulation. BioEssays 24 (2002) 1095-1109
    • (2002) BioEssays , vol.24 , pp. 1095-1109
    • Tyson, J.J.1    Csikasz-Nagy, A.2    Novak, B.3
  • 31
    • 0037376655 scopus 로고    scopus 로고
    • Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
    • Tyson J.J., Chen K.C., and Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opinion Cell Biol. 15 (2003) 221-231
    • (2003) Curr. Opinion Cell Biol. , vol.15 , pp. 221-231
    • Tyson, J.J.1    Chen, K.C.2    Novak, B.3


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