메뉴 건너뛰기




Volumn 98, Issue 3, 2009, Pages 149-159

Temporal constraints of a gene regulatory network: Refining a qualitative simulation

Author keywords

Delay parameter synthesis; Escherichia coli; Gene regulatory network; Hybrid automaton; Model checking

Indexed keywords

CARBON;

EID: 71849105753     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biosystems.2009.05.002     Document Type: Article
Times cited : (15)

References (23)
  • 1
    • 47749089525 scopus 로고    scopus 로고
    • Parametric analysis and abstraction of genetic regulatory networks
    • Proceedings of the 2nd Workshop on Concurrent Models in Molecular Biology, BioCONCUR'04, Comp. Sci. Amsterdam, Elsevier
    • Adélaïde, M., Sutre, G., 2004. Parametric analysis and abstraction of genetic regulatory networks. In: Proceedings of the 2nd Workshop on Concurrent Models in Molecular Biology, BioCONCUR'04. Electronic Notes in Theor. Comp. Sci. Amsterdam, Elsevier.
    • (2004) Electronic Notes in Theor
    • Adélaïde, M.1    Sutre, G.2
  • 2
    • 36949019568 scopus 로고    scopus 로고
    • Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks With Delays
    • Karger Publisher
    • Ahmad, J., Bernot, G., Comet, J.-P., Lime, D., Roux, O., 2007. Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks With Delays. ComPlexUs, Karger Publisher, vol. 3, no. 4, pp. 231-251.
    • (2007) ComPlexUs , vol.3 , Issue.4 , pp. 231-251
    • Ahmad, J.1    Bernot, G.2    Comet, J.-P.3    Lime, D.4    Roux, O.5
  • 3
    • 0028413052 scopus 로고
    • A theory of timed automata
    • Alur R., and Dill D.L. A theory of timed automata. Theor. Comput. Sci. 126 (1994) 183-235
    • (1994) Theor. Comput. Sci. , vol.126 , pp. 183-235
    • Alur, R.1    Dill, D.L.2
  • 4
    • 0023430342 scopus 로고
    • Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli
    • Balke V., and Gralla J. Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli. J. Bacteriol. 169 10 (1987) 4499-4506
    • (1987) J. Bacteriol. , vol.169 , Issue.10 , pp. 4499-4506
    • Balke, V.1    Gralla, J.2
  • 5
    • 84860513120 scopus 로고    scopus 로고
    • Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli
    • Batt G., Ropers D., de Jong H., Geiselmann J., Mateescu R., Page M., and Schneider D. Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. Bioinformatics 21 Suppl. 1 (2005) i19-i28
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 1
    • Batt, G.1    Ropers, D.2    de Jong, H.3    Geiselmann, J.4    Mateescu, R.5    Page, M.6    Schneider, D.7
  • 6
    • 3042693879 scopus 로고    scopus 로고
    • Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic
    • Bernot G., Comet J.-P., Richard A., and Guespin J. Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. J. Theor. Biol. 229 3 (2004) 339-347
    • (2004) J. Theor. Biol. , vol.229 , Issue.3 , pp. 339-347
    • Bernot, G.1    Comet, J.-P.2    Richard, A.3    Guespin, J.4
  • 7
    • 0036069537 scopus 로고    scopus 로고
    • Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model
    • Chang D., Smalley D., and Conway T. Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model. Mol. Microbiol. 45 2 (2002) 289-306
    • (2002) Mol. Microbiol. , vol.45 , Issue.2 , pp. 289-306
    • Chang, D.1    Smalley, D.2    Conway, T.3
  • 8
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: a literature review
    • doi: 10.1089/10665270252833208
    • de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 1 (2002) 67-103 doi: 10.1089/10665270252833208
    • (2002) J. Comput. Biol. , vol.9 , Issue.1 , pp. 67-103
    • de Jong, H.1
  • 9
    • 1242333310 scopus 로고    scopus 로고
    • Qualitative simulation of genetic regulatory networks using piecewise-linear models
    • de Jong H., Gouzé J.L., Hernandez C., Page M., Sari T., and Geiselmann J. Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull. Math. Biol. 66 2 (2004) 301-340
    • (2004) Bull. Math. Biol. , vol.66 , Issue.2 , pp. 301-340
    • de Jong, H.1    Gouzé, J.L.2    Hernandez, C.3    Page, M.4    Sari, T.5    Geiselmann, J.6
  • 11
    • 0015609281 scopus 로고
    • The logical analysis of continuous non linear biochemical control networks
    • Glass L., and Kauffman S.A. The logical analysis of continuous non linear biochemical control networks. J. Theor. Biol. 1 39 (1973) 103-129
    • (1973) J. Theor. Biol. , vol.1 , Issue.39 , pp. 103-129
    • Glass, L.1    Kauffman, S.A.2
  • 12
    • 0036953237 scopus 로고    scopus 로고
    • DNA topology-mediated control of global gene expression in Escherichia coli
    • doi: 10.1146/annurev.genet.36.032902.111815
    • Hatfield G.W., and Benham C.J. DNA topology-mediated control of global gene expression in Escherichia coli. Annu. Rev. Genet. 36 (2002) 175-203 doi: 10.1146/annurev.genet.36.032902.111815
    • (2002) Annu. Rev. Genet. , vol.36 , pp. 175-203
    • Hatfield, G.W.1    Benham, C.J.2
  • 13
    • 84947944522 scopus 로고
    • Algorithmic analysis of nonlinear hybrid systems
    • CAV: Computer-Aided Verification, Springer, pp
    • Henzinger, T.A., Ho, P.-H., 1995. Algorithmic analysis of nonlinear hybrid systems. CAV: Computer-Aided Verification, Lecture Notes in Computer Science 939. Springer, pp. 225-238.
    • (1995) Lecture Notes in Computer Science , vol.939 , pp. 225-238
    • Henzinger, T.A.1    Ho, P.-H.2
  • 15
    • 33646377419 scopus 로고    scopus 로고
    • Qualitative simulation of the carbon starvation response in Escherichia coli
    • doi: 10.1016/j.biosystems.2005.10.005
    • Ropers D., de Jong H., Page M., Schneider D., and Geiselmann J. Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems 2 84 (2006) 124-152 doi: 10.1016/j.biosystems.2005.10.005
    • (2006) Biosystems , vol.2 , Issue.84 , pp. 124-152
    • Ropers, D.1    de Jong, H.2    Page, M.3    Schneider, D.4    Geiselmann, J.5
  • 16
    • 33845198572 scopus 로고    scopus 로고
    • Incorporating time delays into the logical analysis of gene regulatory networks
    • Computational Methods in Systems Biology, CMSB'06, Corrado Priami, Trento, Italy, Springer
    • Siebert, H., Bockmayr, A., 2006. Incorporating time delays into the logical analysis of gene regulatory networks. Computational Methods in Systems Biology, CMSB'06, Corrado Priami, Trento, Italy, Lecture Notes in Computer Science, Springer, vol. 4210, pp. 169-183.
    • (2006) Lecture Notes in Computer Science , vol.4210 , pp. 169-183
    • Siebert, H.1    Bockmayr, A.2
  • 17
    • 39049120743 scopus 로고    scopus 로고
    • Temporal constraints in the logical analysis of regulatory networks
    • Siebert H., and Bockmayr A. Temporal constraints in the logical analysis of regulatory networks. Theor. Comput. Sci. 391 3 (2008) 258-275
    • (2008) Theor. Comput. Sci. , vol.391 , Issue.3 , pp. 258-275
    • Siebert, H.1    Bockmayr, A.2
  • 18
    • 0024916497 scopus 로고
    • Qualitative dynamics of a piecewise-linear differential equations: a discrete mapping approach
    • Snoussi E.H. Qualitative dynamics of a piecewise-linear differential equations: a discrete mapping approach. Dyn. Stab. Syst. 4 3 & 4 (1989) 189-207
    • (1989) Dyn. Stab. Syst. , vol.4 , Issue.3-4 , pp. 189-207
    • Snoussi, E.H.1
  • 19
    • 0001723411 scopus 로고
    • Logical identification of all steady states: the concept of feedback loop characteristic states
    • Snoussi E.H., and Thomas R. Logical identification of all steady states: the concept of feedback loop characteristic states. Bull. Math. Biol. 55 5 (1993) 973-991
    • (1993) Bull. Math. Biol. , vol.55 , Issue.5 , pp. 973-991
    • Snoussi, E.H.1    Thomas, R.2
  • 20
    • 0025948178 scopus 로고
    • Regulatory networks seen as asynchronous automata: a logical description
    • Thomas R. Regulatory networks seen as asynchronous automata: a logical description. J. Theor. Biol. 153 (1991) 1-23
    • (1991) J. Theor. Biol. , vol.153 , pp. 1-23
    • Thomas, R.1
  • 22
    • 0029267491 scopus 로고
    • Dynamical behaviour of biological regulatory networks: I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
    • Thomas R., Thieffry D., and Kaufman M. Dynamical behaviour of biological regulatory networks: I. 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    Kaufman, M.3
  • 23
    • 0035082155 scopus 로고    scopus 로고
    • DNA supercoiling and transcription in Escherichia coli: the FIS connection
    • doi: 10.1016/S0300-9084(00)01217-7
    • Travers A., Schneider R., and Muskhelishvili G. DNA supercoiling and transcription in Escherichia coli: the FIS connection. Biochimie 2 (2001) 1213-1217 doi: 10.1016/S0300-9084(00)01217-7
    • (2001) Biochimie , vol.2 , pp. 1213-1217
    • Travers, A.1    Schneider, R.2    Muskhelishvili, G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.