메뉴 건너뛰기




Volumn 53, Issue SPECIAL ISSUE, 2008, Pages 215-229

Temporal logic analysis of gene networks under parameter uncertainty

Author keywords

Discrete abstraction; Genetic regulatory network; Model checking; Piecewisemultiaffine (PMA) system; Synthetic biology

Indexed keywords

ABSTRACT SYSTEMS; ABSTRACTION PROCESS; BIOLOGICAL PARAMETER; DISCRETE ABSTRACTION; DYNAMICAL PROPERTIES; E. COLI; GENE NETWORKS; GENETIC REGULATORY NETWORKS; LIVENESS PROPERTIES; NUMERICAL INFORMATION; PARAMETER SET; PARAMETER SPACES; PARAMETER UNCERTAINTY; PARAMETER VALUES; PIECE-WISE; SYNTHETIC BIOLOGY; SYNTHETIC NETWORKS; TRANSIENT REGION; UNCERTAIN PARAMETERS; GENETIC REGULATORY NETWORK; PIECEWISE-MULTIAFFINE SYSTEM;

EID: 39849098741     PISSN: 00189286     EISSN: None     Source Type: Journal    
DOI: 10.1109/TAC.2007.911330     Document Type: Article
Times cited : (59)

References (53)
  • 1
    • 34548804054 scopus 로고    scopus 로고
    • Model checking genetic regulatory networks with parameter uncertainty
    • ser. Lecture Notes in Computer Science, A. Bemporad, A. Bicchi, and G. Buttazzo, Eds. New York: Springer
    • G. Batt, C. Belta, and R. Weiss, "Model checking genetic regulatory networks with parameter uncertainty," in Proceedings of the Tenth International Workshop Hybrid Systems: Computation and Control, ser. Lecture Notes in Computer Science, A. Bemporad, A. Bicchi, and G. Buttazzo, Eds. New York: Springer, 2007, vol.4416, pp. 61-75.
    • (2007) Proceedings of the Tenth International Workshop Hybrid Systems: Computation and Control , vol.4416 , pp. 61-75
    • Batt, G.1    Belta, C.2    Weiss, R.3
  • 3
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: A brief overview
    • H. Kitano, "Systems biology: A brief overview," Science, vol. 295, no. 5560, pp. 1662-1664, 2002.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1662-1664
    • Kitano, H.1
  • 4
    • 33745454125 scopus 로고    scopus 로고
    • Synthetic biology: New engineering rules for an emerging discipline
    • E. Andrianantoandro, S. Basu, D. Karig, and R. Weiss, "Synthetic biology: New engineering rules for an emerging discipline," Mol. Syst. Biol., vol.2, p. 28, 2006.
    • (2006) Mol. Syst. Biol. , vol.2 , pp. 28
    • Andrianantoandro, E.1    Basu, S.2    Karig, D.3    Weiss, R.4
  • 6
    • 33845459947 scopus 로고    scopus 로고
    • Qualitative approaches to the analysis of genetic regulatory networks
    • Z. Szallasi, J. Stelling, and V. Periwal, Eds. Cambridge, MA: MIT Press
    • H. de Jong and D. Ropers, "Qualitative approaches to the analysis of genetic regulatory networks," in System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, Z. Szallasi, J. Stelling, and V. Periwal, Eds. Cambridge, MA: MIT Press, 2006, pp. 125-148.
    • (2006) System Modeling in Cellular Biology: From Concepts to Nuts and Bolts , pp. 125-148
    • De Jong, H.1    Ropers, D.2
  • 7
    • 37149035291 scopus 로고    scopus 로고
    • Controlling a class of nonlinear systems on rectangles
    • Nov.
    • C. Belta and L. C. G. J. M. Habets, "Controlling a class of nonlinear systems on rectangles," IEEE Trans. Autom. Control, vol. 51, no. 11, pp. 1749-1759, Nov. 2006.
    • (2006) IEEE Trans. Autom. Control , vol.51 , Issue.11 , pp. 1749-1759
    • Belta, C.1    L.Habets, C.G.J.M.2
  • 8
    • 0000333926 scopus 로고    scopus 로고
    • Discrete abstractions of hybrid systems
    • Jul.
    • R. Alur, T.A. Henzinger,G. Lafferriere, and G. J. Pappas, "Discrete abstractions of hybrid systems," Proc. IEEE, vol. 88, no. 7, pp. 971-984, Jul. 2000.
    • (2000) Proc. IEEE , vol.88 , Issue.7 , pp. 971-984
    • Alur, R.1    Henzinger, T.A.2    Lafferriere, G.3    Pappas, G.J.4
  • 11
    • 0035135204 scopus 로고    scopus 로고
    • Analysis of timed systems using time-abstracting bisimulations
    • S. Tripakis and S. Yovine, "Analysis of timed systems using time-abstracting bisimulations," Form. Method Syst. Des., vol. 18, no. 1, pp. 25-68, 2001.
    • (2001) Form. Method Syst. Des. , vol.18 , Issue.1 , pp. 25-68
    • Tripakis, S.1    Yovine, S.2
  • 12
    • 0023558367 scopus 로고
    • Recognizing safety and liveness
    • B. Alpern and F. B. Schneider, "Recognizing safety and liveness," Distrib. Computing, vol. 2, no. 3, pp. 117-126, 1986.
    • (1986) Distrib. Computing , vol.2 , Issue.3 , pp. 117-126
    • Alpern, B.1    Schneider, F.B.2
  • 13
    • 84945924340 scopus 로고
    • Concurrency and automata on infinite sequences
    • ser. Lecture Notes in Computer Science, P. Deussen, Ed. New York: Springer
    • D. Park, "Concurrency and automata on infinite sequences," in Proceedings of the Fifth GI Conference on Theoretical Computer Science, ser. Lecture Notes in Computer Science, P. Deussen, Ed. New York: Springer, 1981, vol.104, pp. 167-183.
    • (1981) Proceedings of the Fifth GI Conference on Theoretical Computer Science , vol.104 , pp. 167-183
    • Park, D.1
  • 14
    • 0001449325 scopus 로고
    • Temporal and modal logic
    • J. van Leeuwen, Ed. Cambridge, MA: MIT Press, Formal Models and Sematics
    • E. A. Emerson, "Temporal and modal logic," in Handbook of Theoretical Computer Science, J. van Leeuwen, Ed. Cambridge, MA: MIT Press, 1990, vol.B, Formal Models and Sematics, pp. 995-1072.
    • (1990) Handbook of Theoretical Computer Science , vol.B , pp. 995-1072
    • Emerson, E.A.1
  • 15
    • 0024035719 scopus 로고
    • Characterizing finite Kripke structures in propositional temporal logic
    • M. C. Browne, E. M. Clarke, and O. Grumberg, "Characterizing finite Kripke structures in propositional temporal logic," Theoret. Comput. Sci., vol.59, pp. 115-131, 1988.
    • (1988) Theoret. Comput. Sci. , vol.59 , pp. 115-131
    • Browne, M.C.1    Clarke, E.M.2    Grumberg, O.3
  • 16
    • 33745700843 scopus 로고    scopus 로고
    • Reachability and control synthesis for piecewise-affine hybrid systems on simplices
    • Jun.
    • L. C. G. J. M. Habets, P. J. Collins, and J. H. van Schuppen, "Reachability and control synthesis for piecewise-affine hybrid systems on simplices," IEEE Trans. Autom. Control, vol. 51, no. 6, pp. 938-948, Jun. 2006.
    • (2006) IEEE Trans. Autom. Control , vol.51 , Issue.6 , pp. 938-948
    • L.Habets, C.G.J.M.1    Collins, P.J.2    Van Schuppen, J.H.3
  • 17
    • 1242333310 scopus 로고    scopus 로고
    • Qualitative simulation of genetic regulatory networks using piecewise-linear models
    • H. de Jong, J.-L. Gouzé, C. Hernandez, M. Page, T. Sari, and J. Geiselmann, "Qualitative simulation of genetic regulatory networks using piecewise-linear models," Bull. Math. Biol., vol. 66, no. 2, pp. 301-340, 2004.
    • (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
  • 21
    • 0028844979 scopus 로고
    • A mathematical framework for describing and analysing gene regulatory networks
    • T. Mestl, E. Plahte, and S. W. Omholt, "A mathematical framework for describing and analysing gene regulatory networks," J. Theor. Biol., vol. 176, no. 2, pp. 291-300, 1995.
    • (1995) J. Theor. Biol. , vol.176 , Issue.2 , pp. 291-300
    • Mestl, T.1    Plahte, E.2    Omholt, S.W.3
  • 22
    • 0015609281 scopus 로고
    • The logical analysis of continuous nonlinear biochemical control networks
    • L. Glass and S. A. Kauffman, "The logical analysis of continuous nonlinear biochemical control networks," J. Theor. Biol., vol. 39, no. 1, pp. 103-129, 1973.
    • (1973) J. Theor. Biol. , vol.39 , Issue.1 , pp. 103-129
    • Glass, L.1    Kauffman, S.A.2
  • 23
    • 0014671878 scopus 로고
    • Homeostasis and differentiation in random genetic control networks
    • S. A. Kauffman, "Homeostasis and differentiation in random genetic control networks," Nature, vol.224, pp. 177-178, 1969.
    • (1969) Nature , vol.224 , pp. 177-178
    • Kauffman, S.A.1
  • 24
    • 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
    • R. Thomas, D. Thieffry, and M. Kaufman, "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., vol. 57, no. 2, pp. 247-276, 1995.
    • (1995) Bull. Math. Biol. , vol.57 , Issue.2 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufman, M.3
  • 25
    • 0013823048 scopus 로고
    • Oscillatory behavior in enzymatic control processes
    • G. Weber, Ed. Oxford, U.K.: Pergamon
    • B. C. Goodwin, "Oscillatory behavior in enzymatic control processes," in Advances in Enzyme Regulation, G. Weber, Ed. Oxford, U.K.: Pergamon, 1965, pp. 425-438.
    • (1965) Advances in Enzyme Regulation , pp. 425-438
    • Goodwin, B.C.1
  • 26
    • 0014974440 scopus 로고
    • On the relation between effector concentration and the rate of induced enzyme synthesis
    • G. Yagil and E. Yagil, "On the relation between effector concentration and the rate of induced enzyme synthesis," Biophys. J., vol. 11, no. 1, pp. 11-27, 1971.
    • (1971) Biophys. J. , vol.11 , Issue.1 , pp. 11-27
    • Yagil, G.1    Yagil, E.2
  • 27
    • 33745787278 scopus 로고    scopus 로고
    • Reachability analysis of multiaffine systems
    • ser. Lecture Notes in Computer Science, J. P. Hespanha and A. Tiwari, Eds. New York: Springer
    • M. Kloetzer and C. Belta, "Reachability analysis of multiaffine systems," in Proceedings of the Ninth International Workshop on Hybrid Systems : Computational Control, ser. Lecture Notes in Computer Science, J. P. Hespanha and A. Tiwari, Eds. New York: Springer, 2006, vol.3927, pp. 348-362.
    • (2006) Proceedings of the Ninth International Workshop on Hybrid Systems : Computational Control , vol.3927 , pp. 348-362
    • Kloetzer, M.1    Belta, C.2
  • 28
    • 21144455474 scopus 로고    scopus 로고
    • Progress on reachability analysis of hybrid systems using predicate abstraction
    • ser. Lecture Notes in Computer Science, A. Pnueli and O. Maler, Eds. New York: Springer
    • R. Alur, T. Dang, and F. Ivancic, "Progress on reachability analysis of hybrid systems using predicate abstraction," in Proceedings of the Sixth International Workshop on Hybrid Systems : Computational Control, ser. Lecture Notes in Computer Science, A. Pnueli and O. Maler, Eds. New York: Springer, 2003, vol.2623, pp. 4-19.
    • (2003) Proceedings of the Sixth InternationalWorkshop on Hybrid Systems : Computational Control , vol.2623 , pp. 4-19
    • Alur, R.1    Dang, T.2    Ivancic, F.3
  • 29
    • 0038036084 scopus 로고    scopus 로고
    • Safety and reachability of piecewise linear hybrid dynamical systems based on discrete abstractions
    • X. D. Koutsoukos and P. J. Antsaklis, "Safety and reachability of piecewise linear hybrid dynamical systems based on discrete abstractions," J. Discr. Event Dynam. Syst., vol. 13, no. 3, pp. 203-243, 2003.
    • (2003) J. Discr. Event Dynam. Syst. , vol.13 , Issue.3 , pp. 203-243
    • Koutsoukos, X.D.1    Antsaklis, P.J.2
  • 30
    • 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
    • DOI 10.1093/bioinformatics/bti1048
    • G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, and D. Schneider, "Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli," Bioinformatics, vol. 21, no. suppl. 1, pp. i19-i28, 2005. (Pubitemid 41794471)
    • (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
  • 31
    • 33947108848 scopus 로고    scopus 로고
    • TCTL inevitability analysis of dense-time systems: From theory to engineering
    • F. Wang, G.-D. Huang, and F. Yu, "TCTL inevitability analysis of dense-time systems: From theory to engineering," IEEE Trans. Softw. Eng., vol. 32, no. 7, pp. 510-526, 2006.
    • (2006) IEEE Trans. Softw. Eng. , vol.32 , Issue.7 , pp. 510-526
    • Wang, F.1    Huang, G.-D.2    Yu, F.3
  • 34
    • 33646407491 scopus 로고    scopus 로고
    • A heuristic for the automatic generation of ranking functions
    • ser. Lecture Notes in Computer Science, G. Gopalakrishnan, Ed. New York: Springer
    • D. Dams, R. Gerth, and O. Grumberg, "A heuristic for the automatic generation of ranking functions," in Proceedings of the Workshop on Advances in Verification, ser. Lecture Notes in Computer Science, G. Gopalakrishnan, Ed. New York: Springer, 2000, pp. 1-8.
    • (2000) Proceedings of the Workshop on Advances in Verification , pp. 1-8
    • Dams, D.1    Gerth, R.2    Grumberg, O.3
  • 38
    • 39849107429 scopus 로고    scopus 로고
    • Stanford Univ., Stanford, CA [Online]. Available
    • D. Gleich, "Matlab Boost Graph Library (MatlabBGL)," Stanford Univ., Stanford, CA, 2006 [Online]. Available: http://www.stanford.edu/~dgleich/ programs/matlab-bgl/
    • (2006) Matlab Boost Graph Library (MatlabBGL)
    • Gleich, D.1
  • 40
    • 14844358192 scopus 로고    scopus 로고
    • Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
    • S. Hooshangi, S. Thiberge, and R. Weiss, "Ultrasensitivity and noise propagation in a synthetic transcriptional cascade," Proc. Natl. Acad. Sci. USA, vol. 102, no. 10, pp. 3581-3586, 2005.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.10 , pp. 3581-3586
    • Hooshangi, S.1    Thiberge, S.2    Weiss, R.3
  • 41
    • 34548747486 scopus 로고    scopus 로고
    • Robustness analysis and tuning of synthetic gene networks
    • G. Batt, B. Yordanov, R.Weiss, and C. Belta, "Robustness analysis and tuning of synthetic gene networks," Bioinformatics, vol. 23, no. 18, pp. 2415-2422, 2007.
    • (2007) Bioinformatics , vol.23 , Issue.18 , pp. 2415-2422
    • Batt, G.1    Yordanov, B.2    Weiss, R.3    Belta, C.4
  • 42
    • 31444433490 scopus 로고    scopus 로고
    • Synthetic promoter libraries - Tuning of gene expression
    • K. Hammer, I. Mijakovic, and P. R. Jensen, "Synthetic promoter libraries - Tuning of gene expression," Trends Biotechnol., vol. 24, no. 2, pp. 53-55, 2006.
    • (2006) Trends Biotechnol. , vol.24 , Issue.2 , pp. 53-55
    • Hammer, K.1    Mijakovic, I.2    Jensen, P.R.3
  • 43
    • 2342578714 scopus 로고    scopus 로고
    • Spatiotemporal control of gene expression with pulse-generating networks
    • S. Basu, R. Mehreja, S. Thiberge, M.-T. Chen, and R. Weiss, "Spatiotemporal control of gene expression with pulse-generating networks," Proc. Natl. Acad. Sci. USA, vol. 101, no. 17, pp. 6355-6360, 2004.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.17 , pp. 6355-6360
    • Basu, S.1    Mehreja, R.2    Thiberge, S.3    Chen, M.-T.4    Weiss, R.5
  • 44
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • H. de Jong, "Modeling and simulation of genetic regulatory systems: A literature review," J. Computat. Biol., vol. 9, no. 1, pp. 69-105, 2002.
    • (2002) J. Computat. Biol. , vol.9 , Issue.1 , pp. 69-105
    • De Jong, H.1
  • 46
    • 84944407299 scopus 로고    scopus 로고
    • Symbolic techniques for parametric reasoning about counter and clock systems
    • ser. Lecture Notes in Computer Science, E. A. Emerson and A. P. Sistla, Eds. New York: Springer
    • A. Annichini, E. Asarin, and A. Bouajjani, "Symbolic techniques for parametric reasoning about counter and clock systems," in Proceedings of the Twelfth International Conference on Computer-Aided Verification, ser. Lecture Notes in Computer Science, E. A. Emerson and A. P. Sistla, Eds. New York: Springer, 2000, vol.1855, pp. 419-434.
    • (2000) Proceedings of the Twelfth International Conference on Computer-Aided Verification , vol.1855 , pp. 419-434
    • Annichini, A.1    Asarin, E.2    Bouajjani, A.3
  • 47
    • 17644425262 scopus 로고    scopus 로고
    • Symbolic parametric safety analysis of linear hybrid systems with BDD-like data-structures
    • Jan.
    • F.Wang, "Symbolic parametric safety analysis of linear hybrid systems with BDD-like data-structures," IEEE Trans. Softw. Eng., vol. 31, no. 1, pp. 38-51, Jan. 2005.
    • (2005) IEEE Trans. Softw. Eng. , vol.31 , Issue.1 , pp. 38-51
    • Wang, F.1
  • 49
    • 14344265954 scopus 로고    scopus 로고
    • Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling
    • R. Ghosh and C. J. Tomlin, "Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling," Proc. IEE Syst. Biol., vol. 1, no. 1, pp. 170-183, 2004.
    • (2004) Proc. IEE Syst. Biol. , vol.1 , Issue.1 , pp. 170-183
    • Ghosh, R.1    Tomlin, C.J.2
  • 50
    • 3042693879 scopus 로고    scopus 로고
    • Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic
    • G. Bernot, J.-P. Comet, A. Richard, and J. Guespin, "Application of formal methods to biological regulatory networks: Extending Thomas' asynchronous logical approach with temporal logic," J. Theor. Biol., vol. 229, no. 3, pp. 339-347, 2004.
    • (2004) J. Theor. Biol. , vol.229 , Issue.3 , pp. 339-347
    • Bernot, G.1    Comet, J.-P.2    Richard, A.3    Guespin, J.4
  • 52
    • 8744267839 scopus 로고    scopus 로고
    • Robust regulation of polytopic uncertain linear hybrid systems with networked control system applications
    • P. J. Antsaklis and D. Liu, Eds. Basel, Switzerland: Birkhauser
    • H. Lin and P. J. Antsaklis, "Robust regulation of polytopic uncertain linear hybrid systems with networked control system applications," in Stability and Control of Dynamical Systems with Applications, P. J. Antsaklis and D. Liu, Eds. Basel, Switzerland: Birkhauser, 2003.
    • (2003) Stability and Control of Dynamical Systems with Applications
    • Lin, H.1    Antsaklis, P.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.