Model checking genetic regulatory networks with parameter uncertainty

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4416 LNCS, Issue , 2007, Pages 61-75

  Batt, Grégory ^a   Belta, Calin ^a   Weiss, Ron ^b  

^a Boston University   (United States)

^b Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENTIAL EQUATIONS; MATHEMATICAL MODELS; MODEL CHECKING; PROBLEM SOLVING; TEMPORAL LOGIC;

DISCRETE ABSTRACTIONS; GENETIC REGULATORY NETWORKS; PARAMETER SPACE; PARAMETER UNCERTAINTY;

UNCERTAINTY ANALYSIS;

EID: 34548804054     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-71493-4_8     Document Type: Conference Paper

References (27)

1. Kitano, H.: Systems biology: A brief overview. Science 295(5560) (2002) 1662-1664
2. Andrianantoandro, E., Basu, S., Karig, D., Weiss, R.: Synthetic biology: New engineering rules for an emerging discipline. Mol. Syst. Biol. (2006)
3. Szallasi, Z., Stelling, J., Periwal, V., eds.: System Modeling in Cellular Biology: From Concepts to Nuts and Bolts. MIT Press (2006)
4. de Jong, H., Ropers, D.: Qualitative approaches to the analysis of genetic regulatory networks. In [3] (2006) 125-148
5. Belta, C., Habets, L.C.G. J.M.: Controlling a class of nonlinear systems on rectangles. IEEE Trans. Aut. Control 51(11) (2006) 1749-1759
6. Alur, R., Henzinger, T.A., Lafferriere, G., Pappas, G.J.; Discrete abstractions of hybrid systems. Proc, IEEE 88(7) (2000) 971-984
7. Clarke, E.M., Grumberg, O., Peled, D.A.: Model Checking. MIT Press (1999)
8. Batt, G., Belta, C.: Model checking genetic regulatory networks with applications to synthetic biology. CISE Tech. Rep. 2006-IR-0030, Boston University (2006)
9. de Jong, H., Gouzé, J.-L., Hernandez, C., Page, M., Sari, T., Geiselmann, J.: Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull. Math. Biol. 66(2) (2004) 301-340
10. Abate, A., Tiwari, A.: Box invariance of hybrid and switched systems. In: Proc. ADHS'06. (2006)
11. Belta, C., Habets, L.C.G.J.M., Kumar, V.: Control of multi-affine systems on rectangles with applications to hybrid biomolecular networks. In: Proc. CDC'02. (2002)
12. Mestl, T., Plahte, E., Omholt, S.: A mathematical framework for describing and analysing gene regulatory networks. J. Theor. Biol. 176 (1995) 291-300
13. Glass, L., Kauffman, S.: The logical analysis of continuous non-linear biochemical control networks. J. Theor. Biol. 39(1) (1973) 103-129
14. Kloetzer, M., Belta, C.: Reachability analysis of multi-affine systems. In Hespanha, J., Tiwari, A., eds.: Proc. HSCC'06. LNCS 3927, Springer (2006) 348-362
15. Alur, R., Dang, T., Ivanèic, F.: Progress on reachability analysis of hybrid systems using predicate abstraction. In Pnueli, A., Maler, O., eds.: Proc. HSCC'03. LNCS 2623, Springer (2003) 4-19
16. Koutsoukos, X., Antsaklis, P.J.: Safety and reachability of piecewise linear hybrid dynamical systems based on discrete abstractions. J. Discrete Event Dynamic Systems 13(3) (2003) 203-243
17. Batt, G., Ropers, D., de Jong, H., Geiselmann, J., Mateescu, R., Page, M., Schneider, D.: Validation of qualitative models of genetic regulatory networks by model checking : Analysis of the nutritional stress response in E. coli. Bioinformatics 21(Suppl.l) (2005) i19-i28
18. Batt, G., Belta, C., Weiss, R.: Model checking liveness properties of genetic regulatory networks. To appear in Grumberg, O., Huth, M., eds.: Proc. TACAS'07. LNCS, Springer (2007)
19. Hooshangi, S., Thiberge, S., Weiss, R.: Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. USA 102(10) (2005) 3581-3586
20. Annichini, A., Asarin, E., Bouajjani, A.: Symbolic techniques for parametric reasoning about counter and clock systems. In Emerson, E., Sistla, A., eds.: Proc. CAV'OO. LNCS 1855, Springer (2000) 419-434
21. Wang, F.: Symbolic parametric safety analysis of linear hybrid systems with BDDlike data-structures. IEEE Trans. Softw. Eng. 31(1) (2005) 38-51
22. Henzinger, T., Ho, P.-H., Wong-Toi, H.: HYTECH: A model checker for hybrid systems. Software Tools Technology Transfer 1(1-2) (1997) 110-122
23. Ghosh, R., Tomlin, C.J.: Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling. IEE Proc. Syst. Biol. 1(1) (2004) 170-183
24. Lin, H., Antsaklis, P.J.: Robust regulation of polytopic uncertain linear hybrid systems with networked control system applications. In Antsaklis, P., Liu, D., eds.: Stability and Control of Dynamical Systems with Applications. Birkhauser (2003)
25. Antoniotti, M., Piazza, C., Policriti, A., Simeoni, M., Mishra, B.: Taming the complexity of biochemical models through bisimulation and collapsing: Theory and practice. Theor. Comput. Sci. 325(1) (2004) 45-67
26. Calzone, L., Chabrier-Rivier, N., Fages, F., Soliman, S.: Machine learning biochemical networks from temporal logic properties. In Priami, C., Plotkin, G., eds: Trans. Comput. Syst. Biol. VI. LNBI 4220, Springer (2006) 68-94
27. Bernot, G., Comet, J.-P., Richard, A., 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