Timed modelling of gene networks with arbitrarily precise expression discretization

Electronic Notes in Theoretical Computer Science

Volumn 293, Issue , 2013, Pages 67-81

  Van Goethem, S ^a   Jacquet, J M ^a   Brim, L ^b   Safranek D ^b  

^a UNIVERSITY OF NAMUR   (Belgium)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

Boolean logic; Discrete modeling; gene regulatory network; UPAAL

Indexed keywords

ACTIVITY LEVELS; BENCHMARK MODELS; BOOLEAN LOGIC; DISCRETE ABSTRACTION; DISCRETE MODELING; DISCRETIZATIONS; GENE REGULATORY NETWORKS; UPAAL;

AUTOMATA THEORY;

GENE EXPRESSION;

EID: 84875252085     PISSN: 15710661     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.entcs.2013.02.019     Document Type: Conference Paper

References (21)

1. E. Andréa, T. Chatain, L. Fribourg, and E. Encrenaz An inverse method for parametric timed automata Electron. Notes Theor. Comput. Sci. 223 2008 29 46
2. G. Batt, C. Belta, and R. Weiss Model checking liveness properties of genetic regulatory networks TACAS 2007 LNCS vol. 4424 2007 323 338
3. G. Batt, R.B. Salah, and O. Maler On timed models of gene networks Formal Modeling and Analysis of Timed Systems LNCS vol. 4763 2007 38 52
4. G. Behrmann, A. David, K.G. Larsen, O. Müller, P. Pettersson, and W. Yi Uppaal - Present and Future Proc. of 40th IEEE Conference on Decision and Control IEEE vol. 3 2001 2881 2886
5. G. Bernot, J.-P. Comet, A. Richard, and J. Guespin Application of formal methods to biological regulatory networks: Extending thomasE' asynchronous logical approach with temporal logic Journal of Theoretical Biology 229 2004 339 347
6. W. Bos, Interactive signaling network analysis tool, MasterE's thesis, University of Twente, 2009, URL http://essay.utwente.nl/59184/.
7. M. Bozga, S. Graf, I. Ober, I. Ober, and J. Sifakis The if toolset M. Bernardo, F. Corradini, Formal Methods for the Design of Real-Time Systems Lecture Notes in Computer Science vol. 3185 2004 Springer Berlin / Heidelberg 131 132
8. C. Chaouiya Qualitative analysis of regulatory graphs: A computational tool based on a discrete formal framework Positive Systems Lecture Notes in Control and Information Sciences vol. 294 2003 Springer Berlin 830 832
9. T. Dang, C.L. Guernic, and O. Maler Computing reachable states for nonlinear biological models CMSBE'09 LNCS vol. 5688 2009 126 141
10. H. de Jong, J. Geiselmann, C. Hernandez, and M. Page Genetic network analyzer: qualitative simulation of genetic regulatory networks Bioinformatics 19 2003 336 344
11. S.V. Goethem, Modelling gene regulatory networks with timed automata, MasterE's thesis, University of Namur, 2011, URL http://anna.fi.muni.cz/ ~xsafran1/Work/cs2bio/.
12. R. Grosu, G. Batt, F. Fenton, J. Glimm, C.L. Guernic, S. Smolka, E. Bartocci, From cardiac cells to genetic regulatory networks, in: Proceedings of the 23rd international conference on Computer aided verification, CAVE'11, 2011, pp. 396-411.
13. R. Guantes, and J. Poyatos Dynamical principles of two-component genetic oscillators PLoS Comput Biol 2 2006
14. A. Halász, V. Kumar, M. Imielinski, C. Belta, O. Sokolsky, S. Pathak, and H. Rubin Analysis of lactose metabolism in e. coli using reachability analysis of hybrid systems Systems Biology, IET 1 2007 130 148
15. F. Jacob, and J. Monod Genetic regulatory mechanisms in the synthesis of proteins Journal of Molecular Biology 3 1961 318 356
16. O. Maler, G. Batt, Approximating continuous systems by timed automata, in: Proceedings of the 1st international workshop on Formal Methods in Systems Biology, FMSB E'08, 2008, pp. 77-89.
17. H. Siebert and A. Bockmayr, Incorporating time delays into the logical analysis of gene regulatory networks, in: CMSB, 2006, pp. 169-183.
18. E.H. Snoussi Qualitative dynamics of piecewise-linear differential equations: A discrete mapping approach. dynamics and stability of systems Dynamics and Stability of Systems 4 1989
19. M. Swat, A. Kel, and H. Herzel Bifurcation Analysis of the Regulatory Modules of the Mammalian G1/S Transition Bioinformatics 20 2004 1506 1511
20. D. Thieffry, and R. Thomas Dynamical Behavior of Biological Regulatory Networks Bulletin of Mathematical Biology 57 1995 277 297
21. R. Thomas Boolean formalization of genetic control circuits Journal of Theoretical Biology 42 1973