Compositional reachability analysis of genetic networks

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

Volumn 4210 LNBI, Issue , 2006, Pages 212-226

  Gössler, Gregor ^a  

^a INRIA RHÔNE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL METHODS; COMPUTER SIMULATION; FORMAL LOGIC; GENETIC ALGORITHMS; MATHEMATICAL MODELS;

DISCRETE TRANSITION SYSTEMS; FORMAL VERIFICATION; REGULATORY NETWORKS;

NEURAL NETWORKS;

EID: 33845219747     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11885191_15     Document Type: Conference Paper

References (29)

1. R. Alur, T. Dang, and F. Ivancić. Reachability analysis of hybrid systems via predicate abstraction. Trans. on Embedded Computing Systems, 2004.
2. G. Batt, D. Bergamini, H. de Jong, H. Garavel, and R. Mateescu. Model checking genetic regulatory networks using GNA and CADP. In proc. SPIN'04, volume 2989 of LNCS, pages 158-163. Springer-Verlag, 2004.
3. G. Batt, H. de Jong, J. Geiselmann, M. Page, D. Ropers, and D. Schneider. Symbolic reachability analysis of genetic regulatory networks using qualitative abstraction. Research Report 5362, INRIA, France, 2004.
4. G. Batt, D. Ropers, H. de Jong, J. Geiselmann, M. Page, and D. Schneider. Qualitative analysis and verification of hybrid models of genetic regulatory networks: Nutritional stress response in escherichia coli. In proc. HSCC'05, volume 3414 of LNCS, pages 134-150. Springer-Verlag, 2005.
5. 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. Journal of Theoretical Biology, 229(3):339-348, 2004.
6. R. Blossey, L. Cardelli, and A. Phillips. A compositional approach to the stochastic dynamics of gene networks. Trans. on Comput Syst. Biol., 4:99-122, 2006.
7. R. Casey, H. de Jong, and J.-L. Gouzé. Piecewise-linear models of genetic regulatory networks: Equilibria and their stability. Mathematical Biology, 52(1):27-56, 2006.
8. N. Chabrier and F. Fages. Symbolic model checking of biochemical networks. In proc. CMSB'03, 2003.
9. C. Chaouiya, E. Remy, P. Ruet, and D. Thieffry. Qualitative modelling of genetic networks: From logical regulatory graphs to standard petri nets. In J. Cortadella and W. Reisig, editors, proc. ICATPN'04, volume 3099 of LNCS, pages 137-156. Springer-Verlag, 2004.
10. J.-P. Comet, H. Klaudel, and S. Liauzu. Modeling multi-valued genetic regulatory networks using high-level petri nets. In G. Ciardo and P. Darondeau, editors, proc. ICATPN'05, volume 3536 of LNCS, pages 208-227. Springer-Verlag, 2005.
11. H. de Jong. Modeling and simulation of genetic regulatory systems: A literature review. Journal of Computational Biology, 9(1):69-105, 2002.
12. H. de Jong, J. Geiselmann, G. Batt, C. Hernandez, and M. Page. Qualitative simulation of the initiation of sporulation in Bacillus subtilis. Bulletin of Mathematical Biology, 66(2):261-300, 2004.
13. H. de Jong, J. Geiselmann, C. Hernandez, and M. Page. Genetic Network Analyzer: Qualitative simulation of genetic regulatory networks. Bioinformatics, 19(3) :336-344, 2003.
14. 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. Bulletin of Mathematical Biology, 66:301-340, 2004.
15. S. Eker, M. Knapp, K. Laderoute, P. Lincoln, and C. Talcott. Pathway logic: Executable models of biological networks. ENTCS, 71, 2002,
16. F. Fages, S. Soliman, and N. Chabrier-Rivier. Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM. J. of Biological Physics and Chemistry, 4(2):64-72, 2004.
17. A.F. Filippov. Differential equations with discontinuous righthand side. Mathematics and its Applications, 18, 1988.
18. R. Ghosh, A. Tiwari, and C. Tomlin. Automated symbolic reachability analysis; with application to delta-notch signaling automata. In O. Maler and A. Pnueli, editors, proc. HSCC'03, volume 2623 of LNCS, pages 233-248. Springer-Verlag, 2003.
19. L. Glass and S.A. Kauffman. The logical analysis of continuous, non-linear biochemical control networks. Journal of Theoretical Biology, 39(1):103-129, 1973.
20. G. Gössler and J. Sifakis. Component-based construction of deadlock-free systems (extended abstract). In proc. FSTTCS'03, volume 2914 of LNCS. Springer-Verlag, 2003.
21. J.-L. Gouzé and T. Sari. A class of piecewise linear differential equations arising in biological models. Dynamical Systems, 17(4):299-316, 2003.
22. M. Heiner and I. Koch. Petri net based model validation in systems biology. In J. Cortadella and W. Reisig, editors, proc. ICATPN'04, volume 3099 of LNCS, pages 216-237. Springer-Verlag, 2004.
23. A. Larrinaga, A. Naldi, L. Sánchez, D. Thieffry, and C. Chaouiya. GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems, 2005.
24. G. Marnellos, G.A. Deblandre, E. Mjolsness, and G. Kintner. Delta-Notch lateral inhibitory patterning in the emergence of ciliated cells in Xenopus: Experimental observations and a gene network model. In proc. PSB'00, volume 5, pages 326-337. World Scientific Publishing, 2000.
25. Z.N. Oltvai and A.L. Barabási. Life's complexity pyramid. Science, 298:763-764, 2002.
26. C. Piazza, M. Antoniotti, V. Mysore, A. Policriti, F. Winkler, and B. Mishra. Algorithmic algebraic model checking I: Challenges form systems biology. In proc. CAV'05, volume 3576 of LNCS, pages 5-19. Springer-Verlag, 2005.
27. O. Resendis-Antonio, J.A. Freyre-González, R. Menchaca- Méndez, R.M. Gutiérrez-Ríos, A. Martínez-Antonio, C. Avila-Sánchez, and J. Collado-Vides. Modular analysis of the transcriptional regulatory network of e. coli. Trends in Genetics, 21(1):16-20, 2005.
28. E. Simão, E. Remy, D, Thieffry, and C. Chaouiya. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in e.coli. Bioinformatics, 21(Suppl. 2):ii190-ii196, 2005.
29. R. Thomas. Boolean formalisation of genetic control circuits. J. Theor. Biol., 42:565-583, 1973.