Genetic network analyzer: A tool for the qualitative modeling and simulation of bacterial regulatory networks

Methods in Molecular Biology

Volumn 804, Issue , 2012, Pages 439-462

  Batt, Grégory ^a   Besson, Bruno ^b   Ciron, Pierre Emmanuel ^b   De Jong, Hidde ^c   Dumas, Estelle ^c   Geiselmann, Johannes ^d   Monte, Regis ^c   Monteiro, Pedro T ^c   Page, Michel ^c   Rechenmann, François ^c   Ropers, Delphine ^c  

^a INRIA   (France)

^b Genostar   (France)

^c INRIA RHÔNE ALPES   (France)

^d UNIV GRENOBLE ALPES   (France)

Author keywords

Carbon starvation; Escherichia coli; Gene regulatory networks; Genetic Network Analyzer; Model checking; Piecewise linear differential equations; Qualitative modeling and simulation

Indexed keywords

ARTICLE; BACTERIUM; BIOLOGICAL MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE REGULATORY NETWORK; GENETICS; MATHEMATICAL PHENOMENA; METHODOLOGY; SYSTEMS BIOLOGY;

BACTERIA; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; MATHEMATICAL CONCEPTS; MODELS, GENETIC; SOFTWARE; SYSTEMS BIOLOGY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 84855869711     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-361-5_22     Document Type: Article

References (41)

1. Bolouri H. (2008) Computational Modelling of Gene Regulatory Networks: A Primer. Imperial College Press, London.
2. Heinrich R, Schuster S. (1996) The Regulation of Cellular Systems. Chapman & Hall, New York.
3. de Jong H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput Biol, 9:67-103. (Pubitemid 34264287)
4. Fisher J, Henzinger T. (2007) Executable cell biology. Nat Biotechnol, 25(11):1239-1250.
5. Karlebach G, Shamir R. (2008) Modelling and analysis of gene regulatory networks. Nat Rev Mol Cell Biol, 9(10):770-780.
6. Thomas R, d'Ari R. (1990) Biological Feedback. CRC Press, Boca Raton, FL.
7. Chaouiya C. (2007) Petri net modelling of biological networks. Brief Bioinform, 8(4):210-219. (Pubitemid 47336806)
8. Palsson B. (2006) Systems Biology: Properties of Reconstructed Networks. Cambridge University Press, New York.
9. Ciocchetta F, Hillston J. (2008) Process Algebras in Systems Biology. In Proc. 8th. School on Formal Methods for the Design of Computer, Communication, and Software Systems (SFM 2008), Volume 5016 of LNCS. Edited by Bernardo M, Degano P, ZavattaroG, Springer-Verlag, Berlin, 313-365
10. Glass L, Kauffman S. (1973) The logical analysis of continuous non-linear biochemical control networks. J Theor Biol, 39:103-129.
11. Batt G, de Jong H, Page M, Geiselmann J. (2008) Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Automatica, 44(4):982-989.
12. Casey R, de Jong H, Gouzé JL. (2006) Piecewise-linear models of genetic regulatory networks: equilibria and their stability. J Math Biol, 52:27-56. (Pubitemid 41830874)
13. Edwards R. (2006) Analysis of continuoustime switching networks. Physica D, 146 (1-4): 165-199.
14. Farcot E, Gouzé JL. (2009) Periodic solutions of piecewise affine gene network models with non uniform decay rates: the case of a negative feedback loop. Acta Biotheor, 57(4):429-455.
15. Gouzé JL, Sari T. (2002) A class of piecewise linear differential equations arising in biological models. Dyn Syst, 17(4):299-316.
16. Mestl T, Plahte E, Omholt S. (1995) A mathematical framework for describing and analysing gene regulatory networks. J Theor Biol, 176(2):291-300.
17. Glass L, Pasternack J. (1978) Stable oscillations in mathematical models of biological control systems. J Math Biol, 6:207-223. (Pubitemid 9015991)
18. Plahte E, Kjøglum S. (2005) Analysis and generic properties of gene regulatory networks with graded response functions. Physica D, 201:150-176. (Pubitemid 40183516)
19. de Jong H, Geiselmann J, Hernandez C, Page M. (2003) Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics, 19(3):336-344. (Pubitemid 36284933)
20. de Jong H, Page M. (2008) Search for steady states of piecewise-linear differential equation models of genetic regulatory networks. ACM/IEEE Trans Comput Biol Bioinform, 5(2):208-222. (Pubitemid 351695261)
21. Monteiro P, Ropers D, Mateescu R, Freitas A, de Jong H. (2008) Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics, 24(16): i227-i233.
22. Ropers D, de Jong H, Page M, Schneider D, Geiselmann J. (2006) Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems, 84(2):124-152. (Pubitemid 43670488)
23. Ropers D, Baldazzi V, de Jong H. (2011) Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli. ACM/IEEE Trans Comput Biol Bioinform, 8(1):166-181.
24. Novère NL, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem M, Wimalaratne S, Bergman F, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd S, Calzone L, Courtot M, Dogrusoz U, Freeman T, Funahashi A, Ghosh S, Jouraku S, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell D, Sander C, Sauro H, Snoep J, Kohn K, Kitano H. (2009) The systems biology graphical notation. Nat Biotechnol, 27(8):735-742.
25. MH Saier J, Ramseier T, Reizer J. (1996) Regulation of Carbon Utilization. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. Edited by Neidhardt et al., ASM Press, Washington, DC, 1325-1343.
26. Gonzalez-Gil G, Bringmann P, Kahmann R: Fis is a regulator of metabolism in Escherichia coli. Mol. Microbiol. 1996, 22:21-29. (Pubitemid 26338326)
27. Ishizuka H, Hanamura A, Inada T, Aiba H. (1994) Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene. EMBO J, 13(13):3077-3082. (Pubitemid 24213459)
28. Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama A. (1999) Growth phase dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol, 181 (20):6361-6370. (Pubitemid 29512946)
29. de Jong H, Gouzé JL, Hernandez C, Page M, Sari T, Geiselmann J. (2004) Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull Math Biol, 66(2):301-340. (Pubitemid 38215331)
30. Kuipers B. (1994) Qualitative Reasoning: Modeling and Simulation with Incomplete Knowledge. MIT Press, Cambridge, MA.
31. Farcot E. (2006) Geometric properties of a class of piecewise affine biological network models. J Math Biol, 52(3):373-418. (Pubitemid 43237828)
32. Clarke E, Grumberg O, Peled D. (1999) Model Checking. MIT Press, Boston, MA.
33. Batt G, Ropers D, de Jong H, Geiselmann J, Mateescu R, Page M, Schneider D. (2005) Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli. Bioinformatics, 21(Suppl 1):i19-i28. (Pubitemid 41794471)
34. Monteiro P, Dumas E, Besson B, Mateescu R, Page M, Freitas A, de Jong H. (2009) A service-oriented architecture for integrating the modeling and verification of genetic regulatory networks. BMC Bioinform, 10:450.
35. Cimatti A, Clarke EM, Giunchiglia E, Giunchiglia F, Pistore M, Roveri M, Sebastiani R, Tacchella A. (2002) NuSMV2: An Open-Source Tool for Symbolic Model Checking. In Proc. 14th Intl. Conf. Computer Aided Verification (CAV 2002), Volume 2404 of LNCS. Edited by Brinksma D, Larsen K, Springer-Verlag, Berlin, 359-364.
36. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. (2006) COPASI - a Complex Pathway Simulator. Bioinformatics, 22(24):3067-3074. (Pubitemid 44884083)
37. Chen K, Calzone L, Csikasz-Nagy A, Cross F, Novak B, Tyson J. (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell, 15(8):3841-3862. (Pubitemid 38989719)
38. Tyson J. (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc Natl Acad Sci U S A, 88:7328-7332. (Pubitemid 21915144)
39. Snoussi E. (1989) Qualitative dynamics of piecewise-linear differential equations: a discrete mapping approach. Dynam Stab Syst, 4(3-4): 189-207. (Pubitemid 20614063)
40. Plahte E, Mestl T, Omholt S. (1998) A methodological basis for description and analysis of systems with complex switch-like interactions. J Math Biol, 36(4):321-348. (Pubitemid 128735352)
41. Bernot G, Comet JP, Richard A, Guespin J. (2004) Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic. J Theor Biol, 229(3):339-348.