Genetic network analyzer: Qualitative simulation of genetic regulatory networks

Bioinformatics

Volumn 19, Issue 3, 2003, Pages 336-344

  de Jong, Hidde ^a   Geiselmann, Johannes ^b   Hernandez, Céline ^a   Page, Michel ^a,b  

^a INRIA RHÔNE ALPES   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACILLUS SUBTILIS; CASE STUDY; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; CONTROLLED STUDY; GENE INTERACTION; GENETIC ANALYSIS; GENETIC REGULATION; NONHUMAN; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; SPOROGENESIS;

BACILLUS SUBTILIS; POSIBACTERIA;

EID: 0345269975     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btf851     Document Type: Article

References (22)

1. Bai,U. and Mandić-Mulec,I. (1993) SinI modulates the activity of SinR, a developmental switch protein of Bacillus subtilis, by protein-protein interaction. Genes Dev., 7, 139-148.
2. Burkholder,W.F. and Grossman,A.D. (2000) Regulation of the initiation of endospore formation in Bacillus subtilis. In Brun,Y.V. and Shimkets,L.J. (eds), Prokaryotic Development. ASM, pp. 151-166.
3. de Jong,H., Geiselmann,J., Batt,G., Hernandez,C. and Page,M. (2002a) Qualitative simulation of the initiation of sporulation in B.subtilis. Technical Report RR-4527. INRIA.
4. de Jong,H., Gouzé,J.-L., Hernandez,C., Page,M., Sari,T. and Geiselmann,H. (2002b) Qualitative simulation of genetic regulatory networks using piecewise-linear models. Technical Report RR-4407. INRIA.
5. de Jong,H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comput. Biol., 9, 69-105.
6. Glass,L. and Kauffman,S.A. (1973) The logical analysis of continuous non-linear biochemical control networks. J. Theor. Biol., 39, 103-129.
7. Goryanin,J., Hodgman,T.C. and Selkov,E. (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics, 15, 749-758.
8. Gouzé,J.-L. and Sari,J. (2002) A class of piecewise linear differential equations arising in biological models. Dyn. Syst, in press.
9. Grossman,A.D. (1995) Genetic networks controlling the initiation of sporulation and the development of genetic competence in Bacillus subtilis. Annu. Rev. Genet., 29, 477-508.
10. Heidtke,K.R. and Schulze-Kremer,S. (1998) Design and implementation of a qualitative simulation model of λ phage infection. Bioinformatics, 14, 81-91.
11. Hoch,J.A. (1993) Regulation of the phosphorelay and the initiation of sporulation in Bacillus subtilis. Ann. Rev. Microbiol., 47, 441-465.
12. Kohn,K.W. (2001) Molecular interaction maps as information organizers and simulation guides. Chaos, 11, 1-14.
13. Kuipers,B. (1994) Qualitative Reasoning. MIT Press.
14. Mendes,P. (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. CABIOS, 9, 563-571.
15. Mestl,T., Plahte,E. and Omholt,S.W. (1995) A mathematical framework for describing and analysing gene regulatory networks. J Theor. Biol., 176, 291-300.
16. Perego,M. and Hoch,J.A. (1987) Isolation and sequence of the spo0E gene: Its role in initiation of sporulation in Bacillus subtilis. Mol. Microbiol., 1, 125-132.
17. Perego,M. and Hoch,J.A. (1991) Negative regulation of Bacillus subtilis sporulation by the spo0E gene product. J. Bacteriol., 173, 2514-2520.
18. Snoussi,E.H. (1989) Qualitative dynamics of piecewise-linear differential equations. Dyn. Stab. Syst., 4, 189-207.
19. Stragier,P. and Losick,R. (1996) Molecular genetics of Bacillus subtilis. Ann. Rev. Genet., 30, 297-341.
20. Strauch,M.A., Spiegelman,G.B., Perego,M., Johnson,W.C., Burbulys,D. and Hoch,J.A. (1989) The transition state transcription regulator abrB of Bacillus subtilis is a DNA binding protein. EMBO J., 8, 1615-1621.
21. Thomas,R., Thieffry,D. and Kaufman,M. (1995) Dynamical behaviour of biological regulatory networks: I. Biological rule of feedback loops. Bull. Math. Biol., 57, 247-276.
22. Voit,E.O. (2000) Computational Analysis of Biochemical Systems. Cambridge University Press, Cambridge.