Mapping multivalued onto Boolean dynamics

Journal of Theoretical Biology

Volumn 270, Issue 1, 2011, Pages 177-184

  Didier, Gilles ^a   Remy, Elisabeth ^a   Chaouiya, Claudine ^b,c  

^a AIX MARSEILLE UNIVERSITÉ   (France)

^b INSTITUTO GULBENKIAN DE CIÊNCIA   (Portugal)

^c Aix Marseille university   (France)

Author keywords

Boolean modelling; Cell dynamics; Gene Regulatory Networks; Multivalued modelling

Indexed keywords

CELL ORGANELLE; GENE EXPRESSION; MAPPING METHOD; NUMERICAL MODEL;

ARTICLE; GENE REGULATORY NETWORK; INFORMATION SCIENCE; PRIORITY JOURNAL; THEORETICAL MODEL;

ALGORITHMS; CELL NUCLEUS; CYTOPLASM; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL; PROTO-ONCOGENE PROTEINS C-MDM2; TUMOR SUPPRESSOR PROTEIN P53;

EID: 78650754127     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.09.017     Document Type: Article

References (29)

1. Abou-Jaoude W., Ouattara D.A., Kaufman M. From structure to dynamics: frequency tuning in the p53-Mdm2 network I. Logical approach. J. Theor. Biol. 2009, 258(4):561-577.
2. Ansótegui, C., Manyà, F., 2004. Mapping problems with finite-domain variables to problems with boolean variables. In: Hoos, H.H., Mitchell, D.G. (Eds.), SAT (Selected Papers), Lecture Notes in Computer Science, vol. 3542, pp. 1-15.
3. Aracena J., Demongeot J., Goles E. Positive and negative circuits in discrete neural networks. IEEE Trans. Neural Networks 2004, 15(1):77-83.
4. Bornholdt S. Boolean network models of cellular regulation: prospects and limitations. J. Roy. Soc. Interface 2008, 5:S85-S94.
5. Chaves M., Albert R., Sontag E.D. Robustness and fragility of Boolean models for genetic regulatory networks. J. Theor. Biol. 2005, 235(3):431-449.
6. Ciliberto A., Novak B., Tyson J.J. Steady states and oscillations in the p53/Mdm2 network. Cell Cycle 2005, 4(3):488-493.
7. Fauré A., Thieffry D. Logical modelling of cell cycle control in eukaryotes: a comparative study. Mol. Biosyst. 2009, 5:1569-1581.
8. Garg, A., Xenarios, I., Mendoza, L., De Micheli, G., 2007. An efficient method for dynamic analysis of gene regulatory networks and in silico gene perturbation experiments. In: Recomb, Lecture Notes in Computer Science, vol. 4453, pp. 62-76.
9. Glass L., Kauffman S.A. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 1973, 39:103-129.
10. Kauffman S.A. The Origins of Order. Self-Organization and Selection in Evolution 1993, Oxford University Press.
11. Kaufman M., Urbain J., Thomas R. Towards a logical analysis of the immune response. J. Theor. Biol. 1985, 114(4):527-561.
12. Kaufman M., Thomas R. Model analysis of the bases of multistationarity in the humoral immune response. J. Theor. Biol. 1987, 129(2):141-162.
13. Mendoza L. A network model for the control of the differentiation process in Th cells. Biosystems 2006, 84(2):101-114.
14. Naldi A., Berenguier D., Fauré A., Lopez F., Thieffry D., Chaouiya C. Logical modelling of regulatory networks with GINsim 2.3. Biosystems 2009, 97(2):134-139.
15. Naldi, A., Remy, E., Thieffry, D., Chaouiya, C., 2009. A reduction of logical regulatory graphs preserving essential dynamical properties. In: CMSB'09, Lecture Notes in Computer Science, vol. 5688, pp. 266-280.
16. Remy E., Ruet P. From minimal signed circuits to the dynamics of Boolean regulatory networks. Bioinformatics 2008, 24(16):i220-i226.
17. Richard A., Comet J.-P. Necessary conditions for multistationarity in discrete dynamical systems. Discrete Appl. Math. 2007, 155(18):2403-2413.
18. Saez-Rodriguez J., Simeoni L., Lindquist J.A., Hemenway R., Bommhardt U., Arndt B., Haus U.-U., Weismantel R., Gilles E.D., Klamt S., Schraven B. A logical model provides insights into T cell receptor signaling. PLoS Comput. Biol. 2007, 3(8):e163.
19. Sánchez L., Chaouiya C., Thieffry D. Segmenting the fly embryo: a logical analysis of the segment polarity cross-regulatory module. Int. J. Dev. Biol. 2008, 52(8):1059-1075.
20. Sánchez L., Thieffry D. A logical analysis of the drosophila gap-gene system. J. Theor. Biol. 2001, 211(2):115-141.
21. Sánchez L., Thieffry D. Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J. Theor. Biol. 2003, 224(4):517-537.
22. Siebert H. Deriving behavior of Boolean bioregulatory networks from subnetwork dynamics. Math. Comput. Sci. 2009, 2(3):421-442.
23. Snoussi E.H., Thomas R. Logical identification of all steady states: the concept of feedback loop characteristic states. Bull. Math. Biol. 1993, 55(5):973-991.
24. Thieffry D. Dynamical roles of biological regulatory circuits. Brief Bioinform. 2007, 8(4):220-225.
25. Thomas R. Regulatory networks seen as asynchronous automata: a logical description. J. Theor. Biol. 1991, 153:1-23.
26. Thomas R., D'Ari R. Biological Feedback 1990, CRC Press.
27. Tournier L., Chaves M. Uncovering operational interactions in genetic networks using asynchronous Boolean dynamics. J. Theor. Biol. 2009, 260(2):196-209.
28. Van Ham, P., 1979. How to deal with variables with more than two levels. In: Thomas, R. (Ed.), Kinetic Logic: A Boolean Approach to the Analysis of Complex Regulatory Systems. Lecture notes in Biomathematics, vol. 29.
29. Willadsen K., Wiles J. Robustness and state-space structure of Boolean gene regulatory models. J. Theor. Biol. 2007, 249(4):749-765.