A. C. Antoulas, D. C. Sorensen, and S. Gugercin, A survey of model reduction methods for large-scale systems, Contemporary Mathematics, vol.280, pp.193-219, 2001.
DOI : 10.1090/conm/280/04630

A. Berman and R. J. Plemmons, Nonnegative matrices in the mathematical sciences, Classics in Applied Mathematics, 1994.
DOI : 10.1137/1.9781611971262

S. Bornholdt, SYSTEMS BIOLOGY: Less Is More in Modeling Large Genetic Networks, Science, vol.310, issue.5747, pp.449-451, 2005.
DOI : 10.1126/science.1119959

R. Casey, H. De-jong, and J. L. Gouzé, Piecewise-linear Models of Genetic Regulatory Networks: Equilibria and their Stability, Journal of Mathematical Biology, vol.52, issue.1, pp.27-56, 2006.
DOI : 10.1007/s00285-005-0338-2

URL : https://hal.archives-ouvertes.fr/inria-00071250

C. Chaouiya, E. Remy, B. Mossé, and D. Thieffry, Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework, First Multidisciplinary International Symposium on Positive Systems: Theory and Applications (POSTA'03), pp.119-126, 2003.
DOI : 10.1007/978-3-540-44928-7_17

M. Chaves, R. Albert, and E. D. Sontag, Robustness and fragility of Boolean models for genetic regulatory networks, Journal of Theoretical Biology, vol.235, issue.3, pp.431-449, 2005.
DOI : 10.1016/j.jtbi.2005.01.023

M. Chaves, T. Eissing, and F. Allgöwer, Regulation of Apoptosis via the NF??B Pathway: Modeling and Analysis, Dynamics on and of complex networks. Birkhauser, 2008.
DOI : 10.1007/978-0-8176-4751-3_2

T. H. Cormen, C. E. Leiserson, R. L. Rivest, and C. Stein, Introduction to algorithms, 2001.

N. N. Danial and S. J. Korsmeyer, Cell Death, Cell, vol.116, issue.2, pp.205-216, 2004.
DOI : 10.1016/S0092-8674(04)00046-7

T. Eissing, H. Conzelmann, E. D. Gilles, F. Allgöwer, E. Bullinger et al., Bistability Analyses of a Caspase Activation Model for Receptor-induced Apoptosis, Journal of Biological Chemistry, vol.279, issue.35, pp.36892-36897, 2004.
DOI : 10.1074/jbc.M404893200

B. Faryabi, J. Chamberland, G. Vahedi, A. Datta, and E. R. Dougherty, Optimal Intervention in Asynchronous Genetic Regulatory Networks, IEEE Journal of Selected Topics in Signal Processing, vol.2, issue.3, pp.412-423, 2008.
DOI : 10.1109/JSTSP.2008.923853

A. Fauré, A. Naldi, C. Chaouiya, and D. Thieffry, Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle, Bioinformatics, vol.22, issue.14, pp.22-124, 2006.
DOI : 10.1093/bioinformatics/btl210

C. Frelin, V. Imbert, V. Bottero, N. Gonthier, A. K. Samraj et al., Inhibition of the NF-??B survival pathway via caspase-dependent cleavage of the IKK complex scaffold protein and NF-??B essential modulator NEMO, Cell Death and Differentiation, vol.13, issue.1, pp.152-160, 2008.
DOI : 10.1016/S0092-8674(00)80153-1

A. G. Gonzalez, A. Naldi, L. S-`-anchez, D. Thieffry, and C. Chaouiya, GINsim: A software suite for the qualitative modelling, simulation and analysis of regulatory networks, Biosystems, vol.84, issue.2, pp.91-100, 2006.
DOI : 10.1016/j.biosystems.2005.10.003

URL : https://hal.archives-ouvertes.fr/hal-00088152

J. Gouzé, Positive and Negative Circuits in Dynamical Systems, Journal of Biological Systems, vol.06, issue.01, pp.11-15, 1998.
DOI : 10.1142/S0218339098000054

C. M. Grinstead and J. L. Snell, Introduction to probability, 1997.

A. Hoffmann, A. Levchenko, M. L. Scott, and D. Baltimore, The Ikappa B-NF-kappa B Signaling Module: Temporal Control and Selective Gene Activation, Science, vol.298, issue.5596, pp.1241-1245, 2002.
DOI : 10.1126/science.1071914

S. A. Kauffman, The origins of order, 1993.

B. N. Kholodenko, A. Kiyatkin, F. J. Bruggeman, E. Sontag, H. V. Westerhoff et al., Untangling the wires: A strategy to trace functional interactions in signaling and gene networks, Proc. Natl. Acad. Sci USA, pp.12841-12846, 2002.
DOI : 10.1073/pnas.192442699

S. Klamt, J. Saez-rodriguez, J. Lindquist, L. Simeoni, and E. Gilles, A methodology for the structural and functional analysis of signaling and regulatory networks, BMC Bioinformatics, vol.7, issue.1, p.56, 2006.
DOI : 10.1186/1471-2105-7-56

S. Liang, S. Fuhrman, and R. Somogyi, REVEAL, a general reverse engineering algorithm for inference of genetic network architecture, Pacific Symposium on Biocomputing, pp.18-29, 1998.

T. Lipniacki, P. Paszek, A. R. Brasier, B. Luxon, and M. Kimmel, Mathematical model of NF-??B regulatory module, Journal of Theoretical Biology, vol.228, issue.2, pp.195-215, 2004.
DOI : 10.1016/j.jtbi.2004.01.001

N. D. Perkins, Integrating cell-signalling pathways with NF-??B and IKK function, Nature Reviews Molecular Cell Biology, vol.206, issue.1, pp.49-62, 2007.
DOI : 10.1038/nrm2083

E. Remy, P. Ruet, and D. Thieffry, Graphic requirements for multistability and attractive cycles in a Boolean dynamical framework, Advances in Applied Mathematics, vol.41, issue.3, p.41, 2008.
DOI : 10.1016/j.aam.2007.11.003

URL : https://hal.archives-ouvertes.fr/hal-00692086

D. Ropers, H. De-jong, M. Page, D. Schneider, and J. Geiselmann, Qualitative simulation of the carbon starvation response in Escherichia coli, Biosystems, vol.84, issue.2, pp.124-152, 2006.
DOI : 10.1016/j.biosystems.2005.10.005

URL : https://hal.archives-ouvertes.fr/hal-00171698

J. Saez-rodriguez, L. Simeoni, A. Jonathan, R. Lindquist, U. Hemenway et al., A Logical Model Provides Insights into T Cell Receptor Signaling, PLoS Computational Biology, vol.284, issue.8, p.163, 2007.
DOI : 10.1371/journal.pcbi.0030163.st002

L. Sánchez and D. Thieffry, A Logical Analysis of the Drosophila Gap-gene System, Journal of Theoretical Biology, vol.211, issue.2, pp.115-141, 2001.
DOI : 10.1006/jtbi.2001.2335

M. Schliemann, Modelling and experimental validation of TNF? induced pro-and antiapoptotic signalling, 2006.

H. Schmidt and E. W. Jacobsen, Identifying feedback mechanisms behind complex cell behavior, IEEE Control Syst. Mag, vol.4, pp.91-102, 2004.
DOI : 10.1109/mcs.2004.1316656

I. Shmulevich, E. R. Dougherty, S. Kim, and W. Zhang, Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks, Bioinformatics, vol.18, issue.2, pp.261-274, 2002.
DOI : 10.1093/bioinformatics/18.2.261

H. Siebert and A. Bockmayr, Temporal constraints in the logical analysis of regulatory networks, Theoretical Computer Science, vol.391, issue.3, pp.258-275, 2008.
DOI : 10.1016/j.tcs.2007.11.010

C. Soulé, Graphic Requirements for Multistationarity, Complexus, vol.1, issue.3, pp.123-133, 2003.
DOI : 10.1159/000076100

R. Thomas and R. D. Ari, Biological feedback, 1990.
URL : https://hal.archives-ouvertes.fr/hal-00087681

R. Thomas and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.170-179, 2001.
DOI : 10.1063/1.1350439

R. Thomas and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.180-195, 2001.
DOI : 10.1063/1.1349893

L. Tournier, Etude et modélisation mathématique de réseaux de régulation génétique et métabolique, Laboratoire Jean Kuntzmann, 2005.

A. Wuensche, Basins of attraction in network dynamics: a conceptual framework for biomolecular networks, Modularity in development and evolution, chapter 13, pp.288-311, 2002.

. Unité-de-recherche-inria-sophia and . Antipolis, route des Lucioles -BP 93 -06902 Sophia Antipolis Cedex (France) Unité de recherche INRIA Futurs : Parc Club Orsay Université -ZAC des Vignes 4, 2004.

I. Unité-de-recherche and . Lorraine, Technopôle de Nancy-Brabois -Campus scientifique 615, rue du Jardin Botanique -BP 101 -54602 Villers-l` es-Nancy Cedex (France) Unité de recherche INRIA Rennes : IRISA, Campus universitaire de Beaulieu -35042 Rennes Cedex (France) Unité de recherche INRIA Rhône-Alpes : 655, avenue de l'Europe -38334 Montbonnot Saint-Ismier (France) Unité de recherche INRIA Rocquencourt, Domaine de Voluceau -Rocquencourt -BP 105 -78153 Le Chesnay Cedex

I. Editeur and . De-voluceau-rocquencourt, BP 105 -78153 Le Chesnay Cedex (France) http://www.inria.fr ISSN, pp.249-6399