W. Abou-jaoudé, D. A. Ouattara, and M. Kaufman, From structure to dynamics: Frequency tuning in the p53???Mdm2 network, Journal of Theoretical Biology, vol.258, issue.4, pp.561-577, 2009.
DOI : 10.1016/j.jtbi.2009.02.005

W. Abou-jaoudé, D. A. Ouattara, and M. Kaufman, From structure to dynamics: frequency tuning in the p53?Mdm2 network: II differential and stochastic approaches, Journal of theoretical biology, vol.264, pp.1177-1189, 2010.

D. Angeli and E. D. Sontag, Monotone control systems, IEEE Transactions on Automatic Control, vol.48, issue.10, pp.1684-1698, 2003.
DOI : 10.1109/TAC.2003.817920

URL : http://arxiv.org/abs/math/0206133

G. Batt, B. Besson, P. Ciron, H. De-jong, E. Dumas et al., Genetic Network Analyzer: A Tool for the Qualitative Modeling and Simulation of Bacterial Regulatory Networks, Bacterial Molecular Networks, pp.439-462, 2012.
DOI : 10.1007/978-1-61779-361-5_22

URL : https://hal.archives-ouvertes.fr/hal-00762122

G. Bernot, J. P. Comet, and Z. Khalis, Gene regulatory networks wih multiplexes, Proc of European Simulation and Modelling Conference, pp.423-432, 2008.

C. Chaouiya, Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, 2007.
DOI : 10.1093/bib/bbm029

B. Chazelle, Natural algorithms and influence systems, Communications of the ACM, vol.55, issue.12, pp.101-110, 2012.
DOI : 10.1145/2380656.2380679

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.278.6389

A. Ciliberto, F. Capuani, and J. J. Tyson, Modeling Networks of Coupled Enzymatic Reactions Using the Total Quasi-Steady State Approximation, PLoS Computational Biology, vol.103, issue.3, 2007.
DOI : 10.1371/journal.pcbi.0030045.sd001

J. P. Comet, G. Bernot, A. Das, F. Diener, C. Massot et al., Simplified Models for the Mammalian Circadian Clock, Procedia Computer Science, vol.11, pp.127-138, 2012.
DOI : 10.1016/j.procs.2012.09.014

URL : https://hal.archives-ouvertes.fr/hal-01282923

P. Cousot, R. F. Cousot, S. Gay, S. F. Soliman, and S. Soliman, Abstract interpretation: A unified lattice model for static analysis of programs by construction or approximation of fixpoints Inferring reaction systems from ordinary differential equations Abstract interpretation and types for systems biology, POPL'77: Proceedings of the 6th ACM Symposium on Principles of Programming Languages, pp.238-252, 1977.

F. Fages and S. Soliman, From reaction models to influence graphs and back: a theorem In: Proceedings of Formal Methods in Systems Biology FMSB'08. No. 5054 in Lecture Notes in Computer Science, 2008.

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.
DOI : 10.1021/j100540a008

L. Glass and S. A. Kauffman, The logical analysis of continuous, non-linear biochemical control networks, Journal of Theoretical Biology, vol.39, issue.1, pp.103-129, 1973.
DOI : 10.1016/0022-5193(73)90208-7

A. G. González, C. Chaouiya, and D. Thieffry, Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc, Bioinformatics, vol.24, issue.16, pp.234-240, 2008.
DOI : 10.1093/bioinformatics/btn266

L. Grieco, L. Calzone, I. Bernard-pierrot, F. Radvanyi, B. Kahn-perlès et al., Integrative modelling of the influence of mapk network on cancer cell fate decision, PLOS Computational Biology, vol.9, issue.10, 2013.

M. Hucka, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

M. Katsumata, Graphic representation of Botts-Morales equation for enzyme-substrate-modifier system, Journal of Theoretical Biology, vol.36, issue.2, pp.327-338, 1972.
DOI : 10.1016/0022-5193(72)90102-6

H. Klarner, A. Bockmayr, and H. Siebert, Computing Symbolic Steady States of Boolean Networks, Proceedings of the 11th International Conference on Cellular Automata for Research and Industry , ACRI 2014, pp.561-570, 2014.
DOI : 10.1007/978-3-319-11520-7_59

J. C. Leloup and A. Goldbeter, Toward a detailed computational model for the mammalian circadian clock, Proceedings of the National Academy of Sciences, vol.100, issue.12, pp.7051-7056, 2003.
DOI : 10.1073/pnas.1132112100

A. Naldi, D. Berenguier, A. Fauré, F. Lopez, D. Thieffry et al., Logical modelling of regulatory networks with GINsim 2.3, Biosystems, vol.97, issue.2, pp.134-139, 2009.
DOI : 10.1016/j.biosystems.2009.04.008

A. Naldi, R. Remy, D. Thieffry, and C. Chaouiya, A reduction method for logical regulatory graphs preserving essential dynamical properties, CMSB'09: Proceedings of the seventh international conference on Computational Methods in Systems Biology, pp.266-280, 2009.

A. Naldi, J. Carneiro, C. Chaouiya, and D. Thieffry, Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling, PLoS Computational Biology, vol.212, issue.9, p.1000912, 2010.
DOI : 10.1371/journal.pcbi.1000912.s003

URL : https://hal.archives-ouvertes.fr/inserm-00704876

N. Le-novère, B. Bornstein, A. Broicher, M. Courtot, M. Donizelli et al., BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems, Nucleic Acids Research, vol.34, issue.90001, pp.689-691, 2006.
DOI : 10.1093/nar/gkj092

N. Le-novere, M. Hucka, H. Mi, S. Moodie, F. Schreiber et al., The Systems Biology Graphical Notation, Nature Biotechnology, vol.267, issue.8, pp.735-741, 2009.
DOI : 10.1038/nbt.1558

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, pp.335-350, 2008.
DOI : 10.1016/j.aam.2007.11.003

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

D. A. Rosenblueth, S. Muñoz, M. Carrillo, and E. Azpeitia, Inference of Boolean Networks from Gene??Interaction Graphs Using a SAT Solver, AlCoB 2014: Proceedings of the 1st International Conference on Algorithms for Computational Biology, pp.235-246, 2014.
DOI : 10.1007/978-3-319-07953-0_19

P. Ruet, Local cycles and dynamical properties of Boolean networks, Mathematical Structures in Computer Science, vol.26, issue.04, pp.702-718, 2016.
DOI : 10.1016/j.aam.2007.11.003

R. Thomas, Boolean formalisation of genetic control circuits, Journal of Theoretical Biology, vol.42, pp.565-583, 1973.
DOI : 10.1016/0022-5193(74)90172-6

R. Thomas and R. D-'ari, Biological Feedback, 1990.
URL : https://hal.archives-ouvertes.fr/hal-00087681

P. Traynard, A. Fauré, F. Fages, and D. Thieffry, Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation, Bioinformatics, vol.32, issue.17, 2016.
DOI : 10.1093/bioinformatics/btw457

URL : https://hal.archives-ouvertes.fr/hal-01378465