F. Fages and S. Soliman, Formal Cell Biology in Biocham, 8th Int. School on Formal Methods for the Design of Computer, Communication and Software Systems: Computational Systems Biology SFM'08, pp.54-80, 2008.
DOI : 10.1007/978-3-540-68894-5_3

L. Calzone, F. Fages, and S. Soliman, BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, pp.1805-1807, 2006.
DOI : 10.1093/bioinformatics/btl172
URL : https://hal.archives-ouvertes.fr/hal-01431364

R. Thomas, A. Gathoye, and L. Lambert, A Complex Control Circuit. Regulation of Immunity in Temperate Bacteriophages, European Journal of Biochemistry, vol.54, issue.1, pp.211-227, 1976.
DOI : 10.1016/0022-5193(72)90062-8

R. Thomas, On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations, Synergetics, vol.9, pp.180-193, 1981.
DOI : 10.1007/978-3-642-81703-8_24

R. Thomas, Regulatory networks seen as asynchronous automata: A logical description, Journal of Theoretical Biology, vol.153, issue.1, pp.1-23, 1991.
DOI : 10.1016/S0022-5193(05)80350-9

S. Eker, M. Knapp, K. Laderoute, P. Lincoln, J. Meseguer et al., PATHWAY LOGIC: SYMBOLIC ANALYSIS OF BIOLOGICAL SIGNALING, Biocomputing 2002, pp.400-412, 2002.
DOI : 10.1142/9789812799623_0038

G. Bernot, J. Comet, A. Richard, and J. Guespin, Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-347, 2004.
DOI : 10.1016/j.jtbi.2004.04.003

N. Chabrier-rivier, M. Chiaverini, V. Danos, F. Fages, and V. Schächter, Modeling and querying biomolecular interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.25-44, 2004.
DOI : 10.1016/j.tcs.2004.03.063
URL : http://doi.org/10.1016/j.tcs.2004.03.063

F. Fages, S. Soliman, and N. , Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM, Journal of Biological Physics and Chemistry, vol.4, issue.2, pp.64-73, 2004.
DOI : 10.4024/2040402.jbpc.04.02
URL : https://hal.archives-ouvertes.fr/hal-01431345

L. Calzone, N. Chabrier-rivier, F. Fages, and S. Soliman, Machine Learning Biochemical Networks from Temporal Logic Properties, Transactions on Computational Systems Biology VI, pp.68-94, 2006.
DOI : 10.1007/11880646_4
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.75.5250

V. N. Reddy, M. L. Mavrovouniotis, and M. N. Liebman, Petri net representations in metabolic pathways, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB), pp.328-336, 1993.

I. Zevedei-oancea and S. Schuster, Topological analysis of metabolic networks based on petri net theory, In Silico Biology, vol.3, issue.29

D. Angeli, P. D. Leenheer, and E. D. Sontag, A Petri Net Approach to Persistence Analysis in Chemical Reaction Networks, Biology and Control Theory: Current Challenges, pp.181-216, 2007.
DOI : 10.1007/978-3-540-71988-5_9

C. Chaouiya, E. Remy, and D. Thieffry, Petri net modelling of biological regulatory networks, Journal of Discrete Algorithms, vol.6, issue.2, pp.165-177, 2008.
DOI : 10.1016/j.jda.2007.06.003

C. Rohr, W. Marwan, and M. Heiner, Snoopy--a unifying Petri net framework to investigate biomolecular networks, Bioinformatics, vol.26, issue.7, pp.974-975, 2010.
DOI : 10.1093/bioinformatics/btq050

S. Soliman, Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem, Algorithms for Molecular Biology, vol.7, issue.1, pp.10-1186
DOI : 10.1007/BF01211911
URL : https://hal.archives-ouvertes.fr/hal-00784404

S. Gay, S. Soliman, and F. Fages, A graphical method for reducing and relating models in systems biology, Bioinformatics, vol.26, issue.18, pp.575-581, 2010.
DOI : 10.1093/bioinformatics/btq388
URL : https://hal.archives-ouvertes.fr/hal-01431335

S. Gay, F. Fages, T. Martinez, S. Soliman, and C. Solnon, On the subgraph epimorphism problem, Discrete Applied Mathematics, vol.162, 2014.
DOI : 10.1016/j.dam.2013.08.008
URL : https://hal.archives-ouvertes.fr/hal-01098527

C. Kaleta, S. Richter, and P. Dittrich, Using chemical organization theory for model checking, Bioinformatics, vol.25, issue.15, 1915.
DOI : 10.1093/bioinformatics/btp332

S. Schuster, D. A. Fell, and T. Dandekar, A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks, Nature Biotechnology, vol.18, issue.3, pp.326-332, 2002.
DOI : 10.1038/73786

A. Varma and B. Palsson, Metabolic Flux Balancing: Basic Concepts, Scientific and Practical Use, Bio/Technology, vol.43, issue.10, pp.994-998, 1994.
DOI : 10.1006/jtbi.1993.1203

P. Dittrich and P. Di-fenizio, Chemical Organisation Theory, Bulletin of Mathematical Biology, vol.96, issue.25, pp.1199-1231, 2007.
DOI : 10.1007/s11538-006-9130-8

M. Feinberg, Mathematical aspects of mass action kinetics, Chemical Reactor Theory: A Review, pp.1-78, 1977.

G. Shinar and M. Feinberg, Structural Sources of Robustness in Biochemical Reaction Networks, Science, vol.327, issue.5971
DOI : 10.1126/science.1183372

G. Koh, H. Teong, M. Clement, D. Hsu, and P. Thiagarajan, A decompositional approach to parameter estimation in pathway modeling: a case study of the Akt and MAPK pathways and their crosstalk, Bioinformatics, vol.22, issue.14, pp.271-280, 2006.
DOI : 10.1093/bioinformatics/btl264

S. Soliman, Finding minimal P/T-invariants as a CSP, Proceedings of the fourth Workshop on Constraint Based Methods for Bioinformatics WCB'08, 2008.

E. Grafahrend-belau, F. Schreiber, M. Heiner, A. Sackmann, B. H. Junker et al., Modularization of biochemical networks based on classification of Petri net t-invariants, BMC Bioinformatics, vol.9, issue.1
DOI : 10.1186/1471-2105-9-90

F. Nabli and S. Soliman, Steady-state solution of biochemical systems, beyond S-systems via T-invariants, Proceedings of the 8th International Conference on Computational Methods in Systems Biology, CMSB '10, pp.14-22, 2010.
DOI : 10.1145/1839764.1839768

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

V. Hárs and J. Tóth, On the inverse problem of reaction kinetics, Colloquia Mathematica Societatis János Bolyai, pp.363-379, 1979.

G. Szederkényi, J. R. Banga, and A. A. Alonso, Inference of complex biological networks: distinguishability issues and optimization-based solutions, BMC Systems Biology, vol.5, issue.1, pp.177-187, 2011.
DOI : 10.1049/iet-syb:20060079

S. Soliman and M. Heiner, A Unique Transformation from Ordinary Differential Equations to Reaction Networks, PLoS ONE, vol.482, issue.12
DOI : 10.1371/journal.pone.0014284.g007
URL : https://hal.archives-ouvertes.fr/hal-01431261

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. Hucka, S. Hoops, S. M. Keating, L. N. Nicolas, S. Sahle et al., Systems biology markup language (SBML) level 2: Structures and facilities for model definitions, Nature

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

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.

F. Fages and S. Soliman, Abstract interpretation and types for systems biology, Theoretical Computer Science, vol.403, issue.1, pp.52-70, 2008.
DOI : 10.1016/j.tcs.2008.04.024
URL : https://hal.archives-ouvertes.fr/hal-01431355

S. Soliman, A Stronger Necessary Condition for the Multistationarity of Chemical Reaction Networks, Bulletin of Mathematical Biology, vol.1, issue.3, pp.2289-230310, 2013.
DOI : 10.1007/s11538-013-9893-7
URL : https://hal.archives-ouvertes.fr/hal-00772438

C. Soulé, Mathematical approaches to differentiation and gene regulation, Comptes Rendus Biologies, vol.329, issue.1, pp.13-20, 2006.
DOI : 10.1016/j.crvi.2005.10.002

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

E. H. Snoussi, Necessary Conditions for Multistationarity and Stable Periodicity, Journal of Biological Systems, vol.06, issue.01, pp.3-9, 1998.
DOI : 10.1142/S0218339098000042

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

M. Kaufman, C. Soulé, and R. Thomas, A new necessary condition on interaction graphs for multistationarity, Journal of Theoretical Biology, vol.248, issue.4, pp.675-685, 2007.
DOI : 10.1016/j.jtbi.2007.06.016

K. W. Kohn, Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems, Molecular Biology of the Cell, vol.10, issue.8, pp.2703-2734, 1999.
DOI : 10.1091/mbc.10.8.2703

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

T. S. Gardner, M. Dolnik, and J. J. Collins, A theory for controlling cell cycle dynamics using a reversibly binding inhibitor, Proceedings of the National Academy of Sciences of the United States of America, pp.14190-14195, 1998.
DOI : 10.1073/pnas.95.24.14190

T. Matsuo, S. Yamaguchi, S. Mitsui, A. Emi, F. Shimoda et al., Control Mechanism of the Circadian Clock for Timing of Cell Division in Vivo, Science, vol.302, issue.5643, pp.255-259, 2003.
DOI : 10.1126/science.1086271

J. J. Tyson, Modeling the cell division cycle: cdc2 and cyclin interactions., Proceedings of the National Academy of Sciences, vol.88, issue.16, pp.7328-7332, 1991.
DOI : 10.1073/pnas.88.16.7328

A. Goldbeter, A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase., Proceedings of the National Academy of Sciences, vol.88, issue.20, pp.9107-9111, 1991.
DOI : 10.1073/pnas.88.20.9107