J. Aracena, Maximum number of fixed points in regulatory boolean networks, Bulletin of Mathematical Biology, vol.70, issue.5, pp.1398-1409, 2008.

J. Aracena, J. Demongeot, and E. Goles, Positive and negative circuits in discrete neural networks, IEEE Transactions of Neural Networks, vol.15, pp.77-83, 2004.

J. Aracena, E. Goles, A. Moreira, and L. Salinas, On the robustness of update schedules in Boolean networks, Biosystems, vol.97, issue.1, pp.1-8, 2009.

J. Aracena, A. Richard, and L. Salinas, Number of fixed points and disjoint cycles in monotone boolean networks, SIAM Journal on Discrete Mathematics, vol.31, issue.3, pp.1702-1725, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01630477

J. Baetens, P. V. Der-weeën, and B. D. Baets, Effect of asynchronous updating on the stability of cellular automata, Chaos, Solitons & Fractals, vol.45, issue.4, pp.383-394, 2012.

S. Balaguer, T. Chatain, and S. Haar, A concurrency-preserving translation from time Petri nets to networks of timed automata, Formal Methods in System Design, vol.40, issue.3, pp.330-355, 2012.
URL : https://hal.archives-ouvertes.fr/inria-00638283

P. Baldan, A. Bruni, A. Corradini, B. König, C. Rodríguez et al., Efficient unfolding of contextual Petri nets, TCS, vol.449, pp.2-22, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00776752

P. Baldan, A. Corradini, and U. Montanari, Contextual Petri nets, asymmetric event structures, and processes, Information and Computation, vol.171, issue.1, pp.1-49, 2001.

N. Busi and G. M. Pinna, Non sequential semantics for contextual P/T nets, Application and Theory of Petri Nets, vol.1091, pp.113-132, 1996.

C. Chaouiya, Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, pp.210-219, 2007.

C. Chaouiya, A. Naldi, E. Remy, and D. Thieffry, Petri net representation of multi-valued logical regulatory graphs, Natural Computing, vol.10, issue.2, pp.727-750, 2011.

C. Chaouiya, E. Remy, P. Ruet, and D. Thieffry, Qualitative modelling of genetic networks: From logical regulatory graphs to standard Petri nets, 25th International Conference, vol.3099, pp.137-156, 2004.

T. Chatain, S. Haar, L. Jezequel, L. Paulevé, and S. Schwoon, Characterization of reachable attractors using Petri net unfoldings, Computational Methods in Systems Biology, vol.8859, pp.129-142, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01060450

T. Chatain, S. Haar, M. Koutny, and S. Schwoon, Non-atomic transition firing in contextual nets, Applications and Theory of Petri Nets, vol.9115, pp.117-136, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01241129

T. Chatain, S. Haar, and L. Paulevé, Boolean Networks: Beyond Generalized Asynchronicity, Cellular Automata and Discrete Complex Systems (AUTOMATA 2018), vol.10875, pp.29-42, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01768359

T. Chatain and L. Paulevé, Goal-Driven Unfolding of Petri Nets, Leibniz International Proceedings in Informatics (LIPIcs), vol.85, pp.1-18, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01392203

A. Cheng, J. Esparza, and J. Palsberg, Complexity results for 1-safe nets, Theoretical Computer Science, vol.147, issue.1&2, pp.117-136, 1995.

S. Collombet, C. Van-oevelen, J. L. Sardina-ortega, W. Abou-jaoudé, B. Di-stefano et al., Logical modeling of lymphoid and myeloid cell specification and transdifferentiation, Proc. Natl. Acad. Sci, vol.114, issue.23, pp.5792-5799, 2017.

J. Courtiat and D. Saïdouni, Relating maximality-based semantics to action refinement in process algebras, Formal Description Techniques VII, Proceedings of the 7th IFIP WG6.1 International Conference on Formal Description Techniques, vol.6, pp.293-308, 1994.

J. Esparza and K. Heljanko, Unfoldings -A Partial-Order Approach to Model Checking, 2008.

A. Garg, A. Di-cara, I. Xenarios, L. Mendoza, and G. De-micheli, Synchronous versus asynchronous modeling of gene regulatory networks, Bioinformatics, vol.24, issue.17, pp.1917-1925, 2008.

P. J. Goss and J. Peccoud, Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Proceedings of the National Academy of Sciences, vol.95, issue.12, pp.6750-6755, 1998.

R. Janicki and M. Koutny, Structure of concurrency, Theoretical Computer Science, vol.112, issue.1, pp.5-52, 1993.

R. Janicki and M. Koutny, Fundamentals of modelling concurrency using discrete relational structures, Acta Inf, vol.34, pp.367-388, 1997.

R. Janicki, P. E. Lauer, M. Koutny, and R. R. Devillers, Concurrent and maximally concurrent evolution of nonsequential systems, Theor. Comput. Sci, vol.43, issue.86, pp.90177-90182, 1986.

S. A. Kauffman, Metabolic stability and epigenesis in randomly connected nets, Journal of Theoretical Biology, vol.22, pp.437-467, 1969.

J. Kol?ák, D. ?afránek, S. Haar, and L. Paulevé, Parameter Space Abstraction and Unfolding Semantics of Discrete Regulatory Networks, Theoretical Computer Science, 2018.

Z. Mai and H. Liu, Boolean network-based analysis of the apoptosis network: Irreversible apoptosis and stable surviving, Journal of Theoretical Biology, vol.259, issue.4, pp.760-769, 2009.

P. Martínez-sosa and L. Mendoza, The regulatory network that controls the differentiation of t lymphocytes, Biosystems, vol.113, issue.2, pp.96-103, 2013.

M. Noual and S. Sené, Synchronism versus asynchronism in monotonic boolean automata networks. Natural Computing, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01479438

E. Palma, L. Salinas, and J. Aracena, Enumeration and extension of non-equivalent deterministic update schedules in boolean networks, Bioinformatics, vol.32, issue.5, pp.722-729, 2016.

L. Paulevé, Reduction of Qualitative Models of Biological Networks for Transient Dynamics Analysis, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017.

L. Popova-zeugmann, M. Heiner, and I. Koch, Time Petri nets for modelling and analysis of biochemical networks, Fundamenta Informaticae, vol.67, issue.1, pp.149-162, 2005.

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

A. Richard, Negative circuits and sustained oscillations in asynchronous automata networks, Advances in Applied Mathematics, vol.44, issue.4, pp.378-392, 2010.

C. Rodríguez and S. Schwoon, Cunf: A tool for unfolding and verifying Petri nets with read arcs, International Symposium on Automated Technology for Verification and Analysis, pp.492-495, 2013.

A. Rougny, C. Froidevaux, L. Calzone, and L. Paulevé, Qualitative dynamics semantics for SBGN process description, BMC Systems Biology, vol.10, issue.1, pp.1-24, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01332679

S. Schwoon,

B. Schönfisch and A. De-roos, Synchronous and asynchronous updating in cellular automata, Biosystems, vol.51, issue.3, pp.123-143, 1999.

L. J. Steggles, R. Banks, O. Shaw, and A. Wipat, Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach, Bioinformatics, vol.23, issue.3, pp.336-343, 2007.

D. Thieffry and R. Thomas, Dynamical behaviour of biological regulatory networks -II. Immunity control in bacteriophage lambda, Bulletin of Mathematical Biology, vol.57, pp.277-297, 1995.

R. Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, vol.42, issue.3, pp.90247-90253, 1973.

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, pp.772-780, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01378465

W. Vogler, Fairness and partial order semantics, Inf. Process. Lett, vol.55, issue.1, pp.33-39, 1995.

W. Vogler, Partial order semantics and read arcs, Theoretical Computer Science, vol.286, issue.1, pp.33-63, 2002.

J. Winkowski, Processes of contextual nets and their characteristics, Fundamenta Informaticae, vol.36, issue.1, 1998.