M. Blinov, J. Faeder, B. Goldstein, and W. Hlavacek, A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity, Bio Systems, vol.83, pp.136-151, 2006.

M. Blinov, J. R. Faeder, B. Goldstein, and W. S. Hlavacek, Bionetgen: software for rule-based modeling of signal transduction based on the interactions of molecular domains, Bioinformatics, p.20, 2004.

P. Boutillier, F. Camporesi, J. Coquet, J. Feret, K. Q. Ly et al., Kasa: a static analyzer for kappa, Proc. CMSB'18, LNCS/LNBI 11095, pp.285-291
URL : https://hal.archives-ouvertes.fr/hal-01888951

F. Camporesi, J. Feret, and K. Q. L´yl´y, Kade: a tool to compile kappa rules into (reduced) odes models, Proc. CMSB 2017, LNCS/LNBI 10545, pp.291-299

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Rule-based modelling of cellular signalling, Proc. CONCUR'07, vol.4703, pp.17-41, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00164297

V. Danos, J. Feret, W. Fontana, and J. Krivine, Abstract interpretation of cellular signalling networks, Proc. VMCAI'08, vol.4905, pp.83-97, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00528352

V. Danos, R. Harmer, and G. Winskel, Constraining rule-based dynamics with types, MSCS, vol.23, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00694492

V. Danos and C. Laneve, Formal molecular biology, TCS, vol.325, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00164591

E. J. Deeds, J. Krivine, J. Feret, V. Danos, and W. Fontana, Combinatorial complexity and compositional drift in protein interaction networks, PLoS ONE, vol.7, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00677889

A. Faure-de-pebeyre, Static analysis of the formation of polymers in rule-based models, 2018.

J. Feret, H. Koeppl, and T. Petrov, Stochastic fragments: A framework for the exact reduction of the stochastic semantics of rule-based models, IJSI, vol.7, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01098561

J. Feret and K. Q. L´yl´y, Reachability analysis via orthogonal sets of patterns, Proc. SASB'16, ENTCS, pp.27-48
URL : https://hal.archives-ouvertes.fr/hal-01379902

B. M. Gyori, J. A. Bachman, K. Subramanian, J. L. Muhlich, L. Galescu et al., From word models to executable models of signaling networks using automated assembly, Molecular Systems Biology, vol.13, 2017.

R. Harmer, Y. L. Cornec, S. Légaré, and I. Oshurko, Bio-curation for cellular signalling: The KAMI project, Proc. CMSB'17, vol.10545, pp.3-19, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01617185

P. Kim, L. Lu, Y. Xia, and M. Gerstein, Relating three-dimensional structures to protein networks provides evolutionary insights, Science, vol.314, 2006.

P. Kreyßig, Chemical Organisation Theory Beyond Classical Models: Discrete Dynamics and Rulebased Models, 2014.

A. Miné, A few graph-based relational numerical abstract domains, Proc. SAS'02, vol.2477, pp.117-132, 2002.

R. Tarjan, Depth first search and linear graph algorithms, SIAM Journal On Computing, vol.1, 1972.