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Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets.

Chaouiya, Claudine; Remy, Elisabeth; Ruet, Paul; Thieffry, Denis

In: Proceedings of Applications and Theory of Petri Nets 2004: 25th International Conference, ICATPN 2004, Bologna, Italy, June 21-25, 2004, pages 137-156. Volume 3099 of Lecture Notes in Computer Science / Cortadella, Reisig (Eds.) --- Springer-Verlag, September 2004.

Abstract: In this paper, a systematic rewriting of logical genetic regulatory graphs in terms of standard Petri net models is proposed. We show that, in the Boolean case, the combination of the logical approach with the standard Petri net framework enables the analysis of isolated regulatory circuits, confirming their most fundamental dynamical properties. Furthermore, two more realistic applications are also presented, the first dealing with the control of the early cell cycles in the developing fly, the second dealing with flower morphogenesis. The combination of logical and Petri net formalisms open new prospects for the delineation of specific relationships between the feedback structure and the dynamical properties of complex regulatory systems. Moreover, this approach should ease the definition of integrated models of networks encompassing various kinds of interactions: genetic or metabolic regulations, signal transduction cascades...

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