Application of formal methods to biological regulatory networks: extending Thomas' asynchronous logical approach with temporal logic.

By G. Bernot, J. Comet, A. Richard, J. Guespin. Journal of Theoretical Biology, 2004

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Robustness and fragility of Boolean models for genetic regulatory networks. (2005, background): “…state variable depends on the update order an , in the absence of temporal information, the Thomas formalism focuses on determining the steady states, where the state and image variables coincide [Mendoza et al., 1999, Sánchez and Thieffry, 2001, Ghysen and Thomas, 2003, Bernot et al., 2004].”
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle (2006, methodology): “Finally, we are presently evaluating the application of temporal logic formalisms (e.g., Computational Tree Logics) to assess the existence of specific dynamical pathways, or to encompass specific temporal information ( Bernot et al., 2004; Batt et al., 2005).”
Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli (2005, unknown): “Most approaches start from discrete models, such as Petri nets [18], process algebras [19], concurrent transition systems [7], rewriting logic [13], and Boolean networks and their generalizations [6].”