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Chaouiya C, Remy E, Mossé B, Thieffry D. 2003. Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework. Positive Systems. 294:830-832.

Mbodj A, Gustafson HE, Ciglar L, Junion G, GONZALEZ A, GIRARDOT C, PERRIN L, Furlong EEM, Thieffry D. 2016. Qualitative Dynamical Modelling Can Formally Explain Mesoderm Specification and Predict Novel Developmental Phenotypes. PLoS Comput Biol. 12:1-17. Abstract

Chaouiya C, REMY E, Ruet P, Thieffry D. 2004. Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. 25th International Conference on Application and Theory of Petri Nets. 3099:137-156.

Simão E, REMY E, Thieffry D, Chaouiya C. 2005. Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.coli.. Bioinformatics (Oxford, England). 21 Suppl 2:ii190-6. Abstract