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Book
Chaouiya C.  2011.  Computational BiologyModeling in Systems BiologyA Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. 16:253-279.
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.
Book Chapter
Naldi A, Thieffry D, Chaouiya C.  2007.  Decision Diagrams for the Representation and Analysis of Logical Models of Genetic Networks. Computational Methods in Systems Biology. 4695:233-247.
Chaouiya C, Naldi A, Thieffry D.  2012.  Logical Modelling of Gene Regulatory Networks with GINsim.. Methods in molecular biology (Clifton, N.J.). 804:463-79. Abstract
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.
Journal Article
Kondratova M, Barillot E, Zinovyev A, Calzone L.  2020.   Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response . Cancers. 12(12)
Verlingue L, Dugourd A, Stoll G, Barillot E, Calzone L, Londoño-Vallejo A.  2016.  A comprehensive approach to the molecular determinants of lifespan using a Boolean model of geroconversion. Aging Cell. :n/a–n/a.
Ciglar L, Furlong EEM.  2009.  Conservation and divergence in developmental networks: a view from Drosophila myogenesis.. Current opinion in cell biology. 21(6):754-60. Abstract
Fauré A, Vreede BMI, Sucena E, Chaouiya C.  2014.  A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects. PLoS Comput Biol. 10(3):e1003527.
Naldi A, Carneiro J, Chaouiya C, Thieffry D.  2010.  Diversity and Plasticity of Th Cell Types Predicted from Regulatory Network Modelling. PLoS Computational Biology. 6(9):e1000912.
Vincent S, Wilson R, Coelho C, Affolter M, Leptin M.  1998.  The Drosophila protein Dof is specifically required for FGF signaling.. Molecular cell. 2(4):515-25. Abstract
Chen Y, Struhl G.  1996.  Dual roles for patched in sequestering and transducing Hedgehog.. Cell. 87(3):553-63. Abstract
Fauré A, Naldi A, Chaouiya C, Thieffry D.  2006.  Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle.. Bioinformatics (Oxford, England). 22(14):e124-31. Abstract
Gonzalez A, Chaouiya C, Thieffry D.  2006.  Dynamical Analysis of the Regulatory Network Defining the Dorsal-Ventral Boundary of the Drosophila Wing Imaginal Disc. Genetics. 174(3):1625-1634.
Checcoli A, Pol JG, Naldi A, Noel V, Barillot E, Kroemer G, Thieffry D, Calzone L, Stoll G.  2020.  Dynamical Boolean Modeling of Immunogenic Cell Death.
Naldi A, Remy E, Thieffry D, Chaouiya C.  2011.  Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science. 412(21):2207-2218.
Gonzalez GA, Naldi A, Sánchez L, Thieffry D, Chaouiya C.  2006.  GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks.. Bio Systems. 84(2):91-100. Abstract
Selvaggio G, Canato S, Pawar A, Monteiro PT, Janody F, Chaouiya C.  2020.  Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors. Cancer Research.
Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ.  2004.  Integrative analysis of cell cycle control in budding yeast.. Molecular biology of the cell. 15(8):3841-62. Abstract
Grieco L, Calzone L, Bernard-Pierrot I, Radvanyi F, Kahn-Perlès B, Thieffry D.  2013.  Integrative modelling of the influence of MAPK network on cancer cell fate decision.. PLoS computational biology. 9(10):e1003286. Abstract
Corral-Jara KF, Chauvin C, Abou-Joudé W, Grandclaudon M, Naldi A, Soumelis V, Thieffry D.  Submitted.  Interplay between Smad2 and STAT5A is a critical determinant of IL- 17A/IL-17F differential expression..
Cacace E, Collombet S, Thieffry D.  2020.  Logical modeling of cell fate specification - Application to T cell commitment. Current Topics in Developmental Biology.
Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D.  2017.  Logical modeling of lymphoid and myeloid cell specification and transdifferentiation.. Proceedings of the National Academy of Sciences of the United States of America. 114(23):5792-5799. Abstract
Gonzalez A, Chaouiya C, Thieffry D.  2008.  Logical modelling of the role of the Hh pathway in the patterning of the Drosophila wing disc. Bioinformatics. 24(16):i234-i240.
Sánchez L, Chaouiya C.  2018.  Logical modelling uncovers developmental constraints in primary sex determination of chicken gonads. J. R. Soc. Interface. . 15


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