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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.
Conference Proceedings
Sánchez-Villanueva J, N’Guyen L, Poplineau M, Duprez E, Remy É, Thieffry D.  2024.  Dynamical modelling of the regulatory network underlying Retinoic Acid resistance in Acute Promyelocytic Leukaemia. European Conference in Computational Biology.
Journal Article
Niarakis A, Bounab Y, Grieco L, Roncagalli R, Hesse A-M, Garin J, Malissen B, Daëron M, Thieffry D.  2014.  Computational modeling of the main signaling pathways involved in mast cell activation. Current topics in microbiology and immunology. 382:69-93. Abstract
Hernadez C, Naldi A, Thomas-Chollier M, Thieffry D.  Submitted.  Computational verification of large logical models - application to the prediction of T cell response to checkpoint inhibitors.
Sanchez-Villanueva JA, Rodriguez-Jorge O, Ramirez-Pliego O, Rosas-Salgado G, Abou-Jaoudé W, Hernandez C, Naldi A, Thieffry D, Santana MA.  2019.  Contribution of ROS and metabolic status to neonatal and adult CD8+ T cell activation. PLoS One.
Rodríguez-Jorge O, Kempis-Calanis LA, Abou-Jaoudé W, Gutiérrez-Reyna DY, Hernandez C, Ramirez-Pliego O, Thomas-Chollier M, Spicuglia S, Santana MA, Thieffry D.  2019.  Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation.. Science Signaling.
Floc’hlay S, Molina MD, Hernandez C, Haillot E, Thomas-Chollier M, Lepage T, Thieffry D.  2020.  Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo. Development.
Flobak Å, Baudot A, Remy E, Thommesen L, Thieffry D, Kuiper M, Lægreid A.  2015.  Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling.. PLoS computational biology. 11(8):e1004426. Abstract
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.
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
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.
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..
Sánchez L, Thieffry D.  2001.  A Logical Analysis of the Drosophila Gap-gene System. Journal of Theoretical Biology. 211(2):115-141.
Traynard P, Fauré A, Fages F, Thieffry D.  2016.  Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. Bioinformatics. 32:i772-i780. Abstract
Cacace E, Collombet S, Thieffry D.  2020.  Logical modeling of cell fate specification - Application to T cell commitment. Current Topics in Developmental Biology.
Nuñez-Reza KJ, Naldi A, Sánchez-Jiménez A, Leon-Apodaca AV, Santana A, Thomas-Chollier M, Thieffry D, Medina-Rivera A.  2021.  Logical modeling of in vitro differentiation of human monocytes into dendritic cells unravels novel transcriptional regulatory interactions.
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
Fauré A, Thieffry D.  2009.  Logical modelling of cell cycle control in eukaryotes: a comparative study. Molecular BioSystems. 5(12):1569.
Mbodj A, Junion G, Brun C, Furlong EEM, Thieffry D.  2013.  Logical modelling of Drosophila signalling pathways.. Molecular bioSystems. 9(9):2248-58. Abstract
Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A.  2010.  Mathematical modelling of cell-fate decision in response to death receptor engagement. PLoS computational biology. 6(3):e1000702. Abstract
Calzone L, Tournier L, Fourquet S, Thieffry D, Zhivotovsky B, Barillot E, Zinovyev A.  2010.  Mathematical modelling of cell-fate decision in response to death receptor engagement.. PLoS computational biology. 6(3):e1000702. Abstract


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