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Cacace E, Collombet S, Thieffry D.  2020.  Logical modeling of cell fate specification - Application to T cell commitment. Current Topics in Developmental Biology.
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
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.
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.
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
Coolen M, Thieffry D, Drivenes Ø, Becker TS, Bally-Cuif L.  2012.  miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors.. Developmental cell. 22(5):1052-64. 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..
F
Fauré A, Thieffry D.  2009.  Logical modelling of cell cycle control in eukaryotes: a comparative study. Molecular BioSystems. 5(12):1569.
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
Fauré A, Naldi A, Lopez F, Chaouiya C, Ciliberto A, Thieffry D.  2009.  Modular logical modelling of the budding yeast cell cycle.. Molecular bioSystems. 5(12):1787-96. Abstract
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
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.
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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
H
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.
M
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
Mbodj A, Junion G, Brun C, Furlong EEM, Thieffry D.  2013.  Logical modelling of Drosophila signalling pathways.. Molecular bioSystems. 9(9):2248-58. Abstract
N
Naldi A, Remy E, Thieffry D, Chaouiya C.  2011.  Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science. 412(21):2207-2218.
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.
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.
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
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.
R
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.
S
Sahin O, Fröhlich H, Löbke C, Korf U, Burmester S, Majety M, Mattern J, Schupp I, Chaouiya C, Thieffry D et al..  2009.  Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC systems biology. 3:1. Abstract


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