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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.

Ptachne M. 1992. Genetic Switch. Phage Lambda and Higher Organisms (second ed.).

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.

Sánchez-Osorio I, Hernández-Martínez1 CA, Martínez-Antonio A. Submitted. Exploring Asymmetric Cell Division in Caulobacter Crescentus Using Logic Modeling.

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)

Ligoxygakis P, Pelte N, Hoffmann JA, Reichhart J-M. 2002. Activation of Drosophila Toll during fungal infection by a blood serine protease.. Science (New York, N.Y.). 297(5578):114-6. Abstract

O'Neill EM, Rebay I, Tjian R, Rubin GM. 1994. The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.. Cell. 78(1):137-47. Abstract

Lee JJ, Ekker SC, von Kessler DP, Porter JA, Sun BI, Beachy PA. 1994. Autoproteolysis in hedgehog protein biogenesis.. Science (New York, N.Y.). 266(5190):1528-37. Abstract

Weber ANR, Tauszig-Delamasure S, Hoffmann JA, Lelièvre E, Gascan H, Ray KP, Morse MA, Imler J-L, Gay NJ. 2003. Binding of the Drosophila cytokine Spätzle to Toll is direct and establishes signaling.. Nature immunology. 4(8):794-800. Abstract

Brooks A, Dou W, Yang X, Brosnan T, Pargett M, Raftery LA, Umulis DM. 2012. BMP signaling in wing development: A critical perspective on quantitative image analysis.. FEBS letters. 586(14):1942-52. Abstract

Sizek H, Hamel A, Deritei D, Campbell S, Regan ER. 2019. Boolean model of growth signaling, cell cycle and apoptosis predicts the molecular mechanism of aberrant cell cycle progression driven by hyperactive PI3K. PLOS Computational Biology. 15(3)

Davidich MI, Bornholdt S. 2008. Boolean network model predicts cell cycle sequence of fission yeast. PloS one. 3(2):e1672. Abstract

Sutherland D, Samakovlis C, Krasnow MA. 1996. branchless encodes a Drosophila FGF homolog that controls tracheal cell migration and the pattern of branching.. Cell. 87(6):1091-101. Abstract

Porter JA, Young KE, Beachy PA. 1996. Cholesterol modification of hedgehog signaling proteins in animal development.. Science (New York, N.Y.). 274(5285):255-9. Abstract

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.

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.

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

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.

Pai LM, Barcelo G, Schüpbach T. 2000. D-cbl, a negative regulator of the Egfr pathway, is required for dorsoventral patterning in Drosophila oogenesis.. Cell. 103(1):51-61. 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.