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Journal Article

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.

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

Zanudo JGT, Steinway SN, Albert R. 2018. Discrete dynamic network modeling of oncogenic signaling: Mechanistic insights for personalized treatment of cancer. Current Opinion in Systems Biology. 9:1-10.

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.

Wood W, Faria C, Jacinto A. 2006. Distinct mechanisms regulate hemocyte chemotaxis during development and wound healing in Drosophila melanogaster.. The Journal of cell biology. 173(3):405-16. Abstract

Amanai K, Jiang J. 2001. Distinct roles of Central missing and Dispatched in sending the Hedgehog signal.. Development (Cambridge, England). 128(24):5119-27. 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.

Irvine KD, Vogt TF. 1997. Dorsal—ventral signaling in limb development. Current Opinion in Cell Biology. 9(6):867-876.

Queralt E, Lehane C, Novak B, Uhlmann F. 2006. Downregulation of PP2A(Cdc55) phosphatase by separase initiates mitotic exit in budding yeast.. Cell. 125(4):719-32. Abstract

Royet J. 2004. Drosophila melanogaster innate immunity: an emerging role for peptidoglycan recognition proteins in bacteria detection.. Cellular and molecular life sciences : CMLS. 61(5):537-46. Abstract

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

Alcedo J, Ayzenzon M, Von Ohlen T, Noll M, Hooper JE. 1996. The Drosophila smoothened gene encodes a seven-pass membrane protein, a putative receptor for the hedgehog signal.. Cell. 86(2):221-32. Abstract

Valanne S, Wang J-H, Rämet M. 2011. The Drosophila Toll signaling pathway.. Journal of immunology (Baltimore, Md. : 1950). 186(2):649-56. Abstract

Gobert V, Gottar M, Matskevich AA, Rutschmann S, Royet J, Belvin M, Hoffmann JA, Ferrandon D. 2003. Dual activation of the Drosophila toll pathway by two pattern recognition receptors.. Science (New York, N.Y.). 302(5653):2126-30. 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.

Thieffry D, Thomas R. 1995. Dynamical behaviour of biological regulatory networks--II. Immunity control in bacteriophage lambda.. Bulletin of mathematical biology. 57(2):277-97. 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.

Wartlick O, Mumcu P, Kicheva A, Bittig T, Seum C, Jülicher F, González-Gaitán M. 2011. Dynamics of Dpp signaling and proliferation control.. Science (New York, N.Y.). 331(6021):1154-9. Abstract

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.

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.