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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.
Book Chapter
Sánchez-Osorio I, Hernández-Martínez1 CA, Martínez-Antonio A.  Submitted.  Exploring Asymmetric Cell Division in Caulobacter Crescentus Using Logic Modeling.
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
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
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
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.
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
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.
Chen Y, Struhl G.  1996.  Dual roles for patched in sequestering and transducing Hedgehog.. Cell. 87(3):553-63. 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.
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
Brunner D, Dücker K, Oellers N, Hafen E, Scholz H, Klämbt C.  1994.  The ETS domain protein pointed-P2 is a target of MAP kinase in the sevenless signal transduction pathway.. Nature. 370(6488):386-9. Abstract
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
Orlando DA, Lin CY, Bernard A, Wang JY, Socolar JES, Iversen ES, Hartemink AJ, Haase SB.  2008.  Global control of cell-cycle transcription by coupled CDK and network oscillators. Nature. 453(7197):944-7. Abstract
Duchek P, Somogyi K, Jékely G, Beccari S, Rørth P.  2001.  Guidance of cell migration by the Drosophila PDGF/VEGF receptor.. Cell. 107(1):17-26. 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.
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..
Kouhara H, Hadari YR, Spivak-Kroizman T, Schilling J, Bar-Sagi D, Lax I, Schlessinger J.  1997.  A lipid-anchored Grb2-binding protein that links FGF-receptor activation to the Ras/MAPK signaling pathway.. Cell. 89(5):693-702. Abstract
Sánchez L, Thieffry D.  2001.  A Logical Analysis of the Drosophila Gap-gene System. Journal of Theoretical Biology. 211(2):115-141.
Saez-Rodriguez J, Simeoni L, Lindquist JA, Hemenway R, Bommhardt U, Arndt B, Haus U-U, Weismantel R, Gilles ED, Klamt S et al..  2007.  A logical model provides insights into T cell receptor signaling.. PLoS computational biology. 3(8):e163. 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.
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


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