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Biblio

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2011
Chaouiya C.  2011.  Computational BiologyModeling in Systems BiologyA Modular, Qualitative Modeling of Regulatory Networks Using Petri Nets. 16:253-279.
Naldi A, Remy E, Thieffry D, Chaouiya C.  2011.  Dynamically consistent reduction of logical regulatory graphs. Theoretical Computer Science. 412(21):2207-2218.
2012
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
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
2013
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
2014
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.
Mombach J, Bugs C, Chaouiya C.  2014.  Modelling the onset of senescence at the G1/S cell cycle checkpoint. BMC Genomics. 15:S7.
2015
Abou-Jaoudé W, Monteiro PT, Naldi A, Grandclaudon M, Soumelis V, Chaouiya C, Thieffry D.  2015.  Model checking to assess T-helper cell plasticity. Frontiers in Bioengineering and Biotechnology. 2(86) Abstract
Remy E, Rebouissou S, Chaouiya C, Zinovyev A, Radvanyi F, Calzone L.  2015.  A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis.. Cancer research. Abstract
Cohen DPA, Martignetti L, Robine S, Barillot E, Zinovyev A, Calzone L.  2015.  Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration.. PLoS computational biology. 11(11):e1004571. Abstract
2016
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.
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
Sánchez L, Chaouiya C.  2016.  Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells.. BMC systems biology. 10(1):37. Abstract
2017
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
2018
Sánchez L, Chaouiya C.  2018.  Logical modelling uncovers developmental constraints in primary sex determination of chicken gonads. J. R. Soc. Interface. . 15
Letort G, Montagud A, Stoll G, Heiland R, Calzone EBAZL, Macklin P.  2018.  PhysiBoSS: a multi-scale agent-based modelling framework integrating physical dimension and cell signalling. Bioinformatics. 35(7):1188–1196.
2020
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)
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.
Cacace E, Collombet S, Thieffry D.  2020.  Logical modeling of cell fate specification - Application to T cell commitment. Current Topics in Developmental Biology.
Selvaggio G, Canato S, Pawar A, Monteiro PT, Janody F, Chaouiya C.  2020.  Hybrid epithelial-mesenchymal phenotypes are controlled by microenvironmental factors. Cancer Research.
2021
Béal J, Pantolini L, Noël V, Barillot E, Calzone L.  2021.  Personalized logical models to investigate cancer response to BRAF treatments in melanomas and colorectal cancers. PLoS Comput. Biol..
Submitted
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..
Montagud A, Béal J, Tobalina L, Traynard P, Subramanian V, Szalai B, Alföldi R, Puskás L, Valencia A, Barillot E et al..  Submitted.  Patient-specific Boolean models of signaling networks guide personalized treatments.


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