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2021

  • TotemBioNet Enrichment Methodology: Application to the Qualitative Regulatory Network of the Cell Metabolism.
    L. Gibart, G. Bernot, H. Collavizza and J.-P. Comet.
    BIOINFORMATICS 2021 : 12th International Conference on Bioinformatics Models, Methods and Algorithms, online. 11-13 February, pp. 85-92, 2021.
    [.pdf ]

2020

  • What is a cell cycle checkpoint? The TotemBioNet answer.
    D. Boyenval, G. Bernot, H. Collavizza and J.-P. Comet.
    the 18th International Conference on Computational Methods in Systems Biology (CMSB), online. September 23-25, 2020. LNCS vol. 12314, pp. 362-372, 2020.
    [.pdf ]
  • Logics, Automata and Biology. MOMI'2020, Sophia-Antipolis (France), 10 march 2020.
    J.-P. Comet
    MOMI'2020, Sophia-Antipolis (France), 10 march 2020.

2019

  • Chemical in vitro bioactivity profiles are not informative about the long-term in vivo endocrine mediated toxicity.
    D. Rouquié, F. Schorsch, I. Grenet, J.-P. Comet, J. Wichard, N. Ryan.
    Computational Toxicology 12:100098, nov. 2019.
    [.pdf ]
  • Stacked Generalization with Applicability Domain Outperforms simple QSAR on in vitro Toxicological Data.
    I. Grenet, K. Merlo, J.-P. Comet, R. Tertiaux, Rouquié, D. and F. Dayan
    J. Chemical Information and Modeling, 59(4):1486--1496, 2019.
    [.pdf ]
  • A Genetically Modified Hoare Logic.
    G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O.F. Roux.
    Theoretical Computer Science, 765:145--157, 2019.
    [.pdf, annexes ]

2018

  • G-networks to predict the outcome of sensing of toxicity.
    I. Grenet, Y. Yin, J.-P. Comet
    Sensors, 18:3483, 2018.
    [.pdf ]
  • Identification of Dynamic Parameters for Gene Networks.
    J. Behaegel, J.-P. Comet and M. Pelleau.
    the 30th IEEE International Conference on Tools with Artificial Intelligence (ICTAI), Volos, Greece. November 5-7, 2018. pp.
  • Machine Learning to Predict Toxicity of Compounds.
    I. Grenet, Y. Yin, J.-P. Comet, E. Gelenbe.
    The 27th International Conference on Artificial Neural Networks (ICANN), Rhodes, Greece. 5-7 October 2018. LNCS vol. 11139, pp. 335-345
    [.pdf ]
  • Identification de paramètres dynamiques de réseaux de gènes
    J. Behaegel, J.-P. Comet, M. Pelleau
    Quatorzièmes Journées Francophones de Programmation par Contraintes, 12-15 juin 2018
    [.pdf ]
  • A Genetically Modified Hoare Logic
    G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O.F. Roux
    Theoretical Computer Science, 2018. DOI 10.1016/j.tcs.2018.02.003,
    [.pdf ]

2017

  • Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks
    J. Behaegel, J.-P. Comet and M. Folschette
    International Symposium on Temporal Representation and Reasoning (TIME), Mons, Belgium. 16-18 October 2017. pp. 5:1-5:21
    [.pdf ]
  • Detecting Toxicity Pathways with a Formal Framework based on Equilibrium Changes
    B. Miraglio, G. Bernot, J.-P. Comet and C. Risso-De Faverney
    Computational Methods for Systems Biology (CMSB), Darmstadt, Germany. 27-29 September 2017. LNBI vol. 10545, pp. 196-213
    [.pdf ]
  • A Qualitative Framework Dedicated to Toxicology
    B. Miraglio, G. Bernot, J.-P. Comet and C. Risso-De Faverney
    International Conference on Bioinformatics Models, Methods and Algorithms, Porto, Portugal. 21-23 february 2017
    [.pdf ]
  • Number of fixed points and disjoint cycles in monotone Boolean networks
    J. Aracena, A. Richard and L. Salinas.
    SIAM Journal on Discrete Mathematics, 31(3):1702-1725, 2017.
    [.pdf ]
  • Fixed points in conjunctive networks and maximal independent sets in graph contractions
    J. Aracena, A. Richard and Lilian Salinas.
    Journal of Computer and System Sciences, 88:145-163, 2017.
    [.pdf ]

2016

  • A hybrid Hoare logic for gene network models.
    J. Behaegel, J.-P. Comet, and M. Folschette.
    ArXiv: 1610.06715, Oct. 2016.
    [.pdf ]
  • (Mathematical) Logic for Systems Biology.
    Joëlle Despeyroux.
    invited paper. 14th Intl. Conference on Computational Methods in Systems Biology (CMSB'2016). Springer LNCS 9859, September 2016.
    [.pdf ]
  • Hybrid and Subexponential Linear Logics.
    Joëlle Despeyroux, Carlos Olarte and Elaine Pimentel.
    11th Workshop on Logical and Semantic Frameworks, with Applications (LSFA'2016) 2016.
    [.pdf ]
  • Event-based run-time adaptation in communication-centric systems.
    Cinzia Di Giusto, Jorge A. Pérez.
    Formal Asp. Comput. 28(4): 531-566, 2016.
  • A hybrid model of cell cycle in mammals.
    J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon, F. Delaunay.
    J. of Bioinformatics and Computational Biology 14(1):1640001, 2016.
    [.pdf ]
  • Reduction and Fixed Points of Boolean Networks and Linear Network Coding Solvability.
    M. Gadouleau, A. Richard and E. Fanchon.
    IEEE Transaction on Information Theory 62(5):2504-2519, 2016.
    [.arxiv ]
  • Simple dynamics on graphs.
    M. Gadouleau and A. Richard.
    Theoretical Computer Science 628:62-77, 2016.
    [.arxiv ]
  • Hybrid Gene Networks: a new Framework and a Software Environment.
    E. Cornillon, J.-P. Comet, G. Bernot, G. Enée.
    In Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology, Modelling Complex Biological Systems in the Context of Genomics eds. P. Amar, F. Képès and V. Norris). EDP Science, 2016.
    [.pdf ]
  • Towards a Computer Aided Toxicology.
    B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-de Faverney.
    In Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology, Modelling Complex Biological Systems in the Context of Genomics eds. P. Amar, F. Képès and V. Norris). EDP Science, 2016.
    [.pdf ]

2015

  • A hybrid model of cell cycle in mammals.
    J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon, F. Delaunay.
    6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2015) November 22-25, 2015
    [.pdf ]
  • Fixed points of Boolean networks, guessing graphs, and coding theory.
    M. Gadouleau, A. Richard and S. Riis.
    SIAM Journal on Discrete Mathematics to appear, 2015
    [.pdf ]
  • Disciplined structured communications with disciplined runtime adaptation.
    C. Di Giusto, J. A. Pérez.
    Science of Computer Programming 97: 235-265, 2015
    [.pdf ]
  • Probabilistic Gene Network.
    K.J.E. Carpio, G. Bernot, J.-P. Comet, F. Diener.
    In Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology, Modelling Complex Biological Systems in the Context of Genomics (eds. P. Amar, F. Képès and V. Norris), pp. 77-90, EDP Science, 2015.
    [.pdf ]
  • Fixed point theorems for Boolean networks expressed in terms of forbidden subnetworks.
    A. Richard.
    Theoretical Computer Science 583:1-26, 2015.
    [.pdf ]

2014

  • A Logical Framework for Systems Biology.
    E. de Maria, J. Despeyroux and A.P. Felty.
    1st International Conference on Formal Methods in Macro-Biology (FMMB), Springer LNCS 8738, September 2014, 20 pp., to appear.
    [.pdf ]
  • Formal methods applied to gene network modelling.
    G. Bernot, J.-P. Comet and E.H. Snoussi.
    In Logical Modeling of Biological Systems (eds. K. Inoue and L. Fariñas), preprint de 36 pages, 2014.
    [.pdf ]
  • Maximum number of fixed points in AND-OR-NOT networks.
    J. Aracena, A. Richard, L. Salinas.
    Journal of Computer and System Sciences, 80(7):1175-1190, 2014.
    [.pdf ]
  • Modelisation of the regulation of protein synthesis following fertilization in sea urchin shows requirement of two processes: a destabilization of eIF4E:4E-BP complex and a great stimulation of the 4E-BP-degradation mechanism, both rapamycin-sensitive.
    S. Laurent, A. Richard, O. Mulner-Lorillon, J. Morales, D. Flament, V. Glippa, J. Bourdon, P. Gosselin, A. Siegel, P. Cormier, R. Bellé.
    Frontiers in Genetics, 5(117), 2014.
    [.pdf ]

2013

  • On circuit functionality in Boolean networks.
    J.-P. Comet, A. Richard, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E.H. Snoussi, D. Thieffry.
    Bulletin of Mathematical Biology,, 75(6):906-919, 2013.
    [.pdf ]
  • A Hybrid Linear Logic for Constrained Transition Systems.
    J. Despeyroux and K. Chaudhuri.
    In Types for Proofs and Programs, post- proceedings of TYPES 2013, Leibniz International Proceedings in Informatics, 2013.
    [.pdf ]
  • Regulatory networks.
    G. Bernot, J.-P. Comet and C. Risso-de Faverney.
    In Computational Toxicology,, (eds. B. Reisfeld and A. Mayeno), Volume II, pp 215-234, 2013.
    [.pdf ]
  • From kernels in directed graphs to fixed points and negative cycles in boolean networks.
    A. Richard and P. Ruet.
    Discrete Applied Mathematics,, 161(7-8):1106-1117, 2013.
    [.pdf ]
  • Modeling and analysis of gene regulatory networks.
    G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, and F. Dayan.
    In Modeling in Computational Biology and Biomedicine, A Multidisciplinary Endeavor,, (eds. F. Cazals and P. Kornprobst), pp. 47-80, Springer, 2013.
    [.pdf ]

2012

  • Boolean models of biosurfactants production in Pseudomonas fluorescens.
    A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel and A. Merieau.
    PlosOne,, 7(1):e24651, 2012.
    [.pdf ]
  • On the impact of the distance between two genes on their interaction curve.
    S. Taati, E. Formenti, J.-P. Comet and G. Bernot.
    Journal of Mathematical Biology,, 64(1):131-147, 2012.
    [.pdf ]
  • Simplified models for the mammalian circadian clock.
    J.-P. Comet, G. Bernot, A. Das, F. Diener, C. Massot and A. Cessieux.
    In Proc. of the Evry Spring school on Modelling complex biological systems in the context of genomics,, (eds. P. Amar, F. Képès and V. Norris). pp. 85-106, EDP Science, 2012.
    [.pdf ]
    Also published in 3rd International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2012), Bangkok, Thailand, October 3-5, 2012. Procedia Computer Science n. 11, pp. 127-138, 2012.
    [.pdf ]
  • Simplified models for the mammalian circadian clock.
    J.-P. Comet, G. Bernot, A. Das, F. Diener, C. Massot and A. Cessieux.
    In Proc. of the Evry Spring school on Modelling complex biological systems in the context of genomics,, (eds. P. Amar, F. Képès and V. Norris). pp. 85-106, EDP Science, 2012.
    [.pdf ]

2011

  • Embedding of biological regulatory networks and properties preservation.
    M. Mabrouki, M. Aiguier, J.-P. Comet, P. Le Gall and A. Richard.
    Mathematics in Computer Science,, 5(3):263-288, special issue, 2011.
    [.pdf ]
  • Stable periodicities and negative circuits in differential systems.
    A. Richard, and J.-P. Comet.
    Journal of Mathematical Biology,, 63(3):593-600, 2011. See also Erratum, 2015.
    [.pdf, .pdf  ]
  • Local negative circuits and fixed points in non-expansive boolean networks.
    A. Richard.
    Discrete Applied Mathematics, 159(11):1085-1093, 2011.
    [.pdf ]

2010

  • Introducing continuous time in discrete models of gene regulatory networks.
    J.-P. Comet and G. Bernot.
    In Proc. of the Evry Spring school on Modelling complex biological systems in the context of genomics, (eds. P. Amar, F. Képès and V. Norris). pp. 61-94, EDP Science, ISBN : 978-2-7598-0545-7, 2010.
    [.pdf ]
  • A formal model for gene regulatory networks with time delays.
    J.-P. Comet, J. Fromentin, G. Bernot and O. Roux.
    1st International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2010), Bangkok, Thailand, November 3-5, 2010. Volume 115 of CCIS, pp. 1-13, 2010.
    [.pdf ]
  • Gene regulatory networks: the impact of distance between genes.
    G. Bernot, J.-P. Comet, E. Formenti and S. Taati.
    19th International Symposium in Mathematical Theory of Networks and Systems, MTNS'2010, Budapest (Hungary), July 5-9, 2010.
    [.pdf ]
  • Topological Fixed Points in Boolean Networks.
    L. Paulevé and A. Richard.
    Comptes Rendus de l'Académie des Sciences - Series I - Mathematics, 348(15-16):825 - 828, 2010.
    [.pdf ]
  • Negative circuits and sustained oscillations in asynchronous automata networks.
    A. Richard.
    Advances in Applied Mathematics, 44(4):378-392, 2010.
    [.pdf ]