Publications

[Journals] [Books chapters and editions] [Conferences and workshops] [Miscellaneous]

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Journals

International journals (23)

1arrow J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon and F. Delaunay,. A hybrid model of cell cycle in mammals. J. of Bioinformatics and Computational Biology. 14(1):1640001 [17 pp.], 2016. Preprint, DOI 10.1142/S0219720016400011, © [copyright World Scientific Publishing Company], http://www.worldscientific.com/worldscinet/jbcb. [Cf. Conferences Behaegel et al. 2015]ps-pdf-htmlbib
2arrow J.-P. Comet, A. Richard, J. Aracena, L. Calzone, J. Demongeot, M. Kaufman, A. Naldi, E.H. Snoussi, D. Thieffry. On circuit functionality in Boolean networks. Bulletin of Mathematical Biology. 75(6):906-919, 2013. DOI: 10.1007/s11538-013-9829-2ps-pdf-htmlbib
3arrow A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel and A. Merieau. Boolean models of biosurfactants production in Pseudomonas fluorescens. PlosOne. 7(1):e24651, 2012. doi:10.1371/journal.pone.0024651ps-pdf-htmlbib
4arrow S. Taati, E. Formenti, J.-P. Comet and G. Bernot. On the impact of the distance between two genes on their interaction curve. Journal of Mathematical Biology. 64(1):131-147, 2012. [online First, february 16th, 2011], DOI: 10.1007/s00285-010-0373-5ps-pdf-htmlbib
5arrow M. Mabrouki, M. Aiguier, J.-P. Comet, P. Le Gall and A. Richard. Embedding of biological regulatory networks and properties preservation. Mathematics in Computer Science. 5(3):263-288, 2011. special issueps-pdf-htmlbib
6arrow A. Richard, and J.-P. Comet. Stable periodicities and negative circuits in differential systems. Journal of Mathematical Biology. 63(3):593-600, 2011. [online dec. 1st, 2010]. See also Erratum, 2015.ps-pdf-htmlps-pdf-htmlbib
7arrow Z. Khalis, J.-P. Comet, A. Richard, and G. Bernot. The SMBioNet Method for Discovering Models of Gene Regulatory Networks. Genes, Genomes and Genomics. 3(special issue 1):15-22, 2009. ps-pdf-htmlbib
8arrow S. Troncale, J.-P. Comet, G. Bernot. Enzymatic Competition: Modeling and Verification with Timed Hybrid Petri Nets. Pattern Recognition. 42(4):562-566, 2009. ps-pdf-htmlbib
9arrow M. Poudret, J.-P. Comet, P. Le Gall, F. Képès, A. Arnould, P. Meseure. Topology-based abstraction of complex biological systems: Application to the Golgi apparatus. Theory in Biosciences. 127:79-88, 2008. ps-pdf-htmlbib
10arrow J. Ahmad, O. Roux, G. Bernot, J.-P. Comet and A. Richard. Analysing formal models of genetic regulatory networks with delays: Applications to lambda phage and T-cell activation systems. Int. J. Bioinformatics Research and Applications. 4(3):240-262, 2008. ps-pdf-htmlbib
11arrow J. Ahmad, G. Bernot, J.-P. Comet, D. Lime and O. Roux. Hybrid modelling and dynamical analysis of gene regulatory networks with delays. ComPlexUs. 3(4):231-251, 2006 (Cover Date: November 2007). ps-pdf-htmlbib
12arrow S. Troncale, R. Thuret, C. Ben, N. Pollet, J.-P. Comet and G. Bernot. Modelling of the TH-dependent regulation of tadpole tail resorption. Journal of Biological Physics and Chemistry. 7(2):45-50, 2007. ps-pdf-htmlbib
13arrow A. Richard and J.-P. Comet. Necessary conditions for multistationarity in discrete dynamical systems. Discrete Applied Mathematics. 155(18):2403-2413, 2007. ps-pdf-htmlbib
14arrow D. Mateus, J.-P. Gallois, J.-P. Comet, and P. Le Gall. Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology. 5(2B):627-640, 2007. ps-pdf-htmlbib
15arrow D. Filopon, A. Merieau, G. Bernot, J.-P. Comet, R. Leberre, B. Guery, B. Polack, J. Guespin-Michel. Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa. BMC Bioinformatics. 7:272, 2006. ps-pdf-htmlbib
16arrow A. Richard, J.-P. Comet, G. Bernot. R. Thomas' modeling of biological regulatory networks: Introduction of singular states in the qualitative dynamics. Fundamenta informaticae. 65(4):373-392, 2005. ps-pdf-htmlbib
17arrow J. Guespin-Michel, G. Bernot, J.-P. Comet, A. Mérieau, A. Richard, C. Hulen and B. Polack. Epigenesis and dynamic similarity in two regulatory networks in pseudomonas aeruginosa. Acta Biotheoretica. 52(4):379-390, 2004. ps-pdf-htmlbib
18arrow G. Bernot, J.-P. Comet, A. Richard, J. Guespin. Application of Formal Methods to Biological Regulatory Networks: Extending Thomas' Asynchronous Logical Approach with Temporal Logic. J.T.B.. 229(3):339-347, 2004. ps-pdf-htmlbib
19arrow G. Mercier, N. Berthault, J. Mary, J. Peyre, A. Antoniadis, J.-P. Comet , A. Cornuéjols, Ch. Froidevaux and M. Dutreix. Biological detection of low radiation by combining results of two microarray analysis methods. Nucleic Acids Research. 32(1):e12, 2004. ps-pdf-htmlbib
20arrow J.-P. Comet.. Application of Max-Plus algebra to biological sequence comparisons. Theoretical Computer Science. 293:189-217, 2003. ps-pdf-htmlbib
21arrow J.-P. Comet and J. Henry. Pairwise sequence alignment using a PROSITE pattern-derived similarity score. Computers & Chemistry. 26(5):421-436, 2002. ps-pdf-htmlbib
22arrow J.-N. Bacro and J.-P. Comet. Sequence alignment : an approximation law for the Z-value with applications to databank scanning. Computers & Chemistry. 25:401-410, 2000. ps-pdf-htmlbib
23arrow J.-P. Comet, J.-C. Aude, E. Glémet, A. Hénaut, J.-L. Risler, P. P. Slonimski, and J.-J. Codani. Significance of Z-value statistic of Smith-Waterman Scores for Protein alignments. Computers & Chemistry. 23(3-4):317-331, 1999. Special issueps-pdf-htmlbib

National journals (2)

1arrow G. Bernot, J.-P. Comet, J. Guespin. Méthode informatique de découverte du fonctionnement d'un réseau de régulation biologique. numéro spécial sur la biologie intégrative, coordinateur F. Rechenmann, Mensuel de vulgarisation Biofutur. 275:22-25, mars 2007. ps-pdf-htmlbib
2arrow J. Guespin-Michel, J.-P. Comet, G. Bernot. Les réseaux de régulation biologique: rencontre entre biologie et informatique. T.S.I.. 23(7):939-945, 2004. ps-pdf-htmlbib

Books chapters and editions

Books chapters (16)

1arrow E. Cornillon, J.-P. Comet, G. Bernot, G. Enée. Hybrid Gene Networks: a new Framework and a Software Environment. 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. 57-84, ISBN: 978-2-7598-1971-3, EDP Science, 2016. ps-pdf-htmlbib
2arrow B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-de Faverney. Towards a Computer Aided Toxicology. 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. 85-101, ISBN: 978-2-7598-1971-3, EDP Science, 2016. ps-pdf-htmlbib
3arrow K.J.E. Carpio, G. Bernot, J.-P. Comet, F. Diener. Probabilistic Gene Network. 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. ps-pdf-htmlbib
4arrow G. Bernot, J.-P. Comet and E.H. Snoussi. Formal methods applied to gene network modelling. In Logical Modeling of Biological Systems (eds. K. Inoue and L. Fariñas). pp. 245-289, ISBN 978-1-84821-680-8, ISTE & Wiley, 2014. ps-pdf-htmlbib
5arrow G. Bernot, J.-P. Comet and C. Risso-de Faverney. Regulatory networks. In Computational Toxicology (eds. B. Reisfeld and A. Mayeno). pp. Volume II, pp 215-234, ISBN 978-1-62703-058-8 (print) 978-1-62703-059-5 (online), DOI 10.1007/978-1-62703-059-5_9, 2013. ps-pdf-htmlbib
6arrow G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, and F. Dayan. Modeling and analysis of gene regulatory networks. In Modeling in Computational Biology and Biomedicine, A Multidisciplinary Endeavor (eds. F. Cazals and P. Kornprobst). pp. 47-80, ISBN 978-3-642-31208-3, Springer, 2013. ps-pdf-htmlbib
7arrow J.-P. Comet, G. Bernot, A. Das, F. Diener, C. Massot and A. Cessieux. Simplified models for the mammalian circadian clock. 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. [Cf. Conférences 15]. ps-pdf-htmlbib
8arrow J.-P. Comet and G. Bernot. Introducing continuous time in discrete models of gene regulatory networks. 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, ISBN : 978-2-7598-0545-7, EDP Science, 2010. ps-pdf-htmlps-pdf-htmlbib
9arrow Z. Khalis, G. Bernot, J.-P. Comet and Observability Group. Gene Regulatory Networks: Introduction of multiplexes into R. Thomas' modelling. In Proc. of the Nice Spring school on Modelling complex biological systems in the context of genomics (eds. P. Amar, F. Képès, V. Norris and G. Bernot). pp. 139-151, ISBN : 978-2-7598-0437-5, EDP Science, 2009. ps-pdf-htmlbib
10arrow M. Poudret, J.-P. Comet, Pascale Le Gall, F. Képès, A. Arnould, P. Meseure, J.-M. Verbavatz, A. Rambourg. Toward a computer-aided methodology for topology-based simulation of the Golgi apparatus. In Proc. of the Lille Spring school on Modelling complex biological systems in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 89-104, ISBN : 978-2-7598-0075-9, EDP Science, 2008. ps-pdf-htmlbib
11arrow D. Mateus, J.-P. Comet, J.-P. Gallois and P. Le Gall. Inferring parameters of genetic regulatory networks with symbolic formal methods. In Proc. of the Evry Spring school on Modelling complex biological systems in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 51-70, ISBN : 978-2-7598-0019-3, EDP Science, 2007. ps-pdf-htmlbib
12arrow A. Richard, J.-P. Comet, G. Bernot. Formal Methods for Modeling Biological Regulatory Networks. In Modern Formal Methods and Applications (eds. H.A. Gabbar). pp. 83-122, ISBN: 1-4020-4222-1, Springer, 2006. ps-pdf-htmlbib
13arrow J. Mary, G. Mercier, J.-P. Comet, A. Cornuéjols, C. Froideveaux, et M. Dutreix. Utilisation d'une méthode de sélection d'attributs pour l'analyse du transcriptome de cellules de levures exposées à de faibles doses de radiation. In Informatique pour l'analyse du transcriptome (eds. J.-F. Boulicaut and O. Gandrillon). pp. 189-205, ISBN: 2-7462-0850-4, Hermes, 2004. bib
14arrow G. Bernot, J. Guespin-Michel, J.-P. Comet, P. Amar, A. Zemirline, F. Delaplace, P. Ballet, A. Richard. Modelling, observability and experiment: a case study. In Proc. of the Dieppe Spring school on Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 49-55, ISBN : 2-84704-036-6, Publisher Frontier group, 2003. bib
15arrow J. Mary, G. Mercier, J.-P. Comet, A. Cornuéjols, C. Froidevaux and M. Dutreix. Using an attribute estimation technique for the analysis of microarray data. In Proc. of the Dieppe Spring school on Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, F. Képès, V. Norris and P. Tracqui). pp. 69-77, ISBN : 2-84704-036-6, Publisher Frontier group, 2003. bib
16arrow J.-J. Codani, J.-P. Comet, J.-C. Aude, E. Glémet, A. Wozniak, J.-L. Risler, A. Hénaut, and P.P. Slonimski. Automatic analysis of large scale pairwise alignments of protein sequences. In Methods in microbiology Vol. 28, Automation, Genomic and Functional Analysis pp. 229-244, Academic Press, 1999. bib

Edition of a book (1)

1arrow Modelling and simulation of biological processes in the context of genomics (eds. P. Amar, J.-P. Comet, F. Képès, V. Norris). ISBN : 2 84704 0374, Publisher Frontier group, juin 2004. bib

Edition of a special issue of a national journal (1)

1arrow Modélisation et simulation pour la post-génomique (eds. J.-P. Comet et M. Kaufman), numéro spécial de T.S.I., 26:1-2, [éditorial de 4 pages], 2007. ps-pdf-htmlbib

Conferences and workshops

Refereed international conferences and workshops - with proceedings (19)

1arrow J. Behaegel, J.-P. Comet and M. Folschette. Constraint Identification Using Modified Hoare Logic on Hybrid Models of Gene Networks, International Symposium on Temporal Representation and Reasoning (TIME), Mons, Belgium. 16-18 October 2017. ps-pdf-htmlbib
2arrow B. Miraglio, G. Bernot, J.-P. Comet and C. Risso-De Faverney. Detecting Toxicity Pathways with a Formal Framework based on Equilibrium Changes, Computational Methods for Systems Biology (CMSB), Darmstadt, Germany. 27-29 September 2017. LNBI vol. 10545, pp. 196-213ps-pdf-htmlbib
3arrow B. Miraglio, G. Bernot, J.-P. Comet and C. Risso-De Faverney. A New Formal Approach Dedicated to Toxicology, International Conference on Bioinformatics Models, Methods and Algorithms, Porto, Portugal. 21-23 february 2017. ps-pdf-htmlbib
4arrow J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon, F. Delaunay. A hybrid model of cell cycle in mammals, 6th International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2015), Bangkok, Thailand. November 22-25, 2015. [Cf. Journals Behaegel et al. 2016]. ps-pdf-htmlbib
5arrow J.-P. Comet, G. Bernot, A. Das, F. Diener, C. Massot, A. Cessieux. Simplified models for the mammalian circadian clock, 3rd International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2012), Bangkok, Thailand. October 3-5, 2012. Procedia Computer Science vol. 11, pp. 127-138, 2012. [Cf. Chapitres 11]. ps-pdf-htmlps-pdf-htmlbib
6arrow J.-P. Comet, J. Fromentin, G. Bernot and O. Roux. A formal model for gene regulatory networks with time delays, 1st International Conference on Computational Systems-Biology and Bioinformatics (CSBio'2010), Bangkok, Thailand. November 3-5, 2010. CCIS vol. 115, pp. 1-13, 2010. ps-pdf-htmlps-pdf-htmlbib
7arrow G. Bernot, J.-P. Comet, E. Formenti and S. Taati. Gene regulatory networks: the impact of distance between genes, 19th International Symposium in Mathematical Theory of Networks and Systems, MTNS'2010, Budapest (Hungary). July 5-9, 2010. ps-pdf-htmlbib
8arrow G. Bernot, J.-P. Comet, and Z. Khalis. Gene regulatory networks with multiplexes, European Simulation and Modelling Conference, ESM'2008, Le Havre (France). October 27-29, 2008. ISBN 978-90-77381-44-1, pp. 423-432, 2008. ps-pdf-htmlbib
9arrow M. Poudret, A. Arnould, J.-P. Comet, and P. Le Gall. Graph Transformation for Topology Modelling, International Conference on Graph Transformation, Leicester (United Kingdom). September 7-13, 2008. LNCS vol. 5214, pp. 147-161, 2008. ps-pdf-htmlbib
10arrow M. Mabrouki, M. Aiguier, J.-P. Comet, and P. Le Gall. Property preservation along embedding of biological regulatory networks, Algebraic Biology, Austria. July 31st-August 2d, 2008. LNCS vol. 5147, pp. 125-138, 2008. ps-pdf-htmlbib
11arrow S. Troncale, J.-P. Comet, G. Bernot. Verification of biological models with timed hybrid Petri nets, Proc. of the 2007 Intl Symp on Computational Models for Life Sciences (CMLS07), Gold Coast, Queensland, Australia. December 17-19 , 2007. American Institute of Physics Conference Proc Series (AIP) vol. 952, pp. 287-296, 2007. Pham, Tuan D.; Zhou, Xiaobo Eds, ISBN 978-0-7354-0466-3. ps-pdf-htmlbib
12arrow J. Fromentin, J.-P. Comet, P. Le Gall, O. Roux. Analysing Gene Regulatory Networks by both Constraint Programming and Model-Checking, EMBC'07, 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France. August 23-26, 2007. pp. 4595-4598, 2007. ps-pdf-htmlbib
13arrow S. Troncale, J.-P. Comet, G. Bernot. Validation of biological models with Temporal Logic and Timed Hybrid Petri Nets, EMBC'07, 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France. August 23-26, 2007. pp. 4603-4608, 2007. ps-pdf-htmlbib
14arrow M. Poudret, J.-P. Comet, P. Le Gall, A. Arnould and Ph. Meseure. Topology-based Geometric Modelling for Biological Cellular Processes, LATA 2007, first International Conference on Language and Automata Theory and Applications, Tarragona, Spain. March 29 - April 4, 2007. pp. 497-508, 2007. The proceedings are available on the website of the conference, Taux d'acceptation : 27.5%. ps-pdf-htmlbib
15arrow J. Ahmad, A. Richard, G. Bernot, J.-P. Comet and O. Roux. Delays in Biological Regulatory Networks, IWBRA 2006 / ICCS 2006: 6th International Conference, May 2006. LNCS vol. 3992, pp. 887-894, 2006. Taux d'acceptation : 37%. ps-pdf-htmlbib
16arrow J.-P. Comet, H. Klaudel, S. Liauzu. Modeling multi-valued genetic regulatory networks using high-level Petri nets, ICATPN 2005, June 2005. LNCS vol. 3536, pp. 208-227, 2005. ps-pdf-htmlbib
17arrow A. Richard, J.-P. Comet, G. Bernot. Graph-based Modeling of Biological Regulatory Networks : Introduction of Singular States, International workshop on Computational Methods in Systems Biology (CMSB), Paris, France. May 26-28, 2004. LNBI vol. 3082, pp. 58-72, 2005. ps-pdf-htmlbib
18arrow G. Bernot, F. Cassez, J.-P. Comet, F. Delaplace, C. Müller, O. Roux, O. Roux. Semantics of Biological Regulatory Networks, BioConcur, Workshop on Concurrent Models in Molecular Biology, Marseille, France. 6 September, 2003. ENTCSps-pdf-htmlbib
19arrow S. Pérès and J.-P. Comet. Contribution of computational tree logic to biological regulatory networks: example from pseudomonas aeruginosa, International workshop on Computational Methods in Systems Biology (CMSB), Rovereto, Italy. February 24-26, 2003. LNCS vol. 2602, pp. 47-56, 2003. Taux d'acceptation: 28 %. ps-pdf-htmlbib

Refereed international conferences and workshops without proceedings (6)

1arrow D. Mateus, J.-P. Comet, J.-P. Galois, P. Le Gall. Modeling Genetic Regulatory Networks from specified behaviors, BioSysBio'2007 (Systems Biology, Bioinformatics, synthetic biology), Manchester, UK. Jan. 11th- Jan. 13th , 2007. [abstract will be published in BMC Systems Biology -- feb. 2007]. ps-pdf-htmlbib
2arrow D. Mateus, J.-P. Comet, J.-P. Galois, P. Le Gall. Modeling Genetic Regulatory Networks from specified behaviors, IPG'2006, Lyon, France. November 29th- December 1st, 2006. bib
3arrow J.-P. Comet, H. Klaudel, S. Liauzu. Qualitative Modelling of genetic networks using high level Petri nets, IPG'2004, Lyon, France. October 14-15, 2004. ps-pdf-htmlbib
4arrow G. Bernot, O. Roux, C. Auberger, V. Bassano, F. Cassez, J.-P. Comet, F. Delaplace, A. Richard, O. Roux, F. Tahi. Temporal logics and biological regulatory networks, ECCB Satellite Meeting on Modeling and Simulation of Biological Regulatory Processes, Paris. October 1, 2003. bib
5arrow S. Pérès, J.-P. Comet. A formal approach to modelize biological regulatory networks, Workshop theoretical biophysics, Hiddensee, Germany. April 02-05, 2003. ps-pdf-htmlbib
6arrow J.-C. Aude and J.-P. Comet. Construction of protein sequences families, 24th Aharon Katzir-Katchalsky conference Bioinformatics-Structure, Jerusalem, Israel. November 17-21,1996. ps-pdf-htmlbib

Invited international conferences and workshops (9)

1arrow G. Bernot, J.-P. Comet and O. Roux. A genetically modified Hoare logic that identifies the parameters of a gene network, 13th international Conference on Computational Methods in Systems Biology (CMSB 2015), Nantes, France. Sept. 16-18, 2015. LNBI vol. 9308, pp. 8-12, 2015. ps-pdf-htmlbib
2arrow J.-P. Comet and G. Bernot. A Hoare logic for gene regulatory networks, 2nd Workshop on Computational Structural Biology: Integrative Approaches for Modeling Biomolecular Complexes, Nice, France. May 29-31, 2013. ps-pdf-htmlbib
3arrow G. Bernot and J.-P. Comet. On the use of temporal formal logic to model gene regulatory networks, 6th International Meeting on Computational Intelligence Methods for Bioinformatics and biostatistics (CIBB'2009), Eds. F. Masulli, L. Peterson, and R. Tagliaferri. Genova, Italy. October 15th-17th 2009. LNBI vol. 6160, pp. 112-138, 2010. ps-pdf-htmlbib
4arrow G. Bernot, J.-P. Comet, J. Guespin. A Discrete Approach to Model Biological Gene Regulatory Networks and the Use of Temporal Logic to Propose Wet Experiments, Gene regulatory networks: Dynamics, spatial organization and inference: Gennetec International Conference, Torino, Italy. April 23th-2th 2008. bib
5arrow G. Bernot, J.-P. Comet, J. Guespin. Using Formal Temporal Logic to Model Biological Regulatory Networks and to Propose New Wet Experiments, Genetics meets Systems Biology: Theory and Practice, Paris. November 13-15, 2006. Abstract in Proc. of SGF annual meeting, p.17. bib
6arrow G. Bernot, J.-P. Comet, J. Guespin. Formal methods from computer science to treat temporal properties of biological regulatory networks, applied to mucus production in Pseudomonas aeruginosa, Symposium "Modeling approaches in Systems Biology, Physiology, and Pathophysiology", 4th World Congress of Cell and Molecular Biology, Poitiers (Futuroscope). October 7-12, 2005. bib
7arrow M. Dutreix, J.-P. Comet, A. Cornuejols and C. Froidevaux. Determination of cellular drug targets: Searching for functional informations in the jungle of microarrays data, Current Trends in Drug Discovery Research, India. Feb. 17-20, 2004. bib
8arrow P. P. Slonimski, M.-O. Mossé, P. Golik, A. Hénaut, Y. Diaz, J.-L. Risler, J.-P. Comet, J.-C. Aude, Wozniak A., E. Glémet, and J.-J. Codani. The first laws of genomics. , Microbial and Comparative Genomics in Microbial Genomes II: Sequencing, Functional Analysis and Comparative Genomics, January 31 - February 4, 1998. vol. 3, pp. 46, 1998. bib
9arrow P. P. Slonimski, J.-L. Risler, M.-O. Mossé, A. Hénaut, Y. Diaz, J.-P. Comet, J.-C. Aude, E. Glémet, and J.-J. Codani. What can we learn about proteins from complete sequences of microbial genome, Protein Science, vol. 6 Suppl. 1, , 1997. bib

Invited national conferences and workshops (8)

1arrow J.-P. Comet, A. Richard, A. Muzy. Plasticité des réseaux de neurones: Un modèle de Réseaux Booléens avec règle de Hebb, Workshop sur la Théorie des réseaux booléens et ses applications en biologie, Nice, France. 4-7 novembre 2014. ps-pdf-htmlbib
2arrow G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O. Roux. An extension of Hoare logic to identify the parameters of gene regulatory networks, Modélisation Mathématique des Systèmes Complexes, SMAI & SMF, Ecole Centrale Paris. 11-13 déc, 2013. bib
3arrow F. Diener, A. Das, G. Bernot, J.-P. Comet, F. Eyssette. Correspondence between discrete and piecewise linear models of gene regulatory networks, actes du colloque à la mémoire d'Emmanuel Isambert, "Philosophie, méthodologie et applications de l'analyse non standard", Eds. A. Fruchard, V. Gautheron & T. Sari. Univ. Paris 7. 21-22 décembre 2007. Publications de l'Université de Paris 13, pp. 185-194, 14 février 2012. ps-pdf-htmlbib
4arrow G. Bernot, J.-P. Comet et Z. Khalis. Une extension de la logique de Hoare pour les réseaux génétique, Rencontre scientifique : "Formalisme logique, apports et défis pour la modélisation de réseaux de régulation biologique", Rabat, Maroc. 12-15 avril 2011. ps-pdf-htmlbib
5arrow G. Bernot, J.-P. Comet. Logique temporelle et Model-Checking pour les réseaux de régulation biologiques, 3ème Journées de Post-Génomique de la Doua (JPGD'03), Lyon, France. 14-16 mai 2003. bib
6arrow J. Guespin-Michel, J.-P. Comet, G. Bernot. Comment valider un modèle mathématique en biologie?, AFADL'03, Rennes, France. 15-17 janvier 2003. bib
7arrow G. Bernot, J. Michel-Guespin, A. Zermiline, J.-P. Comet, F. Delaplace, P. Ballet, P. Amar. Modélisation, observabilité et expérimentation : étude d'un cas, boucle de rétroaction positive dans un réseau de régulation génétique, Autran seminar (Isère), . 17-21 Mars 2002. bib
8arrow J.-P. Comet and F. Tahi. Structuration et analyse des données d'expression de gènes, Journées Péri-Bio à l'université d'Evry, Evry, France. 25 avril 2000. bib

Refereed national conferences and workshops - without proceedings (8)

1arrow J. Behaegel, J.-P. Comet, M. Folschette, F. Delaunay. Prise en compte d'informations temporelles dans la modélisation d'oscillateurs circadiens, 45ème congrès de la Société Francophone de Chronobiologie, 14-16 septembre 2016. bib
2arrow S. Troncale, R. Thuret, C. Ben, N. Pollet, J.-P. Comet, G. Bernot. Modélisation de la régulation TH-dépendante de la résoption de la queue du tétard, Journée thématique RIAMS, le 29 novembre 2006. bib
3arrow J. Guespin, G. Bernot, J.-P. Comet, A. Mérieau, B. Pollack. Une approche bio-informatique de la dynamique d'un réseau de régulation chez Pseudomonas aeruginosa, VIème congrès de la SFM, 10 - 12 Mai 2004. bib
4arrow G. Mercier, J. Mary, J.-P. Comet, A. Cornuejols, C. Froidevaux, and M. Dutreix. Information mining of microarray data: comparison of results generated by different analysis methods, Modélisation et simulation de processus dans le contexte de la biologie, Dieppe, France. 11-16 mai 2003. (sera publié dans les Proceedings). bib
5arrow J. Mary, G. Mercier, J.-P. Comet, A. Cornuéjols, C. Froidevaux, M. Dutreix. Utilisation d'une méthode de sélection d'attributs pour l'analyse du transcriptome de cellules de levure exposées à de faibles doses de radiation, 3ème Journées de Post-Génomique de la Doua (JPGD'03), Lyon, France. 14-16 mai 2003. bib
6arrow J.-P. Comet. Méthodes de prédiction à partir des données transcriptionnelles : Prise en compte des erreurs de mesure, IMPG, Marseille. 30 mars 2001. bib
7arrow J.-N. Bacro and J.-P. Comet. Comparaison de séquences : Loi asymptotique du Z-score et applications, XXXIèmes journées de Statistiques, Grenoble, France. 17-21 mai 1999. bib
8arrow J.-P. Comet. Comparaison de séquences biologiques : Interprétation statistique du score Smith et Waterman, Un autre indice de similarité : Le Z-score, XXIXèmes journées de Statistiques, Carcassonne, France. 26-30 Mai 1997. bib

Other national conferences and workshops - without proceedings (5)

1arrow J. Guespin-Michel, D. Filopon, A. Mérieau, G. Bernot, J.-P. Comet, B. Polack. Approche logique, bio-informatique et expérimentale de la dynamique d'un réseau de régulation chez Pseudomonas aeruginosa, Réunion satellite de JOBIM 2005 : "Modélisation Dynamique de Réseaux de Régulation Biologique : Des mesures aux modèles et des modèles aux mesures", 9 juillet 2005. bib
2arrow G. Bernot, J.-P. Comet, J. Guespin. Mise au point de modèles discrets de réseaux de régulation biologiques par le model checking, la mucoidie chez P.aeruginosa, Journées "Logique temporelle et model checking pour les réseaux de régulation biologiques", ACI-IMPBio VICANNE, Evry, France. 13-14 septembre 2004. bib
3arrow G. Bernot, J.-P. Comet. Logique temporelle et Model-Checking pour les réseaux de régulation biologiques, Club SEE "Systemes Informatiques de Confiance", ENST Paris, France. 19 juin 2003. bib
4arrow J.-P. Comet. Automates (max,+) et Alignements de séquences biologiques, GdR/PRC ALP et GdR/PRC Automatique, ENS Ulm. Novembre 1998. ps-pdf-htmlbib
5arrow J.-P. Comet and V. Froidure. Recherche de la meilleure base de décomposition et du meilleur filtre, Journée Ondelettes du pôle hydrodynamique de Rouen, juin 1992. bib

Miscellaneous

Lectures at thematic schools (1)

1arrow J.-P. Comet. Modélisation discrète et modélisation hybride de régulation génétique, Ecole Jeunes Chercheurs «Modélisation formelle de réseaux de régulation biologique», Ile de Porquerolles, 6-11 juin 2010.

Posters (18)

1arrow E. Cornillon, J.-P. Comet, G. Bernot, G. Enée. Hybrid Gene Networks: a new Framework and a Software Environment, 45ème congrès de la Société Francophone de Chronobiologie. Strasbourg. 14-16 septembre 2016. ps-pdf-htmlbib
2arrow B. Miraglio, G. Bernot, J.-P. Comet, R. Risso. Towards a Computer-Aided Toxycology, 3ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique. Porquerolles, France. 6-10 juin 2016. bib
3arrow E. Cornillon, J.-P. Comet, G. Bernot, G. Enée. Hybrid Gene Networks: a new Framework and a Software Environment, 3ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique. Porquerolles, France. 6-10 juin 2016. bib
4arrow J. Behaegel, J.-P. Comet, M. Folschette. A Hybridisation of the Genetically Modified Hoare Logic, 3ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique. Porquerolles, France. 6-10 juin 2016. bib
5arrow A. Das, F. Diener, G. Bernot, J.-P. Comet. Simplified model for the mammalian circadian clock, Thematic school on "Modelling complex biological systems in the context of genomics". Evry, France. 21-25 may 2012. ps-pdf-htmlbib
6arrow A. Das, F. Diener, G. Bernot, J.-P. Comet. Computational model for the mammalian circadian clock, Sophia-Antipolis, France. 23-27 may 2011. ps-pdf-htmlps-pdf-htmlbib
7arrow Z. Khalis, G. Bernot, J.-P. Comet. Using Hoare logic for constraining parameters of discrete models of gene networks, JOBIM'2010. Montpellier. 7-9 septembre 2010. ps-pdf-htmlbib
8arrow Z. Khalis, G. Bernot, J.-P. Comet. Using Hoare logic for constraining parameters of discrete models of gene networks, Ecole thématique "Modélisation de systèmes biologiques complexes dans le contexte de la génomique". Evry. 3-7 mai 2010. ps-pdf-htmlbib
9arrow A. Das, F. Diener, G. Bernot, J.-P. Comet. Correspondence between discrete and continuous models of gene regulatory network, Ecole thématique "Modélisation de systèmes biologiques complexes dans le contexte de la génomique". Evry. 3-7 mai 2010. ps-pdf-htmlbib
10arrow J. Fromentin, J.-P. Comet, P. Le Gall and O. Roux. Analysing gene regulatory networks by both constraint programming and model-checking, Ecole thématique "Modélisation de systèmes biologiques complexes dans le contexte de la génomique". Evry. 30 avril - 4 mai 2007. ps-pdf-htmlbib
11arrow M. Poudret, J.-P. Comet, P. Le Gall, A. Arnould and P. Meseure. Topological Approach of the Golgi Apparatus: Towards a Discriminating Modelling ?, Ecole thématique "Modélisation de systèmes biologiques complexes dans le contexte de la génomique". Evry. 30 avril - 4 mai 2007. ps-pdf-htmlbib
12arrow D. Mateus, J.-P. Gallois, P. Le Gall, J.-P. Comet. Determining constraints in models of genetic regulatory networks using symbolic analysis, Jobim'2006. Bordeaux. 5-7 juillet, 2006. ps-pdf-htmlbib
13arrow J. Ahmad, A. Richard, G. Bernot, J.-P. Comet, O. Roux. Delays in Biological Regulatory networks, IPG'05. Lyon, France. December 1-2, 2005. bib
14arrow J.-P. Comet, P. Le Gall, G. Bernot. Qualitative Modelling of genetic networks: Extracting experiment schema from modelling, IPG'2004. Lyon, France. October 13-15, 2004. ps-pdf-htmlbib
15arrow J.-P. Comet et A. Richard. SMBioNet: a Tool for Modeling Biological Regulatory Networks Driven by Temporal Behavior, ECCB'03. Paris, France. September 27-30, 2003. bib
16arrow J.-P. Comet, S. Pérès, G. Bernot. CTL and biological regulatory networks : Example from P. Aeriginosa, Symposium on Macromolecular networks. Paris, France. July 8-12, 2002. bib
17arrow J.-P. Comet, S. Pérès, G. Bernot. Un langage formel pour les réseaux de régulation : un exemple avec multi-stationarité, Jobim'2002. Saint-Malo, France. 10-12 juin 2002. bib
18arrow J.-P. Comet. Extension of dynamic programming sequence alignment to pattern, WABI'2001. Arhus, Denmark. August 27-31, 2001. bib

Research Reports (9)

1arrow M. Manceny, J.-P. Comet, J.-P. Gallois and P. Le Gall. Model-checking for parametric transition systems based on symbolic execution - Extended version, Rapport de recherche de l'École Centrale Paris. 2008. ps-pdf-htmlbib
2arrow S. Troncale, J.-P. Comet and Gilles Bernot. A Temporal Logic with Event Clock Automata for Timed Hybrid Petri Nets, 2007. ps-pdf-htmlbib
3arrow A. Richard and J.-P. Comet. Necessary conditions for multistationarity in discrete dynamical systems, 2005. bib
4arrow J.-P. Comet, H. Klaudel and S. Liauzu. Modeling Multi-Valued Genetic Regulatory Networks Using High-Level Petri Nets, 2004. ps-pdf-htmlbib
5arrow J.-P. Comet, A. Richard and G. Bernot. Modeling Biological Regulatory Networks with Singular States, 2004. ps-pdf-htmlbib
6arrow G. Bernot, J.-P. Comet, A. Richard and J. Guespin-Michel. A Fruitful Application of Formal Methods to Biological Regulatory Networks: extending Thomas' logical approach with temporal logic, 2003. ps-pdf-htmlbib
7arrow G. Bernot, J. Guespin-Michel, A. Zemirline, J.-P. Comet, P. Amar, F. Delaplace, P. Ballet. Modelling, observability and experiment: a case study, 2002. ps-pdf-htmlbib
8arrow J.-P. Comet and J. Henry. Sequence alignment : Extension of dynamic programming to pattern, 2001. ps-pdf-htmlbib
9arrow J.-N. Bacro and J.-P. Comet. Approximated asymptotic law of Z-value and applications, 2000. ps-pdf-htmlbib

Seminars (19)

1arrow J.-P. Comet, G. Bernot, E. Cornillon. Reductions symboliques de modèles de réseaux génétiques. Séminaire "Réseaux d’interactions: fondements et applications à la biologie", CIRM, Marseille (France), 3 janvier 2017.
2arrow J.-P. Comet, A. Richard, A. Muzy. Plasticité des neurones biologiques: un modèle de Réseaux Booléens avec règle de Hebb. Séminaire pour un groupe d'étudiants en visite à l'I3S, Nice (France), 6 janvier 2015.
3arrow J.-P. Comet. Introduction of time delays in formal models of gene regulatory networks. Séminaire, Impérial College, London, GB, 16 mai 2012.
4arrow G. Bernot, J.-P. Comet, J. Guespin. On the use of temporal formal logic to deduce the parameters of a gene regulatory network. Séminaire, Imperial College, London, GB, 16 mai, 2012.
5arrow J.-P. Comet. A Hoare Logic for discrete dynamical systems: application to gene networks. Séminaire, CI2MA, University of Concepción, Chili, 17 novembre 2011.
6arrow J.-P. Comet. Modélisation discrète et modélisation hybride de régulation génétique. séminaire du pôle MDSC, I3S, Université de Nice-Sophia, 23 juin 2010.
7arrow J.-P. Comet. Modélisation qualitative des Réseaux de régulation génétique. Séminaire BIOALGOME, Prism, UVSQ, 15 décembre 2005.
8arrow J.-P. Comet. Simulation qualitative des Réseaux de régulation biologique, modèle de H. de Jong. groupe de travail "Observabilité", génopole Evry, 24 novembre 2005.
9arrow J.-P. Comet, A. Richard, Gilles Bernot. Quelques problèmes autour de la modélisation des réseaux de régulation de R. Thomas. Séminaire, ENS Ulm, département informatique, Paris, 20 mai 2005.
10arrow J.-P. Comet. Représentation bipartie des réseaux de régulation biologique de R. Thomas. Séminaire du groupe de travail "Observabilité", génopole Evry, 27 janvier 2005.
11arrow J. Guespin et J.-P. Comet. Méthodes formelles appliquées aux réseaux de régulation de R. Thomas. Séminaire IGM, Orsay, France, 21 septembre 2004.
12arrow J.-P. Comet, G. Bernot. Logique temporelle et model-checking pour les réseaux de régulation biologique. Séminaire du groupe de travail "Observabilité", génopole Evry, 28 novembre 2002.
13arrow J.-P. Comet. Méthode de prédiction à partir des données transcriptionnelles: Combien de gènes témoins faut-il prendre en compte?. Séminaire du groupe de travail "Consensus", génopole Evry, 15 mai 2002.
14arrow J.-P. Comet. Recherche des gènes pouvant servir à la prédiction. Séminaire du groupe de travail "Consensus", génopole Evry, 7 mars 2002.
15arrow J.-P. Comet. Méthodes de prédiction à partir des données transcriptionnelles : Prise en compte des erreurs de mesure. Séminaire du groupe de travail "Consensus", génopole Evry, 11 avril 2001.
16arrow J.-P. Comet. Using error propagation for class prediction. Seminar, Whitehead Institute / MIT Center for Genome Research, Cambridge (MA), USA, November 1999.
17arrow J.-P. Comet. Chips quality and error bars. Seminar, Whitehead Institute / MIT Center for Genome Research, Cambridge (MA), USA, June 1999.
18arrow J.-P. Comet. Interprétation statistique du score Smith-Waterman. Un autre indice de similarité : le z-score. Séminaire du groupe "Statistique des Sequences Biologiques", INRA (Jouy-en-Josas, 78), octobre 1997.
19arrow J.-P. Comet. Analyse de données et Biologie moléculaire. Séminaire, LMCP, Jussieu (Paris), mars 1997.

PhD thesis and Habilitation thesis

1arrow J.-P. Comet. De la bio-informatique textuelle à une approche formelle de la biologie des systèmes. mémoire d'Habilitation à Diriger des Recherches, Université d'Evry-Val d'Essonne, 20 Novembre 2006. ps-pdf-htmlbib
2arrow J.-P. Comet. Programmation dynamique et comparaison de séquences biologiques. Thèse de doctorat, Université de Technologie de Compiègne, Novembre 1998. ps-pdf-htmlps-pdf-htmlbib