Publications & communications (sorted by type)

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Journals ▲

International journals (31)

31arrow L. Gibart, H. Collavizza, J.-P. Comet. A Phenotypic Matrix for Greening Qualitative Regulatory Networks with Environments. BMC bioinformatics [accepted]. :, 2024. ps-pdf-htmlbib
30arrow F. Camilleri, J. Wenda, C. Pecoraro-Mercier, J.-P. Comet, D. Rouquié. Cell Painting and chemical structure read-across can complement each other for rat acute oral toxicity prediction in chemical early de-risking. Chemical Research in Toxicology. :, 2024. DOI 10.1021/acs.chemrestox.4c00169 ps-pdf-htmlbib
29arrow J.-P. Comet, H. Collavizza, L. Gibart. Constrained Kripke Structure for Identifying Parameters of Biological Models. Theoretical Computer Science [Available online 19 March 2024]. 996:114505, 2024. DOI 10.1016/j.tcs.2024.114505 ps-pdf-htmlbib
28arrow L. Gibart, R. Khoodeeram, G. Bernot, J.-P. Comet, J.-Y. Trosset. Regulation of Eukaryote Metabolism: An Abstract Model Explaining the Warburg/Crabtree Effect. Processes. 9:1496, 2021. DOI 10.3390/pr9091496 ps-pdf-htmlbib
27arrow I. Grenet, J.-P. Comet, F. Schorsch, N. Ryan, J. Wichard, D. Rouquié. Chemical in vitro bioactivity profiles are not informative about the long-term in vivo endocrine mediated toxicity. Computational Toxicology. 12:100098, 2019. DOI 10.1016/j.comtox.2019.100098 ps-pdf-htmlbib
26arrow I. Grenet, K. Merlo, J.-P. Comet, R. Tertiaux, D. Rouquié, F. Dayan. Stacked Generalization with Applicability Domain Outperforms simple QSAR on in vitro Toxicological Data. JCIM. 59(4):1486--1496, 2019. DOI 10.1021/acs.jcim.8b00553 ps-pdf-htmlbib
25arrow G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O.F. Roux. A Genetically Modified Hoare Logic. Theoretical Computer Science. 765:145-157, 2019. DOI 10.1016/j.tcs.2018.02.003 ps-pdf-htmlps-pdf-htmlbib
24arrow I. Grenet, Y. Yin, J.-P. Comet. G-networks to predict the outcome of sensing of toxicity. Sensors. 18:3483, 2018. DOI 10.3390/s18103483 ps-pdf-htmlbib
23arrow J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon, F. Delaunay. A hybrid model of cell cycle in mammals. J. of Bioinformatics and Computational Biology. 14(1):1640001 [17 pp.], 2016. [Cf. Conferences Behaegel et al. 2015]. DOI 10.1142/S0219720016400011 ps-pdf-htmlbib
22arrow J.-P. Comet, M. Noual, 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/s11538-013-9829-2 ps-pdf-htmlbib
21arrow A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel, A. Merieau. Boolean models of biosurfactants production in Pseudomonas fluorescens. PlosOne. 7(1):e24651, 2012. DOI 10.1371/journal.pone.0024651 ps-pdf-htmlbib
20arrow S. Taati, E. Formenti, J.-P. Comet, G. Bernot. On the impact of the distance between two genes on their interaction curve. Journal of Mathematical Biology. 64(1):131-147, 2012. DOI 10.1007/s00285-010-0373-5 ps-pdf-htmlbib
19arrow M. Mabrouki, M. Aiguier, J.-P. Comet, P. Le Gall, A. Richard. Embedding of biological regulatory networks and properties preservation. Mathematics in Computer Science. 5(3):263-288, 2011. special issue. DOI 10.1007/s11786-011-0092-3 ps-pdf-htmlbib
18arrow A. Richard, 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. DOI 10.1007/s00285-010-0388-y ps-pdf-htmlps-pdf-htmlbib
17arrow Z. Khalis, J.-P. Comet, A. Richard, 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
16arrow S. Troncale, J.-P. Comet, G. Bernot. Enzymatic Competition: Modeling and Verification with Timed Hybrid Petri Nets. Pattern Recognition. 42(4):562-566, 2009. DOI 10.1016/j.patcog.2008.09.019 ps-pdf-htmlbib
15arrow 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. DOI 10.1007/s12064-008-0030-3 ps-pdf-htmlbib
14arrow J. Ahmad, O. Roux, G. Bernot, J.-P. Comet, 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. DOI 10.1504/IJBRA.2008.019573 ps-pdf-htmlbib
13arrow J. Ahmad, G. Bernot, J.-P. Comet, D. Lime, O. Roux. Hybrid modelling and dynamical analysis of gene regulatory networks with delays. ComPlexUs. 3(4):231-251 (Cover Date: November 2007), 2006. DOI 10.1159/000110010 ps-pdf-htmlbib
12arrow S. Troncale, R. Thuret, C. Ben, N. Pollet, J.-P. Comet, G. Bernot. Modelling of the TH-dependent regulation of tadpole tail resorption. Journal of Biological Physics and Chemistry. 7(2):45-50, 2007. URL https://www.amsi.ge/jbpc/20707/20702.htmlps-pdf-htmlbib
11arrow A. Richard, J.-P. Comet. Necessary conditions for multistationarity in discrete dynamical systems. Discrete Applied Mathematics. 155(18):2403-2413, 2007. DOI 10.1016/j.dam.2007.04.019 ps-pdf-htmlbib
10arrow D. Mateus, J.-P. Gallois, J.-P. Comet, P. Le Gall. Symbolic modeling of genetic regulatory networks. Journal of Bioinformatics and Computational Biology. 5(2B):627-640, 2007. DOI 10.1142/S0219720007002850 ps-pdf-htmlbib
9arrow 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. DOI 10.1186/1471-2105-7-272 ps-pdf-htmlbib
8arrow 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
7arrow J. Guespin-Michel, G. Bernot, J.-P. Comet, A. Mérieau, A. Richard, C. Hulen, B. Polack. Epigenesis and dynamic similarity in two regulatory networks in pseudomonas aeruginosa. Acta Biotheoretica. 52(4):379-390, 2004. DOI 10.1023/B:ACBI.0000046604.18092.a7 ps-pdf-htmlbib
6arrow 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. DOI 10.1016/j.jtbi.2004.04.003 ps-pdf-htmlbib
5arrow G. Mercier, N. Berthault, J. Mary, J. Peyre, A. Antoniadis, J.-P. Comet, A. Cornuéjols, C. Froidevaux, M. Dutreix. Biological detection of low radiation by combining results of two microarray analysis methods. Nucleic Acids Research. 32(1):e12, 2004. DOI 10.1093/nar/gnh002 ps-pdf-htmlbib
4arrow J.-P. Comet. Application of Max-Plus algebra to biological sequence comparisons. Theoretical Computer Science. 293:189-217, 2003. DOI 10.1016/S0304-3975(02)00237-2 ps-pdf-htmlbib
3arrow J.-P. Comet, J. Henry. Pairwise sequence alignment using a PROSITE pattern-derived similarity score. Computers & Chemistry. 26(5):421-436, 2002. DOI 10.1016/S0097-8485(02)00005-0 ps-pdf-htmlbib
2arrow J.-N. Bacro, J.-P. Comet. Sequence alignment : an approximation law for the Z-value with applications to databank scanning. Computers & Chemistry. 25:401-410, 2001. DOI 10.1016/S0097-8485(01)00074-2 ps-pdf-htmlbib
1arrow J.-P. Comet, J.-C. Aude, E. Glémet, A. Hénaut, J.-L. Risler, P.P. Slonimski, J.-J. Codani. Significance of Z-value statistic of Smith-Waterman Scores for Protein alignments. Computers & Chemistry. 23(3-4):317-331, 1999. Special issue. DOI 10.1016/S0097-8485(99)00008-X ps-pdf-htmlbib

National journals (2)

2arrow G. Bernot, J.-P. Comet, J. Guespin. Elucider le fonctionnement d'un réseau de régulation biologique par l'informatique. numéro spécial sur la biologie intégrative, coordinateur F. Rechenmann, Mensuel de vulgarisation Biofutur. 275:22-25, 2007. ps-pdf-htmlbib
1arrow J. Guespin, 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

BioRXiv (1)

1arrow F. Camilleri, J. Wenda, C. Pecoraro-Mercier, J.-P. Comet, D. Rouquié. Cell Painting morphological profiles can complement QSAR models for rat acute oral toxicity prediction. BioRXiv. 2024. ps-pdf-htmlbib

Books chapters and editions ▲

Books chapters (18)

18arrow H. Collavizza, G. Bernot, J.-P. Comet. Formal Verification Methods for Modeling in Biology: Biological Regulation Networks. In Symbolic Approaches to Modeling and Analysis of Biological Systems (eds. C. Lhoussaine, E. Remy). pp. 255--312, ISBN: 978-1-78945-029-3, ISTE, 2023. DOI 10.1002/9781394229086.ch8 bib
17arrow H. Collavizza, G. Bernot, J.-P. Comet. Méthodes de vérification formelle pour la modélisation en biologie : le cas des réseaux de régulation biologique. In Approches symboliques de la modélisation et de l’analyse des systèmes biologiques (eds. C. Lhoussaine, E. Remy). pp. 275--335, ISBN: 9781789480290, ISTE, 2022. DOI 10.51926/ISTE.9029.ch8 ps-pdf-htmlbib
16arrow 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, V. Norris). pp. 57-84, ISBN: 978-2-7598-1971-3, EDP Science, 2016. ps-pdf-htmlbib
15arrow 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, V. Norris). pp. 85-101, ISBN: 978-2-7598-1971-3, EDP Science, 2016. ps-pdf-htmlbib
14arrow 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, V. Norris). pp. 77-90, EDP Science, 2015. ps-pdf-htmlbib
13arrow G. Bernot, J.-P. Comet, E.H. Snoussi. Formal methods applied to gene network modelling. In Logical Modeling of Biological Systems (eds. K. Inoue, L. Fariñas). pp. 245-289, ISBN 978-1-84821-680-8, ISTE & Wiley, 2014. ps-pdf-htmlbib
12arrow G. Bernot, J.-P. Comet, C. Risso-de Faverney. Regulatory networks. In Computational Toxicology (eds. B. Reisfeld, A. Mayeno). pp. Volume II, pp 215-234, ISBN 978-1-62703-058-8 (print) 978-1-62703-059-5 (online), 2013. DOI 10.1007/978-1-62703-059-5_9 ps-pdf-htmlbib
11arrow G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, F. Dayan. Modeling and analysis of gene regulatory networks. In Modeling in Computational Biology and Biomedicine, A Multidisciplinary Endeavor (eds. F. Cazals, P. Kornprobst). pp. 47-80, ISBN 978-3-642-31208-3, Springer, 2013. ps-pdf-htmlbib
10arrow J.-P. Comet, G. Bernot, A. Das, F. Diener, C. Massot, 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, V. Norris). pp. 85-106, EDP Science. [Cf. Conférences 15], 2012. ps-pdf-htmlbib
9arrow J.-P. Comet, 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, V. Norris). pp. 61-94, ISBN : 978-2-7598-0545-7, EDP Science, 2010. ps-pdf-htmlps-pdf-htmlbib
8arrow Z. Khalis, G. Bernot, J.-P. Comet, 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, G. Bernot). pp. 139-151, ISBN : 978-2-7598-0437-5, EDP Science, 2009. ps-pdf-htmlbib
7arrow M. Poudret, J.-P. Comet, P. 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, P. Tracqui). pp. 89-104, ISBN : 978-2-7598-0075-9, EDP Science, 2008. ps-pdf-htmlbib
6arrow D. Mateus, J.-P. Comet, J.-P. Gallois, 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, P. Tracqui). pp. 51-70, ISBN : 978-2-7598-0019-3, EDP Science, 2007. ps-pdf-htmlbib
5arrow 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. DOI 10.1007/1-4020-4223-X_5 ps-pdf-htmlbib
4arrow 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 levures exposées à de faibles doses de radiation. In Informatique pour l'analyse du transcriptome (eds. J.-F. Boulicaut, O. Gandrillon). pp. 189-205, ISBN: 2-7462-0850-4, Hermes, 2004. bib
3arrow 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, P. Tracqui). pp. 49-55, ISBN : 2-84704-036-6, Publisher Frontier group, 2003. bib
2arrow J. Mary, G. Mercier, J.-P. Comet, A. Cornuéjols, C. Froidevaux, 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, P. Tracqui). pp. 69-77, ISBN : 2-84704-036-6, Publisher Frontier group, 2003. bib
1arrow J.-J. Codani, J.-P. Comet, J.-C. Aude, E. Glémet, A. Wozniak, J.-L. Risler, A. Hénaut, 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, 2004. bib

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

1arrow Modélisation et simulation pour la post-génomique (eds. J.-P. Comet, 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 (30)

30arrow R. Michelucci, J.-P. Comet, D. Pallez. Comparing diverse planning strategies with continuous Monte Carlo Tree Search applied to hybrid Gene Regulatory Networks, ICTAI 2024 : The 36th IEEE International Conference on Tools with Artificial Intelligence. Herndon, VA, USA. 27-30 Oct. 2024, 2024. DOI 10.1109/ICTAI62512.2024.00018 ps-pdf-htmlbib
29arrow G. Grataloup, D. Pallez, G. Bernot, J.-P. Comet. Single-objective constrained optimization for Gene Regulatory Networks Modeling, EA 2024 : Artificial Evolution. Bordeaux, France. 29-31 Oct. 2024, LNCS, 2024. ps-pdf-htmlbib
28arrow R. Michelucci, D. Pallez, T. Cazenave, J.-P. Comet. Improving continuous Monte Carlo Tree Search for identifying parameters in hybrid Gene Regulatory Networks, 18th International Conference on Parallel Problem Solving From Nature PPSN. Hagenberg, Austria. Sept. 14-18, 2024. DOI 10.1007/978-3-031-70085-9_20 ps-pdf-htmlbib
27arrow R. Michelucci, V. Callegari, J.-P. Comet, D. Pallez. Cellular Genetic Algorithms for identifying variables in hybrid Gene Regulatory Networks, 27th European Conference, EvoApplications 2024, Held as Part of EvoStar . Aberystwyth, Wales, United Kingdom. 3-5 Apr.. vol. 14634 pp. 131-145, 2024. DOI 10.1007/978-3-031-56852-7_9 ps-pdf-htmlbib
26arrow H. Sun, J.-P. Comet, M. Folschette, M. Magnin. Condition for sustained oscillations in repressilator based on a hybrid modeling of gene regulatory networks, Bioinformatics 2023. Lisbon, Portugal. 16-18 Feb. 2023. vol. 12881 pp. 29-40, 2023. . DOI 10.5220/0011614300003414 ps-pdf-htmlbib
25arrow R. Michelucci, J.-P. Comet, D. Pallez. Evolutionary continuous optimization of Hybrid Gene Regulatory Networks, EA 2022 : Artificial Evolution. Exeter, England. 31 Oct. 2022 - 2 Nov. 2022, LNCS, 2022. DOI 10.1007/978-3-031-42616-2_12 ps-pdf-htmlbib
24arrow L. Gibart, H. Collavizza, J.-P. Comet. Greening R. Thomas’ Framework with Environment Variables: a Divide and Conquer Approach, CMSB 2021 : 19th International Conference on Computational Methods in Systems Biology (CMSB). Bordeaux, France. 22-24 September, LNBI. vol. 12881 pp. 36-56, 2021. DOI 10.1007/978-3-030-85633-5_3 ps-pdf-htmlbib
23arrow L. Gibart, G. Bernot, H. Collavizza, J.-P. Comet. TotemBioNet Enrichment Methodology: Application to the Qualitative Regulatory Network of the Cell Metabolism, BIOINFORMATICS 2021 : 12th International Conference on Bioinformatics Models, Methods and Algorithms. online. 11-13 February, 2021. vol. 3 pp. 85-92, 2021. URL https://www.scitepress.org/publishedPapers/2021/101862/pdf/index.html. ps-pdf-htmlbib
22arrow D. Boyenval, G. Bernot, H. Collavizza, J.-P. Comet. What is a cell cycle checkpoint? The TotemBioNet answer, the 18th International Conference on Computational Methods in Systems Biology (CMSB). online. September 23-25, 2020, LNCS. vol. 12314 pp. 362-372, 2020. DOI 10.1007/978-3-030-60327-4_21 ps-pdf-htmlbib
21arrow J. Behaegel, J.-P. Comet, M. Pelleau. Identification of Dynamic Parameters for Gene Networks, the 30th IEEE International Conference on Tools with Artificial Intelligence (ICTAI). Volos, Greece. November 5-7, 2018 pp. 122-129, 2018. DOI 10.1109/ICTAI.2018.00028 ps-pdf-htmlbib
20arrow I. Grenet, Y. Yin, J.-P. Comet, E. Gelenbe. Machine Learning to Predict Toxicity of Compounds, The 27th International Conference on Artificial Neural Networks (ICANN). Rhodes, Greece. 5-7 October 2018, LNCS. vol. 11139 pp. 335-345, 2018. DOI 10.1007/978-3-030-01418-6_33 ps-pdf-htmlbib
19arrow J. Behaegel, J.-P. Comet, 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 pp. 5:1--5:21, 2017. DOI 10.4230/LIPIcs.TIME.2017.5 ps-pdf-htmlbib
18arrow B. Miraglio, G. Bernot, J.-P. Comet, 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. 196-213, 2017. DOI 10.1007/978-3-319-67471-1_12 ps-pdf-htmlbib
17arrow B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-de Faverney. A Qualitative Framework Dedicated to Toxicology, International Conference on Bioinformatics Models, Methods and Algorithms. Porto, Portugal. 21-23 february 2017, 2017. DOI 10.5220/0006168200930103 ps-pdf-htmlbib
16arrow 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, 2015. [Cf. Journals Behaegel et al. 2016]. ps-pdf-htmlbib
15arrow 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. Chapters 11]. DOI 10.1016/j.procs.2012.09.014 ps-pdf-htmlps-pdf-htmlbib
14arrow J.-P. Comet, J. Fromentin, G. Bernot, 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. DOI 10.1007/978-3-642-16750-8_1 ps-pdf-htmlps-pdf-htmlbib
13arrow G. Bernot, J.-P. Comet, E. Formenti, 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, 2010. ps-pdf-htmlbib
12arrow G. Bernot, J.-P. Comet, Z. Khalis. Gene regulatory networks with multiplexes, European Simulation and Modelling Conference, ESM'2008. Le Havre (France). October 27-29, 2008, 2008. ISBN 978-90-77381-44-1, pp. 423-432, 2008. ps-pdf-htmlbib
11arrow M. Poudret, A. Arnould, J.-P. Comet, 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. DOI 10.1007/978-3-540-87405-8_11 ps-pdf-htmlbib
10arrow M. Mabrouki, M. Aiguier, J.-P. Comet, 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. DOI 10.1007/978-3-540-85101-1_10 ps-pdf-htmlbib
9arrow 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
8arrow 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. DOI 10.1109/IEMBS.2007.4353363 ps-pdf-htmlbib
7arrow 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. DOI 10.1109/IEMBS.2007.4353365 ps-pdf-htmlbib
6arrow M. Poudret, J.-P. Comet, P. Le Gall, A. Arnould, 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
5arrow J. Ahmad, A. Richard, G. Bernot, J.-P. Comet, 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%. DOI 10.1007/11758525_118 ps-pdf-htmlbib
4arrow 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. DOI 10.1007/11494744_13 ps-pdf-htmlbib
3arrow 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. DOI 10.1007/978-3-540-25974-9_6 ps-pdf-htmlbib
2arrow 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, ENTCS, 2003. DOI 10.1016/j.entcs.2004.01.038 ps-pdf-htmlbib
1arrow S. Pérès, 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 %. DOI 10.1007/3-540-36481-1_5 ps-pdf-htmlbib

Refereed international conferences and workshops without proceedings (7)

7arrow F. Camilleri, J. Wenda, A. Bassignani, J. Fabjan, C. Pecoraro-Mercier, J.-P. Comet, D. Rouquié. Oral acute toxicity prediction using Cell Painting morphological profiles, Congress of the European Societies of Toxicology (EUROTOX 2023). Ljubljana, Slovenia. Sept. 10th- Sept. 13th, 2023. abstract published in Toxicology Letters, Volume 384, Supplement 1, September 2023, Page S117. DOI 10.1016/S0378-4274(23)00535-0 ps-pdf-htmlbib
6arrow D. Mateus, J.-P. Comet, J.-P. Gallois, P. Le Gall. Modeling Genetic Regulatory Networks from specified behaviors, BioSysBio'2007 (Systems Biology, Bioinformatics, synthetic biology). Manchester, UK. Jan. 11th- Jan. 13th , 2007, 2007. [abstract will be published in BMC Systems Biology -- feb. 2007]. ps-pdf-htmlbib
5arrow D. Mateus, J.-P. Comet, J.-P. Gallois, P. Le Gall. Modeling Genetic Regulatory Networks from specified behaviors, IPG'2006. Lyon, France. November 29th- December 1st, 2006. bib
4arrow 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, 2004. ps-pdf-htmlbib
3arrow 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, 2003. bib
2arrow S. Pérès, J.-P. Comet. A formal approach to modelize biological regulatory networks, Workshop theoretical biophysics. Hiddensee, Germany. April 02-05, 2003, 2003. ps-pdf-htmlbib
1arrow J.-C. Aude, J.-P. Comet. Construction of protein sequences families, 24th Aharon Katzir-Katchalsky conference Bioinformatics-Structure. Jerusalem, Israel. November 17-21,1996, 1996. ps-pdf-htmlbib

Invited international conferences and workshops (9)

9arrow G. Bernot, J.-P. Comet, 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
8arrow J.-P. Comet, 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, 2013. ps-pdf-htmlbib
7arrow G. Bernot, 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, R. Tagliaferri. Genova, Italy. October 15th-17th 2009, LNBI. vol. 6160 pp. 112-138, 2009. ps-pdf-htmlbib
6arrow 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, 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, 2006. Abstract in Proc. of SGF annual meeting, p.17. bib
4arrow 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, 2005. bib
3arrow M. Dutreix, J.-P. Comet, A. Cornuéjols, 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, 2004. bib
2arrow P.P. Slonimski, M.-O. Mossé, P. Golik, A. Hénaut, Y. Diaz, J.-L. Risler, J.-P. Comet, J.-C. Aude, A. Wozniak, E. Glémet, 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
1arrow P.P. Slonimski, J.-L. Risler, M.-O. Mossé, A. Hénaut, Y. Diaz, J.-P. Comet, J.-C. Aude, E. Glémet, 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 (10)

10arrow G. Bernot, J.-P. Comet. Towards a qualitative understanding of Cancer metabolism, Multidisciplinary Approaches in Cancer Research. Sophia Antipolis, France. 25-26 octobre, 2021. ps-pdf-htmlbib
9arrow J.-P. Comet. Automata, Logics and Biology, MOMI'2020. Sophia-Antipolis (France). 10 march, 2020. bib
8arrow 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
7arrow 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 décembre, 2013. bib
6arrow 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
5arrow G. Bernot, J.-P. Comet, 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
4arrow 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
3arrow J. Guespin-Michel, J.-P. Comet, G. Bernot. Comment valider un modèle mathématique en biologie?, AFADL'03. Rennes, France. 15-17 janvier, 2003. bib
2arrow G. Bernot, J. Michel-Guespin, A. Zemirline, 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
1arrow J.-P. Comet, 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 - with proceedings (2)

2arrow G. Grataloup, J.-P. Comet, G. Bernot. Improving Snoussi constraints in the Thomas framework for Gene Networks, JOBIM. 25-28 juin 2024, 2024. ps-pdf-htmlbib
1arrow J. Behaegel, J.-P. Comet, M. Pelleau. Identification de paramètres dynamiques de réseaux de gènes, Quatorzièmes Journées Francophones de Programmation par Contraintes. 12-15 juin 2018, 2018. ps-pdf-htmlbib

Refereed national conferences and workshops - without proceedings (9)

9arrow R. Michelucci, D. Pallez, J.-P. Comet. Parametrisation of hybrid Gene Regulatory Networks using Artificial Evolution and Reinforcement Learning, 26ème congrès de la Société Française de Recherche Opérationnelle et d’Aide à la Décision ROADEF. 26-28 février 2025, 2025. ps-pdf-htmlbib
8arrow 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, 2016. bib
7arrow 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, 2006. bib
6arrow J. Guespin, G. Bernot, J.-P. Comet, A. Mérieau, B. Polack. Une approche bio-informatique de la dynamique d'un réseau de régulation chez Pseudomonas aeruginosa, VIème congrès de la SFM. 10 - 12 Mai 2004, 2004. bib
5arrow G. Mercier, J. Mary, J.-P. Comet, A. Cornuéjols, C. Froidevaux, 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, 2003. (sera publié dans les Proceedings). bib
4arrow 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, 2003. bib
3arrow J.-P. Comet. Méthodes de prédiction à partir des données transcriptionnelles : Prise en compte des erreurs de mesure, IMPG. Marseille. 30 mars 2001, 2001. bib
2arrow J.-N. Bacro, J.-P. Comet. Comparaison de séquences : Loi asymptotique du Z-score et applications, XXXIèmes journées de Statistiques. Grenoble, France. 17-21 mai 1999, 1999. bib
1arrow 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, 1997. bib

Other national conferences and workshops - without proceedings (5)

5arrow 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, 2005. bib
4arrow 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, 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, 2003. bib
2arrow J.-P. Comet. Automates (max,+) et Alignements de séquences biologiques, GdR/PRC ALP et GdR/PRC Automatique. ENS Ulm. Novembre 1998, 1998. ps-pdf-htmlbib
1arrow J.-P. Comet, V. Froidure. Recherche de la meilleure base de décomposition et du meilleur filtre, Journée Ondelettes du pôle hydrodynamique de Rouen. juin 1992, 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 (30)

30arrow F. Camilleri, J. Wenda, A. Farhi, A. Bassignani, B. Kiehr, S. P. Tripathi, C. Buton, C. Pecoraro-Mercier, J.-P. Comet, E. Webb, D. Rouquie. Comparative Analysis of Acceptable Daily Intakes and Administered Equivalent Doses Derived from Cell Painting Points of Departure and Reverse Dosimetry, Abstracts of the 13th ASCCT Annual Meeting, Research Triangle Park, North Carolina (USA). Research Triangle Park, North Carolina (USA). 28-30 October 2024. bib
29arrow F. Camilleri, J. Wenda, A. Farhi, C. Buton, C. Pecoraro-Mercier, J.-P. Comet, D. Rouquié. Comparison of Acceptable Daily Intake (ADI) and in vivo doses extrapolated from in vitro point of departure obtained with cell painting on U2OS}, Abstracts of the 58th Congress of the European Societies of Toxicology (EUROTOX 2024), Copenhagen (Denmark). Copenhagen, Denmark. 8-11 September 2024. ps-pdf-htmlbib
28arrow F. Camilleri, C. Ginet, V. Lejal, A. Bassignani, J.-P. Comet, D. Rouquié. Exploring cell morphological profile information for the de-risking of small molecules, JOBIM Poster session. Rennes, France. 5-8 july 2022. bib
27arrow L. Gibart, G. Bernot, J.-P. Comet, S. Vasseur. An abstract model of the metabolism regulation of pancratic ductal adenocarcinoma, JOBIM Poster session. Rennes, France. 5-8 july 2022. ps-pdf-htmlbib
26arrow L. Gibart, H. Collavizza, J.-P. Comet. Greening R. Thomas’ Framework: a Divide and Conquer, JOBIM Poster session. online, France. 6-9 july 2021. ps-pdf-htmlps-pdf-htmlbib
25arrow D. Boyenval, G. Bernot, J.-P. Comet, F. Delaunay. Logical and incremental formalization of cell cycle checkpoints, JOBIM Poster session. online, France. 6-9 july 2021. ps-pdf-htmlbib
24arrow D. Boyenval, G. Bernot, H. Collavizza, J.-P. Comet. Introduction of Priority Regulation in Biological Regulatory Networks, Modelife annual Days. Cannes Mandelieu, France. 5-6 november 2019. bib
23arrow L. Gibart, G. Bernot, J.-P. Comet, F. Marchai-Guillaumond, S. Vasseur. Pancreas cancer modelling: a metabolic approach, 4ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique (France). Porquerolles, France. 23-28 juin 2019. ps-pdf-htmlbib
22arrow D. Boyenval, G. Bernot, J.-P. Comet, F. Delaunay. A discrete cell cycle model: from phases characterization toward observable properties verification, 4ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique (France). Porquerolles, France. 23-28 juin 2019. bib
21arrow U.D. Appadu, R. Khoodeeram, J.-P. Comet, G. Bernot, J.-Y. Trosset, V.S. Neergheen-Bhujun. Formal modelling of the impact of Pleurotus mushroom on energy metabolism in liver cancer, 4ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique (France). Porquerolles, France. 23-28 juin 2019. bib
20arrow I. Grenet, J.-P. Comet. How in vitro data can contribute to in vivo toxicity prediction using Machine Learning?, JOBIM, Marseille (France). Marseille (France). 3-6 juillet 2018. bib
19arrow I. Grenet, J.-P. Comet, F. Porée, D. Rouquié. Toward In Vivo Toxicity Prediction from Molecular Structures: A Two-Stage Machine Learning Approach, 57th Annual Meeting of Society of Toxicology (SoT). San Antonio (Texas), USA. 10-15 march 2018. bib
18arrow 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
17arrow B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-de Faverney. Towards a Computer-Aided Toxycology, 3ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique. Porquerolles, France. 6-10 juin 2016. bib
16arrow 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
15arrow 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
14arrow 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
13arrow 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
12arrow 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
11arrow 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
10arrow 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
9arrow J. Fromentin, J.-P. Comet, P. Le Gall, 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
8arrow M. Poudret, J.-P. Comet, P. Le Gall, A. Arnould, 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
7arrow 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
6arrow 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
5arrow 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
4arrow J.-P. Comet, A. Richard. SMBioNet: a Tool for Modeling Biological Regulatory Networks Driven by Temporal Behavior, ECCB'03. Paris, France. September 27-30, 2003. bib
3arrow 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
2arrow 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
1arrow J.-P. Comet. Extension of dynamic programming sequence alignment to pattern, WABI'2001. Arhus, Denmark. August 27-31, 2001. bib

Research Reports (9)

9arrow M. Manceny, J.-P. Comet, J.-P. Gallois, 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
8arrow S. Troncale, J.-P. Comet, G. Bernot. A Temporal Logic with Event Clock Automata for Timed Hybrid Petri Nets, 2007. ps-pdf-htmlbib
7arrow A. Richard, J.-P. Comet. Necessary conditions for multistationarity in discrete dynamical systems, 2005. bib
6arrow J.-P. Comet, H. Klaudel, S. Liauzu. Modeling Multi-Valued Genetic Regulatory Networks Using High-Level Petri Nets, 2004. ps-pdf-htmlbib
5arrow J.-P. Comet, A. Richard, G. Bernot. Modeling Biological Regulatory Networks with Singular States, 2004. ps-pdf-htmlbib
4arrow G. Bernot, J.-P. Comet, A. Richard, J. Guespin-Michel. A Fruitful Application of Formal Methods to Biological Regulatory Networks: extending Thomas' logical approach with temporal logic, 2003. ps-pdf-htmlbib
3arrow 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
2arrow J.-P. Comet, J. Henry. Sequence alignment : Extension of dynamic programming to pattern, 2001. ps-pdf-htmlbib
1arrow J.-N. Bacro, J.-P. Comet. Approximated asymptotic law of Z-value and applications, 2000. ps-pdf-htmlbib

Seminars (20)

20arrow J.-P. Comet. some research activities around the modeling of complex biological networks. annual Sparks Day, Sophia-Antipolis (France), 24 septembre 2019.
19arrow 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.
18arrow 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.
17arrow J.-P. Comet. Introduction of time delays in formal models of gene regulatory networks. Séminaire, Impérial College, London, GB, 16 mai 2012.
16arrow 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.
15arrow J.-P. Comet. A Hoare Logic for discrete dynamical systems: application to gene networks. Séminaire, CI2MA, University of Concepción, Chili, 17 novembre 2011.
14arrow J.-P. Comet. Modélisation discrète et modélisation hybride de régulation génétique. séminaire du pôle MDSC, I3S, Université de Nice-Sophia, 23 juin 2010.
13arrow J.-P. Comet. Modélisation qualitative des Réseaux de régulation génétique. Séminaire BIOALGOME, Prism, UVSQ, 15 décembre 2005.
12arrow J.-P. Comet. Simulation qualitative des Réseaux de régulation biologique, modèle de H. de Jong. groupe de travail "Observabilité", génopole Evry, 24 novembre 2005.
11arrow J.-P. Comet, A. Richard, G. 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.
9arrow J. Guespin, J.-P. Comet. Méthodes formelles appliquées aux réseaux de régulation de R. Thomas. Séminaire IGM, Orsay, France, 21 septembre 2004.
8arrow 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.
7arrow 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.
6arrow J.-P. Comet. Recherche des gènes pouvant servir à la prédiction. Séminaire du groupe de travail "Consensus", génopole Evry, 7 mars 2002.
5arrow 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.
4arrow J.-P. Comet. Using error propagation for class prediction. Seminar, Whitehead Institute / MIT Center for Genome Research, Cambridge (MA), USA, November 1999.
3arrow J.-P. Comet. Chips quality and error bars. Seminar, Whitehead Institute / MIT Center for Genome Research, Cambridge (MA), USA, June 1999.
2arrow 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.
1arrow J.-P. Comet. Analyse de données et Biologie moléculaire. Séminaire, LMCP, Jussieu (Paris), mars 1997.

PhD thesis and Habilitation thesis

2arrow 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
1arrow 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
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