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Gilles Bernot| General : | ||
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G. Bernot, J.-P. Comet, Z. Khalis, A. Richard, O. Roux, A Genetically Modified Hoare Logic . Theoret. Comput. Sci. (TCS), Vol.765, p.145-157, DOI: 10.1016/j.tcs.2018.02.003 , 2019. [preliminary version] [preliminary version]
O. Guinaudeau, G. Bernot, A. Muzy, D. Gaffé, F. Grammont, Formal Neuron Models: Delays Offer a Simplified Dendritic Integration for Free . Communications in Computer and Information Science book series, extended selected paper from Biomedical Engineering Systems and Technologies conference (BIOSTEC 2018), p.167-191, , 2019.
J. Behaegel,
J.-P. Comet,
G. Bernot,
E. Cornillon,
F. Delaunay,
A hybrid model of cell cycle in mammals
.
Selected papers from CSBio'2015, J. Bioinform. Comput. Biol. (JBCB), World
Scientific Ed., Vol.14, Num.1, , 17 pages,
DOI: 10.1142/S0219720016400011, ISSN: 0219-7200
,
2016.
Also:
Short version in Proc of the 6th Intl Conf on Computational Systems-Biology
and Bioinformatics (CSBio'2015), Bangkok, Thailand, November 22-25
,
[preliminary version]
A. Richard, G. Rossignol, J.-P. Comet, G. Bernot, J. Guespin-Michel, A. Merieau, Boolean models of biosurfactants production in Pseudomonas fluorescens . PlosOne, Vol.7, Num.1, e24651. doi:10.1371/journal.pone.0024651 , 2012. [preliminary version]
S. Taati, E. Formenti, J.-P. Comet, G. Bernot, On the impact of the distance between two genes on their interaction curve . J. of Mathematical Biology, Vol.64, Num.1, p.131-147 , 2012. [preliminary version]
V. Norris, A. Zemirline, P. Amar, J.-N. Audinot, P. Ballet, E. Ben Jacob, G. Bernot, G. Beslon, A. Cabin, E. Fanchon, J.-L. Giavitto, N. Glade, P. Greussay, Y. Grondin, J.A. Foster, G. Hutzler, F. Kepes, O. Michel, F. Molina, J. Signorini, P. Stano, A.R. Thierry, Computing with bacterial constituents cells and populations: from bioputing to bactoputing . Theory in Biosciences, Springer, Vol.130, p.211-228, , 2011. [preliminary version]
E. Ahmed, R.A. El-Khoribi, G. Darwish, A. Muzy, G. Bernot, Modeling of the development of the fetus cognitive map from the sensorimotor system . Egyptian Informatics Jal 21, No.4, p.191-199, , 2020. [preliminary version]
G. Bernot, J.-P. Comet, H. Collavizza, Méthodes de vérification formelle pour la modélisation en biologie: le cas des réseaux de régulation biologique . A paraître dans Approches symboliques de la modelisation et de l'analyse des systèmes biologiques, E. Rémy & C. Lhoussaine eds, 40 pages, ISTE Sciences pub, , 2021. [preliminary version]
R. Khoodeeram, G. Bernot, J.-Y. Trosset, An Ockham Razor model of energy metabolism . Book chapter in Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology, P. Amar, F. Képès and V. Norris Eds, EDP Science pub., p.81-101, ISBN: 978-2-7598-2116-7 , 2017. [preliminary version]
O. Guinaudeau, G. Bernot, A. Muzy, F. Grammont, Abstraction of the structure and dynamics of the biological neuron for a formal study of the dendritic integration . Book chapter in Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology, P. Amar, F. Képès and V. Norris Eds, EDP Science pub., p.103-119, ISBN: 978-2-7598-2116-7 , 2017. [preliminary version]
E. Cornillon, J.-P. Comet, G. Bernot, G. Enée, Hybrid Gene Networks: a new Framework and a Software Environment. . Book chapter in Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology (aSSB), P. Amar, F. Képès and V. Norris Eds, EDP Science pub., p.57-84, ISBN: 978-2-7598-1971-3 , 2016. [preliminary version]
B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-de Faverney, Towards a Computer Aided Toxicology. . Book chapter in Proc. of the Thematic Research School on Advances in Systems and Synthetic Biology (aSSB), P. Amar, F. Képès and V. Norris Eds, EDP Science pub., p.57-84, ISBN: 978-2-7598-1971-3 , 2016. [preliminary version]
K.J.E. Carpio, G. Bernot, J.-P. Comet, F. Diener, Probabilistic Gene Network . Book chapter in Proc. of the thematic research school on Advances in Systems and Synthetic Biology, P. Amar, F. Képès and V. Norris Eds., EDP Science pub., p.77-90 , 2015. [preliminary version]
G. Bernot, J.-P. Comet, E.H. Snoussi, Formal methods applied to gene network modelling . Book chapter in Logical Modeling of Biological Systems, L. Farinas del Cerro and K. Inoue Eds., Bioengineering and health science series, ISTE & Wiley, p.245-289, ISBN 978-1-84821-680-8 , 2014. [preliminary version]
G. Bernot, J.-P. Comet, C. Risso-de Faverney, Regulatory Networks . Book chapter in Computational Toxicology II, B. Reisfeld and A. Mayeno eds., Methods in Molecular Biology series, Humana Press, Vol.930, p.215-234, ISBN 978-1-62703-058-8 , 2013. [preliminary version]
G. Bernot, J.-P. Comet, A. Richard, M. Chaves, J.-L. Gouzé, F. Dayan, Modeling and analysis of gene regulatory networks . Book chapter in Modeling in Computational Biology and Biomedicine: A Multidisciplinary Endeavor, F. Cazals and P. Kornprobst Eds., Springer, p.47-80, ISBN 978-3-642-31208-3 , 2013. [preliminary version]
J.-P. Comet, G. Bernot, Introducing continuous time in discrete models of gene regulatory networks . Book chapter in Proc. of the Evry Spring school on Modelling of biological processes in the context of genomics, March 3rd-7th, 9th Edition, Amar, Képès, Norris Ed., EDP Sciences pub., p.61-94, ISBN 978-2-7598-0545-7 , 2010. [preliminary version]
V. Norris, A. Zemirline, P. Amar, P. Ballet, E. Ben Jacob, G. Bernot, G. Beslon, E. Fanchon, JL. Giavitto, N. Glade, P. Greussay, Y. Grondin, J. Foster, G. Hutzler, F. Képès, O. Michel, G. Misevic, F. Molina, J. Signorini, P. Stano, A. Thierry, From bioputing to bactoputing: computing with bacteria . Book Chapter in Proc. of the Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics, April 7th-11th, 7th Edition, Amar, Képès, Norris, Vandenbunder Ed., EDP sciences pub., ISBN 978-2-7598-0075-9, p.123-150 , 2008. [preliminary version]
L. Gibart, G. Bernot, H. Collavizza, J.-P. Comet, TotemBioNet Enrichment Methodology: Application to the Qualitative Regulatory Network of the Cell Metabolism . Proc of 14th Intl Joint Conf on Biomedical Engineering Systems and Technologies, Vol.3, p.85-92, Methods and Algorithms, R. Lorenz, A. Fred, H. Gamboa Eds., ISBN: 978-989-758-490-9, SCITEPRESS pub., Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS), vol.3, p.85-92, 11-13 February , 2021. [preliminary version]
D. Boyenval, G. Bernot, H. Collavizza, J.-P. Comet, What is a cell cycle checkpoint? The TotemBioNet answer . Proc of 18th Intl Conf on Computational Methods in Systems Biology (CMSB), Lecture Notes in Computer Science (LNCS) vol.12314, 23-25 Sept , 2020. [preliminary version]
E. Ahmed, R.A. El-Khoribi, A. Muzy, G. Bernot, G. Darwish, Modeling of Goal-oriented Human Motion Evolution using Hidden Markov Models . Proc of 8th Intl Conf on Pattern Recognition Applications and Methods (ICPRAM19), Prague, Czech Republic, p.605-612, (10.5220/0007391906050612) 19-21 February , 2019. [preliminary version]
O. Guinaudeau, G. Bernot, A. Muzy, D. Gaffé, F. Grammont, Computer-aided Formal Proofs about Dendritic Integration within a Neuron . Proc of 11th Intl Joint Conf on Biomedical Engineering Systems and Technologies (BIOSTEC 2018), Vol.3, p.49-60, DOI: 10.5220/0006680500490060, ISBN: 978-989-758-280-6, Funchal, Portugal, 19-21 January , 2018. [preliminary version]
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, LNBI vol.10545, p.196-213, 27-29 sept , 2017. [preliminary version]
B. Miraglio, G. Bernot, J.-P. Comet, C. Risso-De Faverney, A New Formal Approach Dedicated to Toxicology . Proc of 8th Intl Conf on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS 2017), SCITEPRESS Ed., Porto, Portugal, 21-23 February , 2017. [preliminary version]
J. Behaegel, J.-P. Comet, G. Bernot, E. Cornillon, F. Delaunay, A hybrid model of cell cycle in mammals . 6th Intl Conf on Computational Systems-Biology and Bioinformatics (CSBio'2015), Bangkok, Thailand, November 22-25 , 2015. [preliminary version]
J.-P. Comet,
G. Bernot,
A. Das,
F. Diener,
C. Massot,
A. Cessieux,
Simplified models for the mammalian circadian clock.
.
Proc of 3rd Intl Conf on Computational Systems-Biology and Bioinformatics
(CSBio'2012), Bangkok, Thailand, Procedia Computer Science No.11, p.127-138,
October 3-5
,
2012.
Also:
Book chapter In Proc. of the Evry Spring school on Modelling complex
biological systems in the context of genomics,
May 21st-25th, 11th Edition, Amar, Képès, Norris Ed., EDP Science pub.,
p.85-106, 2012
,
[CSBIO preliminary version]
[Chapter preliminary version]
J.-P. Comet, J. Fromentin, G. Bernot, O. Roux, A formal model for gene regulatory networks with time delays . Proc of Intl Conf on Computational Systems-Biology and Bioinformatics (CSBio'2010), Bangkok, Thailand, Springer CCIS, Vol.115, p.1-13, Nov. 3-5 , 2010. [preliminary version]
G. Bernot, J.-P. Comet, E. Formenti, S. Taati, Gene regulatory networks: the impact of distance between genes . Proc of 19th Intl Symp. in Mathematical Theory of Networks and Systems (MTNS'10), 5 pages, Budapest, Hungary, July 5-9 , 2010. [preliminary version]
G Bernot, J.-P. Comet, On the use of temporal formal logic to model gene regulatory networks . Proc of 6th IEEE International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2009, Genova (Italy), October 15th-17th 2009, F. Masulli, L. Peterson, and R. Tagliaferri (Eds.), Lecture Notes in Bioinformatics (LNBI) 6160, p.112-138. Springer , 2010. [preliminary version]
G. Bernot, Discrete and hybrid modelling of gene networks, the example of the circadian rhythm . 30th International Symposium on Computer and Information Sciences (ISCIS 2015), Imperial College, London, UK, Sept. 23-25 , 2015. [abstract]
G. Bernot, J.-P. Comet, O. Roux, A genetically modified Hoare logic that identifies the parameters of a gene network . 13th Intl Conf on Computational Methods in Systems Biology (CMSB 2015) Nantes, France, Springer LNBI 9308, p.8-12, Sept. 16-18 , 2015. [preliminary version]
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.
J.-P. Comet, G. Bernot, E. Cornillon, Reductions symboliques de modèles de réseaux génétiques . Exposé invité, Réseaux d'interactions: fondements et applications à la biologie, CIRM, Marseille, France, 3 janvier , 2017.
G. Bernot, D. Borgis, F. Képès, M. Loreau, A. Méjean, L. Sanders, Modélisation: complexifier ou simplifier? . Table ronde du Colloque "Modélisation: succès et limites" de l'Académie des Technologies, CNRS, Paris, 6 décembre , 2016.
R. Khoodeeram, J.-Y. Trosset, G. Bernot, A formal model of metabolism to decipher Crabtree effect . Invited talk, Metabolism in Systems Biology Workshop, Lille, France, 24-25 Nov , 2016.
G. Bernot, Modelling and analysing of gene networks: A genetically modified Hoare logic . Invited talk, SIGNALIFE LabEx workshop "Mathematics-Biology", Sophia Antipolis, Nov 25th , 2016. [preliminary version]
G Bernot, J.-P. Comet, Z. Khalis, A. Richard, O. Roux, An extension of Hoare logic to identify the parameters of gene regulatory networks . Invited talk, Modélisation Mathématique des Systèmes Complexes, SMAI & SMF, Ecole Centrale Paris, 11-13 déc , 2013. [slides]
G. Bernot, Property Driven Models: Experimental Validations and Simplifications . Exposé invité, BioIntelligence Symposium, june 2-4 , 2012. [slides]
G. Bernot, J.-P. Comet, J. Guespin, On the use of temporal formal logic to deduce the parameters of a gene regulatory network . Invited talk, Biological networks, Imperial College, London, 16-18 may , 2012. [slides]
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, 21-22 décembre 2007, Univ. Paris 7, A. Fruchard, V. Gautheron & T. Sari Eds., Publications de l'Université de Paris 13, p.185-194, 14 février , 2012. [preliminary version]
G. Bernot, Sur les apports de la logique formelle pour la modélisation des systèmes biologiques . Séminaire d'Epistémologie et de Biologie Théorique, Les systèmes complexes vivants, Université de Nice - Sophia Antipolis, 16 février , 2012. [abstract]
G. Bernot, J.-P. Comet, Z. Khalis, Une extension de la logique de Hoare pour l'identification de paramètres dans les réseaux génétiques . Journée AFSEC Méthodes formelles pour la bio-informatique, Paris, 20 octobre , 2011. [abstract]
G. Bernot, J.-P. Comet, Z. Khalis, Une extension de la logique de Hoare pour les réseaux génétique . Rencontre "Formalisme logique, apports et défis pour la modélisation de réseaux de régulation biologique", Rabat, Maroc, 12-15 avril , 2011. [abstract]
G. Bernot, J.-P. Comet, On the use of temporal formal logic to deduce the parameters of a gene regulatory network . Exposé invité, CRIN-CNRS & INRIA Loraine, Nancy, 23 février , 2010. [abstract]
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.
Also:
3ème École thématique de Modélisation Formelle de Réseaux de Régulation
Biologique, Porquerolles, France, 6-10 juin 2016
,
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.
R. Khoodeeram, G. Bernot, J.-Y. Trosset, Coarse grained modelling of the energy metabolism network . 3ème École thématique de Modélisation Formelle de Réseaux de Régulation Biologique, Porquerolles, France, 6-10 juin , 2016.
A. Das, F. Diener, G. Bernot, J.-P. Comet, Simplified model for the mammalian circadian clock . Evry Spring school on Modelling complex biological systems in the context of genomics, May 21st-25th , 2012. [poster]
A. Das, F. Diener, G. Bernot, J.-P. Comet, Computational model for the mammalian circadian clock. . Thematic school on Modelling Complex Biological Systems in the Context of Genomics, Sophia-Antipolis, France, May 23rd-27th , 2011. [abstract]
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.
Also:
Proc of the Thematic school on Modelling Complex Biological Systems in the
Context of Genomics, p.147-148, Evry, 3rd-7th May, 2010
,
[abstract]
F. Das, F. Diener, G. Bernot, J.-P. Comet, Correspondence between discrete and continuous models of gene regulatory network . Proc of the Thematic school on Modelling Complex Biological Systems in the Context of Genomics, p.133-134, Evry, 3rd-7th May , 2010. [abstract]