I3S
CNRS INSII
Polytech'Nice - Sophia Antipolis
Université de Nice - Sophia Antipolis


Ecole Doctorale STIC
Epigenomics Project
Genopole(R)         

Gilles Bernot


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since 2010
2000-2009
until 2000
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Gilles Bernot

Modeling of Biological Processes in the Context of Genomics (2010-...)


BOOKS and BOOK CHAPTERS

G. Bernot, J.-P. Comet, E.H. Snoussi, Formal methods applied to gene network modelling .  Book chapter in Logical Modeling of Biological Systems, L. Fari<n >as 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]


INTERNATIONAL JOURNALS

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]


NATIONAL JOURNALS


REFEREED INTERNATIONAL CONFERENCES and WORKSHOPS

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]


INVITED INTERNATIONAL CONFERENCES and WORKSHOPS

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.


NATIONAL CONFERENCES and WORKSHOPS

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]


SOME REFEREED POSTERS

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]


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