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


Ecole Doctorale STIC
Epigenomics Project
Genopole(R)         

Gilles Bernot


Note: these pages are neither complete nor up to date...

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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 (2000-2009)


BOOKS and BOOK CHAPTERS

P. Amar, F. Képès, V. Norris, G. Bernot, Editors, Annual book of the Nice Spring School on Modelling Complex Biological Systems in the Context of Genomics .  8th Edition, EDP sciences pub. book, Evry, March 30th - April 3rd , 2009.

Z. Khalis, G. Bernot, J.-P. Comet, Observability group, Gene Regulatory Networks: Introduction of multiplexes into R. Thomas' modelling .  Book chapter in Proc. of the Nice Spring school on Modelling of biological processes in the context of genomics, March 30th-April 3rd, 8th Edition, Amar, Képès, Norris, Bernot Ed., EDP Sciences pub., p.139-151, ISBN 978-2-7598-0437-5 , 2009. [preliminary version]

V. Norris, P. Amar, M. Aimar, P. Ballet, A.-F. Batto, G. Barlovatz, G. Bernot, G. Beslon, A. Cabin, S. Chevalier, A. Delaune, J.-M. Delosme, E. Fanchon, H. Gao, N. Glade, Y. Grondin, D. Hernandez-Verdun, L. Janniere, F. Képès, C. Lange, G. Legent, C. Loutelier-Bourhis, F. Molina, N. Orange, D. Raine, C. Ripoll, M. Thellier, A. Thierry, P. Tracqui, A. Zemirline, Hyperstructures 2008-2009 .  Book chapter in Proc. of the Nice Spring school on Modelling of biological processes in the context of genomics, March 30th-April 3rd, 8th Edition, Amar, Képès, Norris, Bernot Ed., EDP Sciences pub., ISBN 978-2-7598-0437-5, p.71-84 , 2009. [preliminary version]

P. Amar, G. Bernot, F. Képès, V. Norris, Editors, Proceedings of the Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics .  6th Edition, EDP sciences pub. book, Evry, April 30th - May 4th , 2007.

V. Norris, P. Amar, M. Thellier, G. Legent, A. Cabin, J.-C. Plaquevent, M. Saier, G. Bernot, G. Misevic, C. Ripoll, Hybolites: novel therapeutical tools based on stochastic automata .  Book Chapter in Proc. of the Evry Spring School on Modelling Complex Biological Systems in the Context of Genomics, 6th Edition, Amar, Bernot, Képès, Norris Ed., EDP sciences pub., Evry, April 30th - May 4th, ISBN 978-2-7598-0019-3, p.83-88 , 2007. [preliminary version]

A. Richard, J-P. Comet, G. Bernot, Formal Methods for Modeling Biological Regulatory Networks .  Book Chapter in Modern Formal Methods and Applications, H.A. Gabbar Ed., Springer, ISBN: 1-4020-4222-1 , 2006. [preliminary version]

P. Amar, G. Bernot, V. Norris, Modelling and simulation of large assemblies of proteins .  Book Chapter, Part 2, Selected papers from the Dieppe spring school on Modelling and simulation of biological processes in the context of genomics, 12-16 may 2003. Amar, Képès, Norris and Tracqui Eds, Platypus Press, pp.41-48, ISBN:2-84704-036-6 , 2003. [preliminary version]

G. Bernot, J. Guespin, J-P. Comet, P. Amar, A. Zemirline, F. Delaplace, P. Ballet, A. Richard, Modelling, observability and experiment: a case study .  Book Chapter, Part 2, Selected papers from the Dieppe spring school on Modelling and simulation of biological processes in the context of genomics, 12-16 may 2003. Amar, Képès, Norris and Tracqui Eds, Platypus Press, p.49-55, ISBN:2-84704-036-6 , 2003. [preliminary version]


INTERNATIONAL JOURNALS

Z. Khalis, J.-P. Comet, A. Richard, G. Bernot, The SMBioNet Method for Discovering Models of Gene Regulatory Networks .  Invited review, Genes Genomes and Genomics, A. Mansour Ed., Global Science Books, Vol.3, Special Issue 1, p.15-22, ISSN:1749-0383, ISBN 978-4-903313-33-7 , 2009. [preliminary version]

G. Bernot, F. Tahi, Behaviour Preservation of a Biological Regulatory Network when Embedded into a Larger Network .  Fundamenta Informaticae, IOS Press Amsterdam, Vol.91, Issue.3-4, p.463-485, ISSN:0169-2968 , 2009. [preliminary version]

S. Troncale, J.-P. Comet, G. Bernot, Enzymatic Competition: Modeling and Verification with Timed Hybrid Petri Nets .  Pattern Recognition, Elsevier, Vol.42, Num.4, p.562-566 , 2009. [preliminary version]

P. Amar, G. Legent, M. Thellier, C. Ripoll, G. Bernot, T. Nystrom, M.H.Jr Saier, V. Norris, A stochastic automaton shows how enzyme assemblies may contribute to metabolic efficiency .  BMC Systems Biology, Vol.2, p.27-39, March , 2008. [link] [preliminary version]

A.C. Fierro, R. Thuret, K. Engelen, G. Bernot, K. Marchal, N. Pollet, Evaluation of time profile reconstruction from complex two-color microarray designs .  BMC Bioinformatics, Vol.9, Num.1, January , 2008. [link] [preliminary version]

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 .  Intl J. of Bioinformatics Research and Applications (IJBRA). Inderscience pub., ISSN (Paper) 1744-5485, Vol.4, Num.3, p.240-262 , 2008. [preliminary version]

J. Ahmad, G. Bernot, J.-P. Comet, D. Lime, O. Roux, Hybrid Modelling and Dynamical Analysis of Gene Regulatory Networks with Delays .  ComPlexUs, Karger Pub., Vol.3, Num.4, 2006, p.231-251, Cover November , 2007. [preliminary version]

K. Sriram, G. Bernot, F. Képès, A minimal mathematical model combining several regulatory cycles from the budding yeast cell cycle .  IET Systems Biology, ISSN 1751-8857, Vol.1, Num.6, p.326-341, November , 2007. [preliminary version]

S. Troncale, R. Thuret, A.C. Fierro, C. Ben, N. Pollet, J.-P. Comet, G. Bernot, Modelling of the TH-dependent regulation of tadpole tail resorption .  J. of Biological Physics and Chemistry (JBPC), Vol.7, Num.2, p.45-50 , 2007. [link] [preliminary version]

D. Filopon, A. Merieau, G. Bernot, J.-P. Comet, R. Leberre, B. Guery, B. Polack, J. Guespin, Epigenetic acquisition of inducibility of type III cytotoxicity in P. aeruginosa .  BMC Bioinformatics, Vol.7, p.272-282 , 2006. [preliminary version]

K. Sriram, G. Bernot, F. Képès, Discrete Delay Model for the Mammalian Circadian Clock .  ComPlexUs, Vol.3, Num.4, p.185-199, August , 2006. [link] [preliminary version]

A.R. Thierry, F. Képès, P. Amar, G. Barlovatz, G. Bernot, M. Beurton-Aimar, M. Dutreix, J-L. Giavitto, J. Guespin, J.-P. Mazat, V. Norris, V. Schachter, P. Tracqui, C. Godin, F. Molina, Modelling of complex biological systems in the context of genomics: an account of a multidisciplinary thematic seminar held in Montpellier (France) in April 2005 .  Jal of Biological Physics and Chemistry (JBPC), Vol.6, p.103-107 , 2006. [preliminary version]

A. Richard, J-P. Comet, G. Bernot, R. Thomas' modeling of biological regulatory networks: introduction of singular states in the qualitative dynamics .  Fundamenta informaticae, Vol.65, Num.4, p.373-392 , 2005. [preliminary version]

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. of Theoretical Biology (JTB), Vol.229, Issue 3, p.339-347 , 2004. [preliminary version]

J. Guespin, 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 (ABT), Vol.52, Num.4, p.379-390, Kluwer Ac. Pub. , 2004. [preliminary version]

P. Amar, G. Bernot, V. Norris, HSIM: a simulation program to study large assemblies of proteins .  Jal of Biological Physics and Chemistry, Vol.4, Num.2, p.79-84 , 2004. [preliminary version]

V. Norris, P. Amar, G. Bernot, A. Delaune, C. Derue, A. Cabin-Flaman, M. Demarty, Y. Grondin, G. Legent, C. Monnier, H. Pollard, D. Raine, Questions for cell cyclists .  Jal of Biological Physics and Chemistry, Vol.4, Num.2, p.124-130 , 2004. [preliminary version]

F. Képès, P. Amar, G. Barlovatz, G. Bernot, C. Froidevaux, J-L. Giavitto, J. Guespin, F. Molina, V. Norris, V. Schachter, P. Tracqui, Modelling and simulating processes in the genomic era: an account of a multidisciplinary thematic school held in Evry (France) in April 2004 .  J. of Biological Physics and Chemistry (JBPC), Vol.4, Num.2, p.131-136 , 2004. [preliminary version]

V. Norris, P. Amar, G. Bernot, J-L. Giavitto, C. Godin, J. Guespin, H. Pollard, P. Tracqui, F. Képès, Modelling and simulation of biological processes in the context of genomics .  J. of Biological Physics and Chemistry (JBPC), Vol.3, p.106-110 , 2003. [preliminary version]

P. Amar, P. Ballet, G. Barlovatz, A. Benecke, G. Bernot, Y. Bouligand, P. Bourgine, F. Delaplace, J-M. Delosme, M. Demarty, I. Fishov, J. Fourmentin-Guilbert, J. Fralick, J-L. Giavitto, B. Gleyse, C. Godin, R. Incitti, F. Képès, C. Lange, L. Le Sceller, C. Loutellier, O. Michel, F, Molina, C. Monnier, R. Natowicz, V. Norris, N. Orange, H. Pollard, D. Raine, C. Ripoll, J. Rouviere-Yaniv, M. Saier, P. Soler, P. Tambourin, M. Thellier, P. Tracqui, D. Ussery, J-C, Vincent, J-P. Vannier, P. Wiggings, A. Zemirline, Hyperstructures, genome analysis and I-cells .  Acta Biotheretica (ABT), Num.50, p.357-373, Kluwer Ac. Pub. , 2002. [preliminary version]


NATIONAL JOURNALS

G. Bernot, F. Képès, Le Programme d'Épigénomique : constitution d'une communauté de recherche en modélisation et simulation dans le contexte de la génomique .  Technique et Science Informatiques (RSTI série TSI), numéro spécial Modélisation et simulation pour la post-génomique, coordinateurs J.-P. Comet & M. Kaufman, Vol.26, Num.1-2, p.237-240 , 2007. [preliminary version]

J. Guespin, G. Bernot, J-P. Comet, Les réseaux de régulation biologique : rencontre entre biologie et informatique. Production de mucus chez P.Aeruginosa .  Technique et Science Informatiques (RSTI série TSI), numéro spécial sur articles sélectionnés de AFADL'03, vol.23, Num.7, p.939-946 , 2004. [preliminary version]


REFEREED INTERNATIONAL CONFERENCES and WORKSHOPS

G. Bernot, J.-P. Comet, Z. Khalis, Gene regulatory networks with multiplexes .  Proc of European Simulation and Modelling Conference, ESM'2008, Le Havre, France, ISBN 978-90-77381-44-1, p.423-432, October 27-29 , 2008. [preliminary version]

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), American Institute of Physics Conference Proc Series (AIP), Pham, Tuan D.; Zhou, Xiaobo Eds, ISBN 978-0-7354-0466-3, Vol.952, p.287-296, Gold Coast, Queensland, Australia, December 17-19 , 2007. [preliminary version]

J. Ahmad, A. Richard, G. Bernot, J.-P. Comet, O. Roux, Delays in Biological Regulatory Networks .  Proc. of the Intl Workshop on Bioinformatics Research and Applications (IWBRA 2006), LNCS 3992, p.887-894, Univ. of Reading, UK, May 28-31 , 2006. [preliminary version]

K. Sriram, G. Bernot, F. Képès, Discrete Models of Mammalian Circadian Rhythms .  Proc. of European Conference on Complex Systems (ECCS'05), p.86-88, Paris, 14-18 November , 2005. [preliminary version]

A. Richard, J-P. Comet, G. Bernot, Graph-Based Modeling of Biological Regulatory Networks: Introduction of Singular States .  Proc. of the Intl Workshop on Computational Methods in Systems Biology (CMSB 04), Springer-Verlag Lecture Notes in BioInformatics (LNBI) Vol.3082, p.58-72, Paris, France, May 26-28 , 2005. [preliminary version]

C. Collet, K. Belhajjame, G. Bernot, C. Bobineau, G. Bruno, B. Finance, F. Jouanot, Z. Kedad, D. Laurent, F. Tahi, G. Vargas-Solar, T. Vu, X. Xue, Towards a Mediation System Framework for Transparent Access to Largely Distributed Sources: The Mediagrid Project. .  Proc. of the First International IFIP Conference on Semantics of a Networked World (ICSNW), Paris, France, June 17-19, 2004. Revised Selected Papers. M. Bouzeghoub, C.A. Goble, V. Kashyap, S. Spaccapietra Eds.: Semantics for Grid Databases, ISBN 3-540-23609-0, Springer-Verlag Heidelberg LNCS 3226, p.65-78 , 2004. [preliminary version]

G. Bernot, O. Roux, C. Auberger, V. Bassano, F. Cassez, J-P. Comet, F. Delaplace, A. Richard, O.H. Roux, F. Tahi, Temporal logics and biological regulatory networks .  European Conf. on Computational Biology (ECCB), Satellite Meeting on Modelling and Simulation of Biological Regulatory Processes, Paris, France, October 1st , 2003. [abstract]

G. Bernot, A. Iartseva, F. Képès, A. Richard, Modeling of Genetic Network Regulating Mammalian Hematopoiesis .  European Conf. on Computational Biology (ECCB), Satellite Meeting on Modelling and Simulation of Biological Regulatory Processes, Paris, France, October 1st , 2003.

B. Finance, Z. Kedad, K. Belhajjame, G. Bernot, G. Bruno, C. Collet, D. Laurent, F. Tahi, T. Vu, X. Xue, Mediagrid : a mediation framework for a transparent access to biological data sources .  Proc. of the 22nd International Conference on Conceptual Modeling, Entity Relationship Conference, Chicago, Illinois, October , 2003.
Also: Poster European Conf. on Computational Biology (ECCB), Paris, p.69-70. September , 2003. [ERC conf] [poster]

G. Bernot, F. Cassez, J-P. Comet, F. Delaplace, C. Müller, O. Roux, O.H. Roux, Semantics of biological regulatory networks .  Proc. of the Workshop on Concurrent Models in Molecular Biology (BioConcur), Concur 2003 satellite Workshop, Marseille, France, 3-5 September 2003, Electronic Notes in Theoretical Computer Science, Elsevier's ENTCS series, Vol.180, Num.3, p.3-14, July , 2007. [preliminary version]

V. Bassano, G. Bernot, Marked Regulatory Graphs: A formal framework to simulate Biological Regulatory Networks with simple automata .  Proc. of the 14th IEEE International Workshop on Rapid System Prototyping, RSP 2003, San Diego, California, USA, pp.93-99, June 9-11 , 2003.


INVITED INTERNATIONAL CONFERENCES and WORKSHOPS

J. Guespin, G. Bernot, Approches logique, informatique et expérimentale de la multistationnarité chez Pseudomonas aeruginosa / Logical, bio-computational and experimental approaches of multistationarity in Pseudomonas aeruginosa .  Invited talk, symposium Intl en l'honneur des 80 ans de René Thomas, The logic of gene regulatory networks / La logique des réseaux de régulation génétiques, ULB et Académie royale des Sciences, des Lettres et des Beaux-Arts de Belgique, A. Goldbeter et M. Kaufman, Bruxelles, 30-31 mai , 2008. [slides]

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 .  Invited talk, Gennetec Intl Conf. on Gene regulatory networks: Dynamics, spatial organization and inference, Torino, Italy, April 23th-24th , 2008. [abstract]

G. Bernot, A Discrete Approach to Model Biological Gene Regulatory Networks and the Use of Temporal Logic to Propose Wet Experiments .  Invited talk, 15th IEEE Intl Symp. on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems (MASCOTS'07), M.U. Çaglayan, A.J. Field and E. Gelenbe Eds, Istanbul, Turkey, Oct. 24-26 , 2007. [abstract]

G. Bernot, A Discrete Approach to Model Gene Regulatory Networks and the Use of Formal Logic to Propose New Wet Experiments .  Invited talk, Intl workshop Toward Systems Biology (TSB), Grenoble, France, 8-10 October , 2007. [abstract]

G. Bernot, A Discrete Approach to Model Gene Regulatory Networks and the Use of Formal Logic to Propose New Wet Experiments .  Invited talk, abstract in Proc of MPG-CNRS joint Workshop on System Biology, Max-Planck-Gesellschaft zur Forderung der Wissenschaften e.V., Berlin, Germany, p.8, Sept. 24-26 , 2007. [abstract]

S. Troncale, J-P. Comet, G. Bernot, Validation of biological models with Temporal Logic and Timed Hybrid Petri Nets .  Invited paper, Proc. 29th Annual Intl Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), p.4603-4608, Lyon, France, August 23-26 , 2007. [preliminary version]

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 .  Invited talk, Symp. Modeling Approaches in System Biology, Physiology and Patophysiology, 11th October 2005, 4th World Congress of Cell and Molecular Biology, Poitiers, France, October 7-12 , 2005. [abstract]

P. Amar, G. Bernot, V. Norris, Metabolons and Hyperstructures in Cell Metabolism and Signaling .  Invited talk, Symp. Modeling Approaches in System Biology, Physiology and Patophysiology, 4th World Congress of Cell and Molecular Biology, Poitiers, France, October 7-12 , 2005. [slides]

C. Auberger, F. Tahi, G. Bernot, Embedding Properties of Biological Regulatory Networks .  Invited talk. Proc. of the NIH Symposium on Biocomputation and Bioinformation. Digital Biology: The Emerging Paradigm. Bethesda, Maryland, USA, November , 2003. [abstract]

B. Finance, Z. Kedad, K. Belhajjame, G. Bernot, G. Bruno, C. Collet, D. Laurent, F. Tahi, T. Vu, X. Xue, A mediation framework for a transparent access to biological data sources, Mediagrid. .  Invited talk and Poster. Proc. of the NIH Symposium on Biocomputation and Bioinformation. Digital Biology: The Emerging Paradigm. Bethesda, Maryland, USA, November , 2003. [abstract]


NATIONAL CONFERENCES and WORKSHOPS

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 .  Exposé invité, SYSDIAG, Montpellier, 16 décembre , 2008. [abstract]

G. Bernot, J.-P. Comet, O. Roux, J. Fromentin, Méthodes formelles informatiques, réseaux de régulation logiques de René Thomas, et extensions aux délais .  Exposé invité, GDR MABEM, Nice, 15-17 octobre , 2008. [abstract]

G. Bernot, J.-P. Comet, J. Guespin, Using Formal Temporal Logic to Model Biological Regulatory Networks and to Propose New Wet Experiments .  Invited talk, abstract in Proc. of French Genetic Soc. annual meeting, Genetics meets Systems Biology: Theory and Practice, p.17, Paris, November 13-15 , 2006.
Also: Exposé invité, Ecole Doctorale de Dijon, octobre 2008 , [abstract]

S. Troncale, R. Thuret, C. Ben, N. Pollet, Comet J.-P., G. Bernot, Modélisation de la régulation TH-dépendante de la résorption de la queue du têtard .  Réseaux d'interaction: Analyse, Modélisation et Simulation (RIAMS), journée thématique adossée à la conférence IPG, Lyon, 29 novembre , 2006. [preliminary version]

G. Bernot, J.-P. Comet, J. Guespin, Formal models of biological regulatory Networks. Example of Mucus Production in Pseudomonas aeruginosa .  Exposé invité au mini-colloque Biothérapies, axe Microbiologie du PRES UniverSud Paris, Villejuif, 23 sept , 2006. [slides]

G. Bernot, Méthodes informatiques d'étude de réseaux biologiques .  Conf. invitée, journée CIBI, Avancées et Enjeux en Biologie Intégrative, Rouen, 9 mars , 2006. [slides]

J. Guespin, D. Filopon, A. Merieau, 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 « Modélisation dynamique de réseaux de régulation biologique : des mesures aux modèles et des modèles aux mesures », Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Lyon, p.2 , 2005. [slides] [abstract]

J. Guespin, G. Bernot, J-P. Comet, A. Mérieau, B. Pollack, Une approche bioinformatique de la dynamique d'un réseau de régulation chez Pseudomonas aeruginosa .  Conf. invitée, VI-ième congrès de la Société Française de Microbiologie (SFM), Bordeaux, 10-12 mai , 2004.

G. Bernot, J.-P. Comet, J. Guespin, Mise au point de modèles discrets de réseaux de régulation biologiques par le Model Checking, la mucoïdie chez P. aeruginosa .  Exposé invité, Journées Logique Temporelle et Model Checking pour les Réseaux de Régulation Biologiques, ACI-IMPBio VICANNE, Évry, France, sept , 2004. [abstract]

G. Bernot, Applications des méthodes formelles informatiques aux réseaux de régulation biologique .  Exposé invité, Séminaire Généthon - Association Française contre les Myopathies (AFM), avril , 2004.

G. Bernot, Expérimentation en biologie et test de logiciel : même combat ! .  Conf. invitée, Intégration modèle-observation en biologie : méthodes et applications, XXIII-ième séminaire de la Société Francophone de Biologie Théorique (SFBT), Saint-Flour, France, 16-18 juin , 2003. [abstract]

J. Guespin, J-P. Comet, B. Polack, A. Richard, P. Amar, C. Hulen, G. Bernot, Epigenesis and dynamic similarity in two regulatory networks in Pseudomonas aeruginosa .  Conf. invitée, Intégration modèle-observation en biologie : méthodes et applications, XXIII-ième séminaire de la Société Francophone de Biologie Théorique (SFBT), Saint-Flour, France, 16-18 juin , 2003.

G. Bernot, J-P. Comet, Logique temporelle et model checking pour les réseaux de régulation biologique .  Conf. invitée. Actes des Troisièmes Journées de Post-Génomique de la Doua (JPGD), Lyon, France, 14-16 mai , 2003.
Also: Club SEE, Systèmes informatiques de confiance, ENST, Paris, France , 2003. [abstract]

G. Bernot, Logique temporelle et vérification de modèles .  Conf. invitée, Actes de l'école thématique Modélisation et simulation de processus biologiques dans le contexte de la génomique. Dieppe, 11-16 mai , 2003. [preliminary version]

G. Bernot, J. Guespin, A. Zemirline, J-P. Comet, F. Delaplace, P. Ballet, P. Amar, Modélisation, observabilité et expérimentation : étude d'un cas .  Conf. invitée, École thématique Modélisation et simulation de processus biologiques dans le contexte de la génomique. Autrans, 17-21 mars , 2002. [preliminary version]

G. Bernot, Description de quelques problèmes informatiques apportés par la biologie moléculaire .  Conférence invitée, journées BDA'01, Bases de Données Avancées, novembre 2001, Agadir, Maroc , 2001. [abstract]


SOME REFEREED POSTERS

A.C. Fierro, R. Thuret, G. Bernot, N. Pollet, Alternative microarray design: a critical assay on methods for profile reconstruction .  Poster JOBIM 2006, Journées de Biologie Informatique et Mathématiques, Bordeaux, France, 5-7 juillet , 2006.

J. Ahmad, A. Richard, G. Bernot, J.-P. Comet, O. Roux, Delays in Biological Regulatory Networks .  Integrative Post-Genomics (IPG), Lyon, France, p.6 30 November-2 December , 2005.

V. Bassano, P. Le Gall, G. Bernot, A propositional logic approach to manipulate topology of biological regulatory networks .  Poster, Computational Methods in Systems Biology, European Conference on Theory And Practice of Software, ETAPS'05, Edimburgh, Scotland, 2-10 April , 2005.

J.-P. Comet, P. Le Gall, G. Bernot, Qualitative Modelling of Genetic Networks: Extracting Experiment Schemas from Modelling .  Proc. of Integrative Post-Genomics (IPG), Lyon, France, p.28 13-15 October , 2004.

F. Tahi, G. Bernot, C. Auberger, Embedding Properties of Biological Regulatory Networks .  Invited Poster I-69, Biomedical Information Science and technology Initiative, BISTI'03 Symposium, Ntl Institutes of Health, Bethesda, Maryland, USA, 6-7 November , 2003.

V. Bassano, G. Bernot, A Formal Framework for the Modelling of Biological Regulatory Networks .  Poster, Actes de l'école thématique Modélisation et simulation de processus biologiques dans le contexte de la génomique. Dieppe, 11-16 mai , 2003.

J-P. Comet, S. Peres, G. Bernot, CTL and Biological Regulatory Networks: Example from P.aeruginosa .  Poster in Intl Symposium on Macromolecular Networks, Institut Pasteur, Paris, France, July 8-12 , 2002.

J-P. Comet, S. Peres, G. Bernot, Un langage formel pour les réseaux de régulation: un exemple avec multistationarité .  Poster JOBIM 2002, Journées de Biologie Informatique et Mathématiques, Saint-Malo, France, 10-12 juin , 2002.

V. Bassano, G. Bernot, D. Thieffry, Graphes de régulation avec marquages, vers un modèle formel informatique des réseaux de régulation biologiques .  Poster JOBIM 2002, Journées de Biologie Informatique et Mathématiques, Saint-Malo, France, 10-12 juin , 2002. [preliminary version] [poster]

V. Bassano, G. Bernot, D. Thieffry, Marked Regulatory Graphs : a Formal Framework for Biological Regulatory Networks .  Poster in Interdisciplinary School on Imaging, Modelling and Manipulating Regulatory Networks. Ambleteuse, France, 17-22 october , 2002.


PROJECT REPORTS

C. Collet, B. Finance, Z. Kedad, F. Tahi, D. Laurent, G. Bernot, G. Bruno, T.-T. Vu, G. Vargas-Solar, Rapport Final projet MEDIAGRID .  40p , 2005.

C. Collet, B. Finance, Z. Kedad, F. Tahi, D. Laurent, G. Bernot, G. Bruno, T.-T. Vu, G. Solar, Spécification du système MEDIAGRID .  Rapport de contrat MEDIAGRID , 2004.

C. Collet, B. Finance, Z. Kedad, F. Tahi, D. Laurent, G. Bernot, G. Bruno, T.-T. Vu, G. Solar, Etat de l'Art Infrastructure Médiation de sources de données : Intégration, Requêtes et Architecture .  Rapport de contrat MEDIAGRID, 150 pages , 2003.


SOME UNPUBLISHED RESEARCH REPORTS

V. Bassano, G. Bernot, D. Thieffry, Graphes de régulation avec marquages, vers un modèle informatique formel des réseaux de régulations biologiques .  LaMI Report 80-2002, Université d'Évry, France , 2002.


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