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Dive into the research topics where Gilles Bernot is active.

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Featured researches published by Gilles Bernot.


Archive | 2013

Modeling and Analysis of Gene Regulatory Networks

Gilles Bernot; Jean-Paul Comet; Adrien Richard; Madalena Chaves; Jean-Luc Gouzé; Frédéric Dayan

This chapter describes basic principles for modeling genetic regulatory networks, using three different classes of formalisms: discrete, hybrid, and continuous differential systems. A short review of the mathematical tools for each formalism is presented. Based on several simple examples, which are worked out in detail, this chapter illustrates the study and analysis of the networks’ dynamics, their temporal evolution and asymptotic behaviors.


PLOS ONE | 2012

Boolean Models of Biosurfactants Production in Pseudomonas fluorescens

Adrien Richard; Gaelle Rossignol; Jean-Paul Comet; Gilles Bernot; Jannine Guespin-Michel; Annabelle Merieau

Cyclolipopeptides (CLPs) are biosurfactants produced by numerous Pseudomonas fluorescens strains. CLP production is known to be regulated at least by the GacA/GacS two-component pathway, but the full regulatory network is yet largely unknown. In the clinical strain MFN1032, CLP production is abolished by a mutation in the phospholipase C gene () and not restored by complementation. Their production is also subject to phenotypic variation. We used a modelling approach with Boolean networks, which takes into account all these observations concerning CLP production without any assumption on the topology of the considered network. Intensive computation yielded numerous models that satisfy these properties. All models minimizing the number of components point to a bistability in CLP production, which requires the presence of a yet unknown key self-inducible regulator. Furthermore, all suggest that a set of yet unexplained phenotypic variants might also be due to this epigenetic switch. The simplest of these Boolean networks was used to propose a biological regulatory network for CLP production. This modelling approach has allowed a possible regulation to be unravelled and an unusual behaviour of CLP production in P. fluorescens to be explained.


Procedia Computer Science | 2012

Simplified Models for the Mammalian Circadian Clock

Jean-Paul Comet; Gilles Bernot; Aparna Das; Francine Diener; Camille Massot; Amélie Cessieux

Numerous biological mechanisms are synchronized by the circadian rhythm in species so diverse as mushrooms, drosophiles or mammals. Because of its ubiquity and of its implication in numerous cellular functions, we believe important to be able to extract the main “coarse-grain” mechanisms common to a majority of organisms. In this article we consider both differential equation models and discrete models and we deliberately choose to push the simplicity of the model as far as possible, focusing only on a few biological behaviours of interest. The hope is to get the essential abstract causalities that govern these behaviours.


Theory in Biosciences | 2011

Computing with bacterial constituents, cells and populations: from bioputing to bactoputing

Vic Norris; Abdallah Zemirline; Patrick Amar; Jean Nicolas Audinot; Pascal Ballet; Eshel Ben-Jacob; Gilles Bernot; Guillaume Beslon; Armelle Cabin; Eric Fanchon; Jean-Louis Giavitto; Nicolas Glade; Patrick Greussay; Yohann Grondin; James A. Foster; Guillaume Hutzler; Jürgen Jost; François Képès; Olivier Michel; Franck Molina; Jacqueline Signorini; Pasquale Stano; Alain R. Thierry

The relevance of biological materials and processes to computing—aliasbioputing—has been explored for decades. These materials include DNA, RNA and proteins, while the processes include transcription, translation, signal transduction and regulation. Recently, the use of bacteria themselves as living computers has been explored but this use generally falls within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions, while microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These could be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments both as individuals and as populations of bacteria plus bacteriophage. New principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. This computing might even extend to developing a high level language appropriate to using populations of bacteria and bacteriophage. Here, we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria for calculating.


international conference computational systems-biology and bioinformatics | 2010

A Formal Model for Gene Regulatory Networks with Time Delays

Jean-Paul Comet; Jonathan Fromentin; Gilles Bernot; Olivier Henri Roux

We introduce a hybrid modelling framework for gene regulatory networks as an extension of the Rene Thomas’ discrete modelling framework. We handle temporal aspects through delays expressing the time mandatory to pass from a qualitative state to another one. It permits one to build, from a specification expressed in terms of paths, the constraints on the temporal parameters in order to assure the consistency between the hybrid model and the specification.


computational intelligence methods for bioinformatics and biostatistics | 2009

On the use of temporal formal logic to model gene regulatory networks

Gilles Bernot; Jean-Paul Comet

Modelling activities in molecular biology face the difficulty of prediction to link molecular knowledge with cell phenotypes. Even when the interaction graph between molecules is known, the deduction of the cellular dynamics from this graph remains a strong corner stone of the modelling activity, in particular one has to face the parameter identification problem. This article is devoted to convince the reader that computers can be used not only to simulate a model of the studied biological system but also to deduce the sets of parameter values that lead to a behaviour compatible with the biological knowledge (or hypotheses) about dynamics. This approach is based on formal logic. It is illustrated in the discrete modelling framework of genetic regulatory networks due to Rene Thomas.


Journal of Mathematical Biology | 2012

On the impact of the distance between two genes on their interaction curve

Siamak Taati; Enrico Formenti; Jean-Paul Comet; Gilles Bernot

We analyze a basic building block of gene regulatory networks using a stochastic/geometric model in search of a mathematical backing for the discrete modeling frameworks. We consider a network consisting only of two interacting genes: a source gene and a target gene. The target gene is activated by the proteins encoded by the source gene. The interaction is therefore mediated by activator proteins that travel, like a signal, from the source to the target. We calculate the production curve of the target proteins in response to a constant-rate production of activator proteins. The latter has a sigmoidal shape (like a simple delay line) that is sharper and taller when the two genes are closer to each other. This provides further support for the use of discrete models in the analysis gene regulatory networks. Moreover, it suggests an evolutionary pressure towards making the interacting genes closer to each other to make their interactions more efficient and more reliable.


Journal of Bioinformatics and Computational Biology | 2016

A hybrid model of cell cycle in mammals

Jonathan Behaegel; Jean-Paul Comet; Gilles Bernot; Emilien Cornillon; Franck Delaunay


Proceedings of the Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics | 2007

From bioputing to bactoputing: computing with bacteria

Victor Norris; Abdallah Zemirline; Patrick Amar; Pascal Ballet; Eshel Ben Jacob; Gilles Bernot; Guillaume Beslon; Eric Fanchon; Jean-Louis Giavitto; Nicolas Glade; Patrick Greussay; Yohann Grondin; James A. Foster; Guillaume Hutzler; François Képès; Olivier Michel; Gradimir Misevic; Franck Molina; Jacqueline Signorini; Pasquale Stano; Alain R. Thierry


2nd Workshop on Computational Structural Biology: Integrative Approaches for Modeling Biomolecular Complexes | 2013

A Hoare logic for gene regulatory networks

Jean-Paul Comet; Gilles Bernot

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Jean-Paul Comet

Centre national de la recherche scientifique

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Adrien Richard

University of Nice Sophia Antipolis

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Aparna Das

University of Nice Sophia Antipolis

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Francine Diener

University of Nice Sophia Antipolis

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