Guillaume Beslon

182

Documents

Publications

Emergence of supercoiling-mediated regulatory networks through the evolution of bacterial chromosome organization

Théotime Grohens , Sam Meyer , Guillaume Beslon

PLoS Computational Biology, 2025, 21, ⟨10.1371/journal.pcbi.1013482⟩

Article dans une revue hal-05357653v1

Structural mutations set an equilibrium non-coding genome fraction

Juliette Luiselli , Paul Banse , Olivier Mazet , Nicolas Lartillot , Guillaume Beslon

Molecular Biology and Evolution, 2025, 42 (12), ⟨10.1093/molbev/msaf315⟩

Article dans une revue hal-05382436v1

Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?

Paul Banse , Santiago F Elena , Guillaume Beslon

Virus Evolution, 2024, 10, ⟨10.1093/ve/veae078⟩

Article dans une revue hal-04801559v1

A Rigorous Framework to Classify the Post-Duplication Fate of Paralogous Genes (extended version)

Reza Kalhor , Guillaume Beslon , Manuel Lafond , Celine Scornavacca

Journal of Computational Biology, In press

Article dans une revue hal-04608855v2

Genome Streamlining: Effect of Mutation Rate and Population Size on Genome Size Reduction

Juliette Luiselli , Jonathan Rouzaud-Cornabas , Nicolas Lartillot , Guillaume Beslon

Genome Biology and Evolution, 2024, 16, ⟨10.1093/gbe/evae250⟩

Article dans une revue hal-04905734v1

Forward‐in‐time simulation of chromosomal rearrangements: The invisible backbone that sustains long‐term adaptation

Paul Banse , Juliette Luiselli , David P Parsons , Théotime Grohens , Marco Foley et al.

Molecular Ecology, 2023, ⟨10.1111/mec.17234⟩

Article dans une revue hal-04350147v1

Digital evolution: Insights for biologists

Miguel A. Fortuna , Guillaume Beslon , Charles Ofria

Frontiers in Ecology and Evolution, 2022, ⟨10.3389/fevo.2022.1037040⟩

Article dans une revue (article de synthèse) hal-03912093v1

A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling

Théotime Grohens , Sam Meyer , Guillaume Beslon

Artificial Life, 2022, CogNet, 28 (4), pp.440-457. ⟨10.1162/artl_a_00373⟩

Article dans une revue hal-03912118v1

Getting higher on rugged landscapes: Inversion mutations open access to fitter adaptive peaks in NK fitness landscapes

Leonardo Trujillo , Paul Banse , Guillaume Beslon

PLoS Computational Biology, 2022, 18 (10), pp.e1010647. ⟨10.1371/journal.pcbi.1010647⟩

Article dans une revue hal-03866346v1

The Surprising Creativity of Digital Evolution: A Collection of Anecdotes from the Evolutionary Computation and Artificial Life Research Communities

Joel Lehman , Jeff Clune , Dusan Misevic , Christoph Adami , Julie Beaulieu et al.

Artificial Life, 2020, 26 (2), pp.274-306. ⟨10.1162/artl_a_00319⟩

Article dans une revue hal-01735473v1

Phenotypic noise and the cost of complexity

Charles Rocabert , Guillaume Beslon , Carole Knibbe , Samuel Bernard

Evolution - International Journal of Organic Evolution, 2020, ⟨10.1111/evo.14083⟩

Article dans une revue hal-02920356v1

The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness

Vincent F Liard , David P. Parsons , Jonathan Rouzaud-Cornabas , Guillaume Beslon

Artificial Life, 2020, 26 (1), pp.38-57. ⟨10.1162/artl_a_00312⟩

Article dans une revue hal-03136077v1

Evolutionary Subspace Clustering Using Variable Genome Length

Sergio Peignier , Christophe Rigotti , Guillaume Beslon

Computational Intelligence, 2020, 36 (2), pp.574-612. ⟨10.1111/coin.12254⟩

Article dans une revue hal-02405598v1

Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure

Jacob Pieter Rutten , Paulien Hogeweg , Guillaume Beslon

BMC Evolutionary Biology, 2019, 19 (1), pp.1-17. ⟨10.1186/s12862-019-1507-z⟩

Article dans une revue hal-02350040v1

Introduction to the ECAL 2017 Special Issue

Carole Knibbe , Guillaume Beslon , Dusan Misevic

Artificial Life, 2019, 25 (4), pp.313-314. ⟨10.1162/artl_a_00298⟩

Article dans une revue hal-02428658v1

Isee-resistance : using in silico experimental evolution to sensitize providers on antibiotic resistance

Guillaume Beslon , Dominique Schneider

Antimicrobial Resistance and Infection Control, 2017, Abstracts from the 4th International Conference on Prevention & Infection Control (ICPIC 2017), 6(Suppl 3) (52), pp.2

Article dans une revue hal-01569262v1

Evolving Instrument Based on Symbiont-Host Metaphor: a Commensal Computation

Jonas Abernot , Guillaume Beslon , Simon Hickinbotham , Sergio Peignier , Christophe Rigotti

Journal of Creative Music Systems, 2017, 2 (1), pp.1-10. ⟨10.5920/JCMS.2017.11⟩

Article dans une revue hal-01596573v1

Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification

Charles Rocabert , Carole Knibbe , Jessika Consuegra , Dominique Schneider , Guillaume Beslon

PLoS Computational Biology, 2017, 13 (3), e1005459 (32 p.). ⟨10.1371/journal.pcbi.1005459.s006⟩

Article dans une revue hal-01508751v1

Erratum to: Temperature-induced variation in gene expression burst size in metazoan cells

O. Arnaud , Sam Meyer , E. Vallin , G. Beslon , O. Gandrillon

BMC Molecular Biology, 2016, 17, pp.2

Article dans une revue hal-02001327v1

Defining and simulating open-ended novelty: requirements, guidelines, and challenges.

Wolfgang Banzhaf , Bert Baumgaertner , Guillaume Beslon , René Doursat , James A Foster et al.

Theorie in den Biowissenschaften / Theory in Biosciences, 2016, ⟨10.1007/s12064-016-0229-7⟩

Article dans une revue hal-01323108v1

Open-Ended Evolution: Perspectives from the OEE Workshop in York

Tim Taylor , Mark Bedau , Alastair Channon , David Ackley , Wolfgang Banzhaf et al.

Artificial Life, 2016, 22 (3), pp.408-423. ⟨10.1162/ARTL_a_00210⟩

Article dans une revue hal-01371116v1

Temperature-induced variation in gene expression burst size in metazoan cells

Ophélie Arnaud , Sam Meyer , Elodie Vallin , Guillaume Beslon , Olivier Gandrillon

BMC Molecular Biology, 2015, 16 (20), ⟨10.1186/s12867-015-0048-2⟩

Article dans une revue hal-01248384v1

A Model for Genome Size Evolution

Stephan Fischer , Samuel Bernard , Guillaume Beslon , Carole Knibbe

Bulletin of Mathematical Biology, 2014, 76 (9), pp.2249 - 2291. ⟨10.1007/s11538-014-9997-8⟩

Article dans une revue hal-01090984v1

Torsion-Mediated Interaction between Adjacent Genes

Sam Meyer , Guillaume Beslon

PLoS Computational Biology, 2014, 10 (9), pp.e1003785. ⟨10.1371/journal.pcbi.1003785⟩

Article dans une revue hal-01090990v1

Comments to the Editor. Reply to the Comment by V.P. Shkilev on "Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium

Hédi Soula , Bertrand Caré , Guillaume Beslon , Hugues Berry

Biophysical Journal, 2014, 106 (11), pp.2544-2546. ⟨10.1016/j.bpj.2014.03.052⟩

Article dans une revue hal-00956603v1

Stochastic Fluctuations and Distributed Control of Gene Expression Impact Cellular Memory

Guillaume Corre , Daniel Stockholm , Ophélie Arnaud , Gaël Kaneko , José Viñuelas et al.

PLoS ONE, 2014, 9 (12), pp.e115574. ⟨10.1371/journal.pone.0115574⟩

Article dans une revue hal-01370311v1

Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts.

José Viñuelas , Gaël Kaneko , Antoine Coulon , Elodie Vallin , Valérie Morin et al.

BMC Biology, 2013, 11 (1), pp.15. ⟨10.1186/1741-7007-11-15⟩

Article dans une revue inserm-00817963v1

In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut , David P. Parsons , Stephan Fischer , Guillaume Beslon , Carole Knibbe

BMC Bioinformatics, 2013, 14 (Suppl 15), pp.S11

Article dans une revue hal-00873232v1

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium

Hédi Soula , Bertrand Caré , Guillaume Beslon , Hugues Berry

Biophysical Journal, 2013, 105 (9), pp.2064-2073. ⟨10.1016/j.bpj.2013.07.023⟩

Article dans une revue hal-00720515v3

Towards experimental manipulation of stochasticity in gene expression.

José Viñuelas , Gaël Kaneko , Antoine Coulon , Guillaume Beslon , Olivier Gandrillon

Progress in Biophysics and Molecular Biology, 2012, 100 (1), epub ahead of print. ⟨10.1016/j.pbiomolbio.2012.04.010⟩

Article dans une revue istex hal-00720054v1

New insights into bacterial adaptation through in vivo and in silico experimental evolution

Thomas Hindré , Carole Knibbe , Guillaume Beslon , Dominique Schneider

Nature Reviews Microbiology, 2012, 10 (5), pp.352-365. ⟨10.1038/nrmicro2750⟩

Article dans une revue (article de synthèse) hal-00696231v1

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Sebastian Grauwin , Guillaume Beslon , Eric Fleury , Sara Franceschelli , Céline Robardet et al.

Journal of the American Society for Information Science and Technology, 2012, 63 (7), pp.10.1002/asi.22644. ⟨10.1002/asi.22644⟩

Article dans une revue hal-00706567v1

Membrane microdomains emergence through non-homogeneous diffusion.

Hédi Soula , Antoine Coulon , Guillaume Beslon

BMC Biophysics, 2012, 5 (1), pp.6. ⟨10.1186/2046-1682-5-6⟩

Article dans une revue inserm-00768564v1

Chance at the heart of the cell

Olivier Gandrillon , Delphine Kolesnik-Antoine , Jean-Jacques Kupiec , Guillaume Beslon

Progress in Biophysics and Molecular Biology, 2012, Special Issue: Chance at the heart of the cell, 110 (1), pp.1-4. ⟨10.1016/j.pbiomolbio.2012.05.006⟩

Article dans une revue istex hal-00720052v1

Les complexités : point de vue d'un institut des systèmes complexes

Eric Bertin , Guillaume Beslon , Olivier Gandrillon , Sebastian Grauwin , Pablo Jensen et al.

Hermès, La Revue - Cognition, communication, politique, 2011, 2 (60), pp.145-150. ⟨10.4267/2042/45459⟩

Article dans une revue hal-00744520v1

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

Victor Norris , Abdallah Zemirline , Patrick Amar , Jean Nicolas Audinot , Pascal Ballet et al.

Theory in Biosciences, 2011

Article dans une revue hal-03469597v1

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

Vic Norris , Abdallah Zemirline , Patrick Amar , Jean Nicolas Audinot , Pascal Ballet et al.

Theorie in den Biowissenschaften / Theory in Biosciences, 2011, 130 (3), pp.211-228. ⟨10.1007/s12064-010-0118-4⟩

Article dans une revue (article de synthèse) hal-00643738v1

Enhanced Stimulus Encoding Capabilities with Spectral Selectivity in Inhibitory Circuits by STDP

Antoine Coulon , Guillaume Beslon , Hédi Soula

Neural Computation, 2011, 23 (4), pp.882-908

Article dans une revue inria-00593704v1

From Digital Genetics to Knowledge Discovery: Perspectives in Genetic Network Understanding

Guillaume Beslon , David P. Parsons , Jose-Maria Pena , Christophe Rigotti , Yolanda Sanchez-Dehesa

Intelligent Data Analysis, 2010, 14 (2), pp.173--191. ⟨10.3233/IDA-2010-0415⟩

Article dans une revue hal-00697024v1

À propos de la validité des modèles

Guillaume Beslon , Joanna Jongwane

Interstices, 2010

Article dans une revue hal-01350237v1

Scaling Laws in Bacterial Genomes: A Side-Effect of Selection of Mutational Robustness

Guillaume Beslon , David P. Parsons , Yolanda Sanchez-Dehesa , Jose-Maria Peña , Carole Knibbe

BioSystems, 2010, 102 (1), pp.32-40. ⟨10.1016/j.biosystems.2010.07.009⟩

Article dans une revue inria-00593709v1

On the spontaneous stochastic dynamics of a single gene: complexity of the molecular interplay at the promoter.

Antoine Coulon , Olivier Gandrillon , Guillaume Beslon

BMC Systems Biology, 2010, 4, pp.2. ⟨10.1186/1752-0509-4-2⟩

Article dans une revue hal-00542455v1

Large multiprotein structures modeling and simulation: the need for mesoscopic models.

Antoine Coulon , Guillaume Beslon , Olivier Gandrillon

Methods in Molecular Biology, 2008, 484, pp.537-58. ⟨10.1007/978-1-59745-398-1_32⟩

Article dans une revue hal-00294029v1

From Molecules to Organisms: Towards Multiscale Integrated Models of Biological Systems

Christophe Lavelle , Hugues Berry , Guillaume Beslon , Francisco Ginelli , Jean-Louis Giavitto et al.

Theoretical Biology Insights, 2008, 1, pp.13-22

Article dans une revue inria-00331281v1

The topology of the protein network influences the dynamics of gene order: from systems biology to a systemic understanding of evolution

C. Knibbe , J.M. Fayard , Guillaume Beslon

Artificial Life, 2008, 14 (1), pp.149-156. ⟨10.1162/artl.2008.14.1.149⟩

Article dans une revue hal-00391448v1

Modelling Evolution of Regulatory Networks in Artificial Bacteria

Yolanda Sanchez-Dehesa , David P. Parsons , Jose Maria Pena , Guillaume Beslon

Mathematical Modelling of Natural Phenomena, 2008, 2, 3, pp.27-66. ⟨10.1051/mmnp:2008054⟩

Article dans une revue hal-01500393v1

Modélisation cellulaire pour l'émergence de structures multiprotéiques auto-organisées

Antoine Coulon , Hédi Soula , Olivier Mazet , Olivier Gandrillon , Guillaume Beslon

Revue des Sciences et Technologies de l'Information - Série TSI : Technique et Science Informatiques, 2007, 1-2, 26, pp.123-148. ⟨10.3166/tsi.26.123-148⟩

Article dans une revue istex hal-01613745v1

Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences

C. Knibbe , O. Mazet , F. Chaudier , J.M. Fayard , G. Beslon

Journal of Theoretical Biology, 2007, 244 (4), pp.621-630

Article dans une revue hal-00391449v1

A long-term evolutionary pressure on the amount of noncoding DNA

Carole Knibbe , Antoine Coulon , Olivier Mazet , Jean-Michel Fayard , Guillaume Beslon

Molecular Biology and Evolution, 2007, 24 (10), pp.2344-2353. ⟨10.1093/molbev/msm165⟩

Article dans une revue hal-00391447v1

Simultaneous optimization of weights and structure of a RBF Neural Network

Vincent Lefort , C. Knibbe , G. Beslon , J. Favrel

Lecture Notes in Computer Science, 2006, 3871, pp.49-60

Article dans une revue hal-00391452v1

Guidelines: From artificial evolution to computational evolution: a research agenda

Wolfgang Banzhaf , Guillaume Beslon , Stephen Christensen , A. James , François Képès et al.

Nature Reviews Genetics, 2006, 7 (9), pp.729--735. ⟨10.1038/nrg1921⟩

Article dans une revue hal-00793902v1

Spontaneous Dynamics of Asymmetric Random Recurrent Spiking Neural Networks

H. Soula , G. Beslon , O. Mazet

Neural Computation, 2006, 18 (1), pp.60-79. ⟨10.1162/089976606774841567⟩

Article dans une revue hal-00119755v1

Modeling the emergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a multi-agent-based software

Hédi Soula , Céline Robardet , Fran\c Cois Perrin , Sébastien Gripon , Guillaume Beslon et al.

BMC Bioinformatics, 2005, 6, pp.228. ⟨10.1186/1471-2105-6-228⟩

Article dans une revue hal-00759509v1

Self-adaptation of genome size in artificial organisms

C. Knibbe , G. Beslon , Vincent Lefort , F. Chaudier , J.M. Fayard

Lecture Notes in Artificial Intelligence, 2005, 3630, pp.423-432

Article dans une revue hal-00391445v1

Modeling the mergence of multi-protein dynamic structures by principles of self-organization through the use of 3DSpi, a Multi-Agent-based Software.

H. Soula , C. Robardet , F. Perrin , S. Gripon , G. Beslon et al.

BMC Bioinformatics, 2005, 6, pp.228

Article dans une revue hal-00124089v1

ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

N. Reymond , H. Charles , L. Duret , Federica Calevro , G. Beslon et al.

Bioinformatics, 2004, 20, pp.271-273

Article dans une revue hal-00427641v1

Aevol 4b: Bridging the gap between artificial life and bioinformatics

Hugo Daudey , David P. Parsons , Eric Tannier , Vincent Daubin , Bastien Boussau et al.

ALIFE 2024 - International Conference for Artificial Life, Jul 2024, Copenhague, Denmark. pp.41-49, ⟨10.1162/isal_a_00716⟩

Communication dans un congrès hal-04667220v1

Classifying the Post-duplication Fate of Paralogous Genes

Reza Kalhor , Guillaume Beslon , Manuel Lafond , Celine Scornavacca

RECOMB-CG 2023 - 20th conference on Comparative Genomics, Apr 2023, Istanbul, Turkey. pp.1-18, ⟨10.1007/978-3-031-36911-7_1⟩

Communication dans un congrès hal-04239853v1

Simulating short-and long-term evolutionary dynamics on rugged landscapes

Leonardo Trujillo , Paul Banse , Guillaume Beslon

ALIFE 2021 - Conference on Artificial Life, Jul 2021, Prague, Czech Republic. pp.1-9

Communication dans un congrès hal-03426019v1

The Complexity Ratchet

Guillaume Beslon , Vincent F Liard , Jonathan Rouzaud-Cornabas

CCS 2021 - International Conference on Complex Systems, Oct 2021, Lyon, France

Communication dans un congrès hal-03511442v1

A Genome-Wide Evolutionary Simulation of the Transcription-Supercoiling Coupling

Théotime Grohens , Sam Meyer , Guillaume Beslon

ALIFE 2021 - Conference on Artificial Life, Jul 2021, Prague, Czech Republic

Communication dans un congrès hal-03242696v2

How to reduce a genome? ALife as a tool to teach the scientific method to school pupils

Quentin Carde , Marco Foley , Carole Knibbe , David P. Parsons , Jonathan Rouzaud-Cornabas et al.

ALIFE 2019 - Conference on Artificial Life, Jul 2019, Newcastle, United Kingdom. pp.497-504, ⟨10.1162/isal_a_00211⟩

Communication dans un congrès hal-02285718v1

Weight-based search to find clusters around medians in subspaces

Sergio Peignier , Christophe Rigotti , Anthony Rossi , Guillaume Beslon

SAC 2018 - ACM Symposium On Applied Computing, Apr 2018, Pau, France. pp.1-10

Communication dans un congrès hal-01869974v1

The Complexity Ratchet: Stronger than selection, weaker than robustness

Vincent F Liard , David P. Parsons , Jonathan Rouzaud-Cornabas , Guillaume Beslon

ALIFE 2018 - the 2018 conference on artificial Life, Jul 2018, Tokyo, Japan. pp.1-8, ⟨10.1162/isal_a_00051⟩

Communication dans un congrès hal-01882628v1

Evolving Living Technologies-Insights from the EvoEvo project

Guillaume Beslon , Santiago F Elena , Paulien Hogeweg , Dominique Schneider , Susan Stepney

SSBSE 2018 - 10th Symposium on Search-Based Software Engineering, Sep 2018, Montpellier, France. pp.46-62, ⟨10.1007/978-3-319-99241-9_2⟩

Communication dans un congrès hal-01882636v1

Environmental seasonality drives digital populations towards stable cross-feeding

Charles Rocabert , Carole Knibbe , Jessika Consuegra , Dominique Schneider , Guillaume Beslon

European Conference on Artificial Life (ECAL), Sep 2017, Villeurbanne, France

Communication dans un congrès hal-01569093v1

A 4-base model for the Aevol in-silico experimental evolution platform

Vincent Liard , Jonathan Rouzaud-Cornabas , Nicolas Comte , Guillaume Beslon

European Conference on Artificial Life, Sep 2017, Villeurbanne, France

Communication dans un congrès hal-01569097v1

EvoMove: Evolutionary-based living musical companion

Sergio Peignier , Jonas Abernot , Christophe Rigotti , Guillaume Beslon

European Conference on Artificial Life (ECAL), Sep 2017, Villeurbanne, France. pp.1-8

Communication dans un congrès hal-01569091v2

Comparative Genomics on Artificial Life

Priscila Biller , Carole Knibbe , Guillaume Beslon , Eric Tannier

Computability in Europe, Jun 2016, Paris, France. pp.35-44

Communication dans un congrès hal-01334930v1

Open-Endedness: Definitions and Shortcuts

Susan Stepney , Guillaume Beslon

2nd EvoEvo Workshop, satellite workshop of CCS2016, Sep 2016, Amsterdam, Netherlands

Communication dans un congrès hal-01375671v1

A Commensal Architecture for Evolving Living Instruments

Jonas Abernot , Guillaume Beslon , Simon Hickinbotham , Sergio Peignier , Christophe Rigotti

Conference on Computer Simulation of Musical Creativity, Jun 2016, Huddersfield, United Kingdom. pp.1-8

Communication dans un congrès hal-01368034v1

In Silico Experimental Evolution suggests a complex intertwining of selection, robustness and drift in the evolution of genetic networks complexity

Yoram Vadée-Le-Brun , Jonathan Rouzaud-Cornabas , Guillaume Beslon

Artificial Life, Jul 2016, Cancun, Mexico

Communication dans un congrès hal-01375645v1

In silico experimental evolution provides independent and challenging benchmarks for comparative genomics

Priscila Biller , Eric Tannier , Guillaume Beslon , Carole Knibbe

Journées ouvertes Biologie Informatique Mathématiques, Jun 2016, Lyon, France. pp.79-82

Communication dans un congrès hal-01375657v1

Evolvability drives innovation in viral genomes

Guillaume Beslon , Vincent F Liard , Santiago F Elena

2nd EvoEvo Workshop, satellite workshop of CCS2016, Sep 2016, Amsterdam, France

Communication dans un congrès hal-01375665v1

Evolution of mutator populations in constant environments

Jacob Pieter Rutten , Paulien Hogeweg , Guillaume Beslon

2nd EvoEvo Workshop, satellite workshop of CCS2016, Sep 2016, Amsterdam, Netherlands

Communication dans un congrès hal-01375669v1

Aevol-4b: Toward a new simulation platform to benchmark phylogenetic tools

Nicolas Comte , Vincent Liard , Carole Knibbe , Guillaume Beslon

ALPHY (ALignments and PHYlogeny), Feb 2017, Villeurbanne, France

Communication dans un congrès hal-01569078v1

In Silico Experimental Evolution Highlights the Influence of Environmental Seasonality on Bacterial Diversification

Charles Rocabert , Carole Knibbe , Jessika Consuegra , Dominique Schneider , Guillaume Beslon

2nd EvoEvo Workshop, satellite workshop of CCS2016, Sep 2016, Amsterdam, Netherlands

Communication dans un congrès hal-01375677v1

Towards a Integrated Evolutionary Model to Study Evolution of Evolution

Charles Rocabert , Carole Knibbe , Guillaume Beslon

EvoEvo Workshop (Satellite workshop of ECAL 2015), Jul 2015, York, United Kingdom

Communication dans un congrès hal-01252796v1

Subspace Clustering for all Seasons

Sergio Peignier , Christophe Rigotti , Guillaume Beslon

EvoEvo Workshop (satellite workshop of ECAL 2015), Jul 2015, york, United Kingdom. pp.1-3

Communication dans un congrès hal-01252793v1

Epigenetic inheritance speeds up evolution of artificial organisms

Yoram Vadée-Le-Brun , Jonathan Rouzaud-Cornabas , Guillaume Beslon

European Conference on Artificial Life, Jul 2015, York, United Kingdom. ⟨10.7551/978-0-262-33027-5-ch078⟩

Communication dans un congrès hal-01248383v1

Subspace Clustering Using Evolvable Genome Structure

Sergio Peignier , Christophe Rigotti , Guillaume Beslon

Genetic and Evolutionary Computation Conference (GECCO), Jul 2015, Madrid, Spain. pp.575-582

Communication dans un congrès hal-01199136v1

In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut , David P. Parsons , Stephan Fischer , Guillaume Beslon , Carole Knibbe

11th RECOMB - Comparative Genomics 2013, Oct 2013, Villeurbane, France

Communication dans un congrès hal-04764366v1

An alife game to teach evolution of antibiotic resistance

Guillaume Beslon , Bérénice Batut , David P. Parsons , Dominique Schneider , Carole Knibbe

ECAL - 12th European Conference on Artificial Life - 2013, Sep 2013, Taormina, Italy. pp.43-50

Communication dans un congrès hal-00849345v1

The Paradoxical Effects of Allelic Recombination on Fitness

David P. Parsons , Carole Knibbe , Guillaume Beslon

Proceedings of Artificial Life XIII, Jul 2012, East Lansing, France. pp.536--537

Communication dans un congrès hal-00759142v1

Parsimonious modeling of scaling laws in genomes and transcriptomes

Carole Knibbe , David P. Parsons , Guillaume Beslon

Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 11), Aug 2011, Paris, France. pp.414--415

Communication dans un congrès hal-00696870v1

Homologous and Nonhomologous Rearrangements: Interactions and Effects on Evolvability.

David P. Parsons , Carole Knibbe , Guillaume Beslon

Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems (ECAL 11), Aug 2011, Paris, France. pp.622--629

Communication dans un congrès hal-00696902v1

Aevol : un modèle individu-centré pour l’étude de la structuration des génomes

David P. Parsons , Carole Knibbe , Guillaume Beslon

MajecSTIC, Oct 2010, Bordeaux, France

Communication dans un congrès hal-01381560v1

Influence of the rearrangement rates on the organization of genome transcription

David P. Parsons , Carole Knibbe , Guillaume Beslon

JOBIM, Jun 2010, Montpellier, France

Communication dans un congrès hal-01381518v1

Influence of the rearrangement rates on the organization of genome transcription

David P. Parsons , Carole Knibbe , Guillaume Beslon

Integrative Post-Genomics, Nov 2010, Lyon, France

Communication dans un congrès hal-01381618v1

Importance of the rearrangement rates on the organization of transcription.

David P. Parsons , Carole Knibbe , Guillaume Beslon

Proceedings of Artificial Life XII, Aug 2010, Odense, Denmark. pp.479--486

Communication dans un congrès hal-00697043v1

Scaling Laws in Digital Organisms

Guillaume Beslon , Yolanda Sanchez-Dehesa , David P. Parsons , Jose Maria Pena , Carole Knibbe

Proc. Information Processing in Cells and Tissues IPCAT'09, Apr 2009, Ascona, Switzerland. pp.111-114

Communication dans un congrès hal-01437632v1

Evolution of scaling laws in artificial regulation networks

David P. Parsons , Guillaume Beslon , Carole Knibbe , Yolanda Sanchez-Dehesa , Jose Maria Pena

Integrative Post-Genomics, Nov 2009, Lyon, France. pp.22-22

Communication dans un congrès hal-01437814v1

Hyperstructures 2008-2009

Victor Norris , Anne-Françoise Batto , Pascal Ballet , Georgia Barlovatz , Gilles Bernot et al.

modelling complex biological systems, 2009, Evry, France

Communication dans un congrès hal-03469577v1

From bioputing to bactoputing: computing with bacteria

Victor Norris , Abdallah Zemirline , Patrick Amar , Pascal Ballet , Eshel Ben Jacob et al.

Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics, Apr 2008, Paris, France. pp.123-150

Communication dans un congrès hal-00340470v1

The topology of the protein network influences the dynamics of gene order: From systems biology to a systemic understanding of evolution

Carole Knibbe , Jean-Michel Fayard , Guillaume Beslon

8. European Conference on Artificial Life, Sep 2005, Canterbury,, United Kingdom. ⟨10.1162/artl.2008.14.1.149⟩

Communication dans un congrès hal-02823137v1

Modeling evolution of genetic regulation in artificial bacteria

Guillaume Beslon , Yolanda Sanchez-Dehesa , Jose Maria Pena

European Conference on Complex Systems, Sep 2008, Jérusalem, Israel. pp.4

Communication dans un congrès hal-01614302v1

Evolution des organismes bactériens

Guillaume Beslon , Federica Calevro , Hubert Charles , Jean-Michel Fayard , Carole Knibbe et al.

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant", Jul 2008, Villeurbanne, France. 12 diapos

Communication dans un congrès hal-02822501v1

Petits bricolages en évolution

Guillaume Beslon , Sara Franceschelli , Carole Knibbe

"Génies de la Bricole et du Bricolage", colloque en hommage à Claude Levy-Strauss, Nov 2008, Lyon, France

Communication dans un congrès hal-01614309v1

Les réseaux métaboliques et génétiques

H. Charles , G. Beslon , Federica Calevro , Jean-François Boulicaut , J.M. Fayard et al.

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant", 2008, Villeurbanne (France), juillet 2008, France. pp.1-1

Communication dans un congrès hal-00391271v1

Optimisation incrémentale de réseaux de neurones RBF pour la régression via un algorithme évolutionnaire : RBF-Gene

Virginie Lefort , Guillaume Beslon

Actes 8° Journées Francophones Extraction et Gestion des Connaissances EGC'08, Jan 2008, Sophia-Antipolis, France. pp.331-336

Communication dans un congrès hal-01614293v1

Evolution of genome structure : a computational approach

Guillaume Beslon

Workshop “Evolutionary Dynamics” , Mar 2008, Utrecht, Netherlands

Communication dans un congrès hal-01615228v1

Evolution des organismes bactériens

G. Beslon , Federica Calevro , H. Charles , J.M. Fayard , C. Knibbe et al.

Journée INSA de Lyon "BioIngénierie / Sciences et Ingénierie du Vivant", 2008, Villeurbanne (France), juillet 2008, France. pp.1-1

Communication dans un congrès hal-00391156v1

RAevol, un modèle de génétique digitale des réseaux de régulation

Yolanda Sanchez-Dehesa , Jose Maria Pena , Guillaume Beslon

Réseaux d'Interactions : Analyse, Modélisation, Simulation, RIAMS 2007, Nov 2007, Lyon, France

Communication dans un congrès hal-01613852v1

Modeling evolution of Regulatory Networks in Artificial Organisms

Yolanda Sanchez-Dehesa , Guillaume Beslon , Jose Maria Pena

3rd International Symposium on Computational Life Science CompLife'07, Oct 2007, Utrecht, Netherlands. pp.87-98, ⟨10.1063/1.2793407⟩

Communication dans un congrès hal-01613768v1

Digital Genetics: Modéliser la dynamique évolutive des génomes

Guillaume Beslon

Journées communes des clusters environnement et informatique à l'INRIA Montbonnot, Nov 2007, Grenoble, France

Communication dans un congrès hal-01615201v1

Effect of bottlenecks on genome size: investigations by digital genetics

Gaël Kaneko , Carole Knibbe , Guillaume Beslon

Integrative Post-Genomics, Nov 2007, Lyon, France

Communication dans un congrès hal-01596355v1

Artificial Regulatory Networks Evolution

Yolanda Sanchez-Dehesa , Loïc Cerf , Jose Maria Pena , Jean-François Boulicaut , Guillaume Beslon

Proc 1st Int Workshop on Machine Learning for Systems Biology MLSB 07, Sep 2007, Evry, France. pp.47-52

Communication dans un congrès hal-01502737v1

Systems Biology, where is the network ?

Guillaume Beslon

Santa-Fe Institute, Jul 2007, Santa-Fe, United States

Communication dans un congrès hal-01615180v1

Generating Data form the Evolution of Artificial Regulatory Networks

Yolanda Sanchez-Dehesa , Jose Maria Pena , Guillaume Beslon

Workshop Data Mining in Functional Genomics and Proteomics. Current Trends and Future Directions co-located with ECML/PKDD 07, Sep 2007, Varsovie, Poland. pp.91-103

Communication dans un congrès hal-01613779v1

Evolution de Second Ordre : le hasard sélectionné.

Guillaume Beslon

Spring school on interdisciplinarity in biology "Hasard et Fluctuations en Biologie", May 2007, Berder, France

Communication dans un congrès hal-01615166v1

Long-term needs for evolvability and robustness shape genome structure: a simulation study

C. Knibbe , G. Beslon , J.M. Fayard

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), 2006, Bordeaux (France), 2006, France. pp.1-1

Communication dans un congrès hal-00391437v1

Multi-Agent Modeling of Nuclear Structures.

Guillaume Beslon

Spring workshop on biological systems modeling, Mar 2006, Bombannes, France

Communication dans un congrès hal-01615151v1

Evolution et Robustesse : un équilibre complexe aux conséquences inattendues.

Guillaume Beslon

Journées de Gerland "Systèmes complexes et biologie", Dec 2006, Lyon, France

Communication dans un congrès hal-01615165v1

Amount of non-coding sequences depends on mutation rate

C. Knibbe , A. Coulon , O. Mazet , J.M. Fayard , G. Beslon

10th Evolutionary Biology Meeting, 2006, Marseille (France), 2006, France. pp.1-1

Communication dans un congrès hal-00391446v1

Designing artificial organisms to study the influence of gene pleitropy on genome evolution

C. Knibbe , G. Beslon , F. Chaudier , J.M. Fayard

8th European Conference on Artificial Life (ECAL 2005), 2005, Canterbury (Royaume-Uni), 2005, France. pp.1-1

Communication dans un congrès hal-00391344v1

Evolutionary influence of the protein network topology on gene organisation in artificial organisms

C. Knibbe , G. Beslon , J.M. Fayard

European Conference on Complex System (ECCS 2005), 2005, Paris (France), 2005, France. pp.1-1

Communication dans un congrès hal-00391436v1

Modelling evolution of prokaryotic genomes: an integrative approach

G. Beslon , C. Knibbe

FEBS Advanced Lecture Course, System Biology: From Molecules and Modeling to Cells, 2005, Gosau (Autriche), 2005, France. pp.1-1

Communication dans un congrès hal-00391254v1

2DS'PI 2 Dimensional Dynamic Simulation of Proteins' Interactions

Tiphaine Martin , Céline Charavay , Audrey Herr , Céline Becquet , Hédi Soula et al.

Journées de post-génomique de la DOUA 2002, JPG'02, Jun 2002, Lyon, France

Communication dans un congrès inria-00615231v1

ROSO: A software to search optimized oligonucleotide probes for microarrays

Hubert Charles , Nancie Reymond , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard

COST853: Agricultural Biomarkers for Array-Technology, Sep 2002, Waedenswill, Switzerland

Communication dans un congrès hal-03506465v1

Towards alife-generated benchmarks for phylogeny

Marco Foley , Jonathan Rouzaud-Cornabas , Eric Tannier , Guillaume Beslon

ALignements and PHYlogénie (Alphy), Jan 2023, Grenoble, France.

Poster de conférence hal-04398854v1

Phenotypic Noise and the Cost of Complexity

Charles Rocabert , Guillaume Beslon , Carole Knibbe , Samuel Bernard

EvoLyon 2019, Nov 2019, Lyon, France

Poster de conférence hal-02402443v1

Jump then Climb: can rearrangements predict the occurrence of mutational bursts?

Guillaume Beslon , Vincent F Liard , Santiago F Elena

Evolution 2018 - Congress on Evolutionary Biology, Aug 2018, Montpellier, France. pp.1

Poster de conférence hal-01938800v1

The complexity ratchet: stronger than selection

Vincent F Liard , Jonathan Rouzaud-Cornabas , David P. Parsons , Guillaume Beslon

Beacon congress 2018, Aug 2018, east-lansing, United States. pp.1

Poster de conférence hal-01938802v1

In silico experimental evolution shows that complexity can rise even in simple environments

Guillaume Beslon , Vincent F Liard , David P. Parsons , Jonathan Rouzaud-Cornabas

ICSB 2018 - 19th International Conference on Systems Biology, Oct 2018, Lyon, France. pp.1

Poster de conférence hal-01939365v1

Testing evolution predictability using the aevol software

Guillaume Beslon , Vincent F Liard , Santiago F Elena

16th international meeting of the European Society of Evolutionary Biology (ESEB 2017) , Aug 2017, Groningen, Netherlands. 2017

Poster de conférence hal-01577115v1

Unexpected genome inflation and streamlining in variable environments

Bérénice Batut , Guillaume Beslon , Carole Knibbe

Journées ouvertes de Biologie Informatique & Mathématiques 2016, Jun 2016, Lyon, France. pp.320-322, 2016

Poster de conférence hal-01375653v1

Simulating evolutionary scenarios to test whether they can induce reductive evolution

Bérénice Batut , Mathilde Dumond , Gabriel Marais , Guillaume Beslon , Carole Knibbe

SMBE 2012 : Society for Molecular Biology and Evolution, Jun 2012, Dublin, Ireland

Poster de conférence hal-00762597v1

Optimization of proton therapy ballistics using a genetic algorithm

François Smekens , Jean-Michel Létang , Nicolas Freud , Bruno Sixou , Guillaume Beslon

Particle Therapy Co-Operative Group, PTCOG, May 2011, Philadelphia (US), United States. 2011

Poster de conférence hal-01354428v1

Chromatin is a major player in regulating gene expression stochasticity in higher eukaryotic cells

José Viñuelas , Gaël Kaneko , Valérie Morin , Elodie Vallin , Antoine Coulon et al.

Stochastic Systems Biology conference, Jul 2011, Ascona, Switzerland. 2011

Poster de conférence hal-01354566v1

Relationship between chromosomal features and gene expression stochasticity in higher eukaryotic cells

José Viñuelas , Gaël Kaneko , Antoine Coulon , Guillaume Beslon , Olivier Gandrillon

Integrative Post-Genomics, Nov 2009, Lyon, France. pp.36-36, 2009

Poster de conférence hal-01437813v1

Gene expression and the dynamics of transcriptional regulation : a model for theoretical and experimental investigations

Antoine Coulon , Olivier Gandrillon , Guillaume Beslon

Integrative Post-Genomics, IPG'08, Nov 2008, Lyon, France. 2008

Poster de conférence hal-01614314v1

Modeling membrane micro-domain formation through inhomogeneous diffusion

Hédi Soula , Guillaume Beslon

Integrative Post-Genomics, IPG'08, Nov 2008, Lyon, France. 2008

Poster de conférence hal-01614515v1

Binding cooperation and competition among transcription factors can cause complex stochastic properties in gene expression

Antoine Coulon , Guillaume Beslon , Olivier Gandrillon

Integrative Post-Genomics, IPG'07, Nov 2007, Lyon, France. 2007

Poster de conférence hal-01613869v1

ROSO: a software to search optimized oligonucleotide probes for microarrays

Nancie Reymond , Hubert Charles , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard

14. Rencontres Régionales de la Recherche, Oct 2003, Saint-Etienne, France

Poster de conférence hal-03506598v1

Bioinformatique du transcriptome de Buchnera, symbiote intracellulaire des pucerons

Hubert Charles , Federica Calevro , Nancie Reymond , Frederique Laforest , Anne Tchounikine et al.

Rencontres 2003 des Microbiologistes de l'INRA, May 2003, Dourdan, France

Poster de conférence hal-03506503v1

ROSO : un logiciel de recherche et d'optimisation des sondes oligonucléotidiques destinées aux puces à ADN

Nancie Reymond , Hubert Charles , Guillaume Beslon , Jean-Michel Fayard

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM), Jun 2002, Saint-Malo, France

Poster de conférence hal-03506488v1

Modeling evolution through a genetic regulation network

Guillaume Beslon , Hubert Charles , Jean-Michel Fayard , Olivier Gandrillon , Olivier Mazet

Journées de Post-Génomique de la Doua - JPGD'02, Mar 2002, Villeurbanne, France

Poster de conférence hal-03506447v1

ROSO : un logiciel de recherche et d'optimisation des sondes oligonucléotidiques destinées aux puces à ADN

Nancie Reymond , Hubert Charles , Guillaume Beslon , Jean-Michel Fayard

Intersciences 2002, Colloque des doctorants scientifiques de Lyon, Apr 2002, Villeurbanne, France

Poster de conférence hal-03506486v1

ROSO : un logiciel de recherche et d'optimisation des sondes oligonucléotidiques

Nancie Reymond , Hubert Charles , Guillaume Beslon , Jean-Michel Fayard

Journées de Post-Génomique de la Doua - JPGD'02, Mar 2002, Villeurbanne, France

Poster de conférence hal-03506485v1

ROSO : A Software to Search Optimized Oligonucleotide Probes for Microarrays

Nancie Reymond , Hubert Charles , Guillaume Beslon , Laurent Duret , Jean-Michel Fayard

10. International Conference on Intelligent Systems for Molecular Biology (ISMB), Aug 2002, Edmonton, Canada

Poster de conférence hal-03506483v1

Functional space approach for evolutionary algorithms

Guillaume Beslon , Hubert Charles , Jean-Michel Fayard , Olivier Gandrillon , Olivier Mazet et al.

Journées de Post-Génomique de la Doua - JPGD'02, Mar 2002, Villeurbanne, France

Poster de conférence hal-03506453v1

Développement d'un logiciel d'optimisation de sondes oligonucléotidiques destinées aux puces à ADN

Nancie Reymond , Hubert Charles , Guillaume Beslon , Jean-Michel Fayard

Journées de Post-Génomique de la Doua - JPGD'01, Apr 2001, villeurbanne, France

Poster de conférence hal-03506436v1

Of Evolution, Systems and Complexity

Guillaume Beslon , Vincent F Liard , David P. Parsons , Jonathan Rouzaud-Cornabas

Evolutionary Systems Biology II, 2021, ⟨10.1007/978-3-030-71737-7_1⟩

Chapitre d'ouvrage hal-03136122v1

De la modélisation comme poésie. La modélisation de systèmes biologiques complexes vue par deux modélisateurs

Hugues Berry , Guillaume Beslon

Franck Varenne and Marc Silberstein. Modéliser & simuler. Epistémologies et pratiques de la modélisation et de la simulation, 1, Editions Matériologiques, Paris, 2013, 978-2-919694-19-8

Chapitre d'ouvrage hal-00815550v1