Main publications


Articles in peer-reviewed journal

Hédi Soula; Bertrand Caré; Guillaume Beslon; Hugues Berry

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

Biophysical Journal, Biophysical Society, 2013, 105 (9), pp. 2064-2073

Bérénice Batut; David Parsons; Stephan Fischer; Guillaume Beslon; Carole Knibbe

In silico experimental evolution: a tool to test evolutionary scenarios

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

José Viñuelas; Gaël Kaneko; Antoine Coulon; Elodie Vallin; Valérie Morin; Camila Mejia-Pous; Jean-Jacques Kupiec; Guillaume Beslon; Olivier Gandrillon

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

BMC Biology, 2013, 11 (1), pp. 15

Thomas Hindré; Carole Knibbe; Guillaume Beslon; Dominique Schneider

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

Nature Reviews Microbiology, nature publishing group, 2012, 10, pp. 352-365

Hédi Soula; Antoine Coulon; Guillaume Beslon

Membrane microdomains emergence through non-homogeneous diffusion

BMC Biophysics, BioMedCentral, 2012, 5 (1), pp. 6

Sebastian Grauwin ; Guillaume Beslon; Eric Fleury; Sara Franceschelli; Céline Robardet; Jean-Baptiste Rouquier; Pablo Jensen

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Journal of the American Society for Information Science and Technology, 2012, pp. 10.1002/asi.22644

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

Chance at the heart of the cell.

Prog Biophys Mol Biol, 2012, epub ahead of print

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

Towards experimental manipulation of stochasticity in gene expression.

Prog Biophys Mol Biol, 2012, epub ahead of print

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; Francois Kepes; Olivier Michel; Franck Molina; Jacqueline Signorini; Pasquale Stano; Alain R Thierry

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

Theorie in den Biowissenschaften / Theory in Biosciences, Springer, 2011, 130 (3), pp. 211-228

Eric Bertin; Guillaume Beslon; Olivier Gandrillon; Sébastian Grauwin; Pablo Jensen; Nicolas Schabanel

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

Hermes, 2011, 60, pp. 145-150

Antoine Coulon; Guillaume Beslon; Hédi Soula

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

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

Antoine Coulon; Olivier Gandrillon; Guillaume Beslon

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

BMC Systems Biology, 2010, 4, pp. 2

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

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

Intelligent Data Analysis, IOS Press, 2010, 14 (2), pp. 173-191

Guillaume Beslon; David Parsons; Yolanda Sanchez-Dehesa; Jose-Maria Peña; Carole Knibbe

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

Biosystems, Elsevier, 2010, 102 (1), pp. 32-40

Antoine Coulon; Guillaume Beslon; Olivier Gandrillon

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

Methods in molecular biology (Clifton, N.J.), 2008, 484, pp. 537-58

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

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

Artificial Life, 2008, 14 (1), pp. 149-156

Christophe Lavelle; Hugues Berry; Guillaume Beslon; Francisco Ginelli; Jean-Louis Giavitto; Zoi Kapoula; André Le Bivic; Nadine Peyrieras; Ovidiu Radulescu; Adrien Six; Véronique Thomas-Vaslin; Paul Bourgine

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

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

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

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

Molecular Biology and Evolution, 2007, 24 (10), pp. 2344-2353

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

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

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

Wolfgang Banzhaf; Guillaume Beslon; Stephen Christensen; James A.; François Képès; Virginie Lefort; Julian F.; Miroslav Radman; Jeremy J. Ramsden

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

Nature Reviews Genetics, Nature Publishing Group, 2006, 7 (9), pp. 729-735

H. Soula; G. Beslon; O. Mazet

Spontaneous Dynamics of Asymmetric Random Recurrent Spiking Neural Networks

Neural Computation, 2006, 18, pp. 60-79

V. Lefort; C. Knibbe; G. Beslon; J. Favrel

Simultaneous optimization of weights and structure of a RBF Neural Network

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

Hédi Soula; Céline Robardet; François Perrin; Sébastien Gripon; Guillaume Beslon; Olivier Gandrillon

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

BMC Bioinformatics, 2005, 6, pp. 228

C. Knibbe; G. Beslon; V. Lefort; F. Chaudier; J.M. Fayard

Self-adaptation of genome size in artificial organisms

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

N. Reymond; H. Charles; L. Duret; F. Calevro; G. Beslon; J.-M. Fayard

ROSO : Research on Optimized Oligonucleotide Probes for Microarrays

Bioinformatics, 2004, 20, pp. 271-273

Peer-reviewed conferences/proceedings

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

An alife game to teach evolution of antibiotic resistance

ECAL - 12th European Conference on Artificial Life - 2013, Sep 2013, Taormina, Italy. MIT Press

David Parsons; Carole Knibbe; Guillaume Beslon

The Paradoxical Effects of Allelic Recombination on Fitness

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

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

Simulating evolutionary scenarios to test whether they can induce reductive evolution

[Poster]. SMBE 2012 : Society for Molecular Biology and Evolution, Jun 2012, Dublin, Ireland

Carole Knibbe; David P. Parsons; Guillaume Beslon

Parsimonious modeling of scaling laws in genomes and transcriptomes

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

David P. Parsons; Carole Knibbe; Guillaume Beslon

Homologous and Nonhomologous Rearrangements: Interactions and Effects on Evolvability.

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

David P. Parsons; Carole Knibbe; Guillaume Beslon

Importance of the rearrangement rates on the organization of transcription.

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

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

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

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

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

Amount of non-coding sequences depends on mutation rate

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

G. Beslon; C. Knibbe

Modelling evolution of prokaryotic genomes: an integrative approach

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

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

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

8th European Conference on Artificial Life (ECAL 2005), 2005, Canterbury (Royaume-Uni), 2005, France. Proceedings of the System Biology Workshop at the 8th European Conference on Artificial Life, pp. 1-1

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

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

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