Publications

Main Publications

Luiselli et al., Genome Biology and Evolution, 2024 Genome streamlining: effect of mutation rate and population size on genome size reduction
Banse et al., Virus Evolution, 2024 Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?
Banse, Luiselli et al., Molecular Ecology, 2023 Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation
Liard et al., Int. Conf. Artif. Life, 2018 <Best Paper Award> The Complexity Ratchet: Stronger than selection, weaker than robustness
Frenoy et al., Plos Comp. Biol., 2013 Genetic Architecture Promotes the Evolution and Maintenance of Cooperation
Batut et al., BMC Bioinfo., 2013 In silico experimental evolution: a tool to test evolutionary scenarios
Misevic et al., Int. Conf. Artif. Life, 2012 <Best Paper Award> Effects of public good properties on the evolution of cooperation
Frenoy et al., Int. Conf. Artif. Life, 2012 Robustness and evolvability of cooperation
Beslon et al., Biosystems, 2010 Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?
Parsons et al., Int. Conf. Artif. Life, 2010 Importance of the Rearrangement Rates on the Organization of Genome Transcription
Knibbe et al., Mol. Biol. Evol., 2007 A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA

PhD Theses

Luiselli, PhD Thesis, INSA-Lyon, 2025 How chromosomal rearrangements shape genomes : a computational and mathematical study
Foley, PhD Thesis, INSA-Lyon, 2023 Dynamique des génomes bactériens : Une étude expérimentale in silico avec la plateforme Aevol
Banse, PhD Thesis, INSA-Lyon, 2023 Évolution au-delà des substitutions : Modélisation informatique de l’impact des réarrangements chromosomiques sur les dynamiques évolutives
Liard, PhD Thesis, INSA-Lyon, 2020 Origine évolutive de la complexité des systèmes biologiques : Une étude par évolution expérimentale in silico
Frénoy, PhD Thesis, Paris-Descartes, 2014 Pressions de sélection de second ordre liées à l’évolution de la coopération dans des systèmes microbiens et numériques
Batut, PhD Thesis, INSA-Lyon, 2014 Étude de l’évolution réductive des génomes bactériens par expériences d’évolution in silico et analyses bioinformatiques
Parsons, PhD Thesis, INSA-Lyon, 2011 Indirect Selection in Darwinian Evolution: Mechanisms and Implications
Sanchez-Dehesa, PhD Thesis, INSA-Lyon, 2009 RÆvol : un modèle de génétique digitale pour étudier l’évolution des réseaux de régulation génétiques
Knibbe, PhD Thesis, INSA-Lyon, 2006 Structuration des génomes par sélection indirecte de la variabilité mutationnelle, une approche de modélisation et de simulation

All Publications

Banse et al., Virus Evolution, 2024 Innovation in viruses: fitness valley crossing, neutral landscapes, or just duplications?
Luiselli et al., Genome Biology and Evolution, 2024 Genome streamlining: effect of mutation rate and population size on genome size reduction
Daudey et al., Int. Conf. Artif. Life, 2024 Aevol_4b: Bridging the gap between artificial life and bioinformatics
Kalhor et al., Journal of Computational Biology, 2024 A rigorous framework to classify the postduplication fate of paralogous genes. , 31(9), 815-833.
Kalhor et al., RECOMB International Workshop on Comparative Genomics, 2023 Classifying the post-duplication fate of paralogous genes
Banse, Luiselli et al., Molecular Ecology, 2023 Forward-in-time simulation of chromosomal rearrangements: The invisible backbone that sustains long-term adaptation
Beslon et al., Evolutionary systems biology: advances, questions, and opportunities, 2020 Of evolution, systems and complexity
Liard et al., Artificial Life, 2020 The complexity ratchet: Stronger than selection, stronger than evolvability, weaker than robustness
Liard et al., Int. Conf. Artif. Life, 2018 <Best Paper Award> The Complexity Ratchet: Stronger than selection, weaker than robustness
Knibbe et al., Int. Conf. Artif. Life, 2014 What happened to my genes? Insights on gene family dynamics from digital genetics experiments
Beslon et al., Europ. Conf. Artif. Life, 2013 An alife game to teach evolution of antibiotic resistance
Misevic et al., Europ. Conf. Artif. Life, 2013 In silico evolution of transferable genetic elements
Frenoy et al., Plos Comp. Biol., 2013 Genetic Architecture Promotes the Evolution and Maintenance of Cooperation
Batut et al., BMC Bioinfo., 2013 In silico experimental evolution: a tool to test evolutionary scenarios
Misevic et al., Int. Conf. Artif. Life, 2012 <Best Paper Award> Effects of public good properties on the evolution of cooperation
Parsons et al., Int. Conf. Artif. Life, 2012 The Paradoxical Effects of Allelic Recombination on Fitness
Hindre et al., Nat. Rev. Microbiol., 2012 New insights into bacterial adaptation through in vivo and in silico experimental evolution
Frenoy et al., Int. Conf. Artif. Life, 2012 Robustness and evolvability of cooperation
Parsons et al., Europ. Conf. Artif. Life, 2011 Homologous and Nonhomologous Rearrangements: Interactions and Effects on Evolvability
Knibbe et al., Europ. Conf. Artif. Life, 2011 Parsimonious Modeling of Scaling Laws in Genomes and Transcriptomes
Beslon et al., Biosystems, 2010 Scaling laws in bacterial genomes: A side-effect of selection of mutational robustness?
Parsons et al., Int. Conf. Artif. Life, 2010 Importance of the Rearrangement Rates on the Organization of Genome Transcription
Parsons et al., MajecSTIC, 2010 Aevol : un modèle individu-centré pour l’étude de la structuration des génomes
Beslon et al., Intel. Data Anal. J., 2010 From digital genetics to knowledge discovery: Perspectives in genetic network understanding
Knibbe et al., Artif. Life, 2008 The Topology of the Protein Network Influences the Dynamics of Gene Order: From Systems Biology to a Systemic Understanding of Evolution
Knibbe et al., Mol. Biol. Evol., 2007 A Long-Term Evolutionary Pressure on the Amount of Noncoding DNA
Knibbe et al., J. Theor. Biol., 2007 Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences
Knibbe et al., Europ. Conf. Artif. Life, 2005 Self-adaptation of genome size in artificial organisms