Louis‐Marie Bobay

Genomic and phenotypic diversification of Pseudomonas aeruginosa during sustained exposure to a ciliate predator

This study shows that exposure to a ciliate predator reshapes evolutionary dynamics in Pseudomonas aeruginosa by maintaining genetic diversity and altering mutation frequency distributions, without consistently increasing virulence.

DEX: an amino acid exchangeability measure for codon substitution modelling and selection inference

This paper evaluates 30 amino acid distance measures, including a new one based on deep mutational scanning, to identify the best for modeling codon substitutions and inferring natural selection across diverse lineages.

MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.

MetaStrainer reconstructs bacterial strain genotypes from short-read metagenomic data with higher accuracy than existing tools.

Prevalence and Dynamics of Genome Rearrangements in Bacteria and Archaea

This study examines genome rearrangement dynamics in bacteria and archaea, finding variable rates and mobile elements as key drivers of genomic changes.

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

The paper investigates the relationship between co-occurrence and horizontal gene transfer (HGT) in marine bacteria, finding a significant association independent of phylogeny.

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy.

The paper quantifies introgression across bacterial lineages, finding varying levels of gene flow and its association with ecological proximity, but not substantial blurring of species borders.

Homologous Recombination Shapes the Architecture and Evolution of Bacterial Genomes

This study estimates recombination rates across 145 bacterial genomes, revealing patterns that shape genome architecture and evolution, including conserved recombination landscapes and functional associations with adaptive regions.