François Blanquart

This study uses community PCR test data to estimate viral dynamics parameters and assess the impact of age, vaccination, and variants on SARS-CoV-2 infection.

The paper traces the evolutionary origin and recent selection of the High Pathogenicity Island in Escherichia coli, linking its acquisition to Neolithic human-animal interactions and modern public health implications.

This study quantifies how antibiotic resistance and within-host competition affect pneumococcal strain fitness using longitudinal carriage data.

This paper introduces a model for bacterial pangenome evolution and applies it to Salmonella genomes to classify genes based on their evolutionary dynamics.

This study tracks E. coli dynamics in a human gut over 20 years, showing how strain properties and environmental factors influence diversity and persistence.

This study combines experimental, theoretical, and statistical approaches to improve the quantitative validation of models predicting virulence evolution in bacteriophages.

This paper theoretically examines how population bottlenecks influence evolutionary paths and adaptation rates in periodically bottlenecked populations.

This study analyzes the genomic evolution of commensal E. coli over 30 years in France, finding increases in virulence and antibiotic resistance genes through clonal expansion and gene frequency changes within clones.

The paper develops a tool to accurately reconstruct whole HIV genomes from short-read data by using tailored references, showing improved accuracy over standard references.