Florent Lassalle

Phylo-Plex is a low-cost amplicon sequencing method for high-resolution genomic epidemiology, achieving fine-scale lineage discrimination comparable to whole-genome sequencing in resource-limited settings.

The paper benchmarks human read removal methods in metagenomics, finding that high-sensitivity Bowtie2 with T2T-CHM13 reference improves removal while preserving microbial data.

The paper uses whole-genome sequencing to reclassify Allorhizobium vitis into a species complex, identifying two distinct species and their ecological adaptations.

The paper presents a population structure-aware method to classify genes in a bacterial pan-genome, revealing distinct evolutionary dynamics in 7,500 E. coli genomes.

The paper introduces Pantagruel, a software pipeline for analyzing bacterial pangenome data to reconstruct gene evolution and identify co-evolved gene modules.