David Vallenet

NetSyn groups protein sequences by conserved genomic context to identify functional relationships beyond sequence similarity.

Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

PANORAMA predicts and compares biological systems across species using pangenome graphs, demonstrating effectiveness on Pseudomonas and Enterobacteriaceae genomes.

The paper identifies lineage-specific metabolic capacities in extraintestinal pathogenic Escherichia coli clones that may contribute to their ecological success and dissemination.

ASMC is a redesigned workflow for analyzing enzyme active sites, improving clustering and prediction through updated methods and unified code.

panModule identifies conserved modules in pangenome graphs to understand functional gene organization in microbial genomes.

panRGP predicts genomic islands and explores their diversity using pangenome graphs across hundreds of genomes.

PPanGGOLiN partitions pangenome graphs to classify gene families into persistent, cloud, and shell partitions, revealing insights into genome dynamics and diversity.

PlaScope improves plasmid detection in E. coli by combining Centrifuge with a curated database, achieving high recall, specificity, and accuracy compared to existing tools.

GROOLS evaluates functional annotations of proteins through biological processes using paraconsistent logic, identifying inconsistencies and uncertainties in 14 microbial organisms.