Benjamin Linard

MSpangenome simulates population pangenomes from coalescent demographic models to benchmark graph construction tools.

The paper identifies a novel gammacoronavirus causing enteritis in broiler chickens in France, distinct from known poultry coronaviruses.

Pan1C is a pipeline that builds chromosome-level pangenome graphs, improving alignment and variant calling by integrating multiple strategies and benchmarked across different species.

This paper constructs cross-taxon pangenomes for tree species, identifies structural variants, and evaluates their functional relevance using the Armeniaca taxonomic section.

SHERPAS rapidly detects viral recombinants by analyzing phylogenetically-informed k-mers, outperforming existing methods in speed with minimal accuracy loss.

RAPPAS provides a fast, alignment-free method for phylogenetic placement of metagenomic sequences, achieving speed improvements over likelihood-based methods while maintaining accuracy.