Valérian Lupo

A new automated pipeline for whole genome shotgun sequencing analysis and hazard characterization of microbial pesticides

The paper introduces an automated pipeline for whole-genome sequencing analysis of microbial pesticides to improve hazard characterization and risk assessment.

Out of Antarctica: new insights into Antarctic Subcluster 5.2 picocyanobacteria based on high-quality genomes

This study reconstructs high-quality genomes of Antarctic and Arctic cyanobacteria, revealing an Out-of-Antarctica dispersal scenario within subcluster 5.2.

Identification and Characterization of Archaeal Pseudomurein Biosynthesis Genes through Pangenomics

This study identifies and characterizes archaeal pseudomurein biosynthesis genes using pangenomics, revealing evolutionary relationships and horizontal gene transfer events.

The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics .

The paper introduces the GEN-ERA toolbox, a unified bioinformatics workflow for microbial genomics that enables reproducible phylogenetic and metabolic analyses on bacteria and small eukaryotes.

CRitical Assessment of genomic COntamination detection at several Taxonomic ranks (CRACOT)

CRACOT benchmarks six contamination detection tools across six taxonomic ranks, finding poor precision and recommending tool combination for better accuracy.