Chloé Loiseau

The paper analyzes the evolutionary dynamics of IS6110 in Mycobacterium tuberculosis complex strains using ancestral state reconstruction and identifies patterns of insertion and selection.

The paper uses long-read assemblies and proteogenomic analysis to discover novel small proteins in Mycobacterium tuberculosis strains.

This study identifies patient and bacterial factors associated with unfavorable tuberculosis treatment outcomes in Georgia using genomic and clinical data from 4,536 patients.

The paper measures drug tolerance in Mycobacterium tuberculosis lineages and finds higher tolerance in L3 and L4 strains, with heritable patterns and enrichment of mutations in specific metabolic pathways.

The paper shows that epistatic interactions between RpoB and GyrA mutations in Mycobacterium tuberculosis can lead to high-fitness double-resistant strains, which are prevalent in clinical isolates.

The paper uses genomic data and phylodynamic models to show that Mycobacterium tuberculosis lineages have similar infectiousness durations but differ in onset timing, affecting transmission dynamics.

The paper analyzes genomes of Mycobacterium africanum strains to identify a new lineage and explore their evolutionary history and phylogeography.

The paper analyzes whole genome sequences of Mycobacterium tuberculosis lineages L1 and L3 to show South Asia's role in their dispersion and identify local adaptation at the esxH locus.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.

Treemmer reduces large phylogenetic datasets by removing redundant leaves, preserving diversity while simplifying the dataset.