Sébastien Gagneux

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 lineage-specific transcriptional network rewiring in Mtb by analyzing proteomic and transcriptomic data from L1 and L2 strains, revealing key regulators like Rv1985c that drive phenotypic differences.

This study introduces ASCT to assess bacterial killing in real-time and links drug tolerance to clinical outcomes in mycobacterial infections.

This study investigates how antibiotic tolerance evolves in Mycobacterium tuberculosis during treatment and finds no evidence that it contributes to delayed culture conversion.

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 investigates how granulysin from immune cells induces dormancy in Mycobacterium tuberculosis, revealing an immune escape mechanism.

The paper characterizes repeat-associated mutations in Mycobacterium tuberculosis genomes using long-read sequencing, revealing their significant contribution to genetic variation in an outbreak.

The paper shows that antibiotic treatment affects Mycobacterium tuberculosis culturability, with differential effects on colony formation and liquid culture growth.

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.

This study examines how different Mycobacterium tuberculosis complex lineages elicit varying granulomatous responses in vitro, linking genetic diversity to immune activation and bacterial growth.

This study examines the relationship between human genetic ancestry, Mycobacterium tuberculosis diversity, and TB disease severity in Dar es Salaam, Tanzania, finding no significant genetic influence on disease severity.

The study infects macrophages from tuberculosis patients with different MTBC lineages to show that bacterial phylogenetic diversity, not local adaptation, drives variable macrophage responses.

This study uses genomic data and a Bayesian phylodynamic model to show HIV co-infection reduces Mycobacterium tuberculosis transmissibility in sub-Saharan Africa.

The paper improves genotype imputation in underrepresented populations by adding population-specific SNPs to existing reference panels, showing improved accuracy in a Tanzanian cohort.

The paper identifies high within-lineage genomic diversity and gene content differences in Mycobacterium tuberculosis complex lineage 5 compared to H37Rv, affecting transmission analysis and suggesting the need for alternative reference genomes.

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 integrates metabolomics and genomics data to identify functional SNPs in Mycobacterium tuberculosis strains, revealing genetic basis for antibiotic sensitivity.

The paper investigates the fitness cost of rifampicin resistance in Mycobacterium tuberculosis using transcriptomic and proteomic profiling, finding that aberrant gene expression causes the cost and that this burden can be suppressed.

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.