François Balloux

Twenty-three new Yersinia pestis genomes from Scandinavia, the Netherlands, Iceland and Armenia extend the Second Plague Pandemic phylogeny, with the first Icelandic plague genome and eastward-spreading pestis secunda strains.

The paper identifies 18 mitochondrial variants associated with climate adaptation using a large dataset of human mtDNA and climate variables.

This study uses nanopore metagenomic sequencing to analyze the microbiomes of HAP patients, revealing high fungal prevalence and multi-drug-resistant microbes.

The paper uses SARS-CoV-2 genomic data to predict the fitness of viral mutations by analyzing intrahost diversity and genetic linkage patterns, showing improved forecasting with machine learning models.

The paper investigates the evolutionary origins of the BA.2.86 SARS-CoV-2 variant, finding it evolved through multiple transmission chains and recombination, not a single chronic infection.

This study investigates the evolutionary drivers of viral host jumps using genomic data, finding that humans can be both sources and sinks for viral spillover and that adaptation varies across viral families.

The paper screens bat samples for coronaviruses, identifies novel strains, and assesses their potential to infect humans.

HMMploidy infers ploidy levels from short-read sequencing data, outperforming existing methods at low-depth with large sample sizes and revealing aneuploidy in Cryptococcus neoformans.

The paper analyzes SARS-CoV-2 genomic mutations in mink and deer to identify potential host-specific adaptations and assess spillover risks.

This study identifies microbial hallmarks of sepsis using metagenomic data and shows that polymicrobial communities, not single pathogens, are key in sepsis diagnosis.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

The paper analyzes SARS-CoV-2 genomic data to determine if genetic recombination is occurring, finding no detectable evidence of it.

The paper reconstructs the time-calibrated genomic evolution of a bacterium during its establishment as a crop pathogen, finding high gene turnover rates in the accessory genome.

This study tests if recurrent mutations in SARS-CoV-2 are linked to increased transmissibility and finds no significant association.

This study analyzes SARS-CoV-2 genomes from Palestine to trace the virus's introduction and circulation, finding at least nine independent introductions and a locally predominant lineage introduced before the first reported cases.

The paper identifies pre-existing bedaquiline resistance variants in Mycobacterium tuberculosis genomes before clinical use of the drug, highlighting the need for rapid susceptibility testing.

This study uses network analysis of over 10,000 bacterial plasmids to uncover population structure, gene content correlations, and drivers of horizontal gene transfer.

The paper analyzes metagenomic data from a blood stain on a newspaper linked to Jean-Paul Marat to investigate potential infectious agents of his skin condition.

The paper generates a genome from a historical European Plasmodium vivax strain, revealing its evolutionary relationship to American strains and the presence of drug resistance variants predating their use.

This study compares whole genome sequencing of Mycobacterium tuberculosis directly from sputum to sequencing from culture, finding greater genetic diversity in sputum-derived samples.

This study compares the transcriptional responses of four C. gattii lineages to macrophages, identifying lineage-specific gene expression patterns and pathogenicity-related processes.

The paper investigates how structural variations in yeast genomes affect gene expression and quantitative traits, finding that copy number variants significantly influence phenotypes and reproductive isolation.