Xavier Didelot

This paper introduces ClonalFrame2, a Bayesian method for phylogenetic inference in bacteria that accounts for recombination, showing improved accuracy in simulated and real datasets.

This paper introduces a parametrisation of phylogenetic tree space using unconstrained Euclidean coordinates, enabling new methods for Bayesian phylogenetic inference.

The paper develops coalescent models to quantify evolutionary predictability by analyzing lineage coalescence rates and applies them to microbial and viral datasets to detect selective effects.

The paper introduces diagnostic methods to evaluate the reliability of dated phylogenies in microbial population genetics without model comparison.

This study characterizes phage-plasmids in clinical Enterobacteriaceae isolates, finding they are common and associated with antimicrobial resistance and disease severity.

KPop provides a scalable method for comparing microbial genomes using sequence embeddings, accurately separating sequences at species and sub-species levels.

The paper presents a Bayesian method for inferring pathogen migration history and population sizes using the structured coalescent model, validated on simulated and real datasets.

The paper presents a macrogenetic atlas of prokaryotes integrating genomic and population genetic data to analyze evolutionary dynamics and selection-driven structures.

This study identifies phage-plasmids in multiple Salmonella serovars, showing their prevalence and serovar-specific distribution, with implications for antimicrobial resistance transmission.

KmerAperture distinguishes core and accessory sequence differences between bacterial genomes using k-mer positions without alignment, outperforming existing k-mer tools.

This paper develops a frequentist non-parametric method for phylodynamic inference and applies it to study cholera and COVID-19 epidemics.

This study investigates the rapid emergence and spread of a Neisseria gonorrhoeae strain with reduced susceptibility to extended-spectrum cephalosporins in Norway.

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 identifies three co-circulating SARS-CoV-2 lineages with distinct demographic dynamics using phylogenetic analysis.

The paper introduces Pantagruel, a software pipeline for analyzing bacterial pangenome data to reconstruct gene evolution and identify co-evolved gene modules.

This paper introduces a framework for analyzing real-time nucleic acid amplification data using multidimensional standard curves to improve absolute quantification and detect outliers.

The paper estimates recombination scaled effective population size in 21 bacterial species and finds only two show signs of panmixia, suggesting panmixia is unstable in bacteria.

The paper introduces a Bayesian method for dating bacterial phylogenies, leveraging precomputed phylogenetic relationships to improve speed and scalability.

The paper analyzes genetic data to show that pneumococcal capsule recombination generates novel serotypes, highlighting risks for vaccine efficacy.