Xavier Didelot

New method to reconstruct phylogenetic and transmission trees with sequence data from infectious disease outbreaks

The paper develops a Bayesian method to reconstruct transmission trees from WGS data by integrating unobserved processes, showing improved results on simulated and real datasets.

Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

This paper develops a method to infer transmission trees from phylogenies in partially sampled and ongoing outbreaks by incorporating within-host genetic diversity and unsampled intermediates.

Declaring a tuberculosis outbreak over with genomic epidemiology

The paper develops a method to infer transmission times from pathogen genomes and applies it to declare a tuberculosis outbreak over.

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

This paper introduces a Bayesian method to infer changes in phenotype distribution across a phylogenetic tree and applies it to study HIV and Salmonella evolution.

Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131

This study traces the evolutionary history of the ST131 E. coli lineage, showing its clonal expansion linked to antibiotic use and plasmid acquisition, with implications for antimicrobial resistance control.

Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

This study analyzes the global population structure and demography of Helicobacter pylori, identifying ancient human association and candidate genes under positive selection.

Bayesian inference of infectious disease transmission from whole genome sequence data

This paper develops a Bayesian method to reconstruct disease outbreaks from genomic data, finding that even with high substitution rates, uncertainty remains in transmission inference.