Daniel Falush

Bayesian phylogenetic inference accounting for recombination in whole bacterial genomes

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

A transcriptome map reveals conserved and lineage-specific sRNAs that regulate motility and metabolism across Vibrio

The paper maps sRNAs in Vibrio parahaemolyticus, identifies conserved and lineage-specific sRNAs, and shows their roles in regulating motility and metabolism.

Wave succession in the pandemic clone of Vibrio parahaemolyticus driven by gene loss

The paper investigates gene loss in Vibrio parahaemolyticus pandemic clones, showing it drives wave succession through environmental and transmission advantages.

Functional coherence of bacterial ecospecies

The paper experimentally links a multilocus ecospecies genotype in Vibrio parahaemolyticus to a swimming phenotype in viscous environments, showing functional coherence of ecospecies.

Macrogenetic atlas of prokaryotes reveals selection-driven structures

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

A putative bacterial ecocline in Klebsiella pneumoniae

The paper identifies a genetic ecocline in Klebsiella pneumoniae using PCA, suggesting diversifying selection on a quantitative trait, with Kpa fimbriae as a potential candidate.

Genealogical inference and more flexible sequence clustering using iterative PopPUNK

The paper introduces iterative-PopPUNK, an extension of PopPUNK that improves flexibility and interpretability in bacterial genome clustering and genealogical inference.

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

The paper estimates molecular clock rates in Campylobacter using a birthday problem analogy to quantify lineage turnover and diversification in environmental bacteria.

A tutorial on how (not) to over-interpret STRUCTURE/ADMIXTURE bar plots

The paper demonstrates how to assess the reliability of genetic clustering results from STRUCTURE/ADMIXTURE using simulated and real data with badMIXTURE.

Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas

This study analyzes H. pylori genome sequences from the Americas to show rapid evolution and genetic exchange leading to distinct subpopulations linked to human demographics and transmission ecology.