William Paul Hanage

SARS-CoV-2 Intra-host Variation Shows Evidence of Transmission and Convergent Evolution in a University Surveillance Cohort

The paper analyzes SARS-CoV-2 intra-host variation in a university cohort to infer transmission events and assess within-host evolution, finding limited transmission of variants and evidence of positive selection at a recurrent site.

Neighbour Typing Using Long Read Sequencing Provides Rapid Prediction of Sequence Type and Antimicrobial Susceptibility of Klebsiella pneumoniae

This paper evaluates RASE, a neighbor typing method using long-read sequencing, for predicting sequence types and antimicrobial susceptibility of Klebsiella pneumoniae in real time.

Bronze Age Yersinia pestis genome from sheep sheds light on hosts and evolution of a prehistoric plague lineage

The paper presents a Yersinia pestis genome from a Bronze Age sheep, showing it belongs to a lineage previously only found in ancient humans and suggests transmission via livestock.

Linkage-based ortholog refinement in bacterial pangenomes with CLARC

CLARC refines bacterial ortholog groups by integrating linkage and annotation data, reducing accessory gene estimates and improving evolutionary predictions in Streptococcus pneumoniae.

Relating Ecological Diversity to Genetic Discontinuity across Bacterial Species

The paper quantifies genetic discontinuity in bacterial species and links it to ecological factors using a large genome dataset.

Beyond consensus sequence: a quantitative scheme for inferring transmission using deep sequencing in a bacterial transmission model

The paper develops a model to infer bacterial transmission using deep sequencing data from a mouse model, showing that within-host variant abundance differences can accurately identify transmission pairs.

The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

The paper reconstructs the evolutionary histories of antibiotic-resistant pneumococcal lineages PMEN3 and PMEN9, showing how interspecies recombination contributes to antibiotic resistance and serotype switching.

Rapid heuristic inference of antibiotic resistance and susceptibility by genomic neighbor typing

This paper introduces a method to rapidly infer antibiotic resistance and susceptibility from bacterial genomes using genomic neighbor typing, achieving high sensitivity and specificity within minutes to hours.

Previously undetected super-spreading of Mycobacterium tuberculosis revealed by deep sequencing

The paper uses deep sequencing to identify a super-spreader of Mycobacterium tuberculosis in an Inuit outbreak, revealing previously undetected transmission patterns.

Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

This paper analyzes pneumococcal carriage genomic data before and after PCV13 introduction, showing reduced vaccine-type strains and limited serotype replacement.

Efficient inference of recent and ancestral recombination within bacterial populations

The paper introduces fastGEAR, an algorithm for detecting both recent and ancestral recombination in bacterial populations, demonstrating its effectiveness on Streptococcus pneumoniae genomes.

Longitudinal samples of bacterial genomes potentially bias evolutionary analyses

The paper shows that longitudinal bacterial genome samples can introduce biases in evolutionary analyses, inflating recombination estimates and rare mutation counts.