Neil MacAlasdair

The major pathogen Haemophilus influenzae experiences pervasive recombination and purifying selection at local and global scales

This study sequenced 4,475 H. influenzae isolates from Thailand and combined them with global data to show pervasive recombination and purifying selection, with MDR lineages widespread and not restricted to disease-causing subpopulations.

Detecting co-selection through excess linkage disequilibrium in bacterial genomes

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

Genome-wide epistasis and co-selection study using mutual information

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.