PANINI: Pangenome Neighbour Identification for Bacterial Populations

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

(2016) David M. Aanensen et al.   mBio

Horizontal DNA Transfer Mechanisms of Bacteria as Weapons of Intragenomic Conflict

(2016) Nicholas J. Croucher et al.   PLOS BIOLOGY

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

(2016) Alan McNally et al.   PLoS Genetics

A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions

(2016) Carine Makendi et al.   PLoS Neglected Tropical Diseases

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

Variable recombination dynamics during the emergence, transmission and ‘disarming’ of a multidrug-resistant pneumococcal clone

(2014) Nicholas J Croucher et al.   BMC BIOLOGY

Evidence for Soft Selective Sweeps in the Evolution of Pneumococcal Multidrug Resistance and Vaccine Escape

(2014) Nicholas J. Croucher et al.   Genome Biology and Evolution

Dense genomic sampling identifies highways of pneumococcal recombination

(2014) Claire Chewapreecha et al.   NATURE GENETICS

Diversification of bacterial genome content through distinct mechanisms over different timescales

(2014) Nicholas J. Croucher et al.   Nature Communications

Population genomics of post-vaccine changes in pneumococcal epidemiology

(2013) Nicholas J Croucher et al.   NATURE GENETICS

Evolution of MRSA During Hospital Transmission and Intercontinental Spread

(2010) S. R. Harris et al.   SCIENCE

Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations

(2008) Jukka Corander et al.   BMC BIOINFORMATICS