John A Lees

RhierBAPS: An R implementation of the population clustering algorithm hierBAPS

Jukka Corander, Gerry Tonkin-Hill, John A Lees, 2018, Wellcome open research.

Producing polished prokaryotic pangenomes with the Panaroo pipeline

Christopher Beaudoin, Stephen D. Bentley, Julian Parkhill, 2020, Genome Biology.

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study

Julian Parkhill, Michelle Kendall, Caroline Colijn, 2018, Wellcome open research.

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

Jukka Corander, Julian Parkhill, Marco Galardini, 2020, mBio.

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

Jukka Corander, Antti Honkela, Niko Välimäki, 2016, Nature Communications.

Fast and flexible bacterial genomic epidemiology with PopPUNK

Jukka Corander, Gerry Tonkin-Hill, Nicholas J Croucher, 2018, bioRxiv.

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

David Goldblatt, Paul Turner, Julian Parkhill, 2017, bioRxiv.

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

Jukka Corander, Johan Pensar, Julian Parkhill, 2019 .