SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences. - Francesc Coll; Kim Mallard; Mark D. Preston; Stephen D. Bentley; Julian Parkhill; Ruth McNerney; Nigel J. Martin 001; Taane G. Clark (Bioinform., 2012)

Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model. - Andries J. van Tonder; Shilan Mistry; James E. Bray; Dorothea M. C. Hill; Alison J. Cody; Chris L. Farmer; Keith P. Klugman; Anne von Gottberg; Stephen D. Bentley; Julian Parkhill; Keith A. Jolley; Martin C. J. Maiden; et al. (PLoS Comput. Biol., 2014)

pyseer: a comprehensive tool for microbial pangenome-wide association studies. - John A. Lees; Marco Galardini; Stephen D. Bentley; Jeffrey N. Weiser; Jukka Corander (Bioinform., 2018)

RCandy: an R package for visualizing homologous recombinations in bacterial genomes. - Chrispin Chaguza; Gerry Tonkin-Hill; Stephanie W. Lo; James Hadfield; Nicholas J. Croucher; Simon R. Harris; Stephen D. Bentley (Bioinform., 2022)

Predicting hosts and cross-species transmission of Streptococcus agalactiae by interpretable machine learning. - Yunxiao Ren; Carmen Li; Dulmini Nanayakkara Sapugahawatte; Chendi Zhu; Sebastian Spänig; Dorota Jamrozy; Julian Rothen; Claudia A. Daubenberger; Stephen D. Bentley; Margaret Ip; Dominik Heider (Comput. Biol. Medicine, 2024)