Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission. - David W. Eyre; Madeleine L. Cule; David Griffiths; Derrick W. Crook; Tim E. A. Peto; A. Sarah Walker; Daniel J. Wilson 001 (PLoS Comput. Biol., 2013)

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes. - Xavier Didelot; Daniel J. Wilson 001 (PLoS Comput. Biol., 2015)

Practical Approaches for Detecting Selection in Microbial Genomes. - Jessica Hedge; Daniel J. Wilson 001 (PLoS Comput. Biol., 2016)

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent. - Nicola De Maio; Chieh-Hsi Wu; Daniel J. Wilson 001 (PLoS Comput. Biol., 2016)

Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data. - Yang Yang 125; Katherine E. Niehaus; Timothy M. Walker; Zamin Iqbal; A. Sarah Walker; Daniel J. Wilson 001; Tim E. A. Peto; Derrick W. Crook; E. Grace Smith; Tingting Zhu 001; David A. Clifton (Bioinform., 2018)

Bayesian reconstruction of transmission within outbreaks using genomic variants. - Nicola De Maio; Colin J. Worby; Daniel J. Wilson 001; Nicole Stoesser (PLoS Comput. Biol., 2018)

Application of machine learning techniques to tuberculosis drug resistance analysis. - Samaneh Kouchaki; Yang Yang 125; Timothy M. Walker; A. Sarah Walker; Daniel J. Wilson 001; Timothy E. A Peto; Derrick W. Crook; CRyPTIC Consortium; David A. Clifton (Bioinform., 2019)

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis. - Yang Yang 125; Timothy M. Walker; A. Sarah Walker; Daniel J. Wilson 001; Timothy E. A Peto; Derrick W. Crook; Farah Shamout; CRyPTIC Consortium; Tingting Zhu 001; David A. Clifton (Bioinform., 2019)

Sequential Monte Carlo with transformations. - Richard G. Everitt; Richard Culliford; Felipe J. Medina-Aguayo; Daniel J. Wilson 001 (Stat. Comput., 2020)

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission. - David W. Eyre; Mirjam Laager; A. Sarah Walker; Ben S. Cooper; Daniel J. Wilson 001 (PLoS Comput. Biol., 2021)