Professor Daniel Wilson

Director of Studies in Data Science

Biography

I am Professor of Infectious Disease Genomics at the University of Oxford, and Director of Studies in Data Science in the Department for Continuing Education. I oversee and plan the Department's course offerings in Data Science, including award-bearing courses, face-to-face classes and online programmes. I am a Fellow of St. Cross College.

I lead a research group in Infectious Diseases and Population Genomics at the Big Data Institute, Nuffield Department of Population Health, supported by the Wellcome Trust and Robertson Foundation. I am a collaborator with the Modernising Medical Microbiology consortium based at the John Radcliffe Hospital, Oxford, and Associate Member of the Department of Statistics.

Research

My research interests are in the genetic risk of infectious disease and the evolution of pathogen populations, which I study through comparative genome analysis. My research activity focuses on the analysis of bacterial diseases and populations, but I also work on viruses and non-pathogenic microorganisms.

Motivating themes in my work are understanding the inheritance of virulence and susceptibility and the effects of transmission, natural selection and recombination in shaping pathogen diversity. I have investigated the evolution of pathogen populations from the colonization of individual hosts and transmission between hosts, through to the whole-species and phylogenetics levels.

I would welcome enquiries from graduate students keen on working in any of these areas, particularly as part of the part-time DPhil programmes offered by Oxford Continuing Education.

Publications

My ORCID is 0000-0002-0940-3311. My ResearcherID is C-1463-2019. My Google Scholar profile is 0FD9NekAAAAJ.

Earle, S. G., Lobanovska, M., Lavender, H., Tang, C., Exley, R. M., Ramos-Sevillano, E., Browning, D., Kostiou, V., Harrison, O. B., Bratcher, H. B., Varani, G., Tang, C. M., Wilson, D. J. and M. C. J. Maiden (2021)
Polymorphisms affecting expression of the vaccine antigen factor H binding protein influence invasiveness of Neisseria meningitidis
medRxiv doi:10.1101/2021.01.08.21249443v1 (abstract preprint)

Arning, N., Sheppard, S. K., Clifton, D. A. and D. J. Wilson (2021)
Machine learning to predict the source of campylobacteriosis using whole genome data
bioRxiv doi:10.1101/2021.02.23.432443 (abstract preprint)

Young, B. C., Wu, C.-H., Charlesworth, J., Earle, S., Price, J. R., Gordon, N. C., Cole, K., Dunn, L., Liu, E., Oakley, S., Godwin, H., Fung, R., Miller, R., Knox, K., Votintseva, A., Quan, T. P., Tilley, R., Scarborough, M., Crook, D. W., Peto, T. E., Walker, A. S., Llewelyn, M. J. and D. J. Wilson (2021)
Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the hospital environment: a bacterial genome-wide association study
medRxiv doi:10.1101/2021.01.13.21249734 (abstract preprint)

Gill, J. L., Hedge, J., Wilson, D. J. and R. C. MacLean (2021)
Evolutionary processes driving the rise and fall of Staphylococcus aureus ST239, a dominant hybrid pathogen
bioRxiv doi:10.1101/2021.01.10.426095 (abstract preprint)

D. J. Wilson (2021)
The Lévy combination test
arXiv 2105.01501 (abstract preprint)

Armstrong, J., Rudkin, J. K., Allen, N., Crook, D. W., Wilson, D. J., Wyllie, D. H. and A. M. O'Connell (2020)
Dynamic linkage of COVID-19 test results between Public Health England's Second Generation Surveillance System and UK Biobank
Microbial Genomics doi:10.1099/mgen.0.000397 (abstract preprint pdf)

The COVID-19 Host Genetics Initiative (2020)
The COVID-19 Host Genetics Initiative, a global initiative to elucidate the role of host genetic factors in susceptibility and severity of the SARS-CoV-2 virus pandemic
European Journal of Human Genetics 28: 715-718 (abstract pdf)

The Severe Covid-19 GWAS Group [includes COVID-19 Host Genetics Initiative consortium authorship] (2020)
Genomewide Association Study of Severe Covid-19 with Respiratory Failure
New England Journal of Medicine 383: 1522-1534 (abstract pdf)

Pairo-Castineira, E., Clohisey, S., Klaric, L., Bretherick, A. D., Rawlik, K., and colleagues [includes COVID-19 Host Genetics Initiative consortium authorship] (2020)
Genetic mechanisms of critical illness in Covid-19
Nature doi: 10.1038/s41586-020-03065-y (abstrac pdf)

Hilton, B., Wilson, D. J., O'Connell A. M., Ironmonger, D., Rudkin, J. K, Allen, N., Oliver, I. and D. Wyllie (2020)
Microbial isolation in English participants in the UK Biobank cohort: comparison with the general population
medRxiv doi:10.1101/2020.03.18.20038281 (abstract preprint)

D. J. Wilson and The CRyPTIC Consortium (2020)
GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes
Molecular Biology and Evolution doi:10.1093/molbev/msaa069 (abstract preprint pdf)

Arning, N. and D. J. Wilson (2020)
The past, present and future of bacterial ancient DNA
Microbial Genomics, in press (abstract)

Eyre, D. W., Laager, M., Walker, A. S., Cooper, B. S. and D. J. Wilson on behalf of the CDC Modeling Infectious Diseases in Healthcare Program (MInD-Healthcare) (2020)
Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission
PLoS Computational Biology, in press (abstract)

D. J. Wilson (2020)
Generalized mean p-values for combining dependent tests: comparison of generalized central limit theorem and robust risk analysis [version 1; peer review: awaiting peer review]
Wellcome Open Research 5:55 (abstract pdf)

Young, B. C., Earle, S. G., Soeng, S., Sar, P., Kumar, V., Hor, S., Sar, V., Bousfield, R., Sanderson, N. D., Barker, L., Stoesser, N., Emary, K. R. W., Parry, C. M., Nickerson, E. K., Turner, P., Bowden, R., Crook, D., Wyllie, D., Day, N. P. J., Wilson, D. J. and C. E. Moore (2019)
Panton-Valentine leukocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study.
eLife 8: e42486 (abstract preprint pdf)

Read more about my publications and research activities on our group website: www.danielwilson.me.uk