Daniel Wilson Publications

Publications and Preprints

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

The CRyPTIC Consortium (2024)
Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach
Nature Communications 15: 488 (abstract pdf preprint)

Arning, N., Fryer, H. R. and D. J. Wilson (2024)
Identifying direct risk factors in UK Biobank with simultaneous Bayesian-frequentist model-averaged hypothesis testing using Doublethink
medRxiv doi: 10.1101/2024.01.01.24300687 (abstract preprint)

Fryer, H. R., Arning, N. and D. J. Wilson (2023)
Doublethink: simultaneous Bayesian-frequentist model-averaged hypothesis testing
arXiv doi: 10.48550/arXiv.2312.17566 (abstract preprint)

Pascoe, B., Futcher, G., Pensar, J., Bayliss, S.C., Mourkas, E., Calland, J.K., Hitchings, M.D., Joseph, L.A., Lane, C.G., Greenlee, T., Arning, N., Wilson, D. J., Jolley, K., Corander, J., Maiden, M. C. J., Parker, C. T., Cooper, K. K., Rose, E. B., Hiett, K., Bruce, B. B. and S. K. Sheppard (2023)
Machine learning the source of Campylobacter infection in the United States of America
SSRN doi: 10.2139/ssrn.4671846 (abstract preprint)

COVID-19 Host Genetics Initiative (2023)
A second update on mapping the human genetic architecture of COVID-19
Nature 621:E7-E26 (abstract pdf)

Hilton, B., Wilson, D. J., O'Connell A. M., Ironmonger, D., Rudkin, J. K., Allen, N., Oliver, I. and D. H. Wyllie (2023)
Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population
Scientific Reports 13:496 (abstract pdf preprint)

Antonaru, L. A., Selinger, V. M., Jung, P., Di Stefano, G., Sanderson, N. D., Barker, L., Wilson, D. J., Büdel, B., Canniffe, D. P., Billi, D. and D. J. Nürnberg (2023)
Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales
ISME Communications 3: 113 (abstract pdf)

Sonnenkalb, L., Carter, J. J., Spitaleri, A., Iqbal, Z., Hunt, M., and colleagues [includes CRyPTIC consortium authorship] (2023)
Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis
Lancet Microbe 4:E358-E368 (abstract pdf)

The CRyPTIC Consortium (2022)
Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms
PLOS Biology 20: e3001755 (abstract pdf preprint)

The CRyPTIC Consortium (2022)
A data compendium associating the genomes of 12,289 Mycobacterium tuberculosis isolates with quantitative resistance phenotypes to 13 antibiotics
PLOS Biology 20: e3001721 (abstract pdf preprint)

COVID-19 Host Genetics Initiative (2022)
A first update on mapping the human genetic architecture of COVID-19
Nature 608:E1-E10 (abstract pdf)

Walker, T. M., Miotto, P., Köser, C. U., Fowler, P. W., Knaggs, J., Iqbal, Z., Hunt, M., Chindelevitch, L., Farhat, M., Cirillo, D. M., Comas, I., Posey, J., Omar, S. V., Peto, T. E. A., Suresh, A., Uplekar, S., Laurent, S., Colman, R., Nathanson, C.-M., Zignol, M., Walker, A. S., Crook, D. W., Ismail, N., Rodwell, T. C., The CRyPTIC Consortium and The Seq&Treat Consortium (2022)
The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis
The Lancet Microbe 3: E265-273 (abstract pdf preprint)

The CRyPTIC Consortium (2022)
Epidemiological cutoff values for a 96-well broth microdilution plate for high-throughput research antibiotic susceptibility testing of M. tuberculosis
European Respiratory Journal doi: 10.1183/13993003.00239-2022 (abstract pdf preprint)

Kousathanas, A., Pairo-Castineira, E., Rawlik, K., Stuckey, A., Odhams, C. A., and colleagues [includes COVID-19 Host Genetics Initiative consortium authorship] (2022)
Whole genome sequencing reveals host factors underlying critical Covid-19
Nature doi: 10.1038/s41586-022-04576-6 (abstract pdf)

Giulieri, S. G., Guérillot, R., Duchene, S., Hachani, A., Daniel, D., Seemann, T., Davis, J. S., Tong, S. Y. C., Young, B. C., Wilson, D. J., Stinear, T. P. and B. P. Howden (2022)
Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections
eLife 11: e77195 (abstract pdf)

Stevens, E. J., Morse, D. J., Bonini, D., Duggan, S., Brignoli, T., Recker, M., Lees, J. A., Croucher, N. J., Bentley, S., Wilson, D. J., Earle, S. G., Dixon, R., Nobbs, A., Jenkinson, H., van Opijn, T., Thibauld, D., Wilkinson, O. J., Dillingham, M. S., Carlile, S., McLoughlin, R. M. and R. C. Massey (2022)
Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae
Microbial Genomics doi: 10.1099/mgen.0.000784 (abstract pdf)

Muloi, D. M., Wee, B. A., McClean, D. M. H., Ward, M. J., Pankhurst, L., Phan, H., Ivens, A. C., Kivali, V., Kiyong'a, A., Ndinda, C., Gitahi, N., Ouko, T., Hassell, J. M., Imboma, T., Akoko, J., Murungi, M. K., Njoroge, S. M., Muinde, P., Nakamura, Y., Alumasa, L., Furmaga, E., Kaitho, T., Öhgren, E. M., Amanya, F., Ogendo, A., Wilson, D. J., Bettridge, J. M., Kiiru, J., Kyobutungi, C., Tacoli, C., Kang’ethe, E. K., Davila, J. D., Kariuki, S., Robinson, T. P., Rushton, J., Woolhouse, M. E. J. and E. M. Fèvre (2022)
Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape
Nature Microbiology 7: 581-589 (abstract pdf)

Hunt, M., Letcher, B., Malone, K. M., Nguyen, G., Hall, M. B., and colleagues [includes CRyPTIC consortium authorship] (2022)
Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes
Genome Biology 23: 147 (abstract pdf preprint)

Fowler, P. W., Wright, C., Spiers, H., Zhu, T., Baeten, E. M. L., and colleagues [includes CRyPTIC consortium authorship] (2022)
A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates
eLife 11: e75046 (abstract pdf preprint)

The COVID-19 Host Genetics Initiative (2021)
Mapping the human genetic architecture of COVID-19
Nature doi: 10.1038/s41586-021-03767-x (abstract pdf)

Lin, S.-K., De Maio, N., Pedergnana, V., Wu, C.-H., Thézé, J., Wilson, D. J., Barnes, E. and M. A. Ansari (2021)
Using host genetics to infer the global spread and evolutionary history of HCV subtype 3a
Virus Evolution doi: 10.1093/ve/veab065 (abstract pdf)

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)
Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis
PLOS Pathogens 17: e1009992 (abstract preprint pdf)

Arning, N., Sheppard, S., Bayliss, S., Clifton, D. A. and D. J. Wilson (2021)
Machine learning to predict the source of campylobacteriosis using whole genome data
PLOS Genetics 17: e1009436 (abstract preprint pdf)

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
Microbial Genomics doi: 10.1099/mgen.0.000700 (abstract preprint pdf)

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
mBio in press. 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 (abstract pdf)

The CRyPTIC Consortium (2021)
A generalisable approach to drug susceptibility prediction for M. tuberculosis using machine learning and whole-genome sequencing
Submitted (preprint)

D. J. Wilson and The CRyPTIC Consortium (2020)
GenomegaMap: within-species genome-wide d_N/d_S 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 doi: 10.1099/mgen.0.000384 (abstract pdf)

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 17: e1008417 (abstract pdf)

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: 2 approved]
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)

D. J. Wilson (2019)
The harmonic mean p-value for combining dependent tests.
Proceedings of the National Academy of Sciences USA 116: 1195-1200. (abstract pdf)

D. J. Wilson (2019)
Reply to Held: When is a harmonic mean p-value a Bayes factor?
Proceedings of the National Academy of Sciences USA 116: 5857-5858. (preprint pdf)

D. J. Wilson (2019)
Correction for Wilson, The harmonic mean p-value for combining dependent tests.
Proceedings of the National Academy of Sciences USA 116: 21948 (pdf)

D. J. Wilson (2019)
Reply to Goeman et al: Trade-offs in model averaging using multilevel tests.
Proceedings of the National Academy of Sciences USA 116: 23384-23385 (preprint pdf)

Everitt, R. G., Culliford, R., Medina-Aguayo, F., D. J. Wilson (2019)
Sequential Monte Carlo with transformations.
Statistics and Computing 30: 663-676 (abstract preprint pdf)

Yang, Y., Walker, T. M., Walker, A. S., Wilson, D. J., Peto, T. E. A., Crook, D. W., Shamout, F., Zhu, T., Clifton, D. A. and CRyPTIC Consortium (2019)
DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis.
Bioinformatics 35: 3240-3249 (abstract pdf)

Crispell, J., Benton, C. H., Balaz, D., De Maio, N., Akhmetova, A., Allen, A., Biek, R., Breadon, E. L., Dale, J., Hewinson, G., Lycett, S. J., Nunez-Garcia, J., Skuce, R. A., Trewby, H., Wilson, D. J., Zadoks, R. N., Delahay, R. J. and R. R. Kao (2019)
Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system.
eLife 8: e45833 (abstract pdf)

Cole, K., Foster, D., Russell, J. E., Golubchik, T., Llewelyn, M., Wilson, D. J., Crook, D., Paul, J. and The Modernising Medical Microbiology Consortium (2019)
Draft genome sequences of 64 type strains of 50 species and 25 subspecies of the genus Staphylococcus Rosenbach 1884.
Microbiology Resource Announcements 8: e00062-19 (abstract pdf)

Didelot, X., Croucher, N., Bentley, S. and D. J. Wilson (2018)
Bayesian inference of ancestral dates on bacterial phylogenetic trees.
Nucleic Acids Research 46: e134. (abstract pdf)

De Maio, N., Worby, C. J., Wilson, D. J. and N. Stoesser (2018)
Bayesian reconstruction of transmission within outbreaks using genomic variants.
PLoS Computational Biology 14: e1006117. (abstract preprint pdf)

Gibson, B., Wilson, D. J., Feil, E. and Eyre-Walker, A. (2018)
The distribution of bacterial doubling times in the wild.
Proceedings of the Royal Society B 285: 20180789. (abstract pdf preprint)

The CRyPTIC Consortium and the 100,000 Genomes Project (2018)
Prediction of susceptibility to first-line tuberculosis drugs by DNA sequencing.
New England Journal of Medicine 379: 1403-1415 (abstract pdf)

Kouchaki, S., Yang, Y., Walker, T. M., Walker, A. S., Wilson, D. J., Peto, T. E. A., Crook, D. W., Clifton, D. A. and the CRyPTIC Consortium (2018)
Application of machine learning to tuberculosis drug resistance analysis.
Bioinformatics 35: 2276-2282 (abstract pdf)

Young, B. C., Wu, C.-H., Gordon, N. C., Cole, K., Price, J. R., Lui, E., Sheppard, A. E., Perera, S., Charlesworth, J., Golubchik, T., Iqbal, Z., Bowden, R., Massey, R. C., Paul, J., Crook, D. W., Peto, T. E. A., Walker, A. S., Llewelyn, M. J., Wyllie, D. H. and D. J. Wilson (2017)
Severe infections emerge from commensal bacteria by adaptive evolution.
eLife 6: e30637. (abstract pdf preprint)

De Maio, N. and D. J. Wilson (2017)
The bacterial sequential Markov coalescent.
Genetics 206: 333-343. (abstract pdf)

Yang, Y., Niehaus, K. E., Walker, T. M., Iqbal, Z., Walker, A. S., Wilson, D. J., Peto, T. E., Crook, D. W., Smith, G. E., Zhu, T. and D. A. Clifton (2017)
Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data.
Bioinformatics 34: 1666-1671 (abstract pdf)

Gordon, N. C., Pichon, B., Golubchik, T., Wilson, D. J., Paul, J., Blanc, D. S., Cole, K., Collins, J. Cortes, N., Cubbon, M., Gould, F. K., Jenks, P. J., Llewelyn, M., Nash, J. Q., Orendi, J. M., Paranthaman, K., Price, J. R., Senn, L., Thomas, H. L., Wyllie, S., Crook, D. W., Peto, T. E. A., Walker, A. S. and A. M. Kearns (2017)
Whole genome sequencing reveals the contribution of long-term carriers in Staphylococcus aureus outbreak investigation.
Journal of Clinical Microbiology 55: 2188-2197. (abstract pdf)

Dingle, K. E., Didelot, X., Quan, T. P., Eyre, D. W., Stoesster, N., Golubchik, T., Harding, R. M., Wilson, D. J., Griffiths, D., Oakley, S. J., the Modernising Medical Microbiology Informatics Group, Fawley, W. N., Freeman, J., Morris, K., Martin, J., Howard, P., Gorbach, S., Goldstein, E. J. C., Citron, D. M., Hopkins, S., Hope, R., Johnson, A. P., Wilcox, M. H., Peto, T. E. A., Walker, A. S. and D. W. Crook (2017)
Effects of control interventions on Clostridium difficile infection in England: an observational study.
Lancet Infectious Diseases 17: 411-421. (abstract pdf)

Price, J. R., Cole, K., Bexley, A., Kostiou, V., Eyre, D. W., Golubchik, T., Wilson, D. J., Crook, D. W., Walker, A. S., Peto, T. E. A., Llewelyn, M. J. and J. Paul (2017)
Transmission of Staphylococcus aureus between health-care workers, the environment, and patients in an intensive care unit: a longitudinal cohort study based on whole-genome sequencing.
Lancet Infectious Diseases 17: 207-214. (abstract pdf)

Earle, S. G., Wu, C.-H., Charlesworth, J., Stoesser, N., Gordon, N. C., Walker, T. M., Spencer, C. C. A., Iqbal, Z., Clifton, D. A., Hopkins, K. L., Woodford, N., Smith, E. G., Ismail, N., Llewelyn, M. J., Peto, T. E., Crook, D. W., McVean, G., Walker, A. S. and D. J. Wilson (2016)
Identifying lineage effects when controlling for population structure improves power in bacterial association studies.
Nature Microbiology 1: 16041 (abstract pdf preprint supplement)

Das, S., Lindemann, C., Young, B. C., Muller, J., Österreich, B., Ternette, N., Winkler, A.-C., Paprotka, K., Reinhardt, R., Förstner, K. U., Allen, E., Flaxman, A., Yamaguchi, Y., Rollier, C. S., Van Diemen, P., Blättner, S., Remmele, C. W., Selle, M., Dittrich, M., Müller, T., Vogel, J., Ohlsen, K., Crook, D., Massey, R., Wilson, D. J., Rudel, T., Wyllie, D. H., and M. J. Fraunholz (2016)
Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation.
Proceedings of the National Academy of Sciences USA 113: E3101-E3110. (abstract pdf)

De Maio, N., Wu, C.-H. and D. J. Wilson (2016)
SCOTTI: Efficient reconstruction of transmission within outbreaks with the structured coalescent.
PLoS Computational Biology 12: e1005130. (abstract pdf preprint)

Didelot, X., Walker, A. S., Peto, T. E., Crook, D. W. and D. J. Wilson (2016)
Within-host evolution of bacterial pathogens.
Nature Reviews Microbiology 14: 150-162. (abstract pdf)

Hedge, J. and D. J. Wilson (2016)
Practical approaches for detecting selection in microbial genomes.
PLoS Computational Biology 12: e1004739 (abstract pdf)

Dearlove, B. L., Cody, A. J., Pascoe, B., Méric, G., Wilson, D. J. and S. K. Sheppard (2016)
Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections.
ISME Journal 10: 721-9. (abstract pdf)

De Silva, D., Peters, J., Cole, K., Cole, M. L., Cresswell, F., Dean, G., Dave, J., Thomas, D. R., Foster, K., Waldram, A., Wilson, D. J., Didelot, X., Grad, Y. H., Crook, D. W., Peto, T. E. A., Walker, A. S., Paul, J. and Eyre, D. W (2016)
Whole-genome sequencing to determine transmission of Neisseria gonorrhoeae: an observational study.
Lancet Infectious Diseases 16: 1295-1303. (abstract pdf)

Stoesser, N., Sheppard, A. E., Pankhurst, L., De Maio, N., Moore, C. E., Sebra, R., Turner, P., Anson, L., Kasarskis, A., Batty, E. M., Kos, V., Wilson, D. J., Phetsouvanh, R., Wyllie, D., Sokurenko, E., Manges, A., Johnson, T. J., Price, L. B., Peto, T. E. A., Johnson, J. R., Didelot, X., Walker, A. S., Crook, D. W. and the Modernizing Medical Microbiology Informatics Group (2016)
Evolutionary history of the global emergence of the Escherichia coli epidemic clone ST131.
mBio 7: e02162-15 (abstract pdf).

Sheppard, A., Stoesser, N., Wilson, D. J., Sebra, R., Kasarskis, A., Anson, L., Giess, A., Pankhurst, L., Vaughan, A., Grim, C., Cox, H., Yeh, A., the Modernising Medical Microbiology Informatics Group, Sifri, C., Walker, A. S., Peto, T., Crook, D. W. and A. Mathers (2016)
Nested Russian Doll-like genetic mobility drives rapid dissemination of the carbapenem resistance gene blaKPC
Antimicrobial Agents and Chemotherapy 60: 3767-3778. (abstract pdf).

van Hal, S. J., Ip, C. L. C., Anzari, M. A., Wilson, D. J., Espedido, B., Jensen, S. O. and R. Bowden (2016)
Evolutionary dynamics of Enterococcus faecium reveals complex genomic relationships between isolates with independent emergence of vancomycin resistance.
Microbial Genomics doi: 10.1099/mgen.0.000048. (abstract pdf)

Brown, T., Didelot, X., Wilson, D. J. and N. De Maio (2016)
SimBac: simulation of whole bacterial genomes with homologous recombination.
Microbial Genomics doi: 10.1099/mgen.0.000044. (abstract pdf)

Leekitcharoenphon, P., Hendriksen, R. S., Le Hello, S., Weill, F. X., Baggesen, D. L., Jun, S.-R., Ussery, D. W., Lund, O., Crook, D. W., Wilson, D. J. and F. M. Aarestrup (2016)
Global genomic epidemiology of Salmonella Typhimurium DT104.
Applied and Environmental Microbiology 82: 2516-2526. (abstract pdf).

Laabei, M., Uhlemann, A.-C., Lowy, F. D., Austin, E. D., Yokoyama, M., Ouadi, K., Feil, E., Thorpe, H. A., Williams, B., Perkins, M., Peacock, S. J., Clarke, S. R., Dordel, J., Holden, M., Votintseva, A. A., Bowden, R., Crook, D. W., Young, B. C., Wilson, D. J., Recker, M. and R. C. Massey (2015)
Evolutionary trade-offs underlie the multi-faceted virulence of Staphylococcus aureus.
PLoS Biology 13: e1002229. (abstract pdf)

De Maio, N., Wu, C.-H., O'Reilly, K. M. and D. J. Wilson (2015)
New routes to phylogeography: a Bayesian structured coalescent approximation.
PLoS Genetics 11: e1005421 (abstract pdf)

Didelot, X. and D. J. Wilson (2015)
ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
PLoS Computational Biology 11: e1004041. (abstract pdf)

Bradley, P., Gordon, N. C., Walker, T. M., Dunn, L., Heys, S., Huang, B., Earle, S. G., Pankhurst, L. J., Anson, L., de Cesare, M., Piazza, P., Votintseva, A. A., Golubchik, T., Wilson, D. J., Wyllie, D., Diel, R., Niemann, S., Feuerriegel, S., Kohl, T. A., Ismail, N., Omar, S. V., Smith, E. G., Buck, D., McVean, G., Walker, A. S., Peto, T. E. A., Crook, D. W. and Z. Iqbal (2015)
Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis
Nature Communications 6: 10063. (abstract pdf)

Walker, T. M., Kohl, T. A., Omar, S. V., Hedge, J., Del Ojo Elias, C., Bradley, P., Iqbal, Z., Feuerriegel, S., Niehaus, K., Wilson, D. J., Clifton, D. A., Kapatai, G., Ip, C. L. C., Bowden, R., Drobniewski, F., Allix-Béguec, C., Gaudin, C., Parkhill, J., Diel, R., Supply, P., Crook, D. W., Smith, E. G., Walker, A. S., Ismail, N., Niemann, S., Peto, T. E. A. and the MMM Informatics Group (2015)
Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.
Lancet Infectious Diseases 15: 1193-1202. (abstract pdf)

Everitt, R. G., Didelot, X., Batty, E. M., Miller, R. R., Knox, K., Young, B. C., Bowden, R., Auton, A., Votintseva, A., Larner-Svensson, H., Charlesworth, J., Golubchik, T., Ip, C. L. C., Godwin, H., Fung, R., Peto, T. E. A., Walker, A. S., Crook, D. W. and D. J. Wilson (2014)
Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.
Nature Communications 5: 3956. (abstract pdf)

Hedge, J. and D. J. Wilson (2014)
Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not.
mBio 5: e02158-14. (abstract pdf)

Laabei, M., Recker, M., Rudkin, J. K., Aldeljawi, M., Gulay, Z., Sloan, T. J., Williams, P., Endres, J., Bayles, K. W., Fey, P. D., Yajjala, V. K., Widhelm, T., Hawkins, E., Lewis, K., Parfett, S., Scowen, L., Peacock, S. J., Holden, M., Wilson, D. J., Read, T. D., van den Elsen, J., Priest, N. K., Feil, E. J., Hurst, L. D., Josefsson, E and R. C. Massey (2014)
Predicting the virulence of MRSA from its genome sequence.
Genome Research 24: 839-849. (abstract pdf)

Price, J. R., Golubchik, T., Wilson, D. J., Crook, D. W., Walker, A. S., Peto, T. E. A., Paul, J. and M. J. Llewelyn (2014)
Reply to Data on whole-genome sequencing is insufficient to rule out patient-to-patient transmission as a significant source of Staphylococcus aureus acquisition in an ICU, Mills and Linkin.
Clinical Infectious Diseases 59: 752-753. (pdf)

Price, J. R., Golubchik, T., Cole, K., Wilson, D. J., Crook, D. W., Thwaites, G. E., Bowden, R., Walker, A. S., Peto, T. E. A., Paul, J. and M. J. Llewelyn (2014)
Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit.
Clinical Infectious Diseases 58: 609-618. (abstract pdf)

Gordon, N. C, Price, J. R., Cole, K., Everitt, R., Morgan, M., Finney, J., Kearns, A. M., Pichon, B., Young, B., Wilson, D. J., Llewelyn, M. J., Paul, J., Peto, T. E. A., Crook, D. W., Walker, A. S. and T. Golubchik (2014)
Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing.
Journal of Clinical Microbiology 52: 1182-1191. (abstract pdf)

Miller, R. R., Price, J. R., Batty, E. M., Didelot, X., Wyllie, D., Golubchik, T., Crook, D. W., Paul, J., Peto, T. E. A., Wilson, D. J., Cule, M., Ip, C. L. C., Day, N. P. J., Moore, C. E., Bowden, R. and M. J. Llewelyn (2014)
Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone.
Journal of Hospital Infection 86: 83-89. (abstract pdf)

Stoesser, N., Giess, A., Batty, E.M., Sheppard, A.E., Walker, A.S., Wilson, D.J., Didelot, X., Bashir, A., Sebra, R., Kasarskis, A., Sthapit, B., Shakya, M., Kelly, D., Pollard, A.J., Peto, T.E., Crook, D.W., Donnelly, P., Thorson, S., Amatya, P. and S. Joshi (2014)
Genome sequencing of an extended series of NDM-Klebsiella pneumoniae neonatal infections in a Nepali hospital characterizes the extent of community versus hospital-associated transmission in an endemic setting.
Antimicrobial Agents and Chemotherapy 58: 7347-7357. (abstract pdf)

Dearlove, B. L. and D. J. Wilson (2013)
Coalescent-based methods for infectious disease: a meta-analysis of hepatis C virus epidemiology.
Philosophical Transactions of the Royal Society B 368: 20120314. (abstract pdf)

Eyre, D. W., Cule, M. L., Griffiths, D., Crook, D. W., Peto, T. E. A., Walker, A. S and D. J. Wilson (2013)
Detection of mixed infection from bacterial whole genome sequence data allows assessment of its role in Clostridium difficile transmission.
PLoS Computational Biology 9: e1003059. (abstract pdf)

Golubchik, T., Batty, E. M., Miller, R. R., Farr, H., Young, B. C., Larner-Svennson, H., Fung, R., Godwin, H., Knox, K., Votintseva, A., Everitt, R. G., Street, T., Cule, M., Ip, C. L. C., Didelot, X., Peto, T. E. A., Harding, R. M., Wilson, D. J., Crook, D. W. and R. Bowden (2013)
Within-host evolution of Staphylococcus aureus during asymptomatic carriage.
PLoS ONE 8: e61319. (abstract pdf F1000)

Eyre, D. W., Cule, M. L., Wilson, D. J., Griffiths, D., Vaughan, A., O'Connor, L., Ip, C. L. C., Golubchik, T., Batty, E. M., Finney, J. M., Wyllie, D. H., Didelot, X., Piazza, P., Bowden, R., Dingle, K. E., Harding, R. M., Crook, D. W., Wilcox, M. H., Peto, T. E. A. and A. S. Walker (2013)
Diverse sources of C. difficile infection identified by whole genome sequencing.
New England Journal of Medicine 369: 1195-1205 (abstract pdf)

Quach, H., Wilson, D. J., Laval, G. Patin, E., Manry, J., Guibert, J., Barreiro, L. B., Nerrienet, E., Verschoor, E., Gessain, A., Przeworski, M. and L. Quintana-Murci (2013)
Different selective pressures shape the evolution of toll-like receptors in human and African great ape populations.
Human Molecular Genetics 22: 4829-4840 (abstract pdf)

Wong, T. H., Dearlove, B. L., Hedge, J., Giess, A. P., Piazza, P., Trebes, A., Paul, J., Smit, E., Smith, E. G., Sutton, J. K., Wilcox, M. H., Dingle, K. E., Peto, T. E., Crook, D. W., Wilson, D. J. and D. H. Wyllie (2013)
Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England.
Virology Journal 10: 335 (abstract pdf)

Batty, E. M., Wong, T. H. N., Trebes, A., Argoud, K., Attar, M., Buck, D., Ip, C. L. C., Golubchik, T., Cule, M., Bowden, R., Manganis, C., Klenerman, P., Barnes, E., Walker, A. S., Wyllie, D., Wilson, D. J., Dingle, K. E., Peto, T. E. A., Crook, D. W. and P. Piazza (2013)
A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples.
PLoS ONE 8: e66129 (abstract pdf)

Young, B. C., Golubchik, T., Batty, E. M., Fung, R., Larner-Svennson, H., Votintseva, A., Miller, R. R., Godwin, H., Knox, K., Everitt, R. G., Iqbal, Z., Rimmer, A. J., Cule, M., Ip C. L. C., Didelot, X., Harding, R. M., Donnelly, P. J., Peto, T. E., Crook, D. W., Bowden, R. and D. J. Wilson (2012)
Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease.
Proceedings of the National Academy of Sciences USA 109: 4550-4555. (abstract pdf F1000)

D. J. Wilson (2012)
Insights from genomics into bacterial pathogen populations.
PLoS Pathogens 8: e1002874. (abstract pdf)

Didelot, X., Bowden, R., Wilson, D. J., Peto, T. E. A. and D. W. Crook (2012)
Transforming clinical microbiology with bacterial genome sequencing.
Nature Reviews Genetics 13: 601-612. (abstract pdf)

Young, B. C. and D. J. Wilson (2012)
On the evolution of virulence during Staphylococcus aureus nasal carriage.
Virulence 3: 454-456. (abstract pdf)

Eyre, D. W., T. Golubchik, N. C. Gordon, R. Bowden, P. Piazza, E. M. Batty, C. L. C. Ip, D. J. Wilson, X. Didelot, L. O'Connor, R. Lay, D. Buck, A. Kearns, A. Shaw, J. Paul, M. Wilcox, P. J. Donnelly, T. E. A. Peto, A. S. Walker and D. W. Crook (2012)
A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance.
BMJ Open 2: e001124. (abstract pdf)

Walker, T. M., Ip, C. L. C., Harrell, R. H., Evans, J. T., Kapatai, G., Dedicoat, M. J., Eyre, D. W., Wilson, D. J., Hawkey, P. M., Crook, D. W., Parkhill, J., Harris, D., Walker, A. S., Bowden, R., Monk, P., Smith, E. G. and T. E. A. Peto (2012)
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study.
Lancet Infectious Diseases doi:10.1016/S1473-3099(12)70277-3. (abstract pdf)

Didelot, X., Eyre, D. W., Cule, M., Ip, C. L. C., Ansari, A., Griffiths, D., Vaughan, A., O'Connor, L., Golubchik, T., Batty, E. M., Piazza, P., Wilson, D. J., Bowden, R., Donnelly, P. J., Dingle, K. E., Wilcox, M., Walker, A. S., Crook, D. W., Peto, T. E. A. and R. M. Harding (2012)
Microevolutionary analysis of Clostridium difficile genomes to investigate transmission.
Genome Biology 13: R118. (abstract pdf)

Wilson, D. J., R. D. Hernandez, P. Andolfatto and M. Przeworski (2011)
A population genetics-phylogenetics approach to inferring natural selection in coding sequences.
PLoS Genetics 7: e1002395. (abstract pdf F1000)

Muellner, P., Marshall, J. C., Spencer, S. E. F., Noble, A. D., Shadbolt, T., Collins-Emerson, J. M., Midwinter, A. C., Carter, P. E., Pirie, R., Wilson, D. J., Campbell, D. M., Stevenson, M. A. and N. P. French (2011)
Utilizing a combination of molecular and spatial tools to assess the effect of a public health intervention.
Preventive Veterinary Medicine 102: 242-253. (abstract pdf)

Sheppard, S. K., Dallas, J. F., Wilson, D. J., Strachan, N. J. C., McCarthy N. D., Jolley, K. A., Colles, F. M., Rotariu, O., Ogden, I. D., Forbes, K. J. and M. C. J. Maiden (2010)
Evolution of an agriculture-associated disease causing Campylobacter coli clade: evidence from national surveillance data in Scotland.
PLoS ONE 5: e15708. (abstract pdf)

Sousa, T. N., Tarazona-Santos, E. M., Wilson, D. J., Madureira, A. P., Falcao, P. R. K., Fontes, C. J. F., Gil, L. H. S., Ferreira, M. U., Carvalho, L. H. and C. F. A. Brito (2010)
Genetic variability and natural selection at the ligand domain of the Duffy binding protein in Brazilian Plasmodium vivax populations.
Malaria Journal 9: 334. (abstract pdf)

Gabriel, E., Wilson, D. J., Leatherbarrow, A. J., Cheesbrough, J., Gee, S., Bolton, E., Fox, A., Fearnhead, P., Hart, C. A. and P. J. Diggle (2010)
Spatio-temporal epidemiology of Campylobacter jejuni enteritis, in an area of Northwest England, 2000-2002.
Epidemiology and Infection 138: 1384-1390. (abstract pdf)

Mullner, P., Shadbolt, T., Collins-Emerson, J. M., Midwinter, A. C., Spencer, S. E. F., Marshall, J., Carter, P. E., Campbell, D. M., Wilson, D. J., Hathaway, S., Pirie, R. and N. P. French (2010)
Molecular and spatial epidemiology of human campylobacteriosis - source association and genotype-related risk factors.
Epidemiology and Infection 138: 1372-1383. (abstract pdf)

Fledel-Alon, A., Wilson, D. J., Broman, K., Wen, X., Ober, C., Coop, G. and M. Przeworski (2009)
Broad-scale recombination patterns underlying proper disjunction in humans.
PLoS Genetics 5: e1000658. (abstract pdf)

Brehony, C., Wilson, D. J. and M. C. J. Maiden (2009)
Variation of the factor H-binding protein of Neisseria meningitidis.
Microbiology 155: 4155-4169. (abstract pdf)

Mullner, P., Spencer, S. E. F., Wilson, D. J., Jones, G., Noble, A. D., Midwinter, A. C., Collins-Emerson, J. M., Carter, P., Hathaway, S. and N. P. French (2009)
Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach.
Infection, Genetics and Evolution 9: 1311-1319. (abstract pdf)

Wilson, D. J., Gabriel, E., Leatherbarrow, A. J. H., Cheesbrough, J., Gee, S., Bolton, E., Fox, A., Hart, C. A., Diggle, P. J. and P. Fearnhead (2009)
Rapid evolution and the importance of recombination to the gastro-enteric pathogen Campylobacter jejuni.
Molecular Biology and Evolution 26: 385-397. (abstract pdf F1000)

Sheppard, S. K., Dallas, J. F., Strachan, N. J. C., MacRae, M., McCarthy, N. D., Wilson, D. J., Gormley, F. J., Falush, D., Ogden, I. D., Maiden, M. C. J. and K. J. Forbes (2009)
Campylobacter genotyping to determine the source of human infection.
Clinical Infectious Diseases 48: 1072-1078. (abstract pdf)

Wilson, D. J., E. Gabriel, A. J. H. Leatherbarrow, J. Cheesbrough, S. Gee, E. Bolton, A. Fox, P. Fearnhead, C. A. Hart and P. J. Diggle (2008)
Tracing the source of campylobacteriosis.
PLoS Genetics 4: e1000203. (abstract pdf press-release)

Wilson, D. J. and G. McVean (2006)
Estimating diversifying selection and functional constraint in the presence of recombination.
Genetics 172: 1411-1425. (abstract pdf software)

Falush, D., M. Torpdahl, X. Didelot, D. F. Conrad, D. J. Wilson and M. Achtman (2006)
Mismatch induced speciation in Salmonella: model and data.
Philosophical Transactions of the Royal Society B 361: 2045-2053. (abstract pdf)

Edwards, C. T. T., E. C. Holmes, O. G. Pybus, D. J. Wilson, R. P. Viscidi, E. J. Abrams, R. E. Phillips and A. J. Drummond (2006)
Evolution of the HIV-1 envelope gene is dominated by purifying selection.
Genetics 174: 1441-1453. (abstract pdf)

Edwards, C. T. T., E. C. Holmes, D. J. Wilson, R. P. Viscidi, E. J. Abrams, R. E. Phillips and A. J. Drummond (2006)
Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.
BMC Evolutionary Biology 6: 28. (abstract pdf)

Wilson, D. J., D. Falush and G. McVean (2005)
Germs, genomes and genealogies.
Trends in Ecology and Evolution 20: 39-45. (abstract pdf)

Wilson, D. J. and D. Falush (2005)
The genetic structure of human pathogens.
In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics edited by L. B. Jorde, P. F. R. Little, M. J. Dunn and S. Subramaniam. Wiley, New York. (abstract)

Jolley, K. A., D. J. Wilson, P. Kriz, G. McVean and M. C. J. Maiden (2005)
The influence of mutation, recombination, population history and selection on patterns of genetic diversity in Neisseria meningitidis.
Molecular Biology and Evolution 22: 562-569. (abstract pdf)

Claus, H., M. C. J. Maiden, D. J. Wilson, N. D. McCarthy, K. A. Jolley, R. Urwin, F. Hessler, M. Frosch and U. Vogel (2005)
Genetic analysis of meningococci carried by children and young adults.
Journal of Infectious Diseases 191: 1263-1271. (abstract pdf)

Yazdankhah, S. P., P. Kriz, G. Tzanakaki, J. Kremastinou, J. Kalmusova, M. Musilek, T. Alvedstad, K. A. Jolley, D. J. Wilson, N. D. McCarthy, D. A. Caugant and M. C. J. Maiden (2004)
Distribution of Serogroups and Genotypes among Disease-Associated and Carried Isolates of Neisseria meningitidis from the Czech Republic, Greece, and Norway.
Journal of Clinical Microbiology 42: 5146-5153. (abstract pdf)

Thesis

Wilson, D. J. (2005)
Multilocus sequence analysis of the pathogen Neisseria meningitidis.
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