D. Wilson

Daniel Falush, Daniel J. Wilson, Daniel J Wilson, 2009, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Germs, genomes and genealogies.

Daniel Falush, Daniel J. Wilson, Gilean McVean, 2005, Trends in ecology & evolution.

Laboratory diagnosed microbial infection in English UK Biobank participants in comparison to the general population

Daniel J. Wilson, D. Wilson, D. Wyllie, 2023, Scientific Reports.

Incidence of Microbial Infections in English UK Biobank Participants: Comparison with the General Population

N. Allen, D. Wilson, D. Wyllie, 2020 .

Microbial isolation in English participants in the UK Biobank cohort: comparison with the general population

N. Allen, D. Wilson, D. Wyllie, 2020 .

Panton-Valentine leucocidin is the key determinant of Staphylococcus aureus 1 pyomyositis in a bacterial GWAS 2

Daniel J. Wilson, D. Crook, R. Bowden, 2019 .

Identifying lineage effects when controlling for population structure improves power in bacterial association studies

David A. Clifton, Gil McVean, Zamin Iqbal, 2015, Nature Microbiology.

Evolutionary History of the Global Emergence of the Escherichia coli Epidemic Clone ST131

Daniel J. Wilson, J. R. Johnson, A. Kasarskis, 2015, mBio.

Assigning the source of human campylobacteriosis in New Zealand: a comparative genetic and epidemiological approach.

Daniel J. Wilson, N. French, D. Wilson, 2009, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

Global Genomic Epidemiology of Salmonella enterica Serovar Typhimurium DT104

Daniel J. Wilson, O. Lund, D. Ussery, 2016, Applied and Environmental Microbiology.

Whole-Genome Sequencing Shows That Patient-to-Patient Transmission Rarely Accounts for Acquisition of Staphylococcus aureus in an Intensive Care Unit

Daniel J. Wilson, T. Peto, D. Crook, 2013, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Diverse sources of C. difficile infection identified on whole-genome sequencing.

Daniel J. Wilson, Paolo Piazza, Xavier Didelot, 2013, The New England journal of medicine.

Broad-Scale Recombination Patterns Underlying Proper Disjunction in Humans

Daniel J. Wilson, G. Coop, X. Wen, 2009, PLoS genetics.

Sequential Monte Carlo with transformations

Daniel J. Wilson, Daniel J Wilson, Richard G Everitt, 2016, Statistics and Computing.

The Bacterial Sequential Markov Coalescent

Daniel J. Wilson, Nicola De Maio, Daniel J Wilson, 2016, Genetics.

Practical Approaches for Detecting Selection in Microbial Genomes

Daniel J. Wilson, Jessica Hedge, D. Wilson, 2016, PLoS Comput. Biol..

SimBac: simulation of whole bacterial genomes with homologous recombination

Nicola De Maio, Daniel J. Wilson, Xavier Didelot, 2016, Microbial genomics.

The past, present and future of ancient bacterial DNA

Daniel J. Wilson, D. Wilson, Nicolas Arning, 2020, Microbial genomics.

Within-Host Evolution of Staphylococcus aureus during Asymptomatic Carriage

Richard G. Everitt, Daniel J. Wilson, Xavier Didelot, 2013, PloS one.

Mismatch induced speciation in Salmonella: model and data

Daniel Falush, Daniel J. Wilson, Xavier Didelot, 2006, Philosophical Transactions of the Royal Society B: Biological Sciences.

Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis

Daniel J. Wilson, G. Varani, D. Wilson, 2021, PLoS pathogens.

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1

Daniel J. Wilson, Alexei J Drummond, Daniel J Wilson, 2006, BMC Evolutionary Biology.

The distribution of bacterial doubling times in the wild

Daniel J. Wilson, A. Eyre-Walker, E. Feil, 2017, bioRxiv.

Genome-wide association studies of global Mycobacterium tuberculosis resistance to thirteen antimicrobials in 10,228 genomes

Daniel J. Wilson, D. Wilson, S. Earle, 2021, bioRxiv.

Genomic network analysis of environmental and livestock F-type plasmid populations

Daniel J. Wilson, R. Sebra, T. Peto, 2021, The ISME Journal.

Population genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban landscape

Daniel J. Wilson, Maurice K. Murungi, J. Dávila, 2022, Nature Microbiology.

Predicting the virulence of MRSA from its genome sequence

Mario Recker, Daniel J. Wilson, Edward J Feil, 2014, Genome research.

Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone

Daniel J. Wilson, M. Cule, X. Didelot, 2014, The Journal of hospital infection.

Rapid host switching in generalist Campylobacter strains erodes the signal for tracing human infections

Daniel J. Wilson, Bethany L. Dearlove, S. Sheppard, 2015, The ISME Journal.

Evolution of an Agriculture-Associated Disease Causing Campylobacter coli Clade: Evidence from National Surveillance Data in Scotland

Daniel J. Wilson, S. Sheppard, D. Wilson, 2010, PloS one.

DNA Sequencing Predicts 1st-Line Tuberculosis Drug Susceptibility Profiles

Phelim Bradley, Zamin Iqbal, Baoli Zhu, 2018, The New England journal of medicine.

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

Phelim Bradley, Zamin Iqbal, Daniel J. Wilson, 2015, The Lancet. Infectious diseases.

Microevolutionary analysis of Clostridium difficile genomes to investigate transmission

Daniel J. Wilson, P. J. Donnelly, P. Donnelly, 2012, Genome Biology.

The genetic structure of human pathogens

Daniel J. Wilson, D. Falush, D. Wilson, 2005 .

Probabilistic transmission models incorporating sequencing data for healthcare-associated Clostridioides difficile outperform heuristic rules and identify strain-specific differences in transmission

Daniel J. Wilson, David W. Eyre, A. Sarah Walker, 2021, PLoS Comput. Biol..

Detection of Mixed Infection from Bacterial Whole Genome Sequence Data Allows Assessment of Its Role in Clostridium difficile Transmission

David Griffiths, A. Sarah Walker, Daniel J. Wilson, 2013, PLoS Comput. Biol..

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

Nicola De Maio, Daniel J. Wilson, Chieh-Hsi Wu, 2016, PLoS Comput. Biol..

Evolutionary Processes Driving the Rise and Fall of Staphylococcus aureus ST239, a Dominant Hybrid Pathogen

Daniel J. Wilson, R. MacLean, D. Wilson, 2021, bioRxiv.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Peter Donnelly, Zamin Iqbal, Richard G. Everitt, 2012, Proceedings of the National Academy of Sciences.

Mobile elements drive recombination hotspots in the core genome of Staphylococcus aureus

Daniel J. Wilson, A. Auton, R. Everitt, 2014, Nature Communications.

Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation

Konrad U. Förstner, Daniel J. Wilson, Christian W. Remmele, 2016, Proceedings of the National Academy of Sciences.

Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not

Daniel J. Wilson, Jessica Hedge, D. Wilson, 2014, mBio.

Genetic analysis of meningococci carried by children and young adults.

Daniel J. Wilson, D. Wilson, K. Jolley, 2005, The Journal of infectious diseases.

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

Daniel J. Wilson, Julian Parkhill, A Sarah Walker, 2013, The Lancet. Infectious diseases.

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

John Paul, Tanya Golubchik, Daniel J Wilson, 2017, The Lancet. Infectious diseases.

Evolutionary Trade-Offs Underlie the Multi-faceted Virulence of Staphylococcus aureus

Daniel J. Wilson, Harry A. Thorpe, F. Lowy, 2015, PLoS biology.

Severe infections emerge from commensal bacteria by adaptive evolution

Zamin Iqbal, John Paul, Tanya Golubchik, 2017, eLife.

Effects of control interventions on Clostridium difficile infection in England: an observational study

Daniel J. Wilson, X. Didelot, T. Peto, 2017, The Lancet. Infectious diseases.

Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections

Daniel J. Wilson, D. Wilson, S. Duchêne, 2022, bioRxiv.

DeepAMR for predicting co-occurrent resistance of Mycobacterium tuberculosis

David A. Clifton, Farah E. Shamout, A. Sarah Walker, 2019, Bioinform..

Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae

Daniel J. Wilson, S. Bentley, N. Croucher, 2020, bioRxiv.

Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis

Phelim Bradley, Gil McVean, Zamin Iqbal, 2015, bioRxiv.

Nested Russian Doll-Like Genetic Mobility Drives Rapid Dissemination of the Carbapenem Resistance Gene blaKPC

Anna E. Sheppard, A. Sarah Walker, Daniel J. Wilson, 2015, Antimicrobial Agents and Chemotherapy.

Application of machine learning techniques to tuberculosis drug resistance analysis

David A. Clifton, Yang Yang, A. Sarah Walker, 2018, Bioinform..

Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data

David A. Clifton, Yang Yang, Zamin Iqbal, 2017, Bioinform..

Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study

Daniel J. Wilson, Y. Grad, X. Didelot, 2016 .

Reply to Held: When is a harmonic mean p-value a Bayes factor?

D. Wilson, 2019, Proceedings of the National Academy of Sciences.

Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study

Daniel J. Wilson, Chieh-Tsai Wu, A. Walker, 2021, medRxiv.

Controlling for population structure in bacterial association studies

Daniel J. Wilson, G. McVean, D. Clifton, 2015 .

The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013

Daniel J. Wilson, J. Quick, J. Gilbert, 2014, Standards in Genomic Sciences.

Sequential Bayesian inference for mixture models and the coalescent using sequential Monte Carlo samplers with transformations

Richard G. Everitt, Daniel J. Wilson, Richard Culliford, 2016 .

Machine learning to predict the source of campylobacteriosis using whole genome data

Daniel J. Wilson, D. Clifton, S. Sheppard, 2021, bioRxiv.

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis

Daniel J. Wilson, Youwen Qin, M. Inouye, 2022, The Lancet. Microbe.

High fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region

Daniel J. Wilson, Z. Iqbal, D. Clifton, 2022, Genome Medicine.

GenomegaMap: Within-Species Genome-Wide dN/dS Estimation from over 10,000 Genomes

Daniel J. Wilson, Z. Iqbal, D. Clifton, 2019, bioRxiv.

Generalized mean p-values for combining dependent tests: comparison of generalized central limit theorem and robust risk analysis

D. Wilson, 2020, Wellcome open research.

Variation of the factor H-binding protein of Neisseria meningitidis

Daniel J. Wilson, D. Wilson, M. Maiden, 2009, Microbiology.

A data compendium of Mycobacterium tuberculosis antibiotic resistance

Daniel J. Wilson, G. Rodger, Z. Iqbal, 2021, bioRxiv.

Bayesian reconstruction of transmission within outbreaks using genomic variants

Nicola De Maio, Colin J. Worby, Daniel J. Wilson, 2017, bioRxiv.

Bedaquiline and clofazimine resistance in Mycobacterium tuberculosis: an in-vitro and in-silico data analysis

Daniel J. Wilson, G. Rodger, Z. Iqbal, 2023, The Lancet. Microbe.

Whole genome sequencing and de novo assembly identifies Sydney-like variant noroviruses and recombinants during the winter 2012/2013 outbreak in England

Daniel J. Wilson, Bethany L. Dearlove, T. Peto, 2013, Virology Journal.

Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

Daniel J. Wilson, D. Crook, D. Wilson, 2019, Microbiology Resource Announcements.

Nested Russian Doll-like Genetic Mobility Drives

A. Kasarskis, R. Sebra, T. Peto, 2015 .

Panton-Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial genome-wide association study

Daniel J. Wilson, D. Crook, R. Bowden, 2018, bioRxiv.