John A Lees
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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes
J Lees, M Vehkala, N Välimäki, S Harris, C Chewapreecha, N Croucher, ...
Nature Communications 7, 12797, 2016
Fast and flexible bacterial genomic epidemiology with PopPUNK
J Lees, S Harris, G Tonkin-Hill, R Gladstone, S Lo, J Weiser, J Corander, ...
Genome Research 29 (2), 304-316, 2019
Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration
JA Lees, NJ Croucher, D Goldblatt, F Nosten, J Parkhill, C Turner, ...
eLife 6, e26255, 2017
Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently
S David, C Rusniok, M Mentasti, L Gomez-Valero, SR Harris, P Lechat, ...
Genome research 26 (11), 1555-1564, 2016
Adults with suspected central nervous system infection: a prospective study of diagnostic accuracy
U Khatib, D van de Beek, JA Lees, MC Brouwer
Journal of Infection 74 (1), 1-9, 2017
Benzalkonium tolerance genes and outcome in Listeria monocytogenes meningitis
PHC Kremer, JA Lees, MM Koopmans, B Ferwerda, AWM Arends, ...
Clinical Microbiology and Infection 23 (4), 265. e1-265. e7, 2017
Potential impact of the COVID-19 pandemic on HIV, tuberculosis, and malaria in low-income and middle-income countries: a modelling study
AB Hogan, BL Jewell, E Sherrard-Smith, JF Vesga, OJ Watson, ...
The Lancet Global Health 8 (9), e1132-e1141, 2020
RhierBAPS: an R implementation of the population clustering algorithm hierBAPS
G Tonkin-Hill, JA Lees, SD Bentley, SDW Frost, J Corander
Wellcome open research 3 (93), 2018
Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole …
SW Lo, RA Gladstone, AJ van Tonder, JA Lees, M du Plessis, R Benisty, ...
The Lancet Infectious Diseases 19 (7), 759-769, 2019
Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics
MR Davies, L McIntyre, A Mutreja, JA Lacey, JA Lees, RJ Towers, ...
Nature genetics 51, 1035–1043, 2019
International Genomic Definition of Pneumococcal Lineages, to Contextualise Disease, Antibiotic Resistance and Vaccine Impact
RA Gladstone, SW Lo, JA Lees, NJ Croucher, AJ van Tonder, J Corander, ...
EBioMedicine 43, 338-346, 2019
pyseer: a comprehensive tool for microbial pangenome-wide association studies
JA Lees, M Galardini, SD Bentley, JN Weiser, J Corander
Bioinformatics 34 (24), 4310--4312, 2018
Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis
JA Lees, PHC Kremer, AS Manso, NJ Croucher, B Ferwerda, MV Serón, ...
Microbial genomics 3 (1), 2017
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study
JA Lees, M Kendall, J Parkhill, C Colijn, SD Bentley, SR Harris
Wellcome Open Research 3 (33), 2018
Report 21: Estimating COVID-19 cases and reproduction number in Brazil
TA Mellan, HH Hoeltgebaum, S Mishra, C Whittaker, RP Schnekenberg, ...
medRxiv, 2020
Sequential evolution of virulence and resistance during clonal spread of community-acquired methicillin-resistant Staphylococcus aureus
R Copin, WE Sause, Y Fulmer, D Balasubramanian, S Dyzenhaus, ...
Proceedings of the National Academy of Sciences 116 (5), 1745-1754, 2019
Fast hierarchical Bayesian analysis of population structure
G Tonkin-Hill, JA Lees, SD Bentley, SDW Frost, J Corander
Nucleic Acids Research 47 (11), 5539–5549, 2019
Report 16: Role of testing in COVID-19 control
N Grassly, M Pons Salort, E Parker, P White, K Ainslie, M Baguelin, ...
Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis
J Lees, B Ferwerda, PHC Kremer, NE Wheeler, MV Serón, NJ Croucher, ...
Nature Communications 10, 2176, 2019
SuperDCA for genome-wide epistasis analysis
S Puranen, M Pesonen, J Pensar, YY Xu, JA Lees, SD Bentley, ...
Microbial Genomics 4 (6), 2018
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Articles 1–20