John A Lees
Title
Cited by
Cited by
Year
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
1132016
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
562019
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
532017
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
492016
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
452017
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
432017
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
40*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
352018
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
312019
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
312019
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
312019
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
282018
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
27*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
262018
Report 21: Estimating COVID-19 cases and reproduction number in Brazil
TA Mellan, HH Hoeltgebaum, S Mishra, C Whittaker, RP Schnekenberg, ...
medRxiv, 2020
192020
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
192019
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
172019
Report 16: Role of testing in COVID-19 control
N Grassly, M Pons Salort, E Parker, P White, K Ainslie, M Baguelin, ...
162020
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
162019
SuperDCA for genome-wide epistasis analysis
S Puranen, M Pesonen, J Pensar, YY Xu, JA Lees, SD Bentley, ...
Microbial Genomics 4 (6), 2018
162018
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Articles 1–20