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John A Lees
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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
879*2020
Reduction in mobility and COVID-19 transmission
P Nouvellet, S Bhatia, A Cori, KEC Ainslie, M Baguelin, S Bhatt, ...
Nature communications 12 (1), 1-9, 2021
5832021
Producing polished prokaryotic pangenomes with the Panaroo pipeline
G Tonkin-Hill, N MacAlasdair, C Ruis, A Weimann, G Horesh, JA Lees, ...
Genome Biology 21 (180), 2020
4872020
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
2762019
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
2142016
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
2102018
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
2032018
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
2002019
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
1982019
The potential public health consequences of COVID-19 on malaria in Africa
E Sherrard-Smith, AB Hogan, A Hamlet, OJ Watson, C Whittaker, ...
Nature medicine 26 (9), 1411-1416, 2020
1782020
State-level tracking of COVID-19 in the United States
HJT Unwin, S Mishra, VC Bradley, A Gandy, TA Mellan, H Coupland, ...
Nature communications 11 (1), 6189, 2020
1712020
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
1662019
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
1652019
Report 21: Estimating COVID-19 cases and reproduction number in Brazil
TA Mellan, HH Hoeltgebaum, S Mishra, C Whittaker, RP Schnekenberg, ...
160*2020
Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study
R Sonabend, LK Whittles, N Imai, PN Perez-Guzman, ES Knock, ...
The Lancet 398 (10313), 1825-1835, 2021
1482021
Within-country age-based prioritisation, global allocation, and public health impact of a vaccine against SARS-CoV-2: A mathematical modelling analysis
AB Hogan, P Winskill, OJ Watson, PGT Walker, C Whittaker, M Baguelin, ...
Vaccine 39 (22), 2995-3006, 2021
136*2021
Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England
ES Knock, LK Whittles, JA Lees, PN Perez-Guzman, R Verity, RG FitzJohn, ...
Science Translational Medicine 13 (602), eabg4262, 2021
118*2021
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
1052017
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
1002017
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
942019
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