John A Lees
John A Lees
Postdoctoral Fellow, NYU Medical Centre
Verified email at - Homepage
TitleCited byYear
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
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
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
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
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
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
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
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, 2018
Genome watch: Bacterial GWAS: not just gilding the lily
JA Lees, SD Bentley
Nature Reviews Microbiology 14 (7), 2016
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
SuperDCA for genome-wide epistasis analysis
S Puranen, M Pesonen, J Pensar, YY Xu, JA Lees, SD Bentley, ...
Microbial Genomics 4 (6), 2018
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
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
Pneumococcal quorum sensing drives an asymmetric owner–intruder competitive strategy during carriage via the competence regulon
P Shen, JA Lees, GCW Bee, SP Brown, JN Weiser
Nature microbiology 4 (1), 198, 2019
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
Bacterial hypervirulence in haemophilus influenzae meningitis identified by whole genome sequencing
D Koelman, P Kremer, J Lees, M Brouwer, S Bentley, D van de Beek
Journal of the Neurological Sciences 381, 181-182, 2017
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
Genome-wide epistasis and co-selection study using mutual information
J Pensar, S Puranen, B Arnold, N MacAlasdair, J Kuronen, G Tonkin-Hill, ...
Nucleic Acids Research, gkz656, 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
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