| 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 | 113 | 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 | 56 | 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 | 53 | 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 | 49 | 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 | 45 | 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 | 43 | 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 | 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 | 35 | 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 | 31 | 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 | 31 | 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 | 31 | 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 | 28 | 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 | 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 | 26 | 2018 |
| Report 21: Estimating COVID-19 cases and reproduction number in Brazil TA Mellan, HH Hoeltgebaum, S Mishra, C Whittaker, RP Schnekenberg, ... medRxiv, 2020 | 19 | 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 | 19 | 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 | 17 | 2019 |
| Report 16: Role of testing in COVID-19 control N Grassly, M Pons Salort, E Parker, P White, K Ainslie, M Baguelin, ... | 16 | 2020 |
| 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 | 16 | 2019 |
| SuperDCA for genome-wide epistasis analysis S Puranen, M Pesonen, J Pensar, YY Xu, JA Lees, SD Bentley, ... Microbial Genomics 4 (6), 2018 | 16 | 2018 |
