| 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 | 957* | 2020 |
| 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 | 691 | 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 | 651 | 2021 |
| 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 | 334 | 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 (93), 2018 | 246 | 2018 |
| 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 | 243 | 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 | 243 | 2018 |
| 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 | 225 | 2016 |
| 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 | 224 | 2019 |
| 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 | 193 | 2020 |
| 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 | 189 | 2020 |
| 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 | 189 | 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 | 184 | 2019 |
| 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 | 171 | 2021 |
| 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 | 165* | 2021 |
| Report 21: Estimating COVID-19 cases and reproduction number in Brazil TA Mellan, HH Hoeltgebaum, S Mishra, C Whittaker, RP Schnekenberg, ... | 165* | 2020 |
| 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 | 140* | 2021 |
| Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era AK Pöntinen, J Top, S Arredondo-Alonso, G Tonkin-Hill, AR Freitas, ... Nature communications 12 (1), 1523, 2021 | 113 | 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 | 113 | 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 | 111 | 2017 |