| A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology A Rambaut, EC Holmes, Á O’Toole, V Hill, JT McCrone, C Ruis, ... Nature microbiology 5 (11), 1403-1407, 2020 | 2608 | 2020 |
| Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool Á O’Toole, E Scher, A Underwood, B Jackson, V Hill, JT McCrone, ... Virus evolution 7 (2), veab064, 2021 | 863 | 2021 |
| Emergence of SARS-CoV-2 omicron lineages BA. 4 and BA. 5 in South Africa H Tegally, M Moir, J Everatt, M Giovanetti, C Scheepers, E Wilkinson, ... Nature medicine 28 (9), 1785-1790, 2022 | 516 | 2022 |
| Producing polished prokaryotic pangenomes with the Panaroo pipeline G Tonkin-Hill, N MacAlasdair, C Ruis, A Weimann, G Horesh, JA Lees, ... Genome biology 21, 1-21, 2020 | 473 | 2020 |
| Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B. 1.1. 7 B Meng, SA Kemp, G Papa, R Datir, IATM Ferreira, S Marelli, WT Harvey, ... Cell reports 35 (13), 2021 | 424 | 2021 |
| Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK L Du Plessis, JT McCrone, AE Zarebski, V Hill, C Ruis, B Gutierrez, ... Science 371 (6530), 708-712, 2021 | 368 | 2021 |
| Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B. 1.1. 7 emergence MUG Kraemer, V Hill, C Ruis, S Dellicour, S Bajaj, JT McCrone, G Baele, ... Science 373 (6557), 889-895, 2021 | 144 | 2021 |
| Continued emergence and evolution of Omicron in South Africa: New BA. 4 and BA. 5 lineages H Tegally, M Moir, J Everatt, M Giovanetti, C Scheepers, E Wilkinson, ... MedRxiv, 2022.05. 01.22274406, 2022 | 106 | 2022 |
| Stepwise pathogenic evolution of Mycobacterium abscessus JM Bryant, KP Brown, S Burbaud, I Everall, JM Belardinelli, ... Science 372 (6541), eabb8699, 2021 | 105 | 2021 |
| Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evol 7: veab064 Á O’Toole, E Scher, A Underwood, B Jackson, V Hill, JT McCrone, ... | 83 | 2021 |
| Norovirus whole-genome sequencing by SureSelect target enrichment: a robust and sensitive method JR Brown, S Roy, C Ruis, E Yara Romero, D Shah, R Williams, J Breuer Journal of clinical microbiology 54 (10), 2530-2537, 2016 | 80 | 2016 |
| The emerging GII. P16-GII. 4 Sydney 2012 norovirus lineage is circulating worldwide, arose by late-2014 and contains polymerase changes that may increase virus transmission C Ruis, S Roy, JR Brown, DJ Allen, RA Goldstein, J Breuer PloS one 12 (6), e0179572, 2017 | 77 | 2017 |
| Context-specific emergence and growth of the SARS-CoV-2 Delta variant JT McCrone, V Hill, S Bajaj, RE Pena, BC Lambert, R Inward, S Bhatt, ... Nature 610 (7930), 154-160, 2022 | 73 | 2022 |
| Addendum: A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology A Rambaut, EC Holmes, Á O’Toole, V Hill, JT McCrone, C Ruis, ... Nature Microbiology 6 (3), 415-415, 2021 | 71 | 2021 |
| Global phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis MA Beale, M Marks, MJ Cole, MK Lee, R Pitt, C Ruis, E Balla, T Crucitti, ... Nature microbiology 6 (12), 1549-1560, 2021 | 64 | 2021 |
| The impact of viral mutations on recognition by SARS-CoV-2 specific T cells TI de Silva, G Liu, BB Lindsey, D Dong, SC Moore, NS Hsu, D Shah, ... Iscience 24 (11), 2021 | 62 | 2021 |
| Progress and challenges in virus genomic epidemiology V Hill, C Ruis, S Bajaj, OG Pybus, MUG Kraemer Trends in Parasitology 37 (12), 1038-1049, 2021 | 53 | 2021 |
| A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020; 5 (11): 1403–7 A Rambaut, EC Holmes, Á O’Toole, V Hill, JT McCrone, C Ruis, ... | 53 | |
| Dissemination of Mycobacterium abscessus via global transmission networks C Ruis, JM Bryant, SC Bell, R Thomson, RM Davidson, NA Hasan, ... Nature microbiology 6 (10), 1279-1288, 2021 | 50 | 2021 |
| Mutagenesis in norovirus in response to favipiravir treatment C Ruis, LAK Brown, S Roy, C Atkinson, R Williams, SO Burns, ... New England Journal of Medicine 379 (22), 2173-2176, 2018 | 48 | 2018 |
