| 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 | 2857 | 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 | 1043 | 2021 |
| 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 | 689 | 2020 |
| 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 | 623 | 2022 |
| 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 | 466 | 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 | 406 | 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 | 171 | 2021 |
| Stepwise pathogenic evolution of Mycobacterium abscessus JM Bryant, KP Brown, S Burbaud, I Everall, JM Belardinelli, ... Science 372 (6541), eabb8699, 2021 | 131 | 2021 |
| A molnupiravir-associated mutational signature in global SARS-CoV-2 genomes T Sanderson, R Hisner, I Donovan-Banfield, H Hartman, A Løchen, ... Nature 623 (7987), 594-600, 2023 | 121 | 2023 |
| 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 | 114 | 2022 |
| 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 | 103 | 2022 |
| 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 | 101 | 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 | 86 | 2016 |
| 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 | 82 | 2021 |
| 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 | 81 | 2017 |
| 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 | 79 | 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 | 75 | 2021 |
| 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 | 75 | 2021 |
| SARS-CoV-2 evolution in the Omicron era C Roemer, DJ Sheward, R Hisner, F Gueli, H Sakaguchi, N Frohberg, ... Nature microbiology 8 (11), 1952-1959, 2023 | 65 | 2023 |
| 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, ... | 62 | |