| Detection of a SARS-CoV-2 variant of concern in South Africa H Tegally, E Wilkinson, M Giovanetti, A Iranzadeh, V Fonseca, ... Nature 592 (7854), 438-443, 2021 | 2867* | 2021 |
| Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa R Viana, S Moyo, DG Amoako, H Tegally, C Scheepers, CL Althaus, ... Nature 603 (7902), 679-686, 2022 | 1630 | 2022 |
| Datamonkey 2.0: a modern web application for characterizing selective and other evolutionary processes S Weaver, SD Shank, SJ Spielman, M Li, SV Muse, SL Kosakovsky Pond Molecular biology and evolution 35 (3), 773-777, 2018 | 833 | 2018 |
| Less is more: an adaptive branch-site random effects model for efficient detection of episodic diversifying selection MD Smith, JO Wertheim, S Weaver, B Murrell, K Scheffler, ... Molecular biology and evolution 32 (5), 1342-1353, 2015 | 722 | 2015 |
| Escape of SARS-CoV-2 501Y. V2 from neutralization by convalescent plasma S Cele, I Gazy, L Jackson, SH Hwa, H Tegally, G Lustig, J Giandhari, ... Nature 593 (7857), 142-146, 2021 | 702 | 2021 |
| Gene-wide identification of episodic selection B Murrell, S Weaver, MD Smith, JO Wertheim, S Murrell, A Aylward, ... Molecular biology and evolution 32 (5), 1365-1371, 2015 | 566 | 2015 |
| HyPhy 2.5—a customizable platform for evolutionary hypothesis testing using phylogenies SL Kosakovsky Pond, AFY Poon, R Velazquez, S Weaver, NL Hepler, ... Molecular biology and evolution 37 (1), 295-299, 2020 | 470 | 2020 |
| The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages DP Martin, S Weaver, H Tegally, JE San, SD Shank, E Wilkinson, ... Cell 184 (20), 5189-5200. e7, 2021 | 275 | 2021 |
| HIV-TRACE (TRAnsmission Cluster Engine): a tool for large scale molecular epidemiology of HIV-1 and other rapidly evolving pathogens SL Kosakovsky Pond, S Weaver, AJ Leigh Brown, JO Wertheim Molecular biology and evolution 35 (7), 1812-1819, 2018 | 256 | 2018 |
| Natural selection in the evolution of SARS-CoV-2 in bats created a generalist virus and highly capable human pathogen OA MacLean, S Lytras, S Weaver, JB Singer, MF Boni, P Lemey, ... PLoS biology 19 (3), e3001115, 2021 | 240* | 2021 |
| Predicting the mutational drivers of future SARS-CoV-2 variants of concern MC Maher, I Bartha, S Weaver, J Di Iulio, E Ferri, L Soriaga, FA Lempp, ... Science translational medicine 14 (633), eabk3445, 2022 | 160 | 2022 |
| Selection analysis identifies clusters of unusual mutational changes in Omicron lineage BA. 1 that likely impact Spike function DP Martin, S Lytras, AG Lucaci, W Maier, B Grüning, SD Shank, S Weaver, ... Molecular biology and evolution 39 (4), msac061, 2022 | 122* | 2022 |
| HIV-1 and SARS-CoV-2: Patterns in the evolution of two pandemic pathogens W Fischer, EE Giorgi, S Chakraborty, K Nguyen, T Bhattacharya, J Theiler, ... Cell host & microbe 29 (7), 1093-1110, 2021 | 96 | 2021 |
| An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic S Kumar, Q Tao, S Weaver, M Sanderford, MA Caraballo-Ortiz, S Sharma, ... Molecular Biology and Evolution 38 (8), 3046-3059, 2021 | 83 | 2021 |
| Evolution of viral genomes: interplay between selection, recombination, and other forces SJ Spielman, S Weaver, SD Shank, BR Magalis, M Li, ... Evolutionary genomics: statistical and computational methods, 427-468, 2019 | 68 | 2019 |
| phylotree. js-a JavaScript library for application development and interactive data visualization in phylogenetics SD Shank, S Weaver, SL Kosakovsky Pond BMC bioinformatics 19, 1-5, 2018 | 57 | 2018 |
| Contrast-FEL—a test for differences in selective pressures at individual sites among clades and sets of branches SL Kosakovsky Pond, SR Wisotsky, A Escalante, BR Magalis, S Weaver Molecular biology and evolution 38 (3), 1184-1198, 2021 | 51 | 2021 |
| IDEPI: rapid prediction of HIV-1 antibody epitopes and other phenotypic features from sequence data using a flexible machine learning platform NL Hepler, K Scheffler, S Weaver, B Murrell, DD Richman, DR Burton, ... PLoS computational biology 10 (9), e1003842, 2014 | 37 | 2014 |
| NGS-SA DP Martin, S Weaver, H Tegally, JE San, SD Shank, E Wilkinson, ... COVID-19 Genomics UK (COG-UK), Gupta RK, Wertheim JO, Nekturenko A, Murrell …, 2021 | 34 | 2021 |
| Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples M Laird Smith, B Murrell, K Eren, C Ignacio, E Landais, S Weaver, ... Virus Evolution 2 (2), vew018, 2016 | 33 | 2016 |
Sergei L Kosakovsky PondProfessor of Biology, Institute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
