| American society for microbiology N Martin, S Weaver, H Tegally, JE San, SD Shank, E Wilkinson, ... Washington, DC, 205-209, 1979 | 6 | 1979 |
| 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 | 78 | 2021 |
| AUTO-TUNE: selecting the distance threshold for inferring HIV transmission clusters S Weaver, VM Dávila Conn, D Ji, H Verdonk, S Ávila-Ríos, L Brown, ... Frontiers in Bioinformatics 4, 1400003, 2024 | | 2024 |
| Characteristics and growth of the genetic HIV transmission network of Mexico City during 2020 V Dávila‐Conn, C García‐Morales, M Matías‐Florentino, E López‐Ortiz, ... Journal of the International AIDS Society 24 (11), e25836, 2021 | 9 | 2021 |
| 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 | 38 | 2021 |
| 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 | 739 | 2018 |
| 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 | 2751* | 2021 |
| Emergence and phenotypic characterization of the global SARS-CoV-2 C. 1.2 lineage C Scheepers, J Everatt, DG Amoako, H Tegally, CK Wibmer, A Mnguni, ... Nature Communications 13 (1), 1976, 2022 | 29 | 2022 |
| 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 | 678 | 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 | 62 | 2019 |
| Extra base hits: widespread empirical support for instantaneous multiple-nucleotide changes AG Lucaci, SR Wisotsky, SD Shank, S Weaver, SL Kosakovsky Pond PloS one 16 (3), e0248337, 2021 | 20 | 2021 |
| Full-Length Envelope Analyzer (FLEA): A tool for longitudinal analysis of viral amplicons K Eren, S Weaver, R Ketteringham, M Valentyn, M Laird Smith, V Kumar, ... PLoS Computational Biology 14 (12), e1006498, 2018 | 5 | 2018 |
| 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 | 516 | 2015 |
| 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 | 87 | 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 | 232 | 2018 |
| 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 | 386 | 2020 |
| 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 | 35 | 2014 |
| 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 | 658 | 2015 |
| 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 | 232* | 2021 |
| 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 | 31 | 2021 |
Sergei L Kosakovsky PondProfessor of Biology, Institute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
