| 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 |
| TopHap: rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity MA Caraballo-Ortiz, S Miura, M Sanderford, T Dolker, Q Tao, S Weaver, ... Bioinformatics 38 (10), 2719-2726, 2022 | 9 | 2022 |
| 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 |
| 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 | 108* | 2022 |
| 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 | 1483 | 2022 |
| 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 | 137 | 2022 |
| 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 |
| 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 | 263 | 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 | 78 | 2021 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| The emergence and ongoing convergent evolution of the N501Y lineages coincided with a major global shift in the SARS-CoV-2 selective landscape DP Martin, S Weaver, H Tegally, EJ San, SD Shank, E Wilkinson, ... medRxiv, 2021 | 23 | 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 |
| No more business as usual: Agile and effective responses to emerging pathogen threats require open data and open analytics D Baker, M Van Den Beek, D Blankenberg, D Bouvier, J Chilton, N Coraor, ... PLoS pathogens 16 (8), e1008643, 2020 | 27 | 2020 |
| 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 |
| 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 |
Sergei L Kosakovsky PondProfessor of Biology, Institute for Genomics and Evolutionary Medicine, Temple UniversityVerified email at temple.edu
