Articles with public access mandates - Steven WeaverLearn more
Available somewhere: 23
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
Mandates: Bill & Melinda Gates Foundation, US National Institutes of Health, UK …
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health, UK Engineering and Physical Sciences …
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
Mandates: US National Science Foundation, US National Institutes of Health, UK Medical …
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
Mandates: US National Science Foundation, Bill & Melinda Gates Foundation, US National …
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health, UK Medical Research Council
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
Mandates: US National Institutes of Health, Howard Hughes Medical Institute, Cancer …
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
Mandates: US Department of Energy, US National Institutes of Health
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
Mandates: US National Science Foundation, US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: US National Institutes of Health
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
Mandates: Bill & Melinda Gates Foundation, US National Institutes of Health, Wellcome …
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
Mandates: US National Science Foundation, US National Institutes of Health, Research …
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
Mandates: US National Institutes of Health
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