Stephen D Shank
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Explore the profile of Stephen D Shank including associated specialties, affiliations and a list of published articles.
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21
Citations
1068
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Recent Articles
11.
Martin D, Weaver S, Tegally H, San J, Shank S, Wilkinson E, et al.
Cell
. 2021 Sep;
184(20):5189-5200.e7.
PMID: 34537136
The independent emergence late in 2020 of the B.1.1.7, B.1.351, and P.1 lineages of SARS-CoV-2 prompted renewed concerns about the evolutionary capacity of this virus to overcome public health interventions...
12.
Lucaci A, Wisotsky S, Shank S, Weaver S, Kosakovsky Pond S
PLoS One
. 2021 Mar;
16(3):e0248337.
PMID: 33711070
Despite many attempts to introduce evolutionary models that permit substitutions to instantly alter more than one nucleotide in a codon, the prevailing wisdom remains that such changes are rare and...
13.
Martin D, Weaver S, Tegally H, San E, Shank S, Wilkinson E, et al.
medRxiv
. 2021 Mar;
PMID: 33688681
The emergence and rapid rise in prevalence of three independent SARS-CoV-2 "501Y lineages", B.1.1.7, B.1.351 and P.1, in the last three months of 2020 prompted renewed concerns about the evolutionary...
14.
RifeMagalis B, Strickland S, Shank S, Autissier P, Schuetz A, Sithinamsuwan P, et al.
Virus Evol
. 2020 May;
6(1):veaa005.
PMID: 32355568
Human immunodeficiency virus (HIV) is a rapidly evolving virus, allowing its genetic sequence to act as a fingerprint for epidemiological processes among, as well as within, individual infected hosts. Though...
15.
Wisotsky S, Kosakovsky Pond S, Shank S, Muse S
Mol Biol Evol
. 2020 Feb;
37(8):2430-2439.
PMID: 32068869
Most molecular evolutionary studies of natural selection maintain the decades-old assumption that synonymous substitution rate variation (SRV) across sites within genes occurs at levels that are either nonexistent or negligible....
16.
Northover D, Shank S, Liberles D
BMC Evol Biol
. 2020 Feb;
20(1):24.
PMID: 32046633
Background: Understanding the origins of genome content has long been a goal of molecular evolution and comparative genomics. By examining genome evolution through the guise of lineage-specific evolution, it is...
17.
Kosakovsky Pond S, Poon A, Velazquez R, Weaver S, Hepler N, Murrell B, et al.
Mol Biol Evol
. 2019 Sep;
37(1):295-299.
PMID: 31504749
HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis...
18.
Spielman S, Weaver S, Shank S, Magalis B, Li M, Kosakovsky Pond S
Methods Mol Biol
. 2019 Jul;
1910:427-468.
PMID: 31278673
Natural selection is a fundamental force shaping organismal evolution, as it both maintains function and enables adaptation and innovation. Viruses, with their typically short and largely coding genomes, experience strong...
19.
Shank S, Weaver S, Kosakovsky Pond S
BMC Bioinformatics
. 2018 Jul;
19(1):276.
PMID: 30045713
Background: While several JavaScript packages for visualizing phylogenetic trees exist, most are best characterized as frameworks that are designed with a specific set of tasks in mind. Extending such packages...
20.
Weaver S, Shank S, Spielman S, Li M, Muse S, Kosakovsky Pond S
Mol Biol Evol
. 2018 Jan;
35(3):773-777.
PMID: 29301006
Inference of how evolutionary forces have shaped extant genetic diversity is a cornerstone of modern comparative sequence analysis. Advances in sequence generation and increased statistical sophistication of relevant methods now...