Steven Weaver
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Explore the profile of Steven Weaver including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Selberg A, Chikina M, Sackton T, Muse S, Lucaci A, Weaver S, et al.
bioRxiv
. 2024 Nov;
PMID: 39605407
Errors in multiple sequence alignments (MSAs) are known to bias many comparative evolutionary methods. In the context of natural selection analyses, specifically codon evolutionary models, excessive rates of false positives...
2.
Weaver S, Davila Conn V, Ji D, Verdonk H, Avila-Rios S, Leigh Brown A, et al.
Front Bioinform
. 2024 Aug;
4():1400003.
PMID: 39086842
Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic...
3.
Weaver S, Davila-Conn V, Ji D, Verdonk H, Avila-Rios S, Leigh Brown A, et al.
bioRxiv
. 2024 Apr;
PMID: 38559140
Molecular surveillance of viral pathogens and inference of transmission networks from genomic data play an increasingly important role in public health efforts, especially for HIV-1. For many methods, the genetic...
4.
Caraballo-Ortiz M, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, et al.
Bioinformatics
. 2022 May;
38(10):2719-2726.
PMID: 35561179
Motivation: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic...
5.
Martin D, Lytras S, Lucaci A, Maier W, Gruning B, Shank S, et al.
Mol Biol Evol
. 2022 Mar;
39(4).
PMID: 35325204
Among the 30 nonsynonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions...
6.
Martin D, Lytras S, Lucaci A, Maier W, Gruning B, Shank S, et al.
bioRxiv
. 2022 Jan;
PMID: 35075456
Among the 30 non-synonymous nucleotide substitutions in the Omicron S-gene are 13 that have only rarely been seen in other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions...
7.
Viana R, Moyo S, Amoako D, Tegally H, Scheepers C, Althaus C, et al.
Nature
. 2022 Jan;
603(7902):679-686.
PMID: 35042229
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were...
8.
Maher M, Bartha I, Weaver S, di Iulio J, Ferri E, Soriaga L, et al.
Sci Transl Med
. 2022 Jan;
14(633):eabk3445.
PMID: 35014856
SARS-CoV-2 evolution threatens vaccine- and natural infection-derived immunity as well as the efficacy of therapeutic antibodies. To improve public health preparedness, we sought to predict which existing amino acid mutations...
9.
Caraballo-Ortiz M, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, et al.
bioRxiv
. 2021 Dec;
PMID: 34931186
Motivation: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic...
10.
Davila-Conn V, Garcia-Morales C, Matias-Florentino M, Lopez-Ortiz E, Paz-Juarez H, Beristain-Barreda A, et al.
J Int AIDS Soc
. 2021 Nov;
24(11):e25836.
PMID: 34762774
Introduction: Molecular surveillance systems could provide public health benefits to focus strategies to improve the HIV care continuum. Here, we infer the HIV genetic network of Mexico City in 2020,...