Publications by authors named "Stephen D Shank"

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Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics.
Lauren E Droske, Andrea S Ramirez-Mata, Melanie N Cash, Jose Estrada, Stephen D Shank

bioRxiv· November 2025

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Defective HIV DNA genomes provide ancestral relevance critical for phylogenetic inference of reservoir dynamics.
Lauren E Droske, Andrea S Ramirez-Mata, Melanie N Cash, Jose Estrada, Stephen D Shank

bioRxiv· November 2025

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Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of the subgenus.
Jordan D Zehr, Sergei L Kosakovsky Pond, Stephen D Shank, Holly McQueary, Jennifer K Grenier

Microbiol Spectr· November 2024

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Ecological diversification of sea catfishes is accompanied by genome-wide signatures of positive selection.
Melissa Rincon-Sandoval, Rishi De-Kayne, Stephen D Shank, Stacy Pirro, Alfred Ko'ou

Nat Commun· November 2024

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Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy.
Aysam Guerler, Dannon Baker, Marius van den Beek, Bjoern Gruening, Dave Bouvier, Stephen D Shank

BMC Bioinformatics· June 2023

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Natural selection differences detected in key protein domains between non-pathogenic and pathogenic feline coronavirus phenotypes.
Jordan D Zehr, Sergei L Kosakovsky Pond, Jean K Millet, Ximena A Olarte-Castillo, Alexander G Lucaci, Stephen D Shank

Virus Evol· March 2023

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Natural selection differences detected in key protein domains between non-pathogenic and pathogenic Feline Coronavirus phenotypes.
Jordan D Zehr, Sergei L Kosakovsky Pond, Jean K Millet, Ximena A Olarte-Castillo, Alexander G Lucaci, Stephen D Shank

bioRxiv· January 2023

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RASCL: Rapid Assessment of Selection in CLades through molecular sequence analysis.
Alexander G Lucaci, Jordan D Zehr, Stephen D Shank, Dave Bouvier, Alexander Ostrovsky

PLoS One· November 2022

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Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City.
Joel O Wertheim, Jade C Wang, Mindy Leelawong, Darren P Martin, Jennifer L Havens, Stephen D Shank

Nat Commun· June 2022

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Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function.
Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank

Mol Biol Evol· April 2022

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Selection analysis identifies unusual clustered mutational changes in Omicron lineage BA.1 that likely impact Spike function.
Darren P Martin, Spyros Lytras, Alexander G Lucaci, Wolfgang Maier, Björn Grüning, Stephen D Shank

bioRxiv· January 2022

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RASCL: Rapid Assessment Of SARS-CoV-2 Clades Through Molecular Sequence Analysis.
Alexander G Lucaci, Jordan D Zehr, Stephen D Shank, Dave Bouvier, Han Mei

bioRxiv· January 2022

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Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.
Alexander G Lucaci, Sadie R Wisotsky, Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

PLoS One· October 2021

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The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages.
Darren P Martin, Steven Weaver, Houriiyah Tegally, James Emmanuel San, Stephen D Shank

Cell· September 2021

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The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape.
Darren P Martin, Steven Weaver, Houryiah Tegally, Emmanuel James San, Stephen D Shank

medRxiv· July 2021

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Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.
Sadie R Wisotsky, Sergei L Kosakovsky Pond, Stephen D Shank, Spencer V Muse

Mol Biol Evol· August 2020

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Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.
David E Northover, Stephen D Shank, David A Liberles

BMC Evol Biol· February 2020

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Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces.
Stephanie J Spielman, Steven Weaver, Stephen D Shank, Brittany Rife Magalis, Michael Li

Methods Mol Biol· January 2020

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HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.
Sergei L Kosakovsky Pond, Art F Y Poon, Ryan Velazquez, Steven Weaver, N Lance Hepler, Stephen D Shank

Mol Biol Evol· January 2020

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Phyloanatomic characterization of the distinct T cell and monocyte contributions to the peripheral blood HIV population within the host.
Brittany RifeMagalis, Samantha L Strickland, Stephen D Shank, Patrick Autissier, Alexandra Schuetz

Virus Evol· January 2020

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phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics.
Stephen D Shank, Steven Weaver, Sergei L Kosakovsky Pond

BMC Bioinformatics· July 2018

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Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes.
Steven Weaver, Stephen D Shank, Stephanie J Spielman, Michael Li, Spencer V Muse

Mol Biol Evol· March 2018

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The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates.
Russell A Hermansen, Benjamin P Oswald, Stormy Knight, Stephen D Shank, David Northover

J Mol Evol· August 2017

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