Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

Steven Weaver, Stephen D. Shank, Stephanie J. Spielman, +3

Molecular Biology and Evolution

Other Evolutionary ProcessesComparative GenomicsGeneticsEvolutionary ForcesNatural Selection +27

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

Sergei L. Kosakovsky Pond, Art F. Y. Poon, Ryan Velazquez, +11

Molecular Biology and Evolution

The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

Darren P. Martin, Steven Weaver, Houriiyah Tegally, +19

Cell

Viral EvolutionVirus PhylogenyOngoing Convergent EvolutionVirologySars-cov-2 N501y Lineages +2

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, +34

Molecular Biology and Evolution

GeneticsViral PathogenesisGenomic MechanismMolecular BiologyMolecular Genetics +21

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, +1

Molecular Biology and Evolution

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, +9

Virus EpidemiologyImmunologyOngoing Convergent EvolutionSequence DiversificationCovid-19 Epidemiology +17

Evolution of Viral Genomes: Interplay Between Selection, Recombination, and Other Forces

Stephanie J. Spielman, Steven Weaver, Stephen D. Shank, +3

Methods in molecular biology

Viral ReplicationGeneticsViral GenomesNatural SelectionGenomics +21

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

Efficient low-rank solution of generalized Lyapunov equations

Stephen D. Shank, Valeria Simoncini, Daniel B. Szyld

Numerische Mathematik

Efficient Low-rank SolutionGeometric Singular Perturbation TheoryLow-rank ApproximationLyapunov Analysis

Detection of SARS-CoV-2 intra-host recombination during superinfection with Alpha and Epsilon variants in New York City

Joel O. Wertheim, Jade Wang, Mindy Leelawong, +21

Nature Communications