Stephen D. Shank

The paper analyzes within- and between-host dynamics of H5 avian influenza in domestic birds and live bird markets, revealing viral evolution, transmission patterns, and risk factors for human spillover.

This study shows that influenza viruses use different evolutionary strategies in avian versus mammalian hosts, with reassortment dominating in birds and adaptation in mammals.

The paper presents a pipeline for predicting genome-wide protein-protein interactions and generating structural models, validated on human and yeast genomes and applied to SARS-CoV2 proteins.

The paper uses single-cell DNA sequencing to show that defective HIV genomes contribute to phylogenetic inference of reservoir dynamics in an animal model.

RASCL rapidly assesses SARS-CoV-2 clades using molecular sequence analysis to detect selection pressures in emerging variants.

The paper finds widespread statistical support for multiple-nucleotide substitutions in codons using empirical data and provides a software tool for analysis.