Joshua T. Herbeck

This study evaluates 74 phylogenetic summary statistics through simulation to assess their relationship to epidemiological quantities and computational efficiency, offering guidelines for their use in genomic epidemiology.

The paper evaluates two tools for HIV transmission direction prediction using short and long-read sequencing data from serodiscordant couples, showing long reads improve phylogenetic resolution and transmission prediction accuracy.

This paper introduces a method to optimize phylogenetic clustering thresholds for HIV-1 sequence data, showing that optimal thresholds vary by population and improve cluster growth prediction.