J. B. Joy

HIV proviral burden, genetic diversity and dynamics in viremic controllers who subsequently initiated suppressive antiretroviral therapy

This study characterizes proviral burden, diversity, and dynamics in viremic controllers before and after ART initiation using phylogenetic analysis and mathematical modeling.

Fundamental identifiability limits in molecular epidemiology

This study identifies fundamental limits in phylodynamic inference, showing that epidemiological parameters cannot be uniquely determined from viral phylogenetic data alone.

A General Birth-Death-Sampling Model for Epidemiology and Macroevolution

The paper unifies various birth-death-sampling models into a general framework, showing they are special cases of a more general model and provides a method to derive likelihoods for complex scenarios.

Assessing in vivo mutation frequencies and creating a high-resolution genome-wide map of fitness costs of Hepatitis C virus

This study estimates in vivo fitness costs of HCV mutations using frequency-based analysis across 195 patients, revealing mutation type and genomic location effects on fitness costs.