A. F. Feder

Elevated HIV viral load is associated with higher recombination rate in vivo.

This study finds that higher HIV viral load correlates with increased recombination rate in vivo, suggesting dynamic variation in recombination across viral populations and over time.

State-dependent evolutionary models reveal modes of solid tumor growth

This paper introduces a Bayesian state-dependent evolutionary model to infer spatially varying cell division rates in tumors using multi-region sequencing data, finding peripheral cells divide 3-6x faster than central cells.

Understanding patterns of HIV multi-drug resistance through models of temporal and spatial drug heterogeneity

The paper analyzes HIV resistance evolution patterns under temporal and spatial drug heterogeneity models, showing resistance develops even after long-term therapy and in predictable sequences.

Evolutionary dynamics in structured populations under strong population genetic forces

This study uses modeling to show how migration and selection interact to create non-monotonic FST patterns in adapting populations and estimates high migration rates in a Simian-HIV population.

The clarifying role of time series data in the population genetics of HIV

This paper uses time series data to show that soft sweeps drove early HIV treatment failure, contrasting with harder sweeps associated with better drugs.

High resolution spatio-temporal assessment of simian/human immunodeficiency virus (SHIV) evolution reveals a highly dynamic process within the host

This study tracks SHIV evolution in macaques to show drug resistance spreads rapidly across compartments but does not equilibrate, with the gut showing faster turnover and less wild-type virus retention.