Alexander Platt

Apollo simulates within-host viral evolution and infection dynamics, validating limitations of transmission inference tools using HIV cohort data.

The paper introduces cLD, a statistic for measuring rare-variant linkage disequilibrium between genomic regions, and shows it identifies novel genomic interactions and associations.

The paper shows that demographic inference models can produce false results when applied to data from sub-populations or genomes with loci under selection.

The paper estimates the age of rare alleles using haplotype sharing to infer demographic history and selection pressures in a UK population.

The paper derives three new properties of coalescent gene trees to characterize the present-day impacts of historical events.

The paper estimates recent African gene flow into the UK population, identifying old rare variants that suggest a 1.2% contribution approximately 400 years ago.