Ben Jeffery

Tracing the evolutionary histories of ultra-rare variants using variational dating of large ancestral recombination graphs

The paper develops a scalable method to estimate allele ages from large genomic datasets, revealing purifying selection and heterogeneity in ultra-rare variants.

Accessible, realistic genome simulation with selection using stdpopsim

The paper extends the stdpopsim simulation framework to include realistic selection models, enabling studies of selection's impact on genetic variation across species.

Tsbrowse: an interactive browser for Ancestral Recombination Graphs

tsbrowse is an open-source web tool for interactive visualization of Ancestral Recombination Graphs, enabling exploration of genetic ancestry data.

Analysis-ready VCF at Biobank scale using Zarr

The paper introduces VCF Zarr, a format for efficiently storing and processing large-scale genetic variation data, demonstrating improved performance and scalability over traditional VCF formats.

On the Genes, Genealogies, and Geographies of Quebec

The paper models French Canadian ancestry using genealogical and genetic data, revealing population structure shaped by geography and migration.

A unified genealogy of modern and ancient genomes

This paper introduces a non-parametric method to infer human genealogical history from modern and ancient genomes, demonstrating its ability to reconstruct relationships and identify descendants of ancient samples.

Efficient ancestry and mutation simulation with msprime 1.0

The paper introduces msprime 1.0, a high-performance simulation tool for ancestry and mutation in population genetics, showing it is faster and more memory efficient than existing alternatives.

Natural diversity of the malaria vector Anopheles gambiae

The paper sequences genomes of 765 malaria vector mosquitoes to study genetic diversity and insecticide resistance.

Genomic epidemiology of the current wave of artemisinin resistant malaria

This study identifies kelch13 mutations associated with artemisinin resistance in Southeast Asia and finds low frequency of these mutations in Africa, suggesting different evolutionary pressures.