F. Jay

The MUC19 Gene: An Evolutionary History of Recurrent Introgression and Natural Selection

The paper identifies a Denisovan-like MUC19 haplotype in Indigenous Americans and Neanderthals, showing it is under positive selection and has high copy numbers of a tandem repeat.

A quantitative theory for genomic offset statistics

The paper develops a theoretical framework to interpret genomic offset statistics and validates it using simulations and empirical data on African pearl millet.

Simulation of bacterial populations with SLiM

This paper demonstrates how to simulate bacterial populations using SLiM, a forward-in-time simulator, and validates its results against existing tools and theoretical expectations.

Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation

This paper proposes deep learning methods for inferring population size history from SNP data and compares them to ABC, showing competitive performance and potential for combination.

Inference of population genetic structure from temporal samples of DNA

This paper introduces a factor analysis method that corrects for allele frequency drift in temporal DNA samples, applied to study hepatitis C virus evolution and ancient European population structure.

An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions

The paper develops an ABC method to infer past human population expansions using whole-genome sequence data, finding a bottleneck followed by Paleolithic and Neolithic expansions best fits Eurasian populations.

Fast Inference of Individual Admixture Coefficients Using Geographic Data

The paper introduces new algorithms that use geographic data to estimate ancestry proportions and frequencies, showing faster runtime without loss of accuracy.