Cole Shanks

ARGformer uses transformers to learn embeddings from ancestral recombination graphs, enabling population structure analysis and ancestry inference without genotype data.

ARGMix uses a graph transformer to infer local ancestry from ancient DNA, showing continuity between Otzi the Iceman and present-day Europeans.

snputils provides a high-performance Python library for handling genetic variation and population structure data, improving efficiency and integration in genomic research.

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

The paper identifies position-dependent codon usage bias in the human transcriptome and shows its relationship with translational efficiency and functional enrichment.