Joshua Daniel Rubin

SAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings

SAFARI improves ancient DNA alignment by using RYmer indices to handle chemical damage patterns, resulting in more accurate alignments and better damage rate estimation.

soibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs

soibean improves species-level classification of ancient environmental DNA using mitochondrial pangenome graphs, revealing new insights from archaeological datasets.

The Limits of Haplotype-Based Approaches: Exploring the Applicability of the Li and Stephens Haplotype-Copying Model to Ancient Samples

This paper evaluates the Li and Stephens haplotype-copying model's performance on ancient DNA by using forward-simulated data and a constant-sized population model, finding it robust for haplotypes up to 900,000 years old.

HaploCart: Human mtDNA Haplogroup Classification Using a Pangenomic Reference Graph

HaploCart classifies human mtDNA haplogroups using a pangenomic reference graph and Bayesian inference, outperforming existing tools with more accurate and unbiased confidence scores.

euka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs.

euka improves taxonomic identification and abundance estimation in ancient eDNA by using pangenomic graphs and maximum-likelihood methods, outperforming existing tools.