Forensic and Genetic Research

Recomb-Mix Cloud: a cost-efficient and scalable cloud-friendly pipeline for local ancestry inference

On the All of Us workbench, a Recomb-Mix-based cloud pipeline runs whole-genome local ancestry inference for an estimated $0.01 per sample, versus $0.43 for FLARE and $4.58 for RFMix.

Local ancestry inference identifies robust evidence of selection in Neolithic Europe

Local ancestry methods on 176 imputed Neolithic genomes disagree on tract lengths; replicated meta-analysis supports selection at SLC24A5 and FADS1/2, while HLA signals look artefactual.

Sparse sampling and rare-variant depletion distort PCA visualizations of population structure: recovery with objective-guided manifold learning

Sparse or clustered sampling plus rare-variant filtering collapse PCA plots into triangles and three-ray patterns; objective-guided manifold learning on high-dimensional classic PC scores recovers obscured structure.

Rapid and robust sex determination from ancient enamel proteomes using protSexInferer

Using the share of AMELY-specific among all sex-specific amelogenin peptides (RAMELY), enamel proteomes are sexed consistently across four search engines, tolerating false-positive AMELY hits without manual checks.

{micro}CT Scanning Effects on DNA and a Multi-Step Workflow for Archaeological Petrous Bones

Fifty micro-CT-scanned archaeological petrous bones from Argentina did not differ significantly from 43 unscanned ones on six ancient DNA metrics, motivating a multi-step workflow that scans bones before destructive sampling.

The Genomic History Of Southeastern Europe

Ancient DNA from 223 people (12,000-500 BCE) reveals a west-east hunter-gatherer cline, largely unadmixed farmers, Caucasus-shifted Aegean farmers, and Balkan steppe ancestry almost 2,000 years early.

ATLAS: Analysis Tools for Low-depth and Ancient Samples

ATLAS, a C++ toolkit that models post-mortem damage when genotyping ancient or low-depth BAM data, avoided GATK's reference bias and made fewer errors at higher depth in simulations.

Identifying Y-chromosome haplogroups in arbitrarily large samples of sequenced or genotyped men

yHaplo walks the Y-chromosome tree with an error-tolerant breadth-first search, labelling the 1,244 1000 Genomes males in 20 seconds and matching every gold-standard call.