Anna‐Sapfo Malaspinas

mixKIN improves kinship estimation from low-coverage genomes by accounting for ancestry, outperforming existing methods in admixed and heterogeneous populations.

This study uses 30 new palaeogenomes to show that Neolithic expansion into Western Anatolia involved both indigenous assimilation and eastern population influx, with cultural diversity decoupled from genetic differences.

This paper compares methods to reduce reference bias and postmortem damage in ancient genome data, finding that graph alignment and bamRefine improve accuracy and genotyped loci.

The paper introduces RESHAPE, a method to anonymize reference panels by simulating descendant genomes, enabling genotype imputation while protecting privacy.

This study evaluates how post-mortem damage and contamination affect imputation performance in ancient DNA, finding that ATLAS improves results for highly damaged genomes and contamination above 5% reduces accuracy.

This study evaluates the accuracy of genotype imputation for ancient genomes and finds it comparable to modern DNA, with some population-specific biases.

This study benchmarks metagenomics classifiers on simulated ancient viral DNA to identify the most effective tool for detecting human DNA viruses in degraded samples.

The paper sequences 24 ancient Brazilian genomes, including 22 Botocudos, revealing Indigenous American ancestry without external gene flow and low heterozygosity, and identifies ancient pathogen lineages.

This paper introduces a likelihood method to estimate present-day human contamination in ancient DNA samples using low-depth haploid chromosome data, showing improved accuracy compared to existing methods.

This study applies Y-chromosome capture-enrichment to ancient DNA libraries, showing increased recovery of Y-DNA sequences and enabling haplogroup assignment.