Tom van der Valk

G-ALN: a GPU-accelerated BWA-aln algorithm for palaeogenomics

G-ALN accelerates BWA-aln for ancient DNA analysis using GPU, achieving faster indexing and alignment speeds with identical output.

DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens

DNAharvester is a Nextflow pipeline designed to process highly degraded DNA from ancient specimens, improving authentic data recovery through modular workflows and contamination mitigation.

Lifestyle impacts the oral microbiome of Classical and Post-classical societies in Italy

This study examines how lifestyle differences between social classes in Classical and Post-classical Italy are reflected in their oral microbiomes, finding significant variations across time periods and social classes.

Genomic and Dietary Insights from Non-Invasive Sampling of Western Capercaillie in Tyresta National Park (Sweden)

This study uses genomic and dietary data from non-invasive samples to assess the genetic health and diet of a Western Capercaillie population in Sweden, finding low inbreeding but risks from small size and isolation.

The Impact of Reference Genome Divergence on Ancient DNA Damage Detection in Metagenomic Contexts

This study shows that reference genome divergence reduces the detectability of aDNA damage patterns in metagenomic data and introduces a correction method to improve damage signal recovery.

Disinfecting eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data

The paper presents a method to identify and mask microbial-like sequences in eukaryotic reference genomes to improve taxonomic inference from ancient environmental metagenomic data.

Multiplex-edited mice recapitulate woolly mammoth hair phenotypes

This study creates a multiplex-edited mouse model with woolly mammoth hair traits, showing curly and textured coats through gene modifications.

aMeta: an accurate and memory-efficient ancient Metagenomic profiling workflow

aMeta is a metagenomic profiling workflow that improves accuracy and reduces memory usage in ancient microbiome analysis.

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

GenErode provides a pipeline to analyze genomic erosion by comparing ancient and modern whole-genome re-sequencing data, producing standardized erosion indices.

Estimates of genetic load suggest frequent purging of deleterious alleles in small populations

The paper estimates genetic load in mammals and finds that species with small population sizes and low diversity have lower genetic load due to purging of deleterious alleles.

Competitive mapping allows to identify and exclude human DNA contamination in ancient faunal genomic datasets

The genome of the endangered dryas monkey provides new insights into the evolutionary history of the vervets

The paper uses whole genome sequencing of a Dryas monkey to show its evolutionary relationship with vervets and suggests the Congo River's dynamic history and the species' genetic resilience.

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies

This study quantifies index hopping rates on the Illumina HiSeqX platform and finds they are low, suggesting multiplexing does not significantly affect results compared to older platforms.