Colin Davenport

Wochenende - modular and flexible alignment-based shotgun metagenome analysis

Wochenende is a modular pipeline for shotgun metagenome analysis that improves alignment filtering and visualization for microbial taxonomy and functional gene analysis.

iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome

The paper analyzes mtDNA variants in iPSCs and finds that culture expansion selects against harmful mitochondrial mutations, while reprogramming and differentiation do not significantly alter mtDNA heteroplasmy.

MinION nanopore sequencing provides similar methylation estimates to Sanger bisulfite sequencing in the TRPA1 promoter region

Reprogramming enriches for somatic cell clones with small scale mutations in cancer-associated genes

The paper shows that reprogramming enriches for mutations in cancer-associated genes in hiPSCs, potentially increasing tumor risk.