Devon Patrick Ryan

Correcting Methylation Calls in Clinically Relevant Low-Mappability Regions

The paper improves methylation calling by filtering reads in low-mappability regions, reducing mixed methylation calls in a clinical dataset.

Foxd3 controls heterochromatin-mediated silencing of repeat elements in mouse embryonic stem cells and represses the 2-cell transcription program

This study identifies FOXD3 as a regulator of repeat element transcription in mouse embryonic stem cells, showing it represses 2-cell state genes and repeat sequences by promoting heterochromatin formation.

snakePipes enable flexible, scalable and integrative epigenomic analysis

snakePipes provides a flexible, scalable pipeline for integrative epigenomic analysis across multiple assays, simplifying reproducibility and extending existing studies.

Parkour LIMS: facilitating high-quality sample preparation in next generation sequencing

Parkour is a web-based software package for managing next generation sequencing sample preparation workflows, improving efficiency and quality through automated tracking and staff assignment.

Community-driven data analysis training for biology

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

Ultra-parallel ChIP-seq by barcoding of intact nuclei

This paper introduces a method for ultra-parallelized ChIP-seq using barcoded intact nuclei, enabling high-throughput analysis of chromatin-associated proteins.