Philip Ewels

This paper explores the use of LLM-based coding agents in scientific computing, presenting case studies in the life sciences and discussing their potential and challenges.

The paper identifies convergent and lineage-specific genomic changes in sugar-feeding birds through genome and transcriptome analyses, revealing adaptive mechanisms in metabolic pathways.

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

This paper discusses the adoption of Nextflow and nf-core frameworks to standardize bioinformatics pipelines, improving collaboration and interoperability across research communities.

This study benchmarks Nanopore long read RNA sequencing in human cell lines, showing improved isoform resolution compared to short reads.

This study uses linked-read whole-genome sequencing to detect structural variants and copy number variations in multiple myeloma, identifying both common and private variants that affect gene regulation and molecular classification.

Sarek provides a portable and reproducible workflow for analyzing germline and somatic variants from whole-genome sequencing data.

A peer-reviewed, community-run framework for Nextflow analysis pipelines, plus helper tooling, meant to make workflows portable and reproducible across institutions rather than tied to one cluster.

Bioconda provides a sustainable, comprehensive distribution of bioinformatics software using Conda for reproducible analysis across platforms.