Paul R. Munn

This paper evaluates three agentic coding systems for constructing bioinformatics pipelines and finds they produce plausible but incomplete implementations requiring expert review.

BLink-seq is a scalable Haplotagging method for generating phased haplotypes and detecting structural variants in non-model species using short-read sequencing.

The paper develops CGAP-HMM and a voting system to improve transcription unit annotation from run-on and sequencing data, showing significant performance gains over existing methods.

This study uses single-nucleus multi-omics to analyze fibrolamellar carcinoma, revealing rewired cell communication and potential therapeutic targets.

The paper identifies gene regulatory programs distinguishing naive CD8+ T cell subsets using RNA-seq and ATAC-seq data, revealing novel regulators and transcriptional networks.

The paper examines evolutionary changes in ANTXR2 expression in humans, finding regulatory changes and recent positive selection linked to adaptation to anthrax disease.

This study shows that chromatin conformation remains stable during heat shock-induced transcriptional changes in human and Drosophila cells.