Joshua Chuck Harrell

The paper evaluates exclusion set generation strategies in short-read sequencing, finding that pre-generated Blacklists are hard to reproduce and proposes sponge sequences as an alternative to reduce artifacts.

EpiTADformer uses epigenomic signal embeddings to detect TAD boundaries with higher resolution than Hi-C-based methods.

The paper introduces scHiCcompare, an R package for differential analysis of single-cell Hi-C data, improving detection of chromatin interactions across various conditions.

The paper provides exclusion region sets for T2T-CHM13, GRCm39, and other genomes through an R/Bioconductor package and API, offering unified access to curated genomic ranges.

This study evaluates the impact of mouse read removal and library preparation on Hi-C data quality in patient-derived xenografts, finding that library strategy has the largest effect.