J. Seth Strattan

Long-read sequencing of 81 human and mouse samples yields 200,000 full-length transcripts plus a triplet framework that separates promoter choice, splicing and 3' end use across tissues.

The paper evaluates 23 imputation models for cross-cell type epigenomic data, finding quality assessment challenging due to distributional shifts, data availability, and redundant metrics.

ENCODE's containerised Workflow Description Language pipelines for ChIP-seq, ATAC-seq, DNase-seq, RNA-seq variants, Hi-C and bisulfite sequencing run on cloud or local clusters, with documented compute costs and provenance.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper quantifies privacy leakage in functional genomics data and proposes a data-sanitization protocol to reduce it while preserving utility.

The paper systematically maps chromatin state landscapes during mouse development by profiling histone modifications across 72 tissue-stages, identifying dynamic enhancers and transcriptional regulators.