Richard S. Sandstrom

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 creates high-precision maps of DNase I hypersensitive sites across 733 human biosamples and develops a regulatory vocabulary to annotate regulatory DNA, concentrating disease-associated signals.

The paper maps transcription factor footprints across 243 human cell and tissue types, revealing their structure, function, and relationship to genetic variation and disease.

The paper creates a mouse regulatory DNA atlas by mapping DNase I hypersensitive sites across development and shows dynamic changes in regulatory elements and transcription factor activity.

This study demonstrates precise control of gene expression levels by targeting the KRAB repressor domain in human cells.