Mark Frerker

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.