Meenakshi S. Kagda

The paper presents ENCODE4 Segway annotations for 234 human cell types, improving sensitivity in capturing regulatory patterns relevant to disease and traits.

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.

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 updates RegulomeDB to improve non-coding variant annotation by integrating new functional genomic data and probabilistic scores from the SURF algorithm.

The paper shows TART-A transposon captures nxf2 sequence to target it for piRNA-mediated repression, revealing antagonistic co-evolution with the host.