Sorena Rahmanian

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.

This paper introduces Long-TUC-seq, a method combining metabolic labeling with long-read sequencing to reliably detect isoform-level transcription dynamics.

TALON annotates and counts full-length reads from PacBio or Nanopore in one framework; in mouse brain, 422 genes showed more novel-isoform reads than annotated ones.

The paper analyzes miRNA expression dynamics across mouse embryonic development, identifying tissue-specific clusters and their regulatory roles.