Dana Wyman

A novel method for predicting Lp(a) levels from routine outpatient genomic testing identifies those at risk of cardiovascular disease across a diverse cohort

This paper develops a method to predict Lp(a) levels from genomic data, combining SNV risk scores and KIV-2 repeat counts, and shows it improves risk prediction for cardiovascular disease in diverse populations.

The ENCODE4 long-read RNA-seq collection reveals distinct classes of transcript structure diversity

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 ENCODE Uniform Analysis Pipelines

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.

Long-TUC-seq is a robust method for quantification of metabolically labeled full-length isoforms

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

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantification

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.