Neva C. Durand

The paper constructs a single-nucleus multi-omic atlas of adult human tissues, identifying regulatory elements and variant effects across 21 tissues.

This study uses CRUDO to show that cohesin and 3D contacts influence enhancer-promoter regulation, with distal enhancers showing stronger cohesin dependence.

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

This paper introduces a low-cost, high-throughput method for SARS-CoV-2 detection using whole genome sequencing, achieving high sensitivity and accuracy comparable to clinical tests.

ENCODE-rE2G, a classifier trained on K562 CRISPR perturbations, maps 13,455,443 enhancer-gene interactions across 352 biosamples, matching or exceeding prior models on CRISPR, eQTL, and GWAS benchmarks.

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 introduces PRINT, a deep learning method to correct chromatin accessibility data and analyze DNA-protein interactions, revealing structural and functional changes in cis-regulatory elements during hematopoiesis and aging.

The paper examines genome architecture changes during medaka gastrulation, finding that CTCF loops form while CTCF binding sites remain fixed, and transcription precedes mature domain formation.

The paper introduces CRISPRi-FlowFISH to perturb enhancers and an Activity-by-Contact model to predict enhancer-gene regulatory connections.

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

The paper introduces Hi-Culfite, a method combining Hi-C and WGBS to study chromatin contacts and DNA methylation together, revealing context-sensitive methylation patterns.

The paper uses Hi-C data to improve the genome assembly of Trifolium subterraneum, resulting in chromosome-length scaffolds covering 95% of the genome.

The paper identifies genetic variants affecting chromatin accessibility in T cells and links them to gene expression and autoimmune disease.

Juicebox.js is a cloud-based tool for visualizing Hi-C data, enabling users to explore and share 3D genome structures through an intuitive interface.

Point-and-click correction of misassemblies on Hi-C heatmaps, paired with the automated 3D-DNA pipeline, gave chromosome-length wombat, opossum and raccoon scaffolds from just short-insert DNA-Seq and in situ Hi-C reads.