Suhas S.P. Rao

Fast and accurate resolution of ecDNA sequence using Cycle-Extractor

Cycle-Extractor accurately reconstructs ecDNA structures from both short- and long-read sequencing data, outperforming existing methods in speed and completeness.

Cohesin-mediated 3D contacts tune enhancer-promoter regulation

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

A rapid, low cost, and highly sensitive SARS-CoV-2 diagnostic based on whole genome sequencing

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.

An encyclopedia of enhancer-gene regulatory interactions in the human genome

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.

Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when adjacent sequences do not

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

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.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

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

The Hi-Culfite assay reveals relationships between chromatin contacts and DNA methylation state

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.

Cohesin Loss Eliminates All Loop Domains, Leading To Links Among Superenhancers And Downregulation Of Nearby Genes

This study shows that cohesin loss eliminates loop domains, causing superenhancer links and gene downregulation, which are reversible upon cohesin restoration.