Muhammad S. Shamim

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.

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 identifies cell type-specific chromatin loops anchored at large DNA methylation nadirs, revealing their role in stem and progenitor cell function.

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 provides multi-genomic maps of the EndoC-βH1 cell model to define gene regulatory programs in human pancreatic β cells and identifies allelic effects on cis-regulatory elements.

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

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.

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

The paper identifies multi-loop activation hubs during macrophage development using Hi-C data, showing they are enriched for AP-1 binding and driven by cell-type specific transcription factors.