Armen Abnousi

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

The paper identifies combinatorial TF-cRE interactions in mouse basal ganglia development, revealing modules that drive GABAergic neurogenesis and suppress other fates.

The paper identifies a transcription factor network and enhancers involved in cortical regional patterning using mouse embryonic data.

HPRep quantifies reproducibility in HiChIP and PLAC-seq data by using a stratified and weighted correlation metric, outperforming existing Hi-C-based measures.

CRISPRpath enables parallel characterization of cis-regulatory elements for multiple genes in a pathway, identifying functional enhancers and distinguishing their impact on gene expression.

MUNIn identifies long-range chromatin interactions across multiple samples by accounting for sequencing depth and heterogeneity, achieving lower false positives and higher power for shared peaks.

HiC-ACT improves chromatin interaction detection from Hi-C data by post-processing independent methods, enhancing sensitivity while controlling type-I error.

FIREcaller detects frequently interacting regions from Hi-C data and shows their association with gene regulation and GWAS variants in human tissues.

SnapHiC identifies high-resolution chromatin loops from scHi-C data and demonstrates cell-type-specific chromatin architecture in mouse and human cells.

This study characterizes 3D epigenomic landscapes during human corticogenesis, revealing chromatin looping and super interactive promoters involved in lineage-specific gene regulation.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.