The rapid increase of genome-wide datasets on gene expression, chromatin states, and
transcription factor (TF) binding locations offers an exciting opportunity to interpret the …

Mammalian chromosomes undergo varying degrees of compression to form three‐
dimensional genome structures. These three‐dimensional structures undergo dynamic and …

ChIA-PET2 is a versatile and flexible pipeline for analyzing different types of ChIA-PET data
from raw sequencing reads to chromatin loops. ChIA-PET2 integrates all steps required for …

In human cells, DNA is hierarchically organized and assembled with histones and DNA-
binding proteins in three dimensions. Chromatin interactions play important roles in genome …

Gene regulatory networks are now at the forefront of precision biology, which can help
researchers better understand how genes and regulatory elements interact to control …

The pairwise interaction between transcription factors (TFs) plays an important role in
enhancer-promoter loop formation. Although thousands of TFs in the human genome have …

Abstract The three-dimensional (3D) organization of the genome is intimately related to
numerous key biological functions including gene expression and DNA replication …

Background Interactions among transcription factors (TFs) and histone modifications (HMs)
play an important role in the precise regulation of gene expression. The context specificity of …

Chromatin interactions play essential roles in chromatin conformation and gene expression.
However, few tools exist to analyze the spatial density of regulatory chromatin interactions …

Background Chromosomal architecture, which is constituted by chromatin loops, plays an
important role in cellular functions. Gene expression and cell identity can be regulated by …