Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …

Recent progress in whole-genome map** and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Fit-Hi-C is a programming application to compute statistical confidence estimates for Hi-C
contact maps to identify significant chromatin contacts. By fitting a monotonically non …

We present Mustache, a new method for multi-scale detection of chromatin loops from Hi-C
and Micro-C contact maps. Mustache employs scale-space theory, a technical advance in …

HiChIP/PLAC-seq is increasingly becoming popular for profiling 3D chromatin contacts
among regulatory elements and for annotating functions of genetic variants. Here we …

Background Hi-C is currently the most widely used assay to investigate the 3D organization
of the genome and to study its role in gene regulation, DNA replication, and disease …

CD8 T cells play an essential role in defense against viral and bacterial infections and in
tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous …

Chromatin is organized into topologically associating domains (TADs) enriched in distinct
histone marks. In cancer, gain-of-function mutations in the gene encoding the enhancer of …

Linking distal enhancers to genes and modeling their impact on target gene expression are
longstanding unresolved problems in regulatory genomics and critical for interpreting …

In cancer cells, enhancer hijacking mediated by chromosomal alterations and/or increased
deposition of acetylated histone H3 lysine 27 (H3K27ac) can support oncogene expression …