DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …

INTRODUCTION Cancer is one of the leading causes of death worldwide. Although the 2%
of the human genome that encodes proteins has been extensively studied, much remains to …

The human body contains thousands of unique cell types, each with specialized functions.
Cell identity is governed in large part by gene transcription programs, which are determined …

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to map
histone marks and transcription factor binding throughout the genome. Here we present …

Methods for single-cell genome and transcriptome sequencing have contributed to our
understanding of cellular heterogeneity, whereas methods for single-cell epigenomics are much …

Genomic datasets are often interpreted in the context of large-scale reference databases.
One approach is to identify significantly overlapping gene sets, which works well for gene-…

Complex patterns of cell-type–specific gene expression are thought to be achieved by
combinatorial binding of transcription factors (TFs) to sequence elements in regulatory regions. …

Sequencing of cell-free DNA in the blood of cancer patients (liquid biopsy) provides
attractive opportunities for early diagnosis, assessment of treatment response, and minimally …

Glioblastoma is characterized by widespread genetic and transcriptional heterogeneity, yet
little is known about the role of the epigenome in glioblastoma disease progression. Here, …

Regulatory elements recruit transcription factors that modulate gene expression distinctly
across cell types, but the relationships among these remains elusive. To address this, we …