The reference human genome sequence set the stage for studies of genetic variation and
its association with human disease, but epigenomic studies lack a similar reference. To …

Genome-wide association studies have identified many noncoding variants associated with
common diseases and traits. We show that these variants are concentrated in regulatory …

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, …

The laboratory mouse shares the majority of its protein-coding genes with humans, making
it the premier model organism in biomedical research, yet the two mammals differ in …

… Significantly enriched regions were identified in both DNase I and glucocorticoid receptor
ChIP-seq datasets using a version of the Hotspot algorithm 31 (and Thurman et al., in …

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins,
which have an impact on cell differentiation, gene regulation and other key cellular …

Regulatory factor binding to genomic DNA protects the underlying sequence from cleavage
by DNase I, leaving nucleotide-resolution footprints. Using genomic DNase I footprinting …

Eukaryotic chromosomes replicate in a temporal order known as the replication-timing
program 1 . In mammals, replication timing is cell-type-specific with at least half the genome …

The large and growing number of genome-wide datasets highlights the need for high-performance
feature analysis and data comparison methods, in addition to efficient data storage …

The orchestrated binding of transcriptional activators and repressors to specific DNA sequences
in the context of chromatin defines the regulatory program of eukaryotic genomes. We …