Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …

Over time, the human DNA methylation landscape accrues substantial damage, which has
been associated with a broad range of age-related diseases, including cardiovascular …

Somatic mutations are a hallmark of tumorigenesis and may be useful for non-invasive
diagnosis of cancer. We analyzed whole-genome sequencing data from 2,511 individuals in …

Cell-free DNA in the blood provides a non-invasive diagnostic avenue for patients with
cancer. However, characteristics of the origins and molecular features of cell-free DNA are …

Liver cancer is a major cause of cancer mortality worldwide. Screening individuals at high
risk, including those with cirrhosis and viral hepatitis, provides an avenue for improved …

Linking regulatory DNA elements to their target genes, which may be located hundreds of
kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies …

The minfi package is widely used for analyzing Illumina DNA methylation array data. Here
we describe modifications to the minfi package required to support the …

The innovation of biotechnologies has allowed the accumulation of omics data at an
alarming rate, thus introducing the era of 'big data'. Extracting inherent valuable knowledge …

Widespread changes to DNA methylation and chromatin are well documented in cancer, but
the fate of higher-order chromosomal structure remains obscure. Here we integrated …

Chromatin is folded into successive layers to organize linear DNA. Genes within the same
topologically associating domains (TADs) demonstrate similar expression and histone …