Abstract Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) is widely
used in studying chromatin biology, but a comprehensive review of the analysis tools has …

The human gene catalogue is essentially complete, but we lack an equivalently vetted
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …

Over one million candidate regulatory elements have been identified across the human
genome, but nearly all are unvalidated and their target genes uncertain. Approaches based …

We present a major update of the HOCOMOCO collection that consists of patterns
describing DNA binding specificities for human and mouse transcription factors. In this …

Associations between genetic variation and traits are often in noncoding regions with strong
linkage disequilibrium (LD), where a single causal variant is assumed to underlie the …

A hallmark of metazoan evolution is the emergence of genomic mechanisms that implement
cell-type-specific functions. However, the evolution of metazoan cell types and their …

In certain human cancers, the expression of critical oncogenes is driven from large
regulatory elements, called super-enhancers, that recruit much of the cell's transcriptional …

Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful
are known to play pathophysiological roles in cancer. We inferred lncRNAs that dysregulate …

Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a strong
genetic basis. Yet, only a small fraction of potentially causal genes—about 65 genes out of …

Epigenetics refers to stable and long-term alterations of cellular traits that are not caused by
changes in the DNA sequence per se. Rather, covalent modifications of DNA and histones …