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 …

DNA sequencing has revolutionized medicine over recent decades. However, analysis of
large structural variation and repetitive DNA, a hallmark of human genomes, has been …

Gene expression is regulated by transcription factors that work together to read cis-
regulatory DNA sequences. The 'cis-regulatory code'—how cells interpret DNA sequences …

Data from both bulk and single-cell whole-genome DNA methylation experiments are under-
utilized in many ways. This is attributable to inefficient map** of methylation sequencing …

The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

Summary Long interspersed element 1 (L1) retrotransposons are implicated in human
disease and evolution. Their global activity is repressed by DNA methylation, but …

Single-cell chromatin accessibility sequencing (scATAC-seq) reconstructs developmental
trajectory by phenotypic similarity. However, inferring the exact developmental trajectory is …

Enhancers are cis-regulatory elements that can stimulate gene expression from distance,
and drive precise spatiotemporal gene expression profiles during development. Functional …

The epigenome—the chemical modifications and chromatin-related packaging of the
genome—enables the same genetic template to be activated or repressed in different …

Eukaryotic cells are thought to arrange nucleosomes into extended arrays with evenly
spaced nucleosomes phased at genomic landmarks. Here we tested to what extent this …