Rapid advances in nanopore technologies for sequencing single long DNA and RNA
molecules have led to substantial improvements in accuracy, read length and throughput …

Cell type-specific gene expression relies on transcription factors (TFs) binding DNA
sequence motifs embedded in chromatin. Understanding how motifs are accessed in …

Epigenomic maps identify gene regulatory elements by their chromatin state. However,
prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate …

Long-read sequencing (LRS) technologies have provided extremely powerful tools to
explore genomes. While in the early years these methods suffered technical limitations, they …

Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied
characteristic of the eukaryotic genome. As active regulatory DNA elements are generally …

Extrachromosomal DNA (ecDNA) is a common mode of oncogene amplification but is
challenging to analyze. Here, we adapt CRISPR-CATCH, in vitro CRISPR-Cas9 treatment …

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 …

Studies of genome regulation routinely use high-throughput DNA sequencing approaches to
determine where specific proteins interact with DNA, and they rely on DNA amplification and …

Gene activation requires the cooperative activity of multiple transcription factors at cis-
regulatory elements (CREs). Yet, most transcription factors have short residence time …

Probing epigenetic features on DNA has tremendous potential to advance our
understanding of the phased epigenome. In this study, we use nanopore sequencing to …