The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a
simple and scalable way to detect the unique chromatin landscape associated with a cell …

Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion,
which is characterized by reduced effector function and proliferation, and the expression of …

The recent development of experimental methods for measuring chromatin state at single-
cell resolution has created a need for computational tools capable of analyzing these …

Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …

In contrast to single-cell approaches for measuring gene expression and DNA accessibility,
single-cell methods for analyzing histone modifications are limited by low sensitivity and …

Genome-wide profiling of histone modifications can reveal not only the location and activity
state of regulatory elements, but also the regulatory mechanisms involved in cell-type …

Single-cell sequencing-based methods for profiling gene transcript levels have revealed
substantial heterogeneity in expression levels among morphologically indistinguishable …

Abstract We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an
epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in …

The recent development of spatial omics methods has enabled single-cell profiling of the
transcriptome and 3D genome organization with high spatial resolution. Expanding the …

DNA methylation is a key layer of epigenetic regulation. The deposition of methylation marks
relies on the catalytic activity of DNA methyltransferases (DNMTs), and their active removal …