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 …

Tumor microenvironment (TME) is a specialized ecosystem of host components, designed
by tumor cells for successful development and metastasis of tumor. With the advent of 3D …

Naïve CD8+ T cells can differentiate into effector (Teff), memory (Tmem) or exhausted (Tex)
T cells. These developmental pathways are associated with distinct transcriptional and …

Clonal hematopoiesis (CH), the clonal expansion of a blood stem cell and its progeny driven
by somatic driver mutations, affects over a third of people, yet remains poorly understood …

Recent technological advances have enabled massively parallel chromatin profiling with
scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here …

In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR)
dependence leads to clinically aggressive tumors with few therapeutic options. We used …

Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …

Computational trajectory inference enables the reconstruction of cell state dynamics from
single-cell RNA sequencing experiments. However, trajectory inference requires that the …

HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently
considered" transcriptionally silent," but active viral gene expression may occur in some …

The advent of single-cell chromatin accessibility profiling has accelerated the ability to map
gene regulatory landscapes but has outpaced the development of scalable software to …