Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

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 …

Although circulating tumor DNA (ctDNA) assays are increasingly used to inform clinical
decisions in cancer care, they have limited ability to identify the transcriptional programs that …

Abstract The Cistrome Data Browser (DB) is a resource of human and mouse cis-regulatory
information derived from ChIP-seq, DNase-seq and ATAC-seq chromatin profiling assays …

Immune checkpoint blockade (ICB) therapy revolutionized cancer treatment, but many
patients with impaired MHC-I expression remain refractory. Here, we combined FACS-based …

Liver fibrosis is a strong predictor of long-term mortality in individuals with metabolic-
associated fatty liver disease; yet, the mechanisms underlying the progression from the …

Abstract We present Model-based AnalysEs of Transcriptome and RegulOme (MAESTRO),
a comprehensive open-source computational workflow (http://github. com/liulab …

Summary H3K9me3, as a hallmark of heterochromatin, is important for cell-fate specification.
However, it remains unknown how H3K9me3 is reprogrammed during human early embryo …

Lineage plasticity, the ability of a cell to alter its identity, is an increasingly common
mechanism of adaptive resistance to targeted therapy in cancer. An archetypal example is …

Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-
associated proteins, but how these are causally connected to transcriptional activation is …