Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming.

ClustoCell reveals cell states and their markers from single-cell transcriptomes

Accurate identification of cell types and states is essential for reliable single-cell RNA-sequencing analyses, yet current methods remain sensitive to continuous biological states, data preprocessing choices, and reference selection. Here we present ClustoCell, a reference-free method that resolves cell identity using...

Multiplexed embryo profiling links cellular state to zygotic genome activation in single cells

The cell cycle phase is the major source of variability in transcription within a division cycle, and combining this with the analysis of key transcription factors and chromatin modifier state enables accurate prediction of transcriptional output during zygotic genome activation in individual cells.

Single-cell epigenomic profiling of H3K27ac reveals the dynamic changes of B cell driving inflammation-cancer transition

Transcriptomic and epigenomic analyses at the single-cell level are critical for demonstrating the composition and regulatory network within the tumor microenvironment. Though single-cell ATAC-seq is widely-used, it is insufficient to fully interpret the functional connections. Here, we performed scRNA-seq and H3K27ac...

A Framework for Analyzing the Epigenetic and Transcriptomic Landscape of Cancers Using Single-Cell Multiomic Data.

EXPRESS: Harnessing Single-Cell Gene Regulatory Networks for Precision Health.

Cellular diversity in multicellular organisms arises from the functional specialization of individual cells and the influence of both the local tissue microenvironment and external stimuli. Understanding this heterogeneity requires accurate characterization of cell types and the molecular dynamics that define them. In...

Recording proteome dynamics in the late-stage embryo at hour-timescale, spatial, and single-cell resolution with MEMBRYO

Cell fate during development is directed by new gene expression states that replace prior ones. When and where a protein is first translated, and how long it will remain in the cell, dictate the timing and extent of a gene’s phenotypic effect. Accessing protein synthesis and turnover information in the rapidly developi...