Cancer stem cells (CSCs) often exhibit stem-like attributes that depend on an intricate
stemness-promoting cellular ecosystem within their niche. The interplay between CSCs and …

Abstract Motivation Cell–cell interactions (CCIs) consist of cells exchanging signals with
themselves and neighboring cells by expressing ligand and receptor molecules and play a …

Spatially resolved transcriptomics technologies have opened new avenues for
understanding gene expression heterogeneity in spatial contexts. However, existing …

Many single cell RNA-sequencing (scRNA-seq) data analysis workflows rely on methods
that embed and visualize the properties of a k-nearest neighbor (kNN) graph in two …

Advances in single-cell analysis have led to a picture of development largely in agreement
with Waddington's eponymous epigenetic landscape, in which a cell's fate is determined by …

Cellular anatomy and signaling vary across niches, which can induce gradated gene
expressions in subpopulations of cells. Such spatial transcriptomic gradient (STG) makes a …

Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with
respect to cell type composition. We present a method for identifying SHRs using spatial …