Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Neuronal development in the human cerebral cortex is considerably prolonged compared
with that of other mammals. We explored whether mitochondria influence the species …

Drug resistance in cancer is often linked to changes in tumor cell state or lineage, but the
molecular mechanisms driving this plasticity remain unclear. Using murine organoid and …

Measurement of the location of molecules in tissues is essential for understanding tissue
formation and function. Previously, we developed Slide-seq, a technology that enables …

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

Current computational workflows for comparative analyses of single-cell datasets typically
use discrete clusters as input when testing for differential abundance among experimental …

RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-
sequencing data. It describes the rate of gene expression change for an individual gene at a …

The high-dimensional data created by high-throughput technologies require visualization
tools that reveal data structure and patterns in an intuitive form. We present PHATE, a …

The recent maturation of single-cell RNA sequencing (scRNA-seq) technologies has
coincided with transformative new methods to profile genetic, epigenetic, spatial, proteomic …