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

The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize
cellular heterogeneity. However, scRNA-seq requires lysing cells, which impedes further …

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

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

A fundamental goal of developmental and stem cell biology is to map the developmental
history (ontogeny) of differentiated cell types. Recent advances in high-throughput single …

Understanding the molecular programs that guide differentiation during development is a
major challenge. Here, we introduce Waddington-OT, an approach for studying …

The functions of epithelial tissues are dictated by the types, abundance and distribution of
the differentiated cells they contain. Attempts to restore tissue function after damage require …

We perform a thorough analysis of RNA velocity methods, with a view towards
understanding the suitability of the various assumptions underlying popular …