Recent experimental developments in genome-wide RNA quantification hold considerable
promise for systems biology. However, rigorously probing the biology of living cells requires …

Idiopathic pulmonary fibrosis (IPF) is a progressive scarring disease arising from impaired
regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar …

Plant scientists are rapidly integrating single-cell RNA sequencing (scRNA-seq) into their
workflows. Maximizing the potential of scRNA-seq requires a proper understanding of the …

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

Abstract Alveolar epithelial type 1 (AT1) cells are necessary to transfer oxygen and carbon
dioxide between the blood and air. Alveolar epithelial type 2 (AT2) cells serve as a partially …

Dimensionality reduction is standard practice for filtering noise and identifying relevant
features in large-scale data analyses. In biology, single-cell genomics studies typically begin …

Deciphering the cell-state transitions underlying immune adaptation across time is
fundamental for advancing biology. Empirical in vivo genomic technologies that capture …

RNA velocity has been rapidly adopted to guide interpretation of transcriptional dynamics in
snapshot single-cell data; however, current approaches for estimating RNA velocity lack …

Individual cells within an otherwise genetically homogenous population constantly undergo
fluctuations in their molecular state, giving rise to non-genetic heterogeneity. Such diversity …

Single-cell RNA sequencing allows us to model cellular state dynamics and fate decisions
using expression similarity or RNA velocity to reconstruct state-change trajectories; however …