As the field of single-cell transcriptomics matures, research is shifting focus from
phenomenological descriptions of cellular phenotypes to a mechanistic understanding of the …

Over the past decade, high-throughput sequencing and high-resolution single-cell
transcriptome sequencing technologies have undergone rapid development, leading to …

Class-switch recombination (CSR) is an integral part of B cell maturation. Here we present
sciCSR (pronounced 'scissor', single-cell inference of class-switch recombination), a …

Assigning single cell transcriptomes to cellular lineage trees by lineage tracing has
transformed our understanding of differentiation during development, regeneration, and …

Highlights•Single-cell temporal transcriptomics expedites the study of cellular dynamics.•The
dynamics of a cell is inferred from the collective states of observed cells.•The inferred …

The development of a multicellular organism is a highly intricate process tightly regulated by
numerous genes and pathways in both spatial and temporal manners. Here, we present …

Single-cell atlases are critical for unraveling the cellular basis of health and disease, yet
their sheer diversity and vast data landscape in time and space pose daunting …

Phylodynamics inference (PI) is a powerful approach for quantifying population dynamics
and evolutionary trajectories of natural species based on phylogenetic trees. The …

In the context of transcriptional dynamics modeled by ordinary differential equations (ODEs),
the RNA level in a single cell is controlled by specific RNA kinetics parameters, which …

Reconstructing temporal cellular dynamics from static single-cell transcriptomics remains a
major challenge. Methods based on RNA velocity are useful, but interpreting their results to …