Single-cell trajectories can unveil how gene regulation governs cell fate decisions. However,
learning the structure of complex trajectories with multiple branches remains a challenging …

Summary Single-cell (sc) RNA-seq, together with RNA velocity and metabolic labeling,
reveals cellular states and transitions at unprecedented resolution. Fully exploiting these …

Transdifferentiation, the process of converting from one cell type to another without going
through a pluripotent state, has great promise for regenerative medicine. The identification of …

Here, we present Scribe (https://github. com/aristoteleo/Scribe-py), a toolkit for detecting and
visualizing causal regulatory interactions between genes and explore the potential for single …

Robust temporal and spatial patterns of cell types emerge in the course of normal
development in multicellular organisms. The onset of degenerative diseases may result from …

The Waddington epigenetic landscape has become an iconic representation of the cellular
differentiation process. Recent single-cell transcriptomic data provide new opportunities for …

Measurement of single-cell gene expression at different timepoints enables the study of cell
development. However, due to the resource constraints and technical challenges associated …

We estimate stochastic processes that govern the dynamics of evolving populations such as
cell differentiation. The problem is challenging since longitudinal trajectory measurements of …

Background Waddington's epigenetic landscape is an intuitive metaphor for the
developmental and evolutionary potential of biological regulatory processes. It emphasises …

Single-cell transcriptome sequencing now routinely samples thousands of cells, potentially
providing enough data to reconstruct causal gene regulatory networks from observational …