We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular …
Non-Markovian models of stochastic biochemical kinetics often incorporate explicit time delays to effectively model large numbers of intermediate biochemical processes. Analysis …
Here we present biVI, which combines the variational autoencoder framework of scVI with biophysical models describing the transcription and splicing kinetics of RNA molecules. We …
Saccharomyces cerevisiae has a sophisticated signalling system that plays a crucial role in cellular adaptation to changing environments. The SNF1 pathway regulates energy …
The question of how cell-to-cell differences in transcription rate affect RNA count distributions is fundamental for understanding biological processes underlying transcription …
Noise in gene expression is one of the hallmarks of life at the molecular scale. Here we derive analytical solutions to a set of models describing the molecular mechanisms …
S Luo, Z Wang, Z Zhang, T Zhou… - Nucleic Acids …, 2023 - academic.oup.com
Gene expression in mammalian cells is highly variable and episodic, resulting in a series of discontinuous bursts of mRNAs. A challenge is to understand how static promoter …
Accessing information on an underlying network driving a biological process often involves interrupting the process and collecting snapshot data. When snapshot data are stochastic …
Gene expression models, which are key towards understanding cellular regulatory response, underlie observations of single-cell transcriptional dynamics. Although RNA …