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Transient and delay chemical master equations

Gorin, G.; Yoshida, S. R.; Pachter, L.

2022-12-21 biophysics
10.1101/2022.10.17.512599 bioRxiv
Show abstract

The serial nature of reactions involved in the RNA life-cycle motivates the incorporation of delays in models of transcriptional dynamics. The models couple a bursty or switching promoter to a fairly general set of Markovian or deterministically delayed monomolecular RNA interconversion reactions with no feedback. We provide numerical solutions for the RNA copy number distributions the models induce, and solve several systems with splicing and degradation. An analysis of single-cell and single-nucleus RNA sequencing data using these models reveals that the kinetics of nuclear export do not appear to require invocation of a non-Markovian waiting time.

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.