Harissa: stochastic simulation and inference of gene regulatory networks based on transcriptional bursting

DOI10.1007/978-3-031-42697-1_7arXiv2309.05112OpenAlexW4386548881MaRDI QIDQ6199817

Ulysse Herbach

Publication date: 28 February 2024

Published in: Computational Methods in Systems Biology (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/2309.05112

zbMATH Keywords

gene expressionregulatory networkssingle-cell data

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Software, source code, etc. for problems pertaining to biology (92-04) Systems biology, networks (92C42)

Cites Work

• Qualitative properties of certain piecewise deterministic Markov processes
• Reduction of a stochastic model of gene expression: Lagrangian dynamics gives access to basins of attraction as cell types and metastabilty
• Averaging and large deviation principles for fully-coupled piecewise deterministic Markov processes and applications to molecular motors
• Stochastic Gene Expression with a Multistate Promoter: Breaking Down Exact Distributions
• Some simple but challenging Markov processes

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