Kinetic Foundation of the Zero-Inflated Negative Binomial Model for Single-Cell RNA Sequencing Data

DOI10.1137/19M1253198zbMath1447.92182arXiv1911.00356OpenAlexW3030642589MaRDI QIDQ5113806

Chen Jia

Publication date: 17 June 2020

Published in: SIAM Journal on Applied Mathematics (Search for Journal in Brave)

Full work available at URL: https://arxiv.org/abs/1911.00356

zbMATH Keywords

overdispersionmultiscale modelingstochastic gene expressionmodel simplificationdropouttranscriptional bursting

Mathematics Subject Classification ID

Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45) Biochemistry, molecular biology (92C40) Protein sequences, DNA sequences (92D20)

Related Items

A Markovian arrival stream approach to stochastic gene expression in cells, Inference on autoregulation in gene expression with variance-to-mean ratio, Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms, Detailed balance, local detailed balance, and global potential for stochastic chemical reaction networks, Martingale structure for general thermodynamic functionals of diffusion processes under second-order averaging, A generalized moment-based method for estimating parameters of stochastic gene transcription

Uses Software

• DEseq
• MAST
• ZIFA
• powsimR
• zinbwave

Cites Work

• Elimination of intermediate species in multiscale stochastic reaction networks
• Multiple-scale stochastic processes: decimation, averaging and beyond
• Simplification of irreversible Markov chains by removal of states with fast leaving rates
• A unified statistical framework for single cell and bulk RNA sequencing data
• Markovian modelling of gene product synthesis
• Reduction of Markov chains with two-time-scale state transitions
• Analytical Results for a Multistate Gene Model
• Gene expression distribution deconvolution in single-cell RNA sequencing