Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models

DOI10.1016/j.jtbi.2007.01.021zbMath1451.92143OpenAlexW2170467788WikidataQ51920734 ScholiaQ51920734MaRDI QIDQ2210114

Rui Zhu, Dennis Salahub, Andre S. Ribeiro, Stuart A. Kauffman

Publication date: 5 November 2020

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1016/j.jtbi.2007.01.021

zbMATH Keywords

time delaystochastic modelsBoolean networkssystems biologygenetic regulatory networks

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Related Items (16)

Evolving kinetics of gene expression in stochastic environments ⋮ Models of transcription factor binding: sensitivity of activation functions to model assumptions ⋮ Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch ⋮ Tuning cell differentiation patterns and single cell dynamics by regulating proteins' functionalities in a toggle switch ⋮ The regulation of gene expression in eukaryotes: bistability and oscillations in repressilator models ⋮ Stochastic and delayed stochastic models of gene expression and regulation ⋮ Bifurcation analysis of a mathematical model for genetic regulatory network with time delays ⋮ Stochastic gene expression with delay ⋮ Dynamics of small genetic circuits subject to stochastic partitioning in cell division ⋮ Bye bye, linearity, bye: quantification of the mean for linear CRNs in a random environment ⋮ Modeling synthetic gene oscillators ⋮ Super-transient scaling in time-delay autonomous Boolean network motifs ⋮ Noisy attractors and ergodic sets in models of gene regulatory networks ⋮ Applications of an expressive statistical model checking approach to the analysis of genetic circuits ⋮ Effects of elongation delay in transcription dynamics ⋮ Interplay of cellular states: role of delay as control mechanism

Uses Software

• Matlab
• Dizzy

Cites Work

• Gene expression time delays and Turing pattern formation systems
• A proposal for using the ensemble approach to understand genetic regulatory networks
• Effect of time delay on pattern formation: Competition between homogenisation and patterning
• Stochastic approaches for modelling in vivo reactions
• MESOSCOPIC DESCRIPTION OF CHEMICAL SUPERCRITICAL HOPF BIFURCATION
• Stability of genetic regulatory networks with time delay

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