Simple mathematical models of gene regulatory dynamics
This book reviews the state of the art and the work conducted since the 1960s for the understanding of the dynamic behaviour of bacterial operons; it covers a broad range of models from simple examples such as repressible and inducible systems to more complicated, real-life ones, presented in the third part. The book is structured in three parts. It commences with a general introduction of deterministic modelling techniques such as inducible and repressible models for the prokaryotic gene regulation (in the first chapter) and other general dynamic considerations (in the second chapter). Here, the authors present the four main operon dynamics: no-control, inducible regulation, repressible regulation and bistable switches. The appearance of cell growth effects and the consequences of transcriptional or translational delays are also discussed; this part concludes with an overview on fast and slow variables. In the second part, the authors focus on the inclusion of noise in the regulatory models. First, the master equation approach is described (third chapter), with an emphasis on its relation to deterministic models and an evaluation of its stability. In the fourth chapter, intrinsic versus extrinsic noise effects are discussed with focus on the dynamics with bursting and the role of the Gaussian distributed noise on the molecular degradation rate. In the third part of the book, the authors present three examples, for which the mathematical model and the quantitative studies are included: the lactose operon pathway (Chapter 5), the tryptophan operon in \textit{E. coli} (Chapter 6) and the lysis-lysogeny switch in the \(\lambda\) phage. The book represents a systematic overview of the field, however, its style makes it accessible mainly to post graduates and established researchers. Nevertheless, the thorough approach based on both definitions, theorems and practical examples makes the book a reliable, self-contained, and comprehensive study.
- Modeling transcriptional control in gene networks -- methods, recent results, and future directions
- Mechanisms of gene regulation: Boolean network models of the lactose operon in \textit{Escherichia coli}
- Dynamic behavior in mathematical models of the tryptophan operon
- scientific article; zbMATH DE number 6308167
- Modeling and analysis of gene regulatory networks
- Mathematical modeling of the lambda switch: a fuzzy logic approach
- The combined effects of Feller diffusion and transcriptional/translational bursting in simple gene networks
- Theoretical study of the one self-regulating gene in the modified Wagner model
- Self-sustaining positive feedback loops in discrete and continuous systems
- Zero, one and two-switch models of gene regulation
- Operon dynamics with state dependent transcription and/or translation delays
- Deciphering environmental signal integration in \(\sigma^{54}\)-dependent promoters with a simple mathematical model
- Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage
- Mathematical model of GAL regulon dynamics in \textit{Saccharomyces cerevisiae}
- Limit theorems for generalized density-dependent Markov chains and bursty stochastic gene regulatory networks
- Mathematical models of gene expression
- Two-layer mathematical modeling of gene expression: incorporating DNA-level information and system dynamics
- Rule-based modeling of transcriptional attenuation at the tryptophan operon
- Mechanisms of gene regulation: Boolean network models of the lactose operon in \textit{Escherichia coli}
- Travelling fronts in time-delayed reaction-diffusion systems
- The \textit{lac} operon
- On a mathematical model of a repressilator
- Stochastic models of regulation of transcription in biological cells
- A spatial measure-valued model for chemical reaction networks in heterogeneous systems
- Order-of-mutation effects on cancer progression: models for myeloproliferative neoplasm
- Homeostasis in input-output networks: structure, classification and applications
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