A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models

DOI10.1007/s41965-020-00046-yzbMath1469.92053OpenAlexW3086251959WikidataQ115371019 ScholiaQ115371019MaRDI QIDQ1982975

Lucia Nasti, Roberta Gori, Roberto Barbuti, Paolo Milazzo

Publication date: 14 September 2021

Published in: Journal of Membrane Computing (Search for Journal in Brave)

Full work available at URL: https://doi.org/10.1007/s41965-020-00046-y

zbMATH Keywords

Petri netsgene regulatory networksBoolean networksreaction systemsmembrane systems

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Systems biology, networks (92C42) Biologically inspired models of computation (DNA computing, membrane computing, etc.) (68Q07)

Related Items (4)

Phenotype control of partially specified Boolean networks ⋮ A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks ⋮ Unnamed Item ⋮ Unnamed Item

Uses Software

• Bio-PEPA
• Virtual Cell
• BioTapestry

Cites Work

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• Investigating dynamic causalities in reaction systems
• Dynamically consistent reduction of logical regulatory graphs
• Spatial P systems
• An excursion in reaction systems: from computer science to biology
• Quorum sensing P systems
• Petri net modelling of biological regulatory networks
• Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation.
• Lectures on Petri nets. 1: Basic models. Advances in Petri nets
• Membrane systems with promoters/inhibitors
• Computing with membranes
• Analysis issues in Petri nets with inhibitor arcs
• Foundations of chemical reaction network theory
• Comparing different ODE modelling approaches for gene regulatory networks
• Attractor analysis of asynchronous Boolean models of signal transduction networks
• BioAmbients: an abstraction for biological compartments
• Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}
• Robustness and fragility of Boolean models for genetic regulatory networks
• Analysis for gene networks based on logic relationships
• A TOUR OF REACTION SYSTEMS
• DYNAMICAL PROBABILISTIC P SYSTEMS
• From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
• Specialized Predictor for Reaction Systems with Context Properties
• Modelling Biological Compartments in Bio-PEPA
• A Guide to Numerical Modelling in Systems Biology
• Hill Kinetics Meets P Systems: A Case Study on Gene Regulatory Networks as Computing Agents in silico and in vivo
• Abstract Interpretation of Cellular Signalling Networks
• Applications and Theory of Petri Nets 2004
• Computational Methods in Systems Biology
• Membrane Computing
• Computing preimages and ancestors in reaction systems

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