A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
DOI10.1007/S41965-020-00046-YzbMATH Open1469.92053OpenAlexW3086251959WikidataQ115371019 ScholiaQ115371019MaRDI QIDQ1982975FDOQ1982975
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
Biochemistry, molecular biology (92C40) Systems biology, networks (92C42) Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.) (68Q85) Biologically inspired models of computation (DNA computing, membrane computing, etc.) (68Q07)
Cites Work
- Title not available (Why is that?)
- Title not available (Why is that?)
- Title not available (Why is that?)
- Title not available (Why is that?)
- Computing with membranes
- BioAmbients: an abstraction for biological compartments
- Investigating dynamic causalities in reaction systems
- A tour of reaction systems
- Spatial P systems
- An excursion in reaction systems: from computer science to biology
- Applications and Theory of Petri Nets 2004
- Computational Methods in Systems Biology
- Comparing different ODE modelling approaches for gene regulatory networks
- Abstract Interpretation of Cellular Signalling Networks
- Petri net modelling of biological regulatory networks
- Modeling the complexity of genetic networks: Understanding multigenic and pleiotropic regulation.
- From Petri Nets to Differential Equations – An Integrative Approach for Biochemical Network Analysis
- Lectures on Petri nets. 1: Basic models. Advances in Petri nets
- Robustness and fragility of Boolean models for genetic regulatory networks
- Dynamically consistent reduction of logical regulatory graphs
- The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in \textit{Drosophila melanogaster}
- Quorum sensing P systems
- DYNAMICAL PROBABILISTIC P SYSTEMS
- Analysis issues in Petri nets with inhibitor arcs
- Membrane systems with promoters/inhibitors
- Modelling Biological Compartments in Bio-PEPA
- Foundations of chemical reaction network theory
- Attractor analysis of asynchronous Boolean models of signal transduction networks
- Specialized Predictor for Reaction Systems with Context Properties
- Analysis for gene networks based on logic relationships
- Encoding Boolean networks into reaction systems for investigating causal dependencies in gene regulation
- 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
- Membrane Computing
- Computing preimages and ancestors in reaction systems
Cited In (7)
- Title not available (Why is that?)
- Title not available (Why is that?)
- The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model
- A kinetic finite volume discretization of the multidimensional PIDE model for gene regulatory networks
- Phenotype control of partially specified Boolean networks
- Compositional techniques for Boolean networks and attractor analysis
- Response to stress via underlying deep gene regulation networks
Uses Software
Recommendations
- Title not available (Why is that?) 👍 👎
- Modeling the dynamics of genetic regulatory networks: continuous and discrete approaches 👍 👎
- Title not available (Why is that?) 👍 👎
- Comparing different ODE modelling approaches for gene regulatory networks 👍 👎
- Title not available (Why is that?) 👍 👎
- The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model 👍 👎
- Modeling and Analysis of Gene Regulatory Networks 👍 👎
- Genetic Regulatory Networks and Co-Regulation of Genes: A Dynamic Model Based Approach 👍 👎
- Modeling transcriptional control in gene networks -- methods, recent results, and future directions 👍 👎
This page was built for publication: A survey of gene regulatory networks modelling methods: from differential equations, to Boolean and qualitative bioinspired models
Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q1982975)
