ArticleAMB Express2011
Modeling formalisms in Systems Biology.
Article in AMB Express, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed.
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- Data-driven discovery of digital twins in biomedical research.Briefings in bioinformatics · 2026Review
- Molecular insights into heart field-specific cardiomyocyte differentiation - A computational study.PloS one · 2026Article
- Review
- Thermodynamically consistent, reduced models of gene regulatory networks.Royal Society open science · 2025Article
- Personalizing computational models to construct medical digital twins.Journal of the Royal Society, Interface · 2025Article
- Personalizing computational models to construct medical digital twins.bioRxiv : the preprint server for biology · 2024Article
- Towards a comprehensive assessment of QSP models: what would it take?Journal of pharmacokinetics and pharmacodynamics · 2024Review
- Maboss for HPC environments: implementations of the continuous time Boolean model simulator for large CPU clusters and GPU accelerators.BMC bioinformatics · 2024Article
- Microbiome modeling: a beginner's guide.Frontiers in microbiology · 2024Review
- Adapting modeling and simulation credibility standards to computational systems biology.Journal of translational medicine · 2023Review
- Leveraging quantum computing for dynamic analyses of logical networks in systems biology.Patterns (New York, N.Y.) · 2023Article
- Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives.Molecular metabolism · 2022Review
- Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.Briefings in bioinformatics · 2022Article
- Joint Realizability of Monotone Boolean Functions.Theoretical computer science · 2022Article
- Hybrid modelling of biological systems: current progress and future prospects.Briefings in bioinformatics · 2022Review
- Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network.PeerJ · 2022Article
- Modeling and Simulation of Cell Signaling Networks for Subsequent Analytics Processes Using Big Data and Machine Learning.Bioinformatics and biology insights · 2022Article
- Homology of process: developmental dynamics in comparative biology.Interface focus · 2021Article
12 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.