ArticleBioinformatics (Oxford, England)2013
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Hybrid modelling of biological systems: current progress and future prospects.Briefings in bioinformatics · 2022Review
- Advances in flux balance analysis by integrating machine learning and mechanism-based models.Computational and structural biotechnology journal · 2021Review
- The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk.Frontiers in physiology · 2020Article
- Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease.Genes · 2019Review
- Towards dynamic genome-scale models.Briefings in bioinformatics · 2019Article
- Systems Biology Approaches Toward Understanding Primary Mitochondrial Diseases.Frontiers in genetics · 2019Review
- Article
- Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease.NPJ systems biology and applications · 2018Article
- Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology.BMC systems biology · 2017Article
- Systems Toxicology: Real World Applications and Opportunities.Chemical research in toxicology · 2017Article
- Predicting Drug Combination Index and Simulating the Network-Regulation Dynamics by Mathematical Modeling of Drug-Targeted EGFR-ERK Signaling Pathway.Scientific reports · 2017Article
- MUFINS: multi-formalism interaction network simulator.NPJ systems biology and applications · 2016Article
- Constraint Based Modeling Going Multicellular.Frontiers in molecular biosciences · 2016Review
- Synergistic interaction between lipid-loading and doxorubicin exposure in Huh7 hepatoma cells results in enhanced cytotoxicity and cellular oxidative stress: implications for acute and chronic care of obese cancer patients.Toxicology research · 2015Article
- Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease.World journal of gastroenterology · 2014Review
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4 authors.
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Abstract
motivationDynamic simulation of genome-scale molecular interaction networks will enable the mechanistic prediction of genotype-phenotype relationships. Despite advances in quantitative biology, full parameterization of whole-cell models is not yet possible. Simulation methods capable of using available qualitative data are required to develop dynamic whole-cell models through an iterative process of modelling and experimental validation.
resultsWe formulate quasi-steady state Petri nets (QSSPN), a novel method integrating Petri nets and constraint-based analysis to predict the feasibility of qualitative dynamic behaviours in qualitative models of gene regulation, signalling and whole-cell metabolism. We present the first dynamic simulations including regulatory mechanisms and a genome-scale metabolic network in human cell, using bile acid homeostasis in human hepatocytes as a case study. QSSPN simulations reproduce experimentally determined qualitative dynamic behaviours and permit mechanistic analysis of genotype-phenotype relationships. AVAILABILITY AND IMPLEMENTATION: The model and simulation software implemented in C++ are available in supplementary material and at http://sysbio3.fhms.surrey.ac.uk/qsspn/.
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