ArticleMolecular systems biology2013
Properties of cell death models calibrated and compared using Bayesian approaches.
Article in Molecular systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
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- Signal execution modes emerge in biochemical reaction networks calibrated to experimental data.iScience · 2024Article
- BioNetGMMFit: estimating parameters of a BioNetGen model from time-stamped snapshots of single cells.NPJ systems biology and applications · 2023Article
- Unified tumor growth mechanisms from multimodel inference and dataset integration.PLoS computational biology · 2023Article
- Model certainty in cellular network-driven processes with missing data.PLoS computational biology · 2023Article
- A biochemical necroptosis model explains cell-type-specific responses to cell death cues.Biophysical journal · 2023Article
- Mechanistic model of MAPK signaling reveals how allostery and rewiring contribute to drug resistance.Molecular systems biology · 2023Article
- Concepts of multi-level dynamical modelling: understanding mechanisms of squamous cell carcinoma development in Fanconi anemia.Frontiers in genetics · 2023Article
- Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit.Bioinformatics (Oxford, England) · 2022Article
- Automated model calibration with parallel MCMC: Applications for a cardiovascular system model.Frontiers in physiology · 2022Article
- Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Differentiable biology: using deep learning for biophysics-based and data-driven modeling of molecular mechanisms.Nature methods · 2021Review
- Bayesian modeling reveals metabolite-dependent ultrasensitivity in the cyanobacterial circadian clock.Molecular systems biology · 2020Article
- Joining and decomposing reaction networks.Journal of mathematical biology · 2020Article
- Dissecting Particle Uptake Heterogeneity in a Cell Population Using Bayesian Analysis.Biophysical journal · 2020Article
- Parallel Tempering with Lasso for model reduction in systems biology.PLoS computational biology · 2020Article
- Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.Cell systems · 2020Article
- A Probabilistic Approach to Explore Signal Execution Mechanisms With Limited Experimental Data.Frontiers in genetics · 2020Article
- Parameter Estimation and Uncertainty Quantification for Systems Biology Models.Current opinion in systems biology · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Using models to simulate and analyze biological networks requires principled approaches to parameter estimation and model discrimination. We use Bayesian and Monte Carlo methods to recover the full probability distributions of free parameters (initial protein concentrations and rate constants) for mass-action models of receptor-mediated cell death. The width of the individual parameter distributions is largely determined by non-identifiability but covariation among parameters, even those that are poorly determined, encodes essential information. Knowledge of joint parameter distributions makes it possible to compute the uncertainty of model-based predictions whereas ignoring it (e.g., by treating parameters as a simple list of values and variances) yields nonsensical predictions. Computing the Bayes factor from joint distributions yields the odds ratio (∼20-fold) for competing 'direct' and 'indirect' apoptosis models having different numbers of parameters. Our results illustrate how Bayesian approaches to model calibration and discrimination combined with single-cell data represent a generally useful and rigorous approach to discriminate between competing hypotheses in the face of parametric and topological uncertainty.
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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.