Properties of cell death models calibrated and compared using Bayesian approaches
Name
Eydgahi-2013-Properties of cell d.pdf
Size
1.5 MB
Format
Adobe PDF
Checksum (MD5)
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Author(s)
Eydgahi, Hoda
Chen, William W.
Muhlich, Jeremy L.
Vitkup, Dennis
Tsitsiklis, John N.
Sorger, Peter K.
Date Issued
February 2013
Journal
Molecular Systems Biology
Publisher
Nature Publishing Group
Citation
Eydgahi, Hoda et al. “Properties of Cell Death Models Calibrated and Compared Using Bayesian Approaches.” Molecular Systems Biology 9 (2013). ©2013 Nature Publishing Group
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution-Noncommercial-Share Alike 3.0
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DOI of Published Version
https://doi.org/10.1038/msb.2012.69
