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Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates

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Dijkstra,  TMH
Department Protein Evolution, Max Planck Institute for Developmental Biology, Max Planck Society;

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Citation

Thijssen, B., Dijkstra, T., Heskes, T., & Wessels, L. (2018). Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates. Bioinformatics, 34(5), 803-811. doi:10.1093/bioinformatics/btx666.


Cite as: https://hdl.handle.net/21.11116/0000-000A-7D62-C
Abstract
Motivation: Computational models in biology are frequently underdetermined, due to limits in our capacity to measure biological systems. In particular, mechanistic models often contain parameters whose values are not constrained by a single type of measurement. It may be possible to achieve better model determination by combining the information contained in different types of measurements. Bayesian statistics provides a convenient framework for this, allowing a quantification of the reduction in uncertainty with each additional measurement type. We wished to explore whether such integration is feasible and whether it can allow computational models to be more accurately determined.

Results: We created an ordinary differential equation model of cell cycle regulation in budding yeast and integrated data from 13 different studies covering different experimental techniques. We found that for some parameters, a single type of measurement, relative time course mRNA expression, is sufficient to constrain them. Other parameters, however, were only constrained when two types of measurements were combined, namely relative time course and absolute transcript concentration. Comparing the estimates to measurements from three additional, independent studies, we found that the degradation and transcription rates indeed matched the model predictions in order of magnitude. The predicted translation rate was incorrect however, thus revealing a deficiency in the model. Since this parameter was not constrained by any of the measurement types separately, it was only possible to falsify the model when integrating multiple types of measurements. In conclusion, this study shows that integrating multiple measurement types can allow models to be more accurately determined.

Availability and implementation: The models and files required for running the inference are included in the Supplementary information.