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Title: A Bayesian non-parametric mixed-effects model of microbial growth curves
Substantive changes in gene expression, metabolism, and the proteome are manifested in overall changes in microbial population growth. Quantifying how microbes grow is therefore fundamental to areas such as genetics, bioengineering, and food safety. Traditional parametric growth curve models capture the population growth behavior through a set of summarizing parameters. However, estimation of these parameters from data is confounded by random effects such as experimental variability, batch effects or differences in experimental material. A systematic statistical method to identify and correct for such confounding effects in population growth data is not currently available. Further, our previous work has demonstrated that parametric models are insufficient to explain and predict microbial response under non-standard growth conditions. Here we develop a hierarchical Bayesian non-parametric model of population growth that identifies the latent growth behavior and response to perturbation, while simultaneously correcting for random effects in the data. This model enables more accurate estimates of the biological effect of interest, while better accounting for the uncertainty due to technical variation. Additionally, modeling hierarchical variation provides estimates of the relative impact of various confounding effects on measured population growth.  more » « less
Award ID(s):
1651117
PAR ID:
10234578
Author(s) / Creator(s):
; ; ; ; ;
Editor(s):
Papin, Jason A.
Date Published:
Journal Name:
PLOS Computational Biology
Volume:
16
Issue:
10
ISSN:
1553-7358
Page Range / eLocation ID:
e1008366
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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