Dataset Information

Topological augmentation to infer hidden processes in biological systems.

ABSTRACT:

Motivation

A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables-usually molecules and their interactions. Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data.

Results

Topological augmentation starts from a simple model that is unable to explain the experimental data and augments its topology by adding new terms that capture the experimental behavior. This process is guided by representing the uncertainty in the model topology through stochastic differential equations whose trajectories contain information about missing model parts. We first apply this semiautomatic procedure to a pharmacokinetic model. This example illustrates that a global sampling of the parameter space is critical for inferring a correct model structure. We also use our method to improve our understanding of glutamine transport in yeast. This analysis shows that transport dynamics is determined by glutamine permeases with two different kinds of kinetics. Topological augmentation can not only be applied to biochemical systems, but also to any system that can be described by ordinary differential equations.

Availability and implementation

Matlab code and examples are available at: http://www.csb.ethz.ch/tools/index

SUBMITTER: Sunnaker M

PROVIDER: S-EPMC3892687 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Publications

Topological augmentation to infer hidden processes in biological systems.

Sunnåker Mikael M Zamora-Sillero Elias E López García de Lomana Adrián A Rudroff Florian F Sauer Uwe U Stelling Joerg J Wagner Andreas A

Bioinformatics (Oxford, England) 20131202 2

<h4>Motivation</h4>A common problem in understanding a biochemical system is to infer its correct structure or topology. This topology consists of all relevant state variables-usually molecules and their interactions. Here we present a method called topological augmentation to infer this structure in a statistically rigorous and systematic way from prior knowledge and experimental data.<h4>Results</h4>Topological augmentation starts from a simple model that is unable to explain the experimental ...[more]

PMID: 24297519

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Dataset Information

Topological augmentation to infer hidden processes in biological systems.

Motivation

Results

Availability and implementation

Publications

Topological augmentation to infer hidden processes in biological systems.

Similar Datasets

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