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NMR-Based Fragment Screening in a Minimum Sample but Maximum Automation Mode

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Finding MEMo: minimum sets of elementary flux modes.

Annika Röhl¹, Alexander Bockmayr²

¹Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, 14195, Berlin, Germany. annika.roehl@fu-berlin.de.

Journal of Mathematical Biology

|August 8, 2019

Summary

This study introduces Minimum Excluded Modes (MEMs), a novel approach to efficiently analyze metabolic networks. MEMs significantly reduce the number of elementary flux modes (EFMs) required to understand cellular metabolism, overcoming computational limitations.

Keywords:

Elementary flux modes Metabolic network Metabolic pathway analysis Minimal generating set Polyhedral cone Steady-state flux cone

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Area of Science:

Computational systems biology
Metabolic network analysis
Bioinformatics

Background:

Metabolic network reconstructions are crucial for in silico studies of cellular metabolism.
Elementary flux modes (EFMs) represent minimal functional units but are computationally challenging to enumerate for large networks.

Purpose of the Study:

To introduce and study Minimum Excluded Modes (MEMs) as a method to identify smaller, sufficient sets of EFMs.
To enable the analysis of metabolic networks where the complete set of EFMs is computationally intractable.

Main Methods:

Development and application of algorithms to identify MEMs.
Comparison of MEMs size with the total number of EFMs.

Main Results:

MEMs can be orders of magnitude smaller than the total set of EFMs.
This approach allows computation of generating sets of EFMs for previously intractable metabolic networks.

Conclusions:

MEMs provide a computationally feasible alternative to analyzing all EFMs in metabolic networks.
This method enhances the utility of metabolic network reconstructions for systems biology research.