Computing knock out strategies in metabolic networks

TL;DR

This paper presents improved algorithms for identifying minimal reaction knockouts in metabolic networks, enhancing efficiency in blocking specific network behaviors by leveraging elementary modes.

Contribution

It introduces new algorithms that compute knock out sets more efficiently, especially when elementary modes are known, and directly from network descriptions with better worst-case complexity.

Findings

Algorithms outperform existing methods in computational efficiency.

Effective computation of knock out strategies demonstrated on metabolic networks.

Provides practical tools for metabolic network analysis.

Abstract

Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of these knock out sets when the elementary modes (minimal functional subsystems) of the network are given. We also describe an algorithm which computes both the knock out sets and the elementary modes containing the blocked reactions directly from the description of the network and whose worst-case computational complexity is better than the algorithms currently in use for these problems. Computational results are included.