Computing chemical organizations in biological networks
Bioinformatics
Enumerating Precursor Sets of Target Metabolites in a Metabolic Network
WABI '08 Proceedings of the 8th international workshop on Algorithms in Bioinformatics
An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Structures and hyperstructures in metabolic networks
WG'11 Proceedings of the 37th international conference on Graph-Theoretic Concepts in Computer Science
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The structural analysis of metabolic networks aims both at understanding the function and the evolution of metabolism. While it is commonly admitted that metabolism is modular, the identification of metabolic modules remains an open topic. Several definitions of what is a module have been proposed. We focus here on the notion of chemical organisations, i.e. sets of molecules which are closed and self-maintaining. We show that finding a reactive organisation is NP-hard even if the network is flux-consistent and that the hardness comes from blocking cycles. We then propose new algorithms for enumerating chemical organisations that are theoretically more efficient than existing approaches.