Reconstructing chemical reaction networks: data mining meets system identification
Proceedings of the 14th ACM SIGKDD international conference on Knowledge discovery and data mining
An Introduction to Metabolic Networks and Their Structural Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Metabolic network analysis demystified
RECOMB'11 Proceedings of the 15th Annual international conference on Research in computational molecular biology
Under-Approximating cut sets for reachability in large scale automata networks
CAV'13 Proceedings of the 25th international conference on Computer Aided Verification
Counting inequivalent monotone Boolean functions
Discrete Applied Mathematics
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Motivation: Structural studies of metabolic networks yield deeper insight into topology, functionality and capabilities of the metabolisms of different organisms. Here, we address the analysis of potential failure modes in metabolic networks whose occurrence will render the network structurally incapable of performing certain functions. Such studies will help to identify crucial parts in the network structure and to find suitable targets for repressing undesired metabolic functions. Results: We introduce the concept of minimal cut sets for biochemical networks. A minimal cut set (MCS) is a minimal (irreducible) set of reactions in the network whose inactivation will definitely lead to a failure in certain network functions. We present an algorithm which enables the computation of the MCSs in a given network related to user-defined objective reactions. This algorithm operates on elementary modes. A number of potential applications are outlined, including network verifications, phenotype predictions, assessing structural robustness and fragility, metabolic flux analysis and target identification in drug discovery. Applications are illustrated by the MCSs in the central metabolism of Escherichia coli for growth on different substrates. Availability: Computation and analysis of MCSs is an additional feature of the FluxAnalyzer (freely available for academic users upon request, special contracts for industrial companies; see web page below). Supplementary information: http://www.mpi-magdeburg.mpg.de/projects/fluxanalyzer