Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A Multiple Alignment Algorithm for Metabolic Pathway Analysis Using Enzyme Hierarchy
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
Parameterized Algorithms and Hardness Results for Some Graph Motif Problems
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
Double iterative optimisation for metabolic network-based drug target identification
International Journal of Data Mining and Bioinformatics
A scale-free graph model based on bipartite graphs
Discrete Applied Mathematics
Parikh matching in the streaming model
SPIRE'12 Proceedings of the 19th international conference on String Processing and Information Retrieval
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The classic view of metabolism as a collection of metabolic pathways is being questioned with the currently available possibility of studying whole networks. Novel ways of decomposing the network into modules and motifs that could be considered as the building blocks of a network are being suggested. In this work, we introduce a new definition of motif in the context of metabolic networks. Unlike in previous works on (other) biochemical networks, this definition is not based only on topological features. We propose instead to use an alternative definition based on the functional nature of the components that form the motif. After introducing a formal framework motivated by biological considerations, we present complexity results on the problem of searching for all occurrences of a reaction motif in a network, and introduce an algorithm that is fast in practice in most situations. We then show an initial application to the study of pathway evolution.