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An approach is presented for computing meaningful pathways in the network of small molecule metabolism comprising the chemical reactions characterized in all organisms. The metabolic network is described as a weighted graph in which all the compounds are included, but each compound is assigned a weight equal to the number of reactions in which it(More)
Metabolic databases contain information about thousands of small molecules and reactions, which can be represented as networks. In the context of metabolic reconstruction, pathways can be inferred by searching optimal paths in such networks. A recurrent problem is the presence of pool metabolites (e.g., water, energy carriers, and cofactors), which are(More)
The analysis of a variety of data sets (transcriptome arrays, phylogenetic profiles, etc.) yields groups of functionally related genes. In order to determine their biological function, associated gene groups are often projected onto known pathways or tested for enrichment of known functions. However, these approaches are not flexible enough to deal with(More)
The aMAZE database (http://www.amaze.ulb.ac.be) manages information on the molecular functions of genes and proteins, their interactions and the biochemical processes in which they participate. Its data model embodies general rules for associating molecules and interactions into large complex networks that can be analysed using graph theory methods. The(More)
(2009). In response to "Can sugars be produced from fatty acids? A test case for pathway analysis tools". Retrieve-ensembl-seq: user-friendly and large-scale retrieval of single or multi-genome sequences from Ensembl. (2008). Machine learning techniques to identify putative genes involved in nitrogen catabolite repression in the yeast Saccharomyces(More)
Increasingly, immediate patient service--whether scheduling an appointment or seeing a physician--is a realistic expectation. Smoothing patient access and hitting service targets takes sophisticated planning and a true scientific approach. The department of medicine at Boston's Children's Hospital has taken a new approach to visit management, using a model(More)
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