Sean Mooney

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A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector(More)
Understanding protein function from its structure is a challenging problem. Sequence based approaches for finding homology have broad use for annotation of both structure and function. 3D structural information of protein domains and their interactions provide a complementary view to structure function relationships to sequence information. We have(More)
Massively parallel pyrosequencing is a high-throughput technology that can sequence hundreds of thousands of DNA/RNA fragments in a single experiment. Combining it with immunoprecipitation-based biochemical assays, such as cross-linking immunoprecipitation (CLIP), provides a genome-wide method to detect the sites at which proteins bind DNA or RNA. In a(More)
Architectural drift is a widely cited problem in software engineering, where the implementation of a software system diverges from the designed architecture over time causing architecture inconsistencies. Previous work suggests that this architectural drift is, in part, due to programmers lack of architecture awareness as they develop code. JITTAC is a tool(More)
Prediction of functionally important amino acids in protein structures is challenging problem in the area of protein function prediction. In the quest of looking for better machine learning approaches to address this problem, we have compared a support vector machine and a neural network trained with a particle swarm algorithm (PSO) to nonlinearly combine a(More)
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