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With the explosive growth of genomic information, the searching of sequence databases has emerged as one of the most computation and data-intensive scientific applications. Our previous studies suggested that parallel genomic sequence-search possesses highly irregular computation and I/O patterns. Effectively addressing these runtime irregularities is thus the key to designing scalable sequence-search...
Computational problems associated with metabolic pathways have been extensively studied in computational biology. The problem of aligning multiple metabolic pathways is very challenging. Tohsato et al.'s algorithm for aligning multiple metabolic pathways is based on similarities between enzymes, however, a metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. In...
Community structure or clustering is ubiquitous in many evolutionary networks including social networks, biological networks and financial market networks. Detecting and tracking community deviations in evolutionary networks can uncover important and interesting behaviors that are latent if we ignore the dynamic information. In biological networks, for example, a small variation in a gene community...
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