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BACKGROUND Experimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval. RESULTS The Ontology for Biomedical Investigations (OBI), developed as a global, cross-community(More)
MOTIVATION Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a(More)
MOTIVATION In silico methods provide efficient ways to predict possible interactions between drugs and targets. Supervised learning approach, bipartite local model (BLM), has recently been shown to be effective in prediction of drug-target interactions. However, for drug-candidate compounds or target-candidate proteins that currently have no known(More)
Multi-tier applications are widely deployed in today's virtualized cloud computing environments. At the same time, management operations in these virtualized environments, such as load balancing, hardware maintenance, workload consolidation, etc., often make use of live virtual machine (VM) migration to control the placement of VMs. Although existing(More)
The emerging open cloud computing model will provide users with great freedom to dynamically migrate virtualized computing services to, from, and between clouds over the wide-area. While this freedom leads to many potential benefits, the running services must be minimally disrupted by the migration. Unfortunately, current solutions for wide-area migration(More)
Several lines of evidence suggest that programmed cell death may play a role in the aging process and the age-related functional declines of multicellular organisms. To pave the way for the use of Drosophila to rigorously test this hypothesis in a genetic model organism, this work examines the pattern of apoptosis in the adult fly during aging. The analysis(More)
The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the(More)
MOTIVATION Expressed sequence tag (EST) databases have grown exponentially in recent years and now represent the largest collection of genetic sequences. An important application of these databases is that they contain information useful for the design of gene-specific oligonucleotides (or simply, oligos) that can be used in PCR primer design, microarray(More)
MOTIVATION Computational prediction of compound-protein interactions (CPIs) is of great importance for drug design and development, as genome-scale experimental validation of CPIs is not only time-consuming but also prohibitively expensive. With the availability of an increasing number of validated interactions, the performance of computational prediction(More)
BACKGROUND Cellular response to external stimuli requires propagation of corresponding signals through molecular signaling pathways. However, signaling pathways are not isolated information highways, but rather interact in a number of ways forming sophisticated signaling networks. Since defects in signaling pathways are associated with many serious(More)