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Summary form only given. It is known that in the human immunodeficiency virus (HIV) genome regions responsible for interactions with the host's immune system, namely, cytotoxic T-lymphocyte (CTL) epitopes, tend to be clustered together, sometimes found in more conserved parts of genome. On the other hand, more variable regions tend to have lower density of CTL epitopes. Furthermore, high recombination...
An important goal for prostate cancer therapy is to identify novel mechanisms of androgen signaling that may provide new targets for androgen blockade therapy. Androgen regulated target genes continue to be identified, and include genes with regulatory regions containing 1) classical dimeric androgen receptor elements, or 2) sites for other transcription factors that tether androgen receptor to a...
In this paper, we propose a novel query-oriented, mediator-based biological data querying tool, SNPMiner. The system searches and queries single nucleotide polymorphisms (SNPs) data from eight widely used web accessible databases. The system provides a domain-specific search utility, which can access and collect data from the deep web. This is a web-based system, so any user can use the system by...
In this paper, we investigate a new approach for literature mining. We use frequent subgraph mining, and its generalization topological structure mining, for finding interesting relationships between gene names and other key biological terms from the text of scientific articles. We show how we can find keywords of interest and represent them as nodes of the graphs. We also propose several methods...
In this paper we present two different exploratory tools for data analysis following a gene microarray experiment. The first tool is based on a novel data mining formulation, called hypergraph mining. In the second tool, we provide a family of expectation based similarity measures between sets of genes or between a set and a single gene. We have evaluated these two tools using output from two different...
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