Querying of Disparate Association and Interaction Data in Biomedical Applications.

In biomedical applications, network models are commonly used to represent interactions and higher-level associations among biological entities. Integrated analyses of these interaction and association data has proven useful in extracting knowledge, and generating novel hypotheses for biomedical research. However, since most datasets provide their own schema and query interface, opportunities for exploratory and integrative querying of disparate data are currently limited.

COKGEN: a software for the identification of rare copy number variation from SNP microarrays.

Until fairly recently, it was believed that essentially all human cells harbor two copies of each locus in the autosomal genome. However, studies have now shown that there are segments of the genome that are polymorphic with regard to genomic copy number. These copy number variations (CNVs) have a role in various diseases such as Alzheimer disease, Crohn's disease, autism and schizophrenia.

An optimization framework for unsupervised identification of rare copy number variation from SNP array data.

Copy number variants (CNVs) have roles in human disease, and DNA microarrays are important tools for identifying them. In this paper, we frame CNV identification as an objective function optimization problem. We apply our method to data from hundreds of samples, and demonstrate its ability to detect CNVs at a high level of sensitivity without sacrificing specificity.

Pathways database system: an integrated system for biological pathways.

Motivation: During the next phase of the Human Genome Project, research will focus on functional studies of attributing functions to genes, their regulatory elements, and other DNA sequences. To facilitate the use of genomic information in such studies, a new modeling perspective is needed to examine and study genome sequences in the context of many kinds of biological information. Pathways are the logical format for modeling and presenting such information in a manner that is familiar to biological researchers.