Computational Biology

Computational analysis in cancer exome sequencing.

Exome sequencing in cancer is a powerful tool for identifying mutational events across the coding region of human genes. Here, we describe computational methods that use exome sequencing reads from cancer samples to identify somatic single nucleotide …

Adjusting for background mutation frequency biases improves the identification of cancer driver genes.

A common goal of tumor sequencing projects is finding genes whose mutations are selected for during tumor development. This is accomplished by choosing genes that have more non-synonymous mutations than expected from an estimated background mutation …

Semantic web data warehousing for caGrid.

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data …

Integrative analysis of epigenetic modulation in melanoma cell response to decitabine: clinical implications.

Decitabine, an epigenetic modifier that reactivates genes otherwise suppressed by DNA promoter methylation, is effective for some, but not all cancer patients, especially those with solid tumors. It is commonly recognized that to overcome resistance …

Introducing meta-services for biomedical information extraction.

We introduce the first meta-service for information extraction in molecular biology, the BioCreative MetaServer (BCMS; http://bcms.bioinfo.cnio.es/). This prototype platform is a joint effort of 13 research groups and provides automatically generated …

Overview of BioCreative II gene normalization.

BACKGROUND: The goal of the gene normalization task is to link genes or gene products mentioned in the literature to biological databases. This is a key step in an accurate search of the biological literature. It is a challenging task, even for the …

The BiolAD-DB system : an informatics system for clinical and genetic data.

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex …

Term identification in the biomedical literature.

Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is …