Apple Bioinformatics Award Winners

Dr. Simon Lin

Dr. Simon Lin (front row, second from the left) with Colleagues

Institution

Duke University Medical Center

Assignment

Manager, Duke Bioinformatics Shared Resource, Duke Comprehensive Cancer Center
Assistant Research Professor, Biostatistics and Bioinformatics

Scientific Discipline

Computational oncology

Challenge

Translating bioinformatics computing into medical practice with a goal of early cancer detection and personalized treatment.

Discoveries

In a collaboration with Drs. Huntington Willard and Katie Rudd, Dr. Lin used scientific visualization and statistical data mining to identify distinctive spatial patterns in the centromere regions of the genome.

Research

“The human genome is very big — three billion base pairs. But the coding region — the part that generates proteins — represents only about one or two percent of the genome. The non-coding region takes up the other 98 to 99 percent. Most people think it’s garbage because it doesn’t encode anything useful. But what is it doing there? We know it’s related to cancer and other diseases, so we want to understand what’s going on.”

“With high-throughput genomics and new technologies, we are seeing a trend of personalized medicine that results from computational analysis. More and more, we will use the computer to project a patient’s disease outcome, determine a diagnosis and identify the best treatment.”

Resources

Dr. Lin’s team includes Kim Johnson, director of Duke’s Bioinformatics Shared Resource; programmer Patrick McConnell; biostatistician Dr. Jennifer Shoemaker; and clinical researchers. He also plans to link the cluster to the National Cancer Institute’s open-source Bioinformatics Grid and the North Carolina BioGrid project.

Apple Workgroup Cluster for Bioinformatics

“Our lab will use the cluster as a bioinformatics tool to mine the non-coding region of the human genome, discover novel biomarkers for lung cancer from proteomics studies, personalize cancer care with computational predictions, and support the development of cancer vaccines via high-throughput screening.”

Why Apple?

“The turnkey solution from Apple and BioTeam will accelerate our research programs and help us break through bottlenecks in our existing computational structure.”