2009 CSL Undergraduate Summer Research Stipend Report
Aram Apyan | Evan Estola | Erik Harpstead | Jae Kwan Lee | Ryan McClure | Jesse Reinhardt | Peter Schemmel | Andrew Yates
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Evan Estola
Third-year undergraduate, Computer Science
Doug Cork
Professor of Biology
DEVELOPING W-CURVE TOOLS AND TECHNIQUES FOR STUDYING MOLECULAR BIOLOGY
Professor Cork researches such things as antibiotic resistance, the toxicity of Salmonella, and—most recently—the HIV-1 virus and its resistance to a vaccine. He developed the W-Curve algorithm to visualize and analyze long genomic sequences and infer the phylogenetic (evolutionary) history of a species. Instead of a string, the W-Curve describes DNA as a three-dimensional curve, making it easier to see patterns.
This summer, Evan built a live CD of the W-Curve so biologists can use it on any PC (which most prefer to Linux). Cork will give the CDs to researchers working on the HIV-1 virus at Walter Reed Army Research Hospital, where he is doing a sabbatical year with the U.S. Military HIV Research Program, Henry Jackson Foundation.
Evan also wrote a program to examine HIV strings by randomly mutating them and comparing them to a value set, drawing on knowledge from his advanced CS classes and work in the Information Retrieval Laboratory, and with help from graduate students. "The difference in speed for the W-Curve algorithm is ridiculous, absurdly useful," Evan noted.
The HIV virus replicates in so many different ways, it is difficult to find the patterns, and difficult to find the viral "ancestor"; being able to look at the trees in 3D might offer up new information.
"With HIV-1, the envelope gene of the virus hypermutates, leading to rapid changes in the envelope protein," said Cork. "Hopefully, with the W-Curve, we can correlate its 3D patterns with clinical symptoms that one monitors in the patient, related to neutralization of the virus."
A student from Grand Rapids, MI, Evan switched from biomedical engineering to computer science by his third semester, because he discovered he loved programming. Part of IIT's a capella singing community, he will graduate in December and may join Cork at Walter Reed, helping the biologists make the most of their computer tools.
Download the 2009 Undergraduate Summer Research Stipend report. (1 MB .pdf)
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