2008 CSL Undergraduate Summer Research Stipends
Kok Ann "Sam" Gan | Scott Justus | Susan Mallgrave | Emily Mick | Christos Mitillos | Yacin Nadji | Angela Pak | Yaofu Zhou
Yacin NadjiThird-year undergraduate, Computer Science Douglas CorkProfessor of Biology Tools for visualizing and analyzing molecular data |  | |
| Yacin brings computer power to biology. |
Today, computers are essential in molecular biology. But most biologists don't know a lot about computer science. Yacin bridges that gap in Professor Cork's lab. A research assistant in the Information Retrieval Laboratory since his freshman year, he also helps Cork's team use computers to understand how some bacteria cause disease.
Cork researches such things as antibiotic resistance at the genetic level in animal proteins, and why and how a cell turns on the protein that causes the toxicity of Salmonella or other bacteria — working with organizations like USA Poultry and pharmaceutical company Alpharma.
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," he explained. It also allows for fuzzy matching and can speed locating genes within chromosomes.
This summer, Yacin helped to develop a tool for the sequencing and clustering of prokaryotic DNA in phylogenic trees. Basic comparative genomic analysis involves alignment and analysis of linear strings of DNA (A, C, G, T). Many tools like BLAST already exist to search for similar strings of DNA. But they can't be used to visualize and analyze genomic patterns. "I generally ran visualizations based on the data the lab team found using more traditional techniques," said Yacin. "For example, the lab group did a BLAST search of a specific protein, and gave me the results from the search. I got the visualizations for them to compare to the BLAST search that they initially did."
Yacin liked that he "could do the work almost anywhere, like the park," but he went to the lab regularly to talk to the biologists. An avid participant in computer science groups and competitions, Yacin now also loves research and plans to get a PhD and teach.
Photographer: Mindy Sherman, IIT Communications & Marketing
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