Making Sure Research Computes
Suppose you were trying to determine the genes that code for the proteins that regulate the body's response to hypoxia, or oxygen deprivation, in solid tumors. (You'd be doing that because cancer can create oxygen-starved areas in tumors, and most solid tumors are more resilient to oxygen deprivation than healthy organs. The body's response to hypoxia thus can contribute to malignancy and offer a pathway to treatment; turn off the tumor cells' ability to adapt to hypoxia and you could kill the tumor.)
Suppose further that you were looking for clues to treatment in the genome of an organism that survives severe and prolonged hypoxia better than humans can - say a particular strain of Drosophila, the common fruit fly. What's the exact mechanism the fly uses? Which genes get switched on or off? What if changes occur in covariant amino acid sites on the protein (that is, when one changes, so does the other)? And how do those changes dictate secondary and tertiary sequences of the proteins they construct?
What's going on is so complex that it's all but impossible for a solitary scientist to figure out without expert computer help.
Enter two new fields: bioinformatics, which involves compiling and maintaining the database of biological information that has erupted since the dawn of genomics, and computational biology, which is the art and skill of analyzing and interpreting those data.
Enter, also, researchers like Vincent Xue (Macaulay Honors College at Hunter College, BA in computer science, minor in biology, 2012).
The National Science Foundation has awarded Xue a coveted 2012 Graduate Research Fellowship to pursue bioinformatics and computational biology. This is the most prestigious award a graduate student in the STEM disciplines (science, technology, engineering and mathematics) can receive. Providing up to $126,000 over three years, it recognizes and supports exceptional students who have proposed graduate-level research projects in their field.
Xue will begin his doctoral work at Massachusetts Institute of Technology in the fall. "Their biology and computational science faculty are definitely at the top," he says. "I intend to do both wet and dry lab. I want to be doing the experiments as well as the analysis. It's essential for biologists to have a strong computational component and knowledge." He intends to work on gene therapy.
He says that his experience at Hunter College has prepared him well. The questions about hypoxia resistance in Drosophila arose from the computational biology lab of Professor Lei Xie. To better understand the mechanisms behind hypoxia, Xue developed a Web tool to analyze and visualize the effect of correlated amino acid mutations on protein structure.
Xue's introduction to the field was in the Evolutionary Bioinformatics Laboratory of Associate Professor of Biology Weigang Qiu, who is interested in the comparative analysis of multiple genomes of the Lyme disease pathogen. "He introduced me to bioinformatics, and I fell in love with it."
In his sophomore year, Xue was invited to a computational biology winter workshop at MIT. The following summer, at the MIT Summer Research Program, he developed a visualization tool to analyze gene splicing.
Macaulay Honors College was "a huge factor in my decision to come to CUNY," Xue says. Besides the financial incentive of free tuition, there was the Opportunities Fund. It provides each student with $7,500 for travel, living expenses and a stipend during internships, fieldwork, research and other educational experiences.
In his junior year, Xue used his Opportunities allocation during a seven-month internship as a trainee at the European Bioinformatics Institute in Hinxton, near Cambridge, U.K. There, he developed a Web application and did high-performance computing. "The experience was one of the most informative and enlightening of my four years," he says.