August 22, 2011

University Communications, UCI Features

Bioinformatics Boosters

By Rizza Barnes

Read the full story below or view it on the UCI website.

Click here to view photos of the summer program participants.

For aspiring computer engineer Anthony Hizon, spending the summer in a biological chemistry lab at UC Irvine’s School of Medicine was quite an eye-opener.

“Talking to the Ph.D. students in the lab gave me new ideas about my future,” says Hizon, one of seven participants in the newly launched UCI Biomedical Informatics Training Undergraduate Summer Research Program for community college students. “I’ve learned that bioinformatics is a viable career option for me, and I’m now thinking about going to graduate school.”

That sentiment is music to the ears of Pierre Baldi, Chancellor’s Professor of computer science at the Donald Bren School of Information & Computer Sciences and director of UCI’s Institute for Genomics & Bioinformatics. He says the BIT-SR program was created to acquaint students with an emerging field that pairs biology and computer science.

“Our main goal is to see students get excited about science in general,” says Baldi, who co-developed BIT-SR with Suzanne Sandmeyer, professor of biological chemistry; G. Wesley Hatfield, professor emeritus of microbiology & molecular genetics; and Debra Mauzy-Melitz, developmental & cell biology faculty member. “Even if just one student each summer decides to take a serious look at pursuing bioinformatics as a career because of this program, I think it will be all the more rewarding for our team.”

Involving both computer and wet lab work, BIT-SR kicked off in June and ended this month with a research symposium. Supported by a five-year, $400,000 National Institutes of Health grant, the program targets first-generation college students from low-income, historically underserved ethnic and racial backgrounds.

This year’s scholars hailed from Rio Hondo, Santa Ana and Santiago Canyon colleges; their research interests included computer science, electrical engineering, pharmacology and microbiology. Each participant worked with a graduate student and faculty adviser for eight weeks and presented findings at the concluding symposium.

In general, bioinformatics calls for experts in life sciences or computational mathematics, but those cross-trained in both areas are invaluable. Computational science has become particularly important to biological research because high-throughput technologies such as human genome sequencing are so data-intensive.

To give the BIT-SR scholars firsthand exposure to the experimental workflow of DNA sequencing, the Institute for Genomics & Bioinformatics co-hosted a daylong workshop Aug. 1 with UCI’s Genomics High-Throughput Facility, which performs next-generation sequence analysis for campus investigators.

At the workshop, students performed the first step of DNA sequencing — making a genomic library — and discussed the preparation for and challenges of a career in bioinformatics.

Hizon stayed on after the BIT-SR program’s conclusion to finish his work in Professor Bogi Andersen’s lab, where members are exploring potential causes of cancer during organ development. Because of his strong computer science background, Hizon was tasked with building a website to help the researchers more speedily process and evaluate DNA information culled from past studies.

“Currently, they’re using Excel to deal with huge data sets involving thousands of genes and 100-plus experiments. It can get very clunky,” he explains. “My goal is to create a website that lets them generate graphs and models in one or two minutes, so they can quickly analyze the data.”

Hizon, who’s headed to Stanford University this fall after attending classes at Rio Hondo and Santiago Canyon colleges, says the cross-training he received this summer — working in the computer lab and observing in the wet lab — has allowed for meaningful customization of the website.

“Even though I’m working on the computer science side of the project, I needed to get an understanding of what they were doing biologically to determine what kinds of data analysis I could provide,” he says. “As my mentors gave me information for my computer application to process, I actually understood what the data meant and where it came from.”

His principal mentor, Rachel Herndon, a doctoral student in the Department of Biological Chemistry, says Hizon’s addition to her group “has been an interesting experience. We’re a biology lab, and being able to work full time with a computer scientist has encouraged us to try different approaches to problem solving.”

“That’s the great thing about UCI’s Biomedical Informatics Training Program,” she says. “It gets computer scientists and biologists talking and collaborating.”

Computer science doctoral student Todd Johnson, who was paired this summer with Christopher Navarro of Santiago Canyon College on a function prediction project, says that serving as a BIT-SR mentor was also valuable in other ways.

“Through the course of my research, I sometimes fall down rabbit holes and go off on a tangent,” he says. “Not only did Chris produce good work, but having him here helped me stay focused.”

Those BIT-SR scholars not yet bound for a four-year university plan to spread the word about their summer experience when they return to community college.

“I will recommend the program to all my friends when I go back to Rio Hondo,” Min Liang says. “I feel really lucky to have been a part of this.”

— Rizza Barnes, Donald Bren School of Information & Computer Sciences


Bioinformatics Boosters