Calit2 Launches Prize Program to Encourage Bioinformatics Research by UCSD Undergraduates

By Doug Ramsey

San Diego, CA, February 3, 2005 -- Inaugurating a new awards program, the California Institute for Telecommunications and Information Technology (Calit2) at the University of California, San Diego will honor undergraduate students whose research in bioinformatics is accepted for publication in a peer-reviewed journal or conference proceeding. The first two Calit2 Undergraduate Bioinformatics Scholar Awards were announced yesterday at a research symposium on the UCSD campus.

Jacobs School of Engineering computer science senior Robin Friedman was cited for his research on protein sequence analysis; and J. Bradley Kohlenberg from the Chemistry department was honored for research on integrating human genetic and physical maps.

Both bioinformatics majors presented their work at the Feb. 2 symposium in the Center for Molecular Genetics auditorium in front of a crowd of roughly 60 undergraduate, graduate students and faculty. The Calit2-sponsored event showcased opportunities for UCSD undergraduates in bioinformatics research. 

Robin Friedman
Bioinformatics major Robin Friedman
talks about his research
honored with a Calit2 Undergraduate
Bioinformatics Scholar Award.
Length: 1:45

“A tremendous number of research opportunities in bioinformatics are available for undergraduate students at UCSD through the Undergraduate Bioinformatics Research Program website,” said Computer Science and Engineering assistant professor Eleazar Eskin (see link below), an organizer of the program. “Over 30 projects are listed, and the laboratories are spread all over campus, including research opportunities in Computer Science, Bioengineering, Biology and the School of Medicine.”

The Calit2 Undergraduate Bioinformatics Scholar Award will be presented periodically to each undergrad publishing a bioinformatics research paper. The amount of the award will vary to cover the expense of sending the student to the conference where the paper is presented.

Robin Friedman’s article, ‘Discrete profile alignment via constrained information bottleneck,’ was co-authored with Eskin, UCSD graduate student Sean O’Rourke, and Stanford post-doctoral researcher Gal Chechik. Presented in mid-December at the Neural Information Processing Systems (NIPS) conference in Vancouver, B.C., the research will be published in the Proceedings of Advances in NIPS. “We have focused on a discrete way to store protein profiles,” said Friedman. “We came up with this way to efficiently store them and then search for them through a database of these protein profiles.”

Friedman plans to graduate in the spring with a major in bioinformatics, and says the NIPS paper was an important asset when he applied to graduate schools. “When I was applying and then talking to the various schools, I was able to give them information about my publication,” said Friedman. “It certainly gives you something important to say in the interview.” Friedman is waiting to hear from several schools, but says MIT is his first choice.

Brad Kohlenberg

Chemistry and bioinformatics major
Brad Kohlenberg presents his
prize-winning research at the
undergrad symposium. Length: 1:57

Kohlenberg’s research was published in the journal Genome Research, one of the most prestigious research journals in bioinformatics. Since he still has another year of study at UCSD, he plans to continue working in Nicholas Schork’s Polymorphism Research Laboratory and continue his research. “Working in this lab has been the most academically rewarding thing that I have done,” said Kohlenberg. “It was cool working with and learning from Ph.D.s such as my mentor on the project, Caroline Nievergelt, and it gave me a good idea of what grad school is like.”

According to Eskin, much of the burden for making the undergraduate program work lies on the shoulders of graduate students in his lab, including Robin Friedman’s advisor, Sean O’Rourke. “Publications reflect very highly on the graduate students who are excellent undergraduate advisors,” said Eskin. “Advising and mentoring by graduate students are crucial parts of making undergraduate research successful, and Sean can take a lot of credit for guiding Robin in his research.”

The bioinformatics major is composed of students whose home departments are in Computer Science and Engineering, Bioengineering, Biology or Chemistry. Undergraduates from these departments can apply for entry into the bioinformatics major during the first four weeks of every quarter. The undergraduate research program in bioinformatics has a similar scope – underscored by the support of Calit2 on numerous projects. Calit2 hosts the HAP webserver (link below), an interactive software tool developed by Eskin’s group, and has committed funds to support the undergrad research symposium. “Given its mandate to promote interdisciplinary research and education,” noted Eskin, “Calit2 was the logical place to turn for support of these programs.”

Eleazar Eskin
Professor Eleazar Eskin outlines efforts to bring more undergraduates into bioinformatics research. Length: 1:50

“The institute has a made an important commitment to reinforcing research programs for undergraduates on the campus, including summer internships with members of the bioinformatics faculty,” said Ramesh Rao, Calit2’s division director at UCSD and a professor of Electrical and Computer Engineering in the Jacobs School. “We hope that the new bioinformatics awards will encourage more undergrads to commit not only to doing research in this field, but also to embarking on a career of publishing and academic advancement.”

The undergraduate research symposium – which Eskin hopes to turn into a quarterly event – is targeted at undergraduates from any of the four bioinformatics host departments (see above) who are not currently enrolled in the bioinformatics program. A 45-minute information session was followed by an informal reception and poster session to showcase the work of undergraduates already in the program. “We want other students on campus to be aware of all the exciting research opportunities that are available to them in this field,” said Eskin. “Participation in research projects can both significantly improve their chances of admittance into top graduate programs and also make them a much more attractive employment candidate.”

Senior Sergey Kushch already has his eye set on the next Calit2 Undergraduate Bioinformatics Scholar Award. The transfer student is expected to co-author a paper this quarter with graduate students Juan Rodriguez and Michael Sanders. His research focuses on predicting how human variation in genes affects protein function.

Media Contacts
Doug Ramsey, (858) 822-5825,

Related Links
Undergraduate Bioinformatics Research Program
HAP Webserver