New Course at UCSD Prepares Undergraduates for Success in Bioinformatics Research

2.22.05 -- There is an almost festive atmosphere at the Tuesday meetings of UCSD undergraduates taking Eleazar Eskin's new course, "Research Training in Bioinformatics." The Computer Science and Engineering (CSE) professor organizes a group lunch that segues into a free-wheeling discussion among the students and their graduate-student advisors about the status of their respective research projects. Guest lecturers or Eskin then talk about the nuts and bolts of doing research and authoring papers, and the undergrads seem to appreciate the relaxed mood in the seminar. "It's much nicer to have a casual class like this one because it makes learning easier," says computer science major Grace Shaw, a junior.

Students participating in Eleazar Eskin's new course for undergrads working on bioinformatics research projects. Sitting (l-r): Jessica Chan. Chun (Jimmie) Ye (Bioinformatics Ph.D.), Grace Shaw, Tiffany Liang, Deborah Lee, Robin Friedman, Kevin Jung, Michael Sanders (Bioinformatics PhD), Jamal Benhamida, Professor Eleazar Eskin, and Dafna Bitton. Standing (l-r): Jeremy Chiu (CSE M.S.), Sandra Chau, Juan Rodriguez (Bioinformatics Ph.D.), Sergey Kushch, Jiwon Youm, Jim Hong, Taurin Tan-atichat, and Edward Shyu. (Students are undergraduate bioinformatics majors except where indicated.)

To be part of the class, each student must be working on an existing research project. Shaw is one of the undergrads working under the supervision of Hyun Min Kang, a Ph.D. student in CSE, on an independent project related to the HAP webserver (see link below). "We try to start with the easier projects such as working on a webserver first, then go on to the next level," notes grad student Kang.

The HAP webserver is an interactive website for scientists studying human variation - how genomes differ from one individual to another. Hosted by Calit2, the webserver was developed by Eskin as a tool to quickly translate genotype information (containing two copies of each chromosome) into haplotypes separately. A haplotype is the sequence of each chromosome.

Eskin's course covers relevant skills related to the students' projects. "They work closely on their projects under the supervision of graduate students who run the labs and do software demonstrations," explained Eskin. "We started out this quarter with mostly computer science students working in our lab, but, in the spring, the course will be open to any students participating in a research project in bioinformatics."

To enhance the ability of students to succeed on their respective projects, Eskin focuses on the basics of reading and understanding research papers, as well as a writing component about authoring articles for scientific journals. Many of the papers covered are recent publications from groups at UCSD -- with discussion on the papers led by the respective authors.

The class meets twice a week from 12:30 to 2 p.m., and the students get together one evening a week on their own to help each other and review material covered as a group. Currently a dozen students are enrolled in the course, but others in the bioinformatics program also attend.

The researchers range from 1st-year to 5th-year undergraduates. Freshman Dafna Bitton first became interested in research as a high-school intern at NASA. Bitton joined a research lab as early as possible in her college career, after contacting Eskin on the very first day of her first week at UCSD.

Deborah Lee is a sophomore in Bioengineering. "I am researching the genes that we study and then analyzing the data," she said. "I know I don't yet have the same skills as some of the other students, but the articles we're reading in class are really interesting. I just like it; it's cool!"

Several students are working on HAP or other webserver-related projects, including undergraduates Eddy Shyu, Taurin Tan-atichat and Tiffany Liang. 

"The students work on a wide variety of projects, and that keeps things interesting," said Eskin. Other projects include senior Kevin Jung's analysis of un-translated regions (UTRs) in C. elegans under the supervision of bioinformatics Ph.D. student Brian Haas; junior Jim Hong's research on analysis of Drosophila promoters; and Sandra Chau's analysis of genes suspected to be involved in hypertension. Concluded Eskin: "Most of these projects are just starting this quarter, but we hope that all will mature to a point where they lead to publication."

If so, the students in Eskin's class will receive a new award announced last week. The Calit2 Undergraduate Bioinformatics Scholar Award will cover the expense of sending each published undergrad to the scientific meeting where his or her research is presented.

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Related Links
Eleazar Eskin Laboratory

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