New Graduate Internship Program Builds Bridges Between DOE JGI, UC Merced
Days after presenting the results of his summer research at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science user facility, Keedrian Olmstead was back on campus at the University of California, Merced to start orientation as a first-year graduate student in the Quantitative Systems Biology (QSB) Group under the School of Natural Sciences (SNS).
During his eight weeks at the DOE JGI, Olmstead saw a few familiar faces, one of them belonged to his research adviser Axel Visel. Both Visel and another DOE JGI researcher, Zhong Wang, have adjunct faculty positions with the SNS, and Wang’s group was hosting another QSB graduate student, Travis Lawrence.
Olmstead and Lawrence were the first participants in the DOE JGI/University of California, Merced Genomics Distinguished Graduate Internship Program. Conceived by Wang and Visel, the program challenges UC Merced graduate students with individual projects at the DOE JGI that provide hands-on experience in cutting-edge genome research and apply experimental and computation tools to solve research problems. In Visel’s group, Olmstead worked with postdoctoral fellow Ben Cole on a project involving bacteria in Arabidopsis plant roots. At the same time, Lawrence worked with Nicole Johnson in Wang’s group on developing an algorithm for RNA-Seq assembly. RNA-Seq is a technique for profiling the small fraction of a genome that contains transcribed instructions for building and maintaining cells through the use of deep-sequencing technologies.
The internship program was born out of a conversation Wang had with UC Merced students. “After class, we met the graduate students and they said they’d like to come to JGI and learn cutting-edge technologies, but there was no mechanism for it,” he recalls. He arranged a meeting with the SNS dean, Juan Meza, who was very familiar with Berkeley Lab; he’d previously served as acting director of the Lab’s Computational Research Division and head of the High Performance Computing Research Department.
“It’s mutually beneficial,” Visel said of the internship program he co-directs with Wang and backed by both Meza and DOE JGI Director Eddy Rubin. “QSB faculty are active DOE JGI Community Science Program collaborators, and UC Merced has many talented graduate students working in genomics and neighboring areas, areas the JGI is interested in. JGI would like to tap into that talent pool. At the same time, this program expands and enriches the QSB program but giving students the opportunity to gain hands-on experience at a major sequencing center.”
The third member of the internship program’s oversight committee is QSB assistant professor Suzanne Sindi. “There is a large interest at UC Merced to establish connections to the labs,” she says. “As a faculty member with research interests in computational biology, I was especially intrigued by this program, as it will foster stronger connections between JGI and UC Merced.”
Sindi thinks the internship program offers a number of benefits to UC Merced graduate students. “First, there is the opportunity to conduct research at JGI. Ideally the research conducted would form a part of the students’ thesis,” she says. “Second, we want our students to gain the opportunity to see what research is like at JGI. After graduating from UC Merced, this experience will help them direct their career trajectories. Finally, we anticipate that as this program grows there will be a strong culture of cross-training and cross-collaboration between UC Merced and JGI. As such, this program will reach beyond the participating students and enrich the experience of our entire graduate program! At this point the focus has been on students in the QSB graduate program, but I believe that a student in any graduate program whose research interests and experiences overlap significantly with the goals of the program could be considered.”
Olmstead’s project focused on the genetic mechanisms of chemotaxis in the Arabidopsis microbiome, particularly, how bacteria can be driven toward compounds produced by the plant roots. He is now working in Fabian Filipp’s lab, which conducts cancer research.
Lawrence’s project had him developing a framework that would allow users to simultaneously run several programs for RNA-Seq assembly to determine which is best for the task at hand. “There are at least 30-40 programs and it is not clear which are the best to use,” he says. “Many academic labs don’t know how to analyze RNA-Seq data very well, sending it out to companies. I’ll take that knowledge back with me.” Now a second-year evolutionary biology student in David Ardell’s lab, he also took a long view of the opportunity. “I’m getting a picture of the amount of data that’s going to be generated at academic level in a few years as it’s getting closer to producing trillion base data sets on daily basis.”
As part of their learning experience, the students had to give a presentation on their data to a large group of DOE JGI researchers at the end of their internships, and are summarizing their data in a report. “QSB is grateful to the JGI-UC Merced Summer Internship Program for a successful launch this year, providing horizon-expanding opportunities to its students,” noted QSB Graduate Program Chair Ardell. He also noted that the two inaugural JGI-UC Merced Summer Internship Program alumni will present their research findings in a special and dedicated session of the QSB Fall Retreat that will take place on the UC Merced campus in late October or early November, at which time they will receive certificates.
With Olmstead and Lawrence back on campus, Visel and Wang are already looking forward to opening the graduate internship program to a new pool of applicants. “This is the first iteration of this program and we started small with just two people,” Visel says. “They were directly assigned to the two of us just to get the structure set up and collect the first round of feedback from the participants to learn how to improve in future years. Knowing that we can establish an eight-week program in which students are active members of our respective research groups program, we expect to grow this program and be able to offer a larger number of spots in the future.”