DNA sequencing – determining the precise order of nucleotides within a DNA molecule – is evolving rapidly. The sequencing of an organism’s entire genome that once took biologists months to map is now done in days.
These “next-generation” sequencing methods mean research breakthroughs for everything from the level of gene activity in developing tissues to identifying individual mutations in cancerous tumors. And the University of Oregon is now at the forefront for careers in this work, having launched the Bioinformatics Applied Masters Program.
Bioinformatics is the development and application of computational techniques for the collection, analysis, management and visualization of the tidal wave of biological data released through next-generation sequencing. The field combines biology, computers and math, said Andy Berglund, co-director of the new program.
“The new master’s program provides cross-disciplinary training to prepare graduates for today’s cutting-edge jobs in biotechnology, medical and pharmaceutical industries,” said Berglund, an associate professor in the Institute of Molecular Biology.
The 54-credit curriculum takes 15 months to complete and breaks into three components: training in all aspects of acquiring and analyzing next-generation sequencing during three intensive four-credit summer courses; three graduate-level electives taken during the fall, winter or spring; and six- to 12-month paid internships in an industrial, medical or academic setting.
Students get hands-on training in all aspects of next-generation sequencing, including the preparation of libraries from DNA or RNA; filtering and mapping of sequencing data; and analysis of genome assembly and differential gene expression.
The UO has partnered with companies and institutions to offer internships that range in salary from $2,000 to $3,600 per month and can lead to permanent positions in genomics.
“In our first year, every one of our six master’s students landed an internship position and our goal is to place every student in future years,” Berglund said. “Our goal for our partners is to provide potential employees with skill sets who can step in and contribute immediately to bioinformatics research projects.”
Adam Struck, a graduate chemistry student, said he’s used his training in bioinformatics to assist labs working with DNA- and/or RNA-sequencing.
“Although many labs are using these technologies, most do not have a designated bioinformaticist to analyze the data,” Struck said. “Because of this, I have been able to incorporate the bioinformatics program very well into my PhD training.”
The program will also support UO genomics research in other ways, added co-director Bill Cresko, an associate biology professor.
For example, members of the new META Center for Systems Biology – Microbial Ecology and Theory of Animals – will host four native Alaskan students each year from the University of Alaska.
The goal of the center is to better understand how humans and other animals live with microbes in our environment. The Alaskan native students and other center members will gain invaluable data in genomics and bioinformatics that advance this area.
“The Alaskan native students may even become candidates for the bioinformatics master's program," Cresko said.
The program makes participants competitive for positions in industry, academic, medical and government laboratories or admission to graduate and medical schools.
“The UO bioinformatics program is ushering through a new generation of student who will be highly effective at managing and analyzing ‘Big Data’ from next-generation sequencing projects,” said Jason Boone, vice president of Eugene-based Floragenex, a program partner that specializes in plant and animal genetic research.
John Letaw, a graduate biology student, expects to be one of those students. He sees career opportunities for people with the scientific and computational skills that the program cultivates.
“(Bioinformatics) is a burgeoning field and it’s one employers are interested in,” Letaw said. “There’s so much data to be sifted through.”