Skip to main content
Premium Trial:

Request an Annual Quote

Outgrowing its Computer Science Roots, UCSC Bioinformatics Group Moves to New Dept.

Premium

The University of California Santa Cruz bioinformatics program is readying for a move to a new facility and a new department — and just in time: The group responsible for the UCSC genome browser has been tapped to coordinate all the sequence-related data for NHGRI’s ENCODE (Encyclopedia of DNA Elements) project, which just awarded its first round of grants on Oct. 9 (see brief, p. 8).

The bioinformatics group, currently housed in the computer science department of UCSC’s Baskin School of Engineering, has grown from two or three people in the pre-human-genome days to over 30 today, said David Haussler, who leads the program. Haussler said that the genome browser currently gets 140,000 page requests per day, and is supported around the clock. “It’s an enormous enterprise now,” he said. “We’re growing too much, too fast, and it would be disproportionate to the rest of the computer science department” to stay, he said.

In January, Haussler and five other UCSC faculty members will move to UCSC’s newly created department of biomolecular engineering, an interdisciplinary program that will combine computational science, engineering, nanotechnology, biology, and chemistry in a “true teaching department,” according to acting chair David Deamer. While there are a number of interdepartmental programs popping up at several US universities to address the challenges of integrated biology, Deamer said that UCSC is “among the first” to host a dedicated academic department in the field.

Jack Baskin, a retired engineer and philanthropist who helped launch the Baskin School of Engineering with a $5 million gift in 1997, has provided an additional $1 million to fund a new 90,000-square-foot engineering building and create an endowed chair in the department of biomolecular engineering. Deamer said the university is currently seeking candidates to fill the position of chair. The department will also double in size to around 14 faculty positions, he said.

Faculty in the new department will be developing a number of new technologies for sequencing, gene expression analysis, biodetection, and environmental monitoring, and new bioinformatics methods will be a core component of that work. “It means a lot to us to be able to have a home that provides the resources to grow in terms of space and laboratories,” Haussler said, but “the most exciting possibility is expanding some of our bioinformatics into more joint work with high-throughput laboratory methodologies.”

The UCSC bioinformatics team has already modified the genome browser to handle new types of functional data from the ENCODE project. “You should soon see a section for ENCODE tracks all ready and waiting for data,” he said. “We’re open for business.”

Haussler said that the depth of data from the project, which is functionally characterizing 1 percent of the human genome, should offer new opportunities for comparative genomics. “Each of these teams is going to work hard to produce their own data … but if it’s anything like what we’ve seen before, we’ll really learn a lot by putting them all together,” he said. “By juxtaposing them, cross-referencing them, and then starting to do some bioinformatics analysis that uses, say, all 12 ENCODE tracks, it leverages each project enormously.”

With a new home, a growing research team, and new data in the pipeline, Haussler is understandably enthusiastic about the future of bioinformatics at UCSC. “I’m like a kid in a candy store,” he said.

— BT

 

Filed under

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.