Grant to support data processing in genetic research

by Erin Lee | 10/9/14 7:07pm

With a five-year, $1.5 million grant, Geisel School of Medicine professor Casey Greene will further his research in genomic data processing.

Greene, who was named a Moore Investigator in Data-Driven Discovery by the Gordon and Betty Moore Foundation earlier this month, said he plans to use the money to develop algorithms that can reveal patterns in genomic data and build web servers to share them with other biology labs. There are currently more than 1.5 million publicly available assays of gene expression, Greene said, and he hopes to develop techniques that will allow researchers to analyze this data and better understand biological mechanisms, such as genetic pathways related to cancer.

Greene is introducing deep learning, which involves data-processing techniques used in computer science for image and video processing, into biology and bioinformatics.

This approach incorporates methods from different disciplines, Greene said.

“The techniques we’re using aren’t based entirely on known biology, whereas other techniques, even the ones that we’ve developed in the past, have always been based given the understanding of biology that we have,” he said.

Greene’s lab emphasizes open source research, which means that anyone will be able to use the code and technology they develop. Lab programmer Rene Zelaya ’12 said that open access to information in academia is important.

Founded by Intel co-founder Gordon Moore and his wife Betty, the Moore Foundation supports projects that range in focus from patient care to conservation . The Moore Investigator award is part of a $60 million initiative in data research within the Moore Foundation’s science program, focused on supporting interdisciplinary research that helps scientists take advantage of data, program director Chris Mentzel said.

“What we started noticing a number of years ago was a growing number of our research areas, everything from astrophysics to marine microbiology, seemed to be struggling with the amount and heterogeneous nature of scientific data, so we started looking at how we might make a difference in this area,” he said. “Where we saw really innovative stuff happening seemed to be when a person could be a bridge between technology and science.”

Greene was one of 14 scientists selected following a January competition that received around 1,100 applications.

The initiative is trying to develop research at the intersection of computer science and biology, Mentzel said.

“We’re focusing on a new, emerging type of researcher, and we’re really interested in bringing a spotlight and attention to the kind of contribution that these researchers often provide to the community,” Mentzel said. “We’re interested in the software, the data, the alternative contributions that are so important in making science happen that often aren’t given enough credit.”

In 2010, Geisel established a graduate program in quantitative biomedical sciences that continues to expand, reflecting the increased interest in computational methods in biology from researchers around the world, interim Geisel dean Duane Compton said.

The Moore Foundation’s recognition is a testament to Greene’s pioneering work in his field, Compton said.