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ODU Computer Scientist Gets Major NSF Grant for Brain Circuitry Analysis

Shuiwang Ji

Shuiwang Ji, an assistant professor of computer science at Old Dominion University, leads a team of researchers that have won grants totaling almost $600,000 from the National Science Foundation (NSF) to explore a new, comprehensive way to map the intricate workings of the mammalian brain.

The researchers will use image-processing tools together with advanced computational methods to try to unravel the brain circuitry that generates high-level cognitive functions.

"Integrative Analysis of the Anatomic and Genetic Landscapes in the Mouse Brain" is the title of the projects, which will extend through February 2015. The grant is from NSF's Directorate for Biological Sciences, Division of Biological Infrastructure.

Ji, who leads the Computational and Biological Learning Laboratory at ODU, will be collaborating with: Patric Lundberg, associate professor in the Department of Microbiology and Molecular Cell Biology at Eastern Virginia Medical School; Axel Visel, staff scientist of the Genomics Division of Lawrence Berkeley National Laboratory in California; and Michael Hawrylycz, senior director for data analysis and annotation for the Allen Institute for Brain Science in Seattle.

ODU was awarded $526,888 for the work, and an additional $42,014 goes to EVMS.

Hawrylycz's role as a project consultant emphasizes the connection between this research and work under way at the Allen Institute, which is an independent, nonprofit medical research organization. The institute is creating a growing collection of unique online public resources for the scientific community, the first of which to be completed is the Allen Mouse Brain Atlas. This three-dimensional map of gene activity throughout the adult mouse brain details which genes are turned on where, and it has become a resource for thousands of brain researchers around the world.

The mouse brain has similar basic parts and organization of other mammalian brains, and is a common model for studies that are designed to shed light on workings of the human brain.

Ji and his collaborators plan to develop novel computational methods for analyzing the Allen Mouse Brain Atlas data set, with the goal of accomplishing a global (brain-wide and genome-wide) analysis that will elucidate the anatomic and genetic landscapes of the mammalian brain.

The announcement of the award was enthusiastically welcomed by top science and technology administrators at ODU.

Mohammad Karim, ODU vice president for research, and Chris Platsoucas, dean of the College of Sciences, praised the dedication to task that allowed Ji to win federal funding for the project. Ji joined ODU only 18 months ago after receiving a Ph.D. in 2010 from Arizona State University.

"Outstanding work! This is a good day for all of us," Karim said.

Platsoucas noted the cluster faculty-hiring approach begun recently in the Department of Computer Science and said, "We are focusing on areas of bioinformatics, medical imaging and computer networks. We are very pleased that Professor Ji has received this very competitive grant in bioinformatics on first submission. He is a young researcher who has accomplished much in a short time."

Desh Ranjan, the computer science chair, said Ji's grant is evidence that "concrete results are beginning to show" from recent departmental initiatives. "This is a significant grant and a credit to Professor Ji," he added.

"As a computer scientist, I am glad that my first federal research grant is awarded by the Directorate for Biological Sciences", Ji said. "This shows that our interdisciplinary work has been recognized by the biological community."

Although the Allen Mouse Brain Atlas contains voluminous data, charts and 3-D images showing where certain genes signal specific functions, not much is known about how the full neurological system operates within a timeframe. Models and simulations available to researchers today might be compared to a series of snapshots. Ji wants to make it possible for the data to be presented in an uninterrupted, full brain simulation - a moving picture in 3-D, if you will.

The problem he and his team faces is the sheer volume of gene-triggered connections within each mammalian brain - many millions of them - that work in concert to drive reactions and interactions relative to outside stimuli.

The researchers propose to develop tensor computation techniques to allow for data compression and visualization. This is a highly sophisticated means of sampling a lot of diverse data in order to come up with coherent patterns and reliable predictions.

Their analysis, the researchers believe, has the potential to enable and accelerate biological insights and generate experimentally testable hypotheses.

According to the project summary: "In particular, this project is expected to enable significant progress in the areas of (1) understanding the structure and development of the mammalian brain through the multidimensional analysis of genetic networks that can be identified through systems-level analysis of gene expression, (2) understanding molecular pathways that are active and contribute to the function of the mammalian brain, and (3) understanding how disruptions of genes and thus molecular pathways might contribute to pathologies of mouse and, ultimately, human brains.

The Allen Brain Atlas resources are widely used in undergraduate and graduate courses at universities, and Ji predicted his project will extract new knowledge from the resources, thereby significantly enriching current curricula and promoting the development of new courses of study.

He also predicted that ODU's distance learning program will allow him to disseminate these new teaching tools to students throughout the United States and the world.

This article was posted on: February 29, 2012

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