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Understanding Protein Network Essential for Healthy Brain Development

Protein networks are essential to almost every process in a cell, so the interactions between these proteins are crucial to understanding cell physiology in both healthy and disease states.

“A new method offering direct and native access to the protein network is available; however, the process is very costly and completed at a tedious speed,” says Xiadong Cai, a professor in the Department of Electrical and Computer Engineering. “Nonetheless, we contend that our method combined with data-mining logistics will, for the first time, allow for the mapping of protein networks within animals.”

In collaboration with Akira Chiba, professor in the College of Arts and Sciences’ Department of Biology, Cai will collect detailed results in order to systematically map the in-situ protein interaction network (isPIN) within the brain.

“Using the same data-mining logistics and image data acquisition methods, we will aim at mapping 228 protein pairs essential for healthy development of the brain,” Cai explains.

The research project, titled “Predicting protein network within animals,” is one of several awards funded by the College of Engineering and the College of Arts and Sciences that focus on the topics related to the Frost Institute of Chemistry and Molecular Science (FICMS), the first of the Frost Institutes for Science and Engineering that will be housed in the new Phillip and Patricia Frost Science and Engineering Building.

“Such a mapping is possible only in the 21st century with the very 21st century technologies all powered by computer,” Cai says. “These technologies include deep data mining, consistent protein labeling, and direct tracking of their interactions with their natural context intact — isPIN.”

The research project will benefit from Cai’s focus on developing machine learning and data mining methods for analyzing big genomic data, as well as his experience collaborating with scientists in the fields of molecular biology, oncology, immunology, genetics and pharmacology.

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