CAREER: Machine Learning Approaches for Genome-wide Biological Network Inference

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NSF-0644366Chen, Xue-WenThe objectives of this research program are (1) to develop and apply novel computationalapproaches for uncovering genome-wide networks of interactions between genes and proteins, and (2) to conduct related educational activities in a newly established bioinformatics program in the Department of Electrical Engineering and Computer Science at the University of Kansas. Specifically, built upon reconstructing biological networks of moderate size, the new research will computationally uncover genome-wide biological networks and map interactions of genes and proteins across a variety of organisms. The research directions include: Simultaneously integrating multiple biological knowledge into dynamic Bayesian networks for learning networks of gene interactions; learning networks of protein interactions from heterogeneous data; learning integrated networks of gene and protein interactions; learning genome-wide networks of gene and protein interactions; and cross-species network learning. It will advance the state of the art by developing machine learning methods for effectively integrating multiple prior knowledge from different sources of data, including learning for highly heterogeneous data and large-scale network. The research will also produce new methods and user-friendly software that can be applied by molecular biologists to gain insight into diverse biological problems, such as how biological processes are regulated on a genome scale and how individual bio-molecules interact with one another in the cell.Learning with prior knowledge and highly heterogeneous data sources are fundamental to computational biology, information theory, machine learning, data mining, and other areas. Thus, the proposed research will benefit a variety of application domains including research in biology and medicine. The biological discovery derived from this project will also contribute to a variety of fields that include agriculture development, rational drug design, and health care. The research program will foster and facilitate collaborations between biologists and the PI. The educational components are closely tied to the research activities, which include (1) developing and improving bioinformatics courses that are closely related to the research outlined here and integrating them into the core bioinformatics curriculum, and (2) providing special training opportunities in the interdisciplinary area of bioinformatics for a wide-range of students, from high school through graduate school, including groups typically underrepresented in the field of science and technology.