COLLOQUIUM Department of Computer Science and Engineering University of South Carolina Discovering Functional Relationships among Proteins Using Computational Techniques Orhan Camoglu Department of Computer Science University of California, Santa Barbara Date: March 23, 2006 Time: 1100-1200 Place: Swearingen 1A03 (Faculty Lounge) Abstract Recent advances in molecular biology have resulted in immense amounts of biological data (DNA sequences, protein sequences and structures, gene expression data, and protein interaction data). As a result of this growth, scalable techniques to mine and analyze this data have become paramount. These new techniques employ principles in many different areas of computer science, especially databases, data mining, machine learning and graph theory. They also impose new challenges. This talk focuses on applying database principles and computational techniques on biological data to infer functional properties of proteins. Functional and evolutionary relationships between proteins can be discovered via structure comparison. As the sizes of experimentally determined and theoretically estimated protein structure databases grow, there is a need for scalable search techniques. In this talk I will present a technique that extracts feature vectors on triplets of SSEs (Secondary Structure Elements) of proteins and uses an index structure to answer similarity queries. Currently, a wide range of information sources is available to provide evidence about the functional relationships among proteins. I will present an automated functional classification methodology that uses these information sources. Protein interaction networks provide a different view of protein functional relationships based on their interaction properties and can be used to infer intricate relations, such as pathway and complex membership. I will present analysis techniques for mining interaction networks to capture functional relationships among proteins. Orhan Camoglu is a Ph.D. candidate in Computer Science at the University of California, Santa Barbara. He received his B.S. degree in Computer Engineering and Information Science from Bilkent University, Turkey, in 2001. He worked at HAVELSAN, Turkey, as a software engineer, and joined University of California at Santa Barbara as a Ph.D. student afterwards. His research focuses on analyzing biological data to infer functional properties of proteins.