Buffalo Center for Biomedical Computing Computational Approaches to

Buffalo Center for Biomedical Computing: Computational Approaches to Disease Causes and Treatment Aidong Zhang Biomedical Computing Center SUNY at Buffalo University at Buffalo The State University of New York

NIH Biomedical Computing Center Program ¢ Goals: Establish partnerships bringing together three types of scientists: q computational scientists q biomedical computational scientists q experimental and clinical biomedical and behavioral researchers The partnerships will be highly interactive and designed to produce, validate, and disseminate tools and computational environments that will be useful to a broad spectrum of biomedical researchers across the nation. University at Buffalo The State University of New York

Buffalo Center Mission ¢A regional (WNY) biomedical computing center with a multi-disciplinary team. ¢Research focus: providing tools of analyzing genomic and protein data for diseases and treatment effects. ¢Education activities: train biomedical computing researchers and offer bioinformatics certificate. University at Buffalo The State University of New York

Pre-Center Goals ¢Forming center organization structure. ¢Foster multi-disciplinary collaborations. ¢Building computational core infrastructure. ¢Fund developmental projects that maximize interactions between computational and experimental scientists. ¢Generate results -> Apply for full center. University at Buffalo The State University of New York

Organizational Infrastructure A. Zhang, PI W. Jusko, Co-PI M. Trevisan, Co-PI Bruce Pitman, Education Director Scientific Steering Committee External Advisors Internal Advisory Committee Genomics Core Executive Committee Project Coordinator Dr. Robert Chau Computational Core Project Directors University at Buffalo The State University of New York Clinical Core Project Directors

Advisory Board ¢Internal advisory board Kenneth Tramposch, chair, Associate VP for Research Bob Genco, Vice Provost, STOR Rich Gronostajski, Dept. of Biochemistry Candace Johnson, VP for Translational Research, RPCI Russ Miller, Center for Computational Research Jeff Skolnick, Center for Excellence in Bioinformatics Bob Straubinger, Dept of Pharmaceutical Sciences ¢External advisory board University at Buffalo The State University of New York

Collaborative Activities ¢Support computer science students working on developmental projects. ¢Support students from biomedical departments as trainees and co-located in CSE. ¢Internal research seminar and external speakers. ¢Center meetings and annual retreat. University at Buffalo The State University of New York

Computational Core Develop and integrate the computational tools to meet the important challenges of biomedical research: ¢ Overall scheme: Raw Data --> Algorithm Development --> Data Mining --> Knowledge Discovery -> New Drugs, Treatments ¢ Computational Research: q q Data warehouse framework Advanced pattern analysis tools Visualization tools Statistics oriented modeling University at Buffalo The State University of New York

Data Warehouse Framework ¢ Integration of heterogeneous data resources including genomic and clinical data. q Data model: representing and linking various data and provide global view of the hierarchy of whole data. q Data manipulation operations: data updates and querying functions q Data analysis operations: online interpretation of analysis results from data warehouse University at Buffalo The State University of New York

Advanced Analysis Algorithms ¢Pattern analysis: existing tools do not provide optimal solutions for bioinformatics dada pattern analysis q Time series data: noise, outliers, nested clusters q Samples data: large number of non-informative genes q Gene, sample, time series data: complex pattern structures q. Our goals: integrate computer science and statistical approaches to provide customized solutions to biomedical data analysis University at Buffalo The State University of New York

Co-expressed Genes Gene Expression Data Matrix Gene Expression Patterns Co-expressed Genes Why looking for co-expressed genes? Co-expression indicates co-function; Co-expression also indicates co-regulation. University at Buffalo The State University of New York

3 -D Microarray Data Each cell mij is a vector! University at Buffalo The State University of New York

Visualization Tools ¢Mapping high-dimensional data to 2 dimensional data q. Handling data loss q. Relationships between original data patterns and mapped data patterns ¢Interactive exploration of data patterns q. Dynamic visualization q. Interactively adjust dimension parameters University at Buffalo The State University of New York

Budget Direct cost $250 K per year for three years ¢$100 K for planning and computational core q. Executive committee efforts q. Project coordinator q. Computational core researchers’ effort ¢$150 K for developmental projects Support 3 -4 developmental projects per year University at Buffalo The State University of New York

Developmental Projects First year supported projects: ¢Project 1: Delineating genomic mechanisms in chronic complex diseases. (Murali Ramanathan, Yulan Liang, Jian Pei) ¢Project 2: Pharmacodynamic analysis of drugresponsive gene expression changes. (Bill Jusko, Richard Almon, Debra Dubois) ¢Project 3: Sequence tag identification and pathway deconvolution. (Steven Pruitt, Ping Liang, Xin He) University at Buffalo The State University of New York

Recruit New Projects ¢Seed fund to support one year pilot project ¢Funding level: $15 K-$30 K in direct cost ¢Submission deadline: June 15, 2004 ¢Submission format: two pages research description The executive committee will review the submissions and make decision by Aug. 1, 2004 University at Buffalo The State University of New York

Center’s Visionary Roles Focus on fusion of biomedicine and information Technology: ¢ Forming new, compelling, synergetic areas for biomedical research. ¢ Providing computational services to the region, including Roswell Park, UB, and UR. q Accessible data resources q Online analysis tools ¢ Becoming a national center leading new research and student training. Web site: http: //biocomputing. cse. buffalo. edu/ University at Buffalo The State University of New York