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APPENDIX B SYMPOSIUM AGENDA Monday, February 25, 2002 8:00 a.m. Registration and Continental breakfast 8:25 Plenary Session Welcome George Kenyon, Ph.D, Symposium Committee Chair, University of Michigan, Ann Arbor, M} Proteomics at NIGMS: Why is Structural Genomics not the Same as Structural Proteomics? Marvin Cassman, Ph.D., Director, National Institute of General Medical Sciences, Bethesda MD Post Genomic Studies of Mitochodria John E. Walker, Ph.D. Director of the Dunn Human Nutrition Unit, Medical Research Council, Cambndge, UK Accelerating Drug Discovery by Targeted Proteomics Scott Patterson, Ph.D. Rockville, MD - Senior Director for Proteomics, Celera Genomics Group, Large Scale Proteomics in a Clinical and an Industria! Setting Denis Hochstrasser, M.D., President of Clinical Medicine, University of Geneva; Head of Clinical Chemistry Laboratory, Geneva University Hospital; founder, Geneva Bioinformatics, Switzerland. 10:15 Coffee 10.30 Proteomic Strategies in Health an`Disease Julio Cells, Ph.D. Institute of Cancer Biology and Danish Centre for Human Genome Research, Danish Cancer Society, Copenhagen, Denmark. Data Collection in Proteomics, What Data and How Much? Ruedi Aebersold, Ph.D., Institute for Systems Biology, Seattle, WA Scaling up Proteomics: Lessons [earnearfrom the Human Genome Project Francis Collins, Ph.D., Director, National Human Genome Research Institute, Bethesda, MD B-]

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12:15 Lunch Structural Proteomics: Genomics/Proteomics Part of an Integrated Approach to Functional Cheryl A~rowsmith, Ph.D., Department of Medical Biophysics, University of Toronto, Canada Manipulating the Proteome; Studying Protein Pun ction in the Genomic Area Joshua LaBaer, M.D., Ph.D., Director of the institute of Proteomics at Harvard Medical School, Boston, MA Proteomic Tools for Dissecting Cellular Function Brian Chait, Ph.D., Rockefeller University, New York, NY 2:45 Break 3-5:00 pm Breakout Sessions tI5 minutes prior to session end, each (co) chair will summarize main points to be presented to all meeting participants] 5:00 Summaries - 5 minutes per breakout session 6-7:30 pm Reception in Great Hall $~0SIUM BREAK-OUT SESSIONS 1) Computational Methods & Bioinformatics This session will focus on the interface between computational and biochemical methods for the prediction and determination of the functions of gene products. Various experimental methodologies exist for the direct and indirect elucidation of protein function, including structure determination, expression and interaction profiling, knockout experiments for phenotype inference, and mutational analyses. We will examine current computational tools designed to analyze and integrate these disparate types of data into a functional picture of an organism, and discuss both what is possible today, and what we need for future research and development in this complex area. Cochairs: Kimmen Sjolander, Ph.D., University of California - Berkeley Dagmar Ringe, Ph.D., Brandeis University, Waltham, MA 2) Platform/Emerging Technologies Interdisciplinary collaboration in computer science, engineering, and the biosciences has generated rapid advances in new technologies. This session will discuss some of the B-2

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technologies for global quantitative analysis of proteins from complex mixtures, and high throughput analysis of protein interactions. These new technologies include protein chips, microarrays, 2D gels, image and data analysis systems. Cochairs: Ruth Van Bogelen, Ph.D., Head of Genomics & Proteomics, Pfizer Global Research and Development, Ann Arbor, MI Norman G. Anderson, Ph.D., Chief Scientist, Large Scale Biology, Rockville, MD 3) Protein Separation' ancildentif cation New uses are being developed for old technologies such as mass spectrometry and gel electrophoresis. These technologies provide the tools scientists use to identify proteins and multi-protein complexes. This session will address the use of mass spectrometry and related techniques to characterize proteins and protein-protein interactions, structure and folding. Cochairs: Alma Burlingame, Ph.D., University of California-San Francisco Julio Cells, Ph.D., Institute of Cancer Biology and Danish Centre for Human Genome Research, Danish Cancer Society, Copenhagen, Denmark. Alain Van Dorsselaer, Ph.D., Pasteur University, Strasbourg, France 4) Protein Structure and Function With the goal of creating an atomic description of each and every constituent of the cell, worldwide, large-scale structural initiatives are beginning to deliver what, over the next decade, will be an enormous wave of structural information to the shores of the biological community. Achieving this goal requires that many new and formidable challenges must be met. While the structural initiatives are underway, the functional/enzymological programs that will articulate the functions of these structures are, as yet, in the concept stage, and have recently been explored in workshops at the NIH/NIGMS. We invite you to help define the important issues that genomic- scale science has created for the structural and functional communities. Cochairs: Greg Petsko, Ph.D., Brandeis University, Waltham, MA Thomas Leyh, Ph.D., The Albert Einstein College of Medicine, New York, NY 5) Metabolic Pathways arid Post - Translationa! Modif cations Proteomics research presents a much more elusive task than the mapping of the human genome. Protein modification during protein translation and various metabolic processes, creates a challenge for defining the mandate of proteomics research. This session will address how scientists might proceed in annotating proteins, while considering how protein modification and the metabolic products will affect function and proteomics research. Cochairs: Edward Dennis, Ph.D., University of California, San Diego Eugene Bruce, Ph.D., Division of Integrative Biology and Neuroscience National Science Foundation, Arlington, VA 6) Implementation: Necessary Policy and Infrastructure Conditions for Collaboration' B-3 at,

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This session will address the unique/critical needs of proteomics research with respect to collaboration including education, funding, international cooperation, data sharing policies, and informatics infrastructure (e.g. software standards, scientific portals, colIaboratories, computing gnds). Cochairs: Jim Myers, Ph.D., Computational Science and Mathematics Department, Pacific Northwest National Laboratory, RichIand, WA Richard W. Morris, Ph.D., Division of Allergy, Immunology & Transplantation, National Institute of Allergy and Infectious Disease, NTH, Bethesda, MD 7) Clinica!Aspects Proteomics research promises to help fundamentally change the practice of medicine in the 2Ist century. This session will focus on how clinical proteomics research can be used to define new molecular markers for risk assessment and disease diagnosis, and how it can be used with other molecular profiling techniques to identify new targets for pharmaceutical development. The use of protein chips in the drug development and clinical settings will also be discussed. Cochairs: Alan Sachs M.D, University of California Berkeley; Director, Clinical Genomic Pharmacology, Merck Research Labs, Inc Denis Hochstrasser, M.D., President of Clinical Medicine, University of Geneva; Director of the Depa~-l~ent of Pathology and Head of the Central Clinical Chemistry Laboratory, Geneva University Hospital B-4