BIOINFORMATICS:Mining the Data

A one-day conference and networking opportunity for scientists, educators, and health & industry professionals

Thursday – 4 June 20099:00 am – 7:00 pm

Seven Hills Conference CenterSan Francisco State University1600 Holloway AvenueSan Francisco, CA 94132

PersonalizedMedicine 2.0PersonalizedMedicine 2.0CONFERENCE

PROGRAM

http://personalizedmedicine.sfsu.edu

Esteban González Burchard, M.D., M.P.H., is the Director of the UCSF DNA Bank and Asthma Genetics Core Facility and an attending physician in Pulmonary and Critical Care Medicine at San Francisco General Hospital. His research focuses on the role of genetic and environmental risk factors for asthma and drug response among racially/ethnically diverse populations. Dr. González Burchard received his B.S. in Cell & Molecular Biology at San Francisco State University (SFSU), and his M.D. degree from Stanford University School of Medicine. He completed clinical training in Internal Medicine at Harvard’s Brigham and Women’s Hospital and Pulmonary/Critical Care Medicine at UCSF.

G.Steven Burrill (See box on Program page)

Ljubomir Buturovic received his Ph.D. degree from the School of Electrical Engineering, University of Belgrade, Serbia. He is currently Chief Scientist at Pathwork Diagnostics, in Redwood City, California, and Adjunct Professor of Computer Science at SFSU. Prior to joining Pathwork Diagnostics and SFSU he was Bioinformatics Director at Incyte Corporation. At Pathwork, he is re-sponsible for the development of the informatics component of Pathwork clinical diagnostics tests.

Guy Cavet is Senior Director of Informatics at Crescendo Bioscience, which develops molecular diagnostic tests for autoimmune diseases. His responsibilities include data management, data analysis, algorithm development and software engineering. He has over ten years experience working in bioinformatics, software development and scientific research. Prior to joining Crescendo Bioscience, Dr. Cavet managed informatics research and software development for diagnostics at Genentech. He also worked in genomics, technology development and scientific software develop-ment at Rosetta. He received a Ph.D. in Molecular Biology from the University of Cambridge in the United Kingdom.

Hilary Clark is a Senior Scientist at Genentech in the Research Department of Bioinformatics, with a Joint Appointment in the Department of Immunology. She collaborates in the discovery of both new drug targets and companion diagnostics for autoimmune diseases. Dr. Clark received her Ph.D. in Genetics at UC Berkeley and did postdoctoral research at Harvard Medical School. She is an alumna of SFSU and is now an Adjunct Professor in the Department of Biology.

Sarah Davis is a Translational Researcher at the UCSF Breast Care Center, where she has worked over the last 3 years with Dr. Laura Esserman, Director of the Breast Care Center, on several clinical trials. Ms. Davis has an MS in Microbiology from the University of Wisconsin. She has most recently been working on the I-SPY trial, which is a correlative science trial that looks for molecular predictors of response to chemotherapy in women with locally advanced breast cancer. Robert Graham is in the Immunology Biomarker Discovery group at Genentech. Dr. Graham has been leading analyses of whole genome association scans in multiple phenotypes to identify genes involved in response to therapy, disease progression and heterogeneity. Dr. Graham trained in human population genetics and immunology. He received his Ph.D. at the University of Min-nesota in Immunology and Genetics in 2002, followed by a post-doctoral fellowship at the Broad Institute of MIT and Harvard.

Michael Hogarth is Director of the Division of Pathology Informatics in the Depart-ment of Pathology and Laboratory Medicine at UC Davis. His current research interests include cancer informatics, the development of public health information systems and frameworks, terminological and ontological systems develop-ment, and understanding collaborative scientific networks through social network analysis and visualization. He is Director of Cancer Informatics at the UC Davis Cancer Center. Dr. Hogarth received his M.D. at the University of Texas - Southwestern and completed fellowship training at the UC Davis School of Medicine.

Carolyn Johnson (See box on Program page)

Keith Jones is Vice President, Assay and Application Product Development at Affymetrix, Inc. where he is responsible for all the molecular biology functions within the company. Dr. Jones led the Genotyping Research group which was responsible for the development of genetic variation technologies and the demonstration of the utility of these technologies in novel applications. He received his Ph.D. from Stanford University in Pharmacology and has Bachelor of Science degrees from UC Irvine in both Chemistry and Biological Sciences.

Tom Paterson, a co-founder of Entelos, leads the development of predictive biosimulation systems and methodologies for Entelos’ PhysioLab® technology. Mr. Paterson has refined hypothesis management as a core methodology for systematically mapping knowledge gaps in the current understanding of disease pathophysiology, and the subsequent formulation and analyses of competing hypotheses to explore those gaps. Mr. Paterson’s work at Entelos builds on his engineering experience in the defense industry designing large-scale aerospace simulation and decision-support systems. He has held leadership positions at Strategic Decisions Group, GTE Government Systems, and the Institute for Defense Analyses. Mr. Paterson received an S.B. in aeronautics and astronautics from the MIT, and an M.S. in decision analysis from Stanford University.

H. Michael Shepard received a Ph.D. from Indiana University. He is president and CSO, as well as a founder, of Receptor BioLogix, a biopharmaceutical company focused on develop-ing a newly discovered class of protein therapeutics called Intron Fusion Proteins (IFP) to treat cancer, autoimmune, metabolic and other diseases. While at Genentech, he led the discovery and development of the breast cancer drug, Trastuzumab (trade name: HerceptinTM). Dr. Shepard shared the 2006 Alpert Prize for his contribution to the development of the breast cancer therapy HerceptinTM, the first target-directed cancer treatment for solid tumors. Dr. Shepard holds over 25 US patents.

Vance Vanier is Chief Medical Officer of Navigenics and a clinical faculty member of Stan-ford University Medical Center. As a former partner at Mohr Davidow Ventures, he has spent years in the molecular diagnostics industry bringing new genomic technologies into clinical practice. Dr. Vanier received his medical degree from the Johns Hopkins School of Medicine. He serves as a member of the Personalized Medicine Coalition’s Clinical Science Committee, Stanford Hospital’s Pharmacy and Therapeutics Committee, and the American College of Preventive Medicine.

Rosanne Welcher is Vice President of Research and Development at Dako North America. Her focus at Dako includes the area of personalized medicine in which she works closely with pharmaceutical companies to enable the co-development of drug and tissue-based companion di-agnostics, termed pharmacodiagnostics at Dako. The best examples of Dako pharmDxTM products include HercepTest and Her2 FISH that identify over-expression of Her2 protein and gene, aiding in identification of patients more likely to respond to the breast cancer therapeutic, HerceptinTM.

Thomas Wu is a Senior Scientist in the Department of Bioinformatics at Genentech, where he directs data management and software development for high-throughput assays, including microarrays and next-generation sequencing technology. Dr. Wu received his undergraduate and masters degrees from Stanford, an M.D. from Harvard Medical School, and a Ph.D. in computer science from MIT. He subsequently did internship and residency in internal medicine at Stanford Hospital, and postdoctoral research training at Stanford School of Medicine.

Featured Speakers & Panelists

Personalized Medicine 2.0

BIOINFORMATICS:Mining the Data

KEYNOTE SPEAKER:G. STEVEN BURRILL, CHIEF EXECUTIVE OFFICERBURRILL & COMPANY

Steven Burrill has been involved in the growth and prosperity of the biotechnol-ogy industry for over 40 years. Mr. Burrill is one of the original architects of the industry and one of its most avid and sustained developers. He serves as Chairman of the Boards of Pharmasset, BioImagene and NewBridge, and is a member of the Boards of Directors of Catalyst Biosciences, CrossCart, DepoMed, Ikano Therapeutics, Phytomedics, ProteoGenix, Proventys, Targacept and XDx. Before founding Burrill & Company in 1994, he spent 28 years with Ernst & Young, directing services to clients in the biotechnology/life sciences/high technology/manufacturing industries worldwide. In 2002, Mr. Burrill was recognized as a biotech investment visionary by the Scientific American magazine (The Scientific American 50).

SYMPOSIUM MODERATOR:CAROLYN JOHNSON, ANCHOR ABC7 NEWS

Carolyn Johnson brings more than 20 years of experience in television production and on-air work to her position. Most evenings, you’ll find Carolyn anchoring ABC7 News at 6 & 11 and reporting on health and science. In 2008 she celebrated 10 years with the station as an anchor and reporter; she won a regional Edward R. Murrow Award from the Radio and Television News Directors Association for best newscast; and she completed a health journalism fellowship with the California Endowment/USC Annenberg School of Com-munication. Carolyn’s prior industry recognitions include Emmy nominations in multiple categories. She’s also been honored as best reporter by the American Women in Radio and Television, Golden Gate Chapter.

9:00Breakfast & Networking

Symposium ModeratorCarolyn Johnson, News Anchor, ABC7 News, San Francisco

9:45Introduction & WelcomeMichael A. Goldman, Ph.D., Professor & Chair, Department of Biology, SF State UniversityLisa White, Ph.D., Associate Dean of the College of Science & Engineering, SF State University

9:55Opening KeynoteG. Steven Burrill, CEO, Burrill & Co.Biotech 2009: Navigating the Sea Change

10:50Coffee break

10:55Clinical Application PerspectiveVance Vanier, M.D., Chief Medical Officer, Navigenics The Advent of Preventive Genomic Medicine

11:45Emerging Science PerspectiveEsteban G. Burchard, M.D., M.P.H., Associate Professor of Medicine, University of California, San FranciscoThe Importance of Race/Ethnicity & Admixture in Clinical Practice and Biomedical Research

12:35Lunch & Networking

1:25Discovery Bioinformatics – Panel DiscussionPanel organizer: Hilary F. Clark, Ph.D., Senior Scientist, Bioinformatics, GenentechThomas Wu, M.D./Ph.D., Senior Scientist, Bioinformatics, GenentechGuy Cavet, Ph.D., Director, Informatics, Crescendo Bioscience

2:45Clinical Bioinformatics – Panel Discussion Keith Jones, Ph.D., Vice President, Assay & Application Product Development, Affymetrix, Inc. Application of molecular genetic analysis in understanding disease.Sarah Davis, M.S., I-SPY Lead Coordinator, University of California, San FranciscoThe use of informatics tools in translational clinical trials, the I-SPY TRIAL.Michael Hogarth, M.D., Associate Professor, Pathology and Laboratory Medicine, University of California, DavisThe Development of information tools for routine use by medical practitioners in patient management.Thomas Paterson, Co-Founder & Chief Innovation Officer, EntelosThe study of patient stratification and the identification of patterns of known physiologic and genetic biomarkers predictive of efficacy and safety clinical endpoints.

4:05 Coffee Break

4:15Bioinformatics in Diagnostics – Panel Discussion Panel organizer: Ljubomir Buturovic, Ph.D., Sr. Director and Chief Scientist, Pathwork DiagnosticsDiagnostics vs. drug development: Prediction vs. explanation.Rosanne Welcher, Ph.D., MBA, Vice President R&D and General Manager, Dako North AmericaRobert Graham, Scientist, Immunology Diagnostics, Genentech

5:20Closing KeynoteH. Michael Shepard, Ph.D., founder, Receptor BiologixCuring Cancer with Personalized Medicine: Where are the Challenges?

6:00-7:00Reception

4 June 2009 Seven Hills Conference Center San Francisco State University

Conference Program

Personalized Medicine 2.0BIOINFORMATICS:Mining the Data

ORGANIZING COMMITTEE

Mary Fermi, M.B.A., Commercial Development ConsultantB.A. Biology, San Francisco State University

Julio Gagne, Executive Director of New Products and Portfolio Strategy, Novartis OncologyM.B.A., San Francisco State University

Michael A. Goldman, Ph.D., Professor and Chair, Department of Biology, San Francisco State University

Ken Hitchner, Vice President, Monogram BiosciencesM.A. Biology, San Francisco State University

Dan Maher, Vice President, BioMarin Pharmaceutical Inc.B.A. Biology, San Francisco State University

John Wulf, Principal, New Frontier Life Sciences ConsultingM.B.A., San Francisco State University

Special thanks to

Wendy Abraham

Kathleen Baker

Diane Fenster

Michael Fong

Karl Giljum

Jennifer Javernick

Lannie Nguyen-Tang

Sally Pasion

THANK YOU TO OUR SPONSORS:

Thank you for supporting the Department of Biology

http://biology.sfsu.edu

Tentative Date: Thursday, 27 May 2010

Watch for updateshttp://personalizedmedicine.sfsu.edu

Personalized Medicine 3.0

Targeting Cancer

Staff of the Department of BiologySan Francisco State University

College of Science & EngineeringSan Francisco State University