John Yates III, Scripps Research Institute

Title: Driving Biological Discovery using Quantitative Mass Spectrometry

Bio: John Yates received his Ph.D. in Chemistry at the University of Virginia under Professor Donald Hunt. His graduate research involved the development and application of tandem mass spectrometry for sequence analysis of proteins. Following a Biotechnology Fellowship at the California Institute of Technology, he moved to the Department of Molecular Biotechnology at the University of Washington where he attained the tenured rank of Associate Professor. He is now a Professor in the Department of Chemical Physiology at The Scripps Research Institute. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and principle developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has extended the use of proteomic techniques to quantitative analysis of protein expression for the discovery of new biology. He has received the American Society for Mass Spectrometry research award, the Pehr Edman Award in Protein Chemistry, the American Society for Mass Spectrometry Biemann Medal, the HUPO Distinguished Achievement Award in Proteomics, Herbert Sober Award from the ASBMB, and the Christian Anfinsen Award from The Protein Society. He has published over 400 scientific articles.

Pieter Dorrestein, Skaggs School of Pharmacy and Pharmaceutical Sciences, UCSD

Title: Post-translational modifications of therapeutics and toxins

Bio:Pieter Dorrestein was born in Utrecht, Netherlands, in 1974. He completed his undergraduate at Northern Arizona University under the guidance of Professor John MacDonald. Pieter continued on to Cornell University for graduate school in the department of Chemistry and Chemical Biology where he worked on metabolite biosynthetic pathways with Professor Tadhg Begley. During his post-doctoral years, at the University of Illinois, as an NIH-NRSA fellow (co)-sponsored by Professor Neil Kelleher and Professor Christopher Walsh, he exploited high-resolution mass spectrometry to elucidate the biosynthesis of natural products of therapeutic value. In September of 2006, Pieter moved to his current position as Assistant Professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences and Departments of Pharmacology, Chemistry and Biochemistry at UC-San Diego. In 2007 Pieter also became a member of the Center for Marine Biotechnology and Biomedicine at the Scripps Institution of Oceanography and the Moores Cancer center. The Dorrestein lab is a chemical biology laboratory that emphasizes mass spectrometric, including proteomic and MALDI-imaging based approaches to understand the functions of orphan genes from microorganisms responsible for the production of natural products and promising therapeutic agents. In addition, the Dorrestein lab aims to detect and understand the function of post-translational modifications as they are involved cancer processes.

Jing Wei, Biogen Idec

Title: Proteomics Platform for Biomarkers Discovery at Biogen Idec

Bio: Dr. Jing Wei leads the proteomics biomarker discovery effort at Biogen Idec Corporation. Jing received her B.S. from Peking University in 1994 and Ph.D. in chemistry from Iowa State University in 1998. After two years of postdoctoral training at the Scripps Research Institute, she joined Novartis Agriculture Institute (later Torrey Mesa Research Institute). Most recently, she led proteomics group at Diversa Corporation in San Diego prior to joining Biogen Idec in 2005.

Zhouxin Shen, Div. of Biological Sciences, UCSD

Title: Quantitative global proteome and phosphoproteome profiling of human embryonic stem cells before and after differentiation

Bio: Zhouxin Shen is a staff research associate at the University of California, San Diego. He received bachelor's degrees from Peking University in Chemistry. He obtained a Ph.D. in Physical Chemistry at the Iowa State University. He was the Vice President and Director of Research at Mass Consortium Corporation, directing research on biomarker discovery using proteomics and metabolomics.

Ansgar Brock, Genomics Institute of the Novartis Research Foundation

Title: Hydrogen/Deuterium Exchange Mass Spectrometry for Structural Genomics

Bio: Ansgar Brock received a Ph.D. in Physical Chemistry from Baylor University in 1996. During a postdoctoral stay at Stanford University from 1996-1999 he worked with Professor Richard N. Zare on the development of Hadamard Transform TOF MS. In 1999 Dr. Brock joined the newly founded Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA, where he currently holds a Senior Principal Investigator position in the Protein Science Department. His main interests are in the areas of bioanalytical chemistry with emphasis on chemical labeling and hydrogen/deuterium exchange, mass analyzer development, and process automation.

Jan Schnitzer, Sidney Kimmel Cancer Center

Title: Speeding up target discovery and validation through "organellar proteomic imaging" in vivo: A drug delivery system

Bio: Dr. Jan E. Schnitzer is the Scientific Director of the Sidney Kimmel Cancer Center, located in San Diego, California. The Sidney Kimmel Cancer Center is an independent, nonprofit research institution dedicated to the development and advancement of biomedical research to eliminate cancer. Dr. Schnitzer joined the faculty of San Diego's Sidney Kimmel Cancer Center in 1999. He is Professor of Molecular and Cellular Biology, Director of Vascular Biology and Angiogenesis Program and Scientific Director. Prior to this appointment, Dr. Schnitzer was Associate Professor at Harvard Medical School, Beth Israel Hospital, Boston, Massachusetts (1994-1999), and an Assistant Professor at the University of California School of Medicine and Institute of Biomedical Engineering (1990-1994). Dr. Schnitzer received a BSE in Chemical Engineering from Princeton University and an M.D. (1985) from the University of Pittsburgh Medical School. He did his postdoctoral training at Yale University Medical School in the Department of Cell Biology. Dr. Schnitzer has been studying protein interactions at the surface of endothelial cells lining blood vessels and how specialized membrane vesicles called caveolae function to transport endogenous molecules as well as possibly targeted drugs, nanoparticles and gene vectors from the circulatory blood across the endothelial cell barrier to reach underlying tissue and even tumor cells.

Huilin Zhou, Ludwig Institute for Cancer Research

Title: Experimental approaches to proteomics

Bio: Huilin Zhou received his Ph.D. from the Stanford University. He is currently an Associate Professor of Cellular and Molecular Medicine as well as an Associate Member of the Ludwig Institute for Cancer Research. Dr. Zhou's research insterests include how cells sense and respond to DNA damage and proteomic technologies for the study of biological processes. He is the recipient of the K22 Genome Scholar Development and Faculty Transition Award.

Pavel Pevzner, Dept. of Computer Science and Engineering, UCSD

Panel Moderator

Bio: Dr. Pevzner is the Ronald R. Taylor Chair Professor of Computer Science and Director of the Center for Algorithmic and Systems Biology at University of California, San Diego. He holds a Ph.D. (1988) from Moscow Institute of Physics and Technology, Russia. Dr. Pevzner is author of the graduate textbook "Computational Molecular Biology: An Algorithmic Approach" in 2000 and the undergraduate textbook "Introduction to Bioinformatics Algorithms" in 2004 (jointly with Neal Jones). He was named Howard Hughes Medical Institute Professor in 2006.

Vineet Bafna, Dept. of Computer Science and Engineering, UCSD

Title: Proteogenomics: using proteomic data for gene annotation

Bio: Vineet Bafna is an Associate Professor in the Computer Science and Engineering Department at UCSD. Prior to joining UCSD in 2003, he spent seven years in the bio-science industry, ultimately as Director of Informatics Research, at Celera Genomics. At Celera, he participated in the human genome project, designing novel tools for gene discovery, and leading the analysis of mass spectrometry data for identifying cancer bio-markers. His current research focus is on computational problems arising is mass spectrometric data analysis, population genetics, non-coding genes, and cancer genomics. He is an Associate Editor for JBCB, IEEE TCBB, and Biology Direct, and has served on the program committees of ISMB, RECOMB, and other conferences. He has co-authored over seventy research articles in refereed journals and conference proceedings.

Gary Siuzdak, Scripps Center for Mass Spectrometry

Title: Metabolomics Clinical Diagnostics and Discovery from Solution and Surfaces

Bio: Gary Siuzdak, Ph.D. is Senior Director of the Scripps Center for Mass Spectrometry and Professor of Molecular Biology at The Scripps Research Institute in La Jolla, California (http://masspec.scripps.edu/). He is also Faculty Guest at Lawrence Berkeley National Laboratory and Vice President of the American Society for Mass Spectrometry. His research includes developing novel approaches to metabolomics and proteomics, the development of nanostructure-initiated desorption/ionization, intact viral analysis, preparative mass spectrometry, and mass-based inhibitor-enzyme screening. He has over 140 peer-reviewed publications and three books, the latest being The Expanding Role of Mass Spectrometry in Biotechnology, 2nd Edition 2006.

Nuno Bandeira, Dept. of Computer Science and Engineering, UCSD

Title: E Pluribus Unum: Revelations from Tandem Mass Spectra of Overlapping Peptides

Bio: Nuno Bandeira is currently the Executive Director of the Center for Computational Mass Spectrometry at UCSD. He received his Ph.D. from UCSD in 2007 and is a project scientist in the Department of Computer Science and Engineering. Dr. Bandeira's research interests include algorithms, machine learning, and their application to computational biology. The current focus of his research is on the detection, assembly, and interpretation of uninterpreted MS/MS spectra from overlapping peptides