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Biography |
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Gilbert S. Omenn, MD, PhD, is Professor of Medicine, Genetics, Public Health, Computational Medicine & Bioinformatics at the University of Michigan. His research is focused on cancer proteomics, biomedical informatics, and science policy. Previously, he was professor of medicine and dean of public health at the University of Washington from 1982-1997; associate director, Office of Science and Technology Policy and Office of Management and Budget for President Carter 1977-81; and Howard Hughes Investigator. He is member of the Institute of Medicine/National Academy of Sciences and American Academy of Arts &Sciences, past president of the AAAS, and director of Amgen Inc. He is author of 473 research papers and scientific reviews and author/editor of 18 books (www.med.umich.edu/omenn). He is a co-leader of the Science Supercourse based at Bibliotheca Alexandrina. He earned the B.A. at Princeton, M.D. at Harvard, and PhD in Genetics at University of Washington.
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Abstract |
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Gilbert S. Omenn
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109-2218
Abstract
Alternative splicing generates protein diversity without increasing genome size. Our analytical pipeline identifies and quantifies known and novel splice isoforms from peptide sequences determined by mass spectrometry. Alternative splice variant peptides are a new class of protein cancer biomarkers. We have conducted extensive proteomic analyses on plasma and tissue specimens from genetically-designed mouse models of human pancreatic and breast cancers and from human colon cancers. Mass spectra are interrogated against a non-redundant database of exhaustive 3-frame translation of Ensembl transcripts and gene models from ECgene using X!Tandem software. The search results are processed for peptide-to-protein integration by Trans Proteomic Pipeline (TPP) and/or Michigan Peptide to Protein Integration (MPPI) [Cancer Res 2009; 69:300]. Over-expressed novel variants are validated by qRT-PCR. The exact splicing findings and the biological annotations for these cancers are quite interesting. Supported by NCI/SAIC 23XS110A., MTTC GR 687, NIH U54 DA021519.
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