November 2019 Meeting Announcement, Delaware Valley Mass Spectrometry Discussion Group
Topic: "Informing Cancer Treatment using Proteogenomics"
  • Speaker: David Fenyo, New York University
  • Date: Monday, November 11, 2019. 7:30 PM
  • Please RSVP to by Thursday November 7.
  • Time: Social Hour: 6:00 PM
    Talk: 7:00 PM.
  • Place:Villanova University, Mendel 154
  • Abstract: Advances in sequencing technologies have revealed large heterogeneity on the genome and transcriptome level in tumors. However, it has often been difficult pinpoint which of the changes are important drivers of tumor growth. Proteomic technologies measuring the functional gene products directly have also improved rapidly, and they provide rich complementary information. The combined application of proteomics and genomicsto the understanding of tumor biology has the potential of driving innovative diagnostics and new treatments for cancer. I will discuss different strategies for the proteogenomic integration of data from tumors analyzed within The Cancer Genome Atlas (TCGA) and the Clinical Proteomics Tumor Analysis Consortium (CPTAC).
  • Bio: David Fenyő studied engineering physics, with a focus on mathematical and numerical methods, at Uppsala University in Sweden. After receiving an M.Sc. in Engineering Physics in 1987, he joined the laboratory of Dr. Bo Sundqvist at Uppsala University, and studied the mechanisms of ion–solid interaction both experimentally, and using molecular dynamics and Monte Carlo simulations. For this work, he received a Ph.D. in Physics in 1991. He then joined the laboratory of Dr. Brian Chait at the Rockefeller University, where he started developing algorithms to analyze proteomic data obtained using mass spectrometry. In 1997 he co-founded ProteoMetrics, a bioinformatics startup that sought to commercialize these algorithms. He served as the president of Proteometrics, LLC and created several software packages, including a distributed software system for fully automated analysis of large-scale proteomics data. Subsequently, he worked for several companies including GE Healthcare before returning to academia. David Fenyő joined the faculty of NYU Medical School in 2010 and currently he is Professor of Biochemistry and Molecular Pharmacology, Director for the Ph.D. program in Systems and Computational Biomedicine and the Master's program in Biomedical Informatics, and Co-Director for informatics for the Clinical and Translational Science Institute (CTSI) at NYU.Dr. Fenyő has over 30 years of experience with all aspects of biomedical data analysis in both academia and industry and his work has resulted in over 150 scientific publications. During these years, he has laid a statistical foundation to test the significance of protein identification results, he has developed algorithms for identifying proteins by matching mass spectrometry data to databases, detecting retrotransposon insertions using next generation sequencing data, analyzing protein interactions using microscopy data, and he has built commercial software packages for fully automated analysis. Dr. Fenyő has extensive experience in software development in academia as well as in small and large biotechnology companies, and he has managed large commercial software projects for customers in the pharmaceutical and biotech industries.
    His research focuses on providing a detailed understanding of the dynamics of cellular processes. He applies mathematical, statistical, and computational methods to optimize experimental design, analyze quantitative data, and model biological systems. In particular, he uses proteomic approaches to develop methods to identify, characterize, and quantify proteins. His efforts to integrate data from multiple technologies - including mass spectrometry, sequencing, and microscopy - have provided a wide array of powerful tools to discover and verify biomarkers and therapeutic targets in cancer.