Title：Reconstruction of protein interaction networks using affinity purification mass spectrometry technology
Speaker：Prof. Alexey I. Nesvizhskii, Ph.D.
Host: Dr. NING Kang
Time：9:30 am, 21 Apr.(Monday）
Venue：Admin Building Rm. 205
Abstract
Affinity purification followed by mass spectrometry (AP-MS) has become a commonly used method for the identification of protein-protein interactions and protein complexes. We will start with a review of the most commonly used experimental AP-MS workflows, with an emphasis on data analysis challenges typically encountered in such studies. We will review computational and informatics strategies for detecting specific protein interaction partners in AP-MS experiments, and will contrast computational methods developed for genome-wide interactome mapping studies with those applicable to more frequently generated small to intermediate-scale datasets. We will discuss the current state of the computational tool such as SAINT and CRAPome (www.crapome.org) that were developed in our lab. We will also discuss related issues such as combining multiple biological or technical replicates, dealing with data generated using different tagging strategies, and integration of AP-MS data with structure-based protein interaction predictions. We will also discuss the use of label-free quantification in clustering of AP-MS protein interaction data for improved reconstruction of protein complexes, as well as for detection of quantitative changes in the composition of protein complexes as a function of the cell state.
Biography
Dr. Alexey Nesvizhskii is a tenured Associate Professor in the Departments of Computational Medicine & Bioinformatics and Pathology at the University of Michigan, Ann Arbor. He received his M.S. degree (with honors) from St. Petersburg State Technical University, Department of Physics and Technology, St. Petersburg, Russia in 1995 and Ph.D. degree in Physics from the University of Washington, Seattle, USA, in 2001. He then completed post doctoral training in the area of bioinformatics and proteomics in Ruedi Aebersold Lab at the Institute for Systems Biology in Seattle, Washington from 2001-2003, and joined the staff as a Research Scientist upon completion of training. He joined the faculty at the University of Michigan in November of 2005.
Dr. Nesvizhskii's research laboratory (www.nesvilab.org) is working in the area of bioinformatics, proteomics, and systems biology. The computational tools previously developed by Dr. Nesvizhskii, such as Trans-Proteomic Pipeline (including PeptideProphet and ProteinProphet), PeptideAtlas, SAINT, and CRAPome, are used by hundreds of laboratories worldwide. His lab actively collaborates with technology developers, biologists, and clinical scientists on a variety of projects, including analysis protein interaction networks, integrative modeling of multi-omics data to reconstruct targetable pathways in cancer, and biomarker discovery. Dr. Nesvizhskii’s research is currently funded by the US National Institutes of Health and the National Institute of Standards and Technology.
Dr. Nesvizhskii has published more than 100 manuscripts in international scientific journals, including first or senior author publications in such leading journals as Science, Nature Methods, Molecular Systems Biology, and Nature Communications. His works are cited more than 11,600 times, H-index of 41 (Google Scholar; April 2014). In 2007, he was named a "Rising Young Investigator" by Genome Technology magazine (USA). Dr. Nesvizhskii serves as Senior Editor in the area of bioinformatics and biostatistics for international journals Proteomics and Proteomics-Clinical Applications, as Section Editor in the area of proteomics for BMC Bioinformatics, and on the Editorial Boards of Molecular and Cellular Proteomics. Dr. Nesvizhskii also serves on the Scientific Advisory Board for Swiss Institute of Bioinformatics and on the Board of Directors for the US Human Proteome Organization. He is frequently invited to present his research at seminars and conferences in the United States and internationally, and to serve on grant review panels for the National Institutes of Health (NIH), National Science Foundation, Genome Canada, Dutch Cancer Society, and other agencies.
As an enthusiastic educator, Dr. Nesvizhskii directs the NIH funded T32 Proteome Informatics of Cancer Training Program at the University of Michigan, and teaches graduate-level courses in the area of bioinformatics, proteomics, and systems biology. In addition, he has developed and taught several internationally recognized hands-on workshops and tutorials, including a five day Proteome Informatics course at the Institute for Systems Biology in Seattle. His educational and research efforts have been recognized by several awards, including induction in the League of Educational Excellence at the University of Michigan Medical School.
