Machine Learning Seminar
Speaker: Gennady Verkhivker, Chapman University and University of California, San Diego
Title: Modeling and Engineering of Regulatory Mechanisms in Biomolecules: A Symbiotic Platform of Computational Biophysics, Network Science and Machine Learning Approaches
Refreshments available at 2 pm.
Date: Mon, 10 Sep 2018, 2:15 pm – 3:15 pm
Location: 1400 BPS Bldg.
The allosteric interactions and regulation of signaling proteins allow for molecular communication and event coupling in signal transduction pathways and networks. We report the results of integrative systems biology studies of signaling proteins offering novel insights into organizing principles of regulation. Network modelling and percolation analysis approaches were used to emulate thermal unfolding and characterize conformational landscapes of a wide range of signaling proteins that explained divergences in their regulatory mechanisms. The results of biophysical and computational systems biology analyses combined with proteomics experiments have been incorporated into a graph-based network model of allosteric regulation. A symbiosis of computational systems biology and machine learning approaches is then used to construct models of allosteric regulation of oncogenic proteins in signaling cascades. Based on these findings, we developed a computational synthetic biology framework for design and re-engineering signal transduction networks and pathways that involve cross-talk between molecular chaperones and protein kinase proteins… We have also analyzed mechaisms by which cancer drugs may act synergistically and exert their pharmacological effect by modulating protein interaction networks. Our study offers a systems-based perspective on drug design and re-engineering of signaling networks by unravelling relationships between protein kinase networks with molecular chaperones and binding specificity of targeted kinase drugs.
Dr. Verkhivker is currently Professor of Computational Biosciences and Translational Medicine at College of Science & Technology, Chapman Univerity and Professor at the Department of Biomedical and Pharmaceutical Sciences at Chapman University School of Pharmacy. He is also Adjunct Professor of Pharmacology at the Department of Pharmacology, and Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego. Dr. Verkhivker received his PhD in Physical Chemistry from Moscow State University and completed a postdoctoral fellowship in computational biophysics from University of Illinois at Chicago in 1992. Dr. Verkhivker was one of the founding scientists at Agouron Pharmaceuticals Inc, in early 1990s and played a leading role in establishing computer-aided structure-based design technology. In 1993–2006, Dr. Verkhivker has held various research and management positions at Agouron Pharmaceuticals, Warner-Lambert, Pfizer Global Research and Development. He has been Director of Computational Sciences at Pfizer Global Research and Development, in 2001–2005. Since 2002, he has been Adjunct Professor of Pharmacology at the Skaggs School of Pharmacy and Pharmaceutical Sciences, UC San Diego. In 2006, he joined School of Pharmacy and Center for Bioinformatics, The University of Kansas as a Full Professor of Pharmaceutical Chemistry and Bioinformatics. In 2011 Dr. Verkhivker assumed position of Full Professor of Computational Biosciences & Translational Medicine at Schmid College of Science & Technology and Founding Professor at Chapman University School of Pharmacy. Dr. Verkhivker authored more than 150 peer reviewed publications and is recognized for his research contributions in the fields of translational bioinformatics, computational biophysics, computational and mathematical biology. His most recent research activities are in the areas of computational systems biology, translational bioinformatics, network science and artificial intelligence with the focus on application of these approaches in translational cancer research.