Pathway Analysis for Drug Discovery – Infrastructure and Applications

ANTON YURYEV, PhD, is the Senior Director of Application Science at Ariadne Genomics Inc. His department studies the topological and evolutionary properties of biological networks and develops algorithms for pathway reconstruction and analysis of high-throughput data. Dr. Yuryev has published more than thirty scientific publications and is the author of several algorithms for primer design and pathway analysis.

Preface. Contributors. 1 Introduction to Pathway Analysis ( Anton Yuryev ). 2 Software Infrastructure and Data Model for Pathway Analysis ( Fedor Bokov and Anton Yuryev ). 3 Automatic Pathway Inference in Heterogeneous Biological Association Networks ( Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia ). 4 Algorithmic Basis for Pathway Visualization ( Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin ). 5 Pathway Analysis of High-Throughput Experimental Data ( Andrey Y. Sivachenko ). 6 Integrative Pathway Analysis of Disease Molecular Data ( Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya ). 7 Whole-Genome Expression Profi ling of Papillary Serous Ovarian Cancer: Activated Pathways, Potential Targets, and Noise ( John Farley, Laurent L. Ozbun, and Michael J. Birrer ). 8 Mammalian Proteome and Toxicant Network Analysis ( Sean Ekins and Craig N. Giroux ). 9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an Illustrative Example ( Mark P. Kuhnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic ). 10 Impact of Chemistry Information on Pathway Analysis ( Sreenivas Devidas ). 11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks ( Sergei Maslov and Iaroslav Ispolatov ). 12 An Adaptive System Model of the Yeast Glucose Sensor System ( Todor Vujasinovic and Andre Sinisa Zampera ). 13 Present and Future of Pathway Analysis in Drug Discovery ( Anton Yuryev ). Index.