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This book introduces drug researchers to the novel computational approaches of pathway analysis and explains the existing applications that can save time and money in the drug discovery process. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. It explains pathway reconstruction of diseases and toxic states, pathway analysis in various phases, dynamic modeling of drug responses, and more. This is a core resource for drug discovery and pharmaceutical industry researchers, chemists, and biologists and for professionals in related fields.
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. Kühnel, 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 André Siniša Žampera).
13 Present and Future of Pathway Analysis in Drug Discovery (Anton Yuryev).