Chapter 1. Introduction to Pathway analysis (Anton Yuryev).

Chapter 2. Software Infrastructure and data model for pathway analysis (Fedor Bokov, and Anton Yuryev).

Chapter 3. Automatic Pathway Inference in Heterogeneous Biological Association Networks (Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia).

Chapter 4. Algorithmic Basis for Pathway Visualization (Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov and Alexander Nikitin).

Chapter 5. Pathway Analysis of High-Throughput Experimental Data (Andrey Y Sivachenko).

Chapter 6. Integrative Pathway analysis of disease molecular data (Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky and Tatiana Nikolskaya).

Chapter 7. Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways, Potential Targets and Noise (John Farley, Laurent L. Ozbun, and Michael J. Birrer).

Chapter 8. Mammalian Proteome and Toxicant Network Analysis (Sean Ekins and Craig N. Giroux).

Chapter 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).

Chapter 10. Impact of Chemistry Information on Pathway Analysis (Sreenivas Devidas).

Chapter 11. Propagation of concentration perturbations in equilibrium protein binding networks (Sergei Maslov).

Chapter 12. An adaptive system model of the Yeast glucose sensor system (Todor Vujasinovic, and André Sinisa Zampera).

Chapter 13. Present and future of pathway analysis in drug discovery (Anton Yuryev).