Pathway Analysis for Drug Discovery

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 vii

Contributors ix

1 Introduction to Pathway Analysis 1
Anton Yuryev

2 Software Infrastructure and Data Model for Pathway Analysis 27
Fedor Bokov and Anton Yuryev

3 Automatic Pathway Inference in Heterogeneous Biological Association Networks 47
Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia

4 Algorithmic Basis for Pathway Visualization 67
Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin

5 Pathway Analysis of High-Throughput Experimental Data 103
Andrey Y. Sivachenko

6 Integrative Pathway Analysis of Disease Molecular Data 121
Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya

7 Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways,Potential Targets, and Noise 149
John Farley, Laurent L. Ozbun, and Michael J. Birrer

8 Mammalian Proteome and Toxicant Network Analysis 165
Sean Ekins and Craig N. Giroux

9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an IllustrativeExample 195
Mark P. Kühnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic

10 Impact of Chemistry Information on Pathway Analysis 219
Sreenivas Devidas

11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks 237
Sergei Maslov and Iaroslav Ispolatov

12 An Adaptive System Model of the Yeast Glucose Sensor System 263
Todor Vujasinovic and André Siniša Žampera

13 Present and Future of Pathway Analysis in Drug Discovery 285
Anton Yuryev

Index 297