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 viiContributors ix1 Introduction to Pathway Analysis 1Anton Yuryev2 Software Infrastructure and Data Model for Pathway Analysis 27Fedor Bokov and Anton Yuryev3 Automatic Pathway Inference in Heterogeneous Biological Association Networks 47Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia4 Algorithmic Basis for Pathway Visualization 67Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin5 Pathway Analysis of High-Throughput Experimental Data 103Andrey Y. Sivachenko6 Integrative Pathway Analysis of Disease Molecular Data 121Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya7 Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways,Potential Targets, and Noise 149John Farley, Laurent L. Ozbun, and Michael J. Birrer8 Mammalian Proteome and Toxicant Network Analysis 165Sean Ekins and Craig N. Giroux9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an IllustrativeExample 195Mark P. Kühnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic10 Impact of Chemistry Information on Pathway Analysis 219Sreenivas Devidas11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks 237Sergei Maslov and Iaroslav Ispolatov12 An Adaptive System Model of the Yeast Glucose Sensor System 263Todor Vujasinovic and André Siniša Žampera13 Present and Future of Pathway Analysis in Drug Discovery 285Anton YuryevIndex 297

"Pathway analysis will help lead to a better understanding of the chemistry of living systems and the aberrations that disrupt health. This new book will serve as a beacon to research interested in this field." (Journal of Medicinal Chemistry, April 9, 2009)

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 viiContributors ix1 Introduction to Pathway Analysis 1Anton Yuryev2 Software Infrastructure and Data Model for Pathway Analysis 27Fedor Bokov and Anton Yuryev3 Automatic Pathway Inference in Heterogeneous Biological Association Networks 47Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia4 Algorithmic Basis for Pathway Visualization 67Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin5 Pathway Analysis of High-Throughput Experimental Data 103Andrey Y. Sivachenko6 Integrative Pathway Analysis of Disease Molecular Data 121Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya7 Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways,Potential Targets, and Noise 149John Farley, Laurent L. Ozbun, and Michael J. Birrer8 Mammalian Proteome and Toxicant Network Analysis 165Sean Ekins and Craig N. Giroux9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an IllustrativeExample 195Mark P. Kühnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic10 Impact of Chemistry Information on Pathway Analysis 219Sreenivas Devidas11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks 237Sergei Maslov and Iaroslav Ispolatov12 An Adaptive System Model of the Yeast Glucose Sensor System 263Todor Vujasinovic and André Siniša Žampera13 Present and Future of Pathway Analysis in Drug Discovery 285Anton YuryevIndex 297

"Pathway analysis will help lead to a better understanding of the chemistry of living systems and the aberrations that disrupt health. This new book will serve as a beacon to research interested in this field." (Journal of Medicinal Chemistry, April 9, 2009)

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 viiContributors ix1 Introduction to Pathway Analysis 1Anton Yuryev2 Software Infrastructure and Data Model for Pathway Analysis 27Fedor Bokov and Anton Yuryev3 Automatic Pathway Inference in Heterogeneous Biological Association Networks 47Anton Yuryev, Andrey Kalinin, and Nikolai Daraselia4 Algorithmic Basis for Pathway Visualization 67Sergey Simakov, Iaroslav Ispolatov, Sergei Maslov, and Alexander Nikitin5 Pathway Analysis of High-Throughput Experimental Data 103Andrey Y. Sivachenko6 Integrative Pathway Analysis of Disease Molecular Data 121Andrej Bugrim, Zoltan Dezso, Yuri Nikolsky, and Tatiana Nikolskaya7 Whole-Genome Expression Profiling of Papillary Serous Ovarian Cancer: Activated Pathways,Potential Targets, and Noise 149John Farley, Laurent L. Ozbun, and Michael J. Birrer8 Mammalian Proteome and Toxicant Network Analysis 165Sean Ekins and Craig N. Giroux9 Unraveling Mechanisms of Toxicity with the Power of Pathways: ToxWiz Tool as an IllustrativeExample 195Mark P. Kühnel, Bojana Cosovic, Goran Medic, Robert B. Russell, and Gordana Apic10 Impact of Chemistry Information on Pathway Analysis 219Sreenivas Devidas11 Propagation of Concentration Perturbations in Equilibrium Protein Binding Networks 237Sergei Maslov and Iaroslav Ispolatov12 An Adaptive System Model of the Yeast Glucose Sensor System 263Todor Vujasinovic and André Siniša Žampera13 Present and Future of Pathway Analysis in Drug Discovery 285Anton YuryevIndex 297

"Pathway analysis will help lead to a better understanding of the chemistry of living systems and the aberrations that disrupt health. This new book will serve as a beacon to research interested in this field." (Journal of Medicinal Chemistry, April 9, 2009)