Biological Networks and Pathway Analysis

1. Front Matter

   Pages i-xiv

   PDF

2. A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq)

   • Yunchen Gong, Darrell Desveaux, David S. Guttman, Jennifer D. Lewis

   Pages 1-20

3. sbv IMPROVER: Modern Approach to Systems Biology

   • Svetlana Guryanova, Anna Guryanova

   Pages 21-29

4. Mathematical Justification of Expression-Based Pathway Activation Scoring (PAS)

   • Alexander M. Aliper, Michael B. Korzinkin, Natalia B. Kuzmina, Alexander A. Zenin, Larisa S. Venkova, Philip Yu. Smirnov et al.

   Pages 31-51

5. Bioinformatics Meets Biomedicine: OncoFinder, a Quantitative Approach for Interrogating Molecular Pathways Using Gene Expression Data

   • Anton A. Buzdin, Vladimir Prassolov, Alex A. Zhavoronkov, Nikolay M. Borisov

   Pages 53-83

6. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks

   • Mark D’Souza, Dinanath Sulakhe, Sheng Wang, Bing Xie, Somaye Hashemifar, Andrew Taylor et al.

   Pages 85-99

7. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated “Knowledge-Based” Platform

   • Alexey Dubovenko, Yuri Nikolsky, Eugene Rakhmatulin, Tatiana Nikolskaya

   Pages 101-124

8. Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond

   • Galina Glazko, Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib

   Pages 125-159

9. Search for Master Regulators in Walking Cancer Pathways

   • Alexander E. Kel

   Pages 161-191

10. Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles

    • Vladimir A. Kuznetsov

    Pages 193-276

11. A Weighted SNP Correlation Network Method for Estimating Polygenic Risk Scores

    • Morgan E. Levine, Peter Langfelder, Steve Horvath

    Pages 277-290

12. Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer

    • Martin Triska, Alexander Ivliev, Yuri Nikolsky, Tatiana V. Tatarinova

    Pages 291-310

13. Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

    • Rabie Saidi, Imane Boudellioua, Maria J. Martin, Victor Solovyev

    Pages 311-331

14. ArrayTrack: An FDA and Public Genomic Tool

    • Hong Fang, Stephen C. Harris, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi et al.

    Pages 333-353

15. Identification of Transcriptional Regulators of Psoriasis from RNA-Seq Experiments

    • Alena Zolotarenko, Evgeny Chekalin, Rohini Mehta, Ancha Baranova, Tatiana V. Tatarinova, Sergey Bruskin

    Pages 355-370

16. Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases

    • Guan Ning Lin, Roser Corominas, Hyun-Jun Nam, Jorge Urresti, Lilia M. Iakoucheva

    Pages 371-402

17. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations

    • Sascha Losko, Klaus Heumann

    Pages 403-423

18. Knowledge-Based Compact Disease Models: A Rapid Path from High-Throughput Data to Understanding Causative Mechanisms for a Complex Disease

    • Anatoly Mayburd, Ancha Baranova

    Pages 425-461

19. Pharmacologic Manipulation of Wnt Signaling and Cancer Stem Cells

    • Yann Duchartre, Yong-Mi Kim, Michael Kahn

    Pages 463-478

20. Functional Network Disruptions in Schizophrenia

    • Irina Rish, Guillermo A. Cecchi

    Pages 479-504

In this volume, expert practitioners present a compilation of methods of functional data analysis (often referred to as “systems biology”) and its applications in drug discovery, medicine, and basic disease research.  It covers such important issues as the elucidation of protein, compound and gene interactions, as well as analytical tools, including networks, interactome and ontologies, and clinical applications of functional analysis.  As a volume in the highly successful Methods in Molecular Biology series, this work provides detailed description and hands-on implementation advice. 

Reputable, comprehensive, and cutting-edge, Biological Networks and Pathway Analysis presents both “wet lab” experimental methods and computational tools in order to cover a broad spectrum of issues in this fascinating new field.

• Protein-protein interaction modeling
• Functional data analysis
• Protein functionality
• Bioinformatics
• Computational biology
• Databases
• Network algorithms
• Software tools

• Keck School of Medicine, University of Southern California, Los Angeles, USA

  Tatiana V. Tatarinova

• Prosapia Genetics, Solana Beach, USA

  Yuri Nikolsky

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