About this book
In Biological Networks and Pathway Analysis, 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 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.
Contents
1. A Practical Guide to Quantitative Interactor Screening with Next-Generation Sequencing (QIS-Seq) / Yunchen Gong, Darrell Desveaux, David S. Guttman, and Jennifer D. Lewis
2. sbv IMPROVER: Modern Approach to Systems Biology / Svetlana Guryanova and Anna Guryanova
3. 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, Alex A. Zhavoronkov, Anton A. Buzdin, and Nikolay M. Borisov
4. Bioinformatics Meets Biomedicine: OncoFinder, a Quantitative Approach for Interrogating Molecular Pathways Using Gene Expression Data / Anton A. Buzdin, Vladimir Prassolov, Alex A. Zhavoronkov, and Nikolay M. Borisov
5. 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, Inna Dubchak, T. Conrad Gilliam, and Natalia Maltsev
6. Functional Analysis of OMICs Data and Small Molecule Compounds in an Integrated "Knowledge-Based" Platform / Alex Dubovenko, Yuri Nikolsky, Eugene Rakhmatulin, and Tatiana Nikolskaya
7. Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond / Galina Glazko, Yasir Rahmatallah, Boris Zybailov, and Frank Emmert-Streib
8. Search for Master Regulators in Walking Cancer Pathways / Alexander E. Kel
9. Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles / Vladimir A. Kuznetsov
10. A Weighted SNP Correlation Network Method for Estimating Polygenic Risk Scores / Morgan E. Levine, Peter Langfelder, and Steve Horvath
11. Analysis of cis-Regulatory Elements in Gene Co-Expression Networks in Cancer / Martin Triska, Alexander Ivliev, Yuri Nikolsky, and Tatiana V. Tatarinova
12. Applying Association Rule Mining Techniquest to Predict Procaryotic Metabolic Pathways / Imane Boudellioua, Rabie Saidi, Robert Hoehndorf, Maria J. Martin, and Victor Solovyev
13. ArrayTrack: An FDA and Public Genomic Tool / Hong Fang, Stephen C. Harris, Zhenjiang Su, Minjun Chen, Feng Qian, Leming Shi, Roger Perkins, and Weida Tong
14. Identification of Transcriptional Regulators of Psoriasis from RNA-Seq Experiments / Alena Zolotarenko, Evgeny Chekalin, Ancha Baranova, Tatiana V. Tatarinova, and Sergey Bruskin
15. Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases / Guan Ning Lin, Roser Corominas, Hyun-Jun Nam, Jorge Urresti, and Lilia M. Iakoucheva
16. Semantic Data Integration and Knowledge Management to Represent Biological Network Associations / Sascha Losko and Klaus Heumann
17. Knowledge-Based Compact Disease Models: A Rapid Path from High-Throughput Data to Understanding Causative Mechanisms for a Complex Disease / Anatoly Mayburd and Ancha Baranova
18. Pharmacologic Manipulation of Wnt Signaling and Cancer Stem Cells / Yann Duchartre, Yong-mi Kim, and Michael Kahn
19. Functional Network Disruptions in Schizophrenia / Irina Rish and Guillermo A. Cecchi
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