Biological Networks and Pathway Analysis

ISBN-13: 9781493970254 / Angielski / Twarda / 2017 / 509 str.

Tatiana V. Tatarinova; Yuri Nikolsky

Opis

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.

Spis treści

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