Biological networks and pathway analysis

✍ Scribed by Nikolsky, Yuri; Tatarinova, Tatiana V

• Publisher: Humana Press
• Year: 2017
• Tongue: English
• Leaves: 513
• Series: Methods in molecular biology
• Category: Library

✦ Synopsis

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. Read more...

Abstract:

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. Read more...

✦ Table of Contents

Front Matter ....Pages i-xiv
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
sbv IMPROVER: Modern Approach to Systems Biology (Svetlana Guryanova, Anna Guryanova)....Pages 21-29
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
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
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
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
Extracting the Strongest Signals from Omics Data: Differentially Expressed Pathways and Beyond (Galina Glazko, Yasir Rahmatallah, Boris Zybailov, Frank Emmert-Streib)....Pages 125-159
Search for Master Regulators in Walking Cancer Pathways (Alexander E. Kel)....Pages 161-191
Mathematical Modeling of Avidity Distribution and Estimating General Binding Properties of Transcription Factors from Genome-Wide Binding Profiles (Vladimir A. Kuznetsov)....Pages 193-276
A Weighted SNP Correlation Network Method for Estimating Polygenic Risk Scores (Morgan E. Levine, Peter Langfelder, Steve Horvath)....Pages 277-290
Analysis of cis-Regulatory Elements in Gene Co-expression Networks in Cancer (Martin Triska, Alexander Ivliev, Yuri Nikolsky, Tatiana V. Tatarinova)....Pages 291-310
Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways (Rabie Saidi, Imane Boudellioua, Maria J. Martin, Victor Solovyev)....Pages 311-331
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
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
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
Semantic Data Integration and Knowledge Management to Represent Biological Network Associations (Sascha Losko, Klaus Heumann)....Pages 403-423
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
Pharmacologic Manipulation of Wnt Signaling and Cancer Stem Cells (Yann Duchartre, Yong-Mi Kim, Michael Kahn)....Pages 463-478
Functional Network Disruptions in Schizophrenia (Irina Rish, Guillermo A. Cecchi)....Pages 479-504
Back Matter ....Pages 505-509

✦ Subjects

Systems biology -- Laboratory manuals;Biomathematics -- Laboratory manuals;Biomathematics;Systems biology