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Next Generation Microarray Bioinformatics

Methods and Protocols

  • Book
  • © 2012

Overview

Editors:
  1. Junbai Wang

    1. Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway

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  2. Aik Choon Tan

    1. School of Medicine, University of Colorado Denver, Aurora, USA

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    You can also search for this editor in PubMed   Google Scholar

  3. Tianhai Tian

    1. School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom

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    You can also search for this editor in PubMed   Google Scholar

  • Next Generation Sequencing technology opens up new research avenues for the investigation of a wide range of biological and medical questions across the entire genome at single base resolution
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 802)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xvi
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  2. Introduction and Resources for Microarray Bioinformatics

    1. Front Matter

      Pages 1-1
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  3. INTRODUCTION AND RESOURCES FOR MICROARRAY BIOINFORMATICS

    1. A Primer on the Current State of Microarray Technologies

      • Alexander J. Trachtenberg, Jae-Hyung Robert, Azza E. Abdalla, Andrew Fraser, Steven Y. He, Jessica N. Lacy et al.
      Pages 3-17

    2. The KEGG Databases and Tools Facilitating Omics Analysis: Latest Developments Involving Human Diseases and Pharmaceuticals

      • Masaaki Kotera, Mika Hirakawa, Toshiaki Tokimatsu, Susumu Goto, Minoru Kanehisa
      Pages 19-39

    3. Strategies to Explore Functional Genomics Data Sets in NCBI’s GEO Database

      • Stephen E. Wilhite, Tanya Barrett
      Pages 41-53

  4. Microarray Data Analysis (Top-Down Approach)

    1. Front Matter

      Pages 55-55
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  5. MICROARRAY DATA ANALYSIS (TOP DOWN APPROACH)

    1. Analyzing Cancer Samples with SNP Arrays

      • Peter Van Loo, Gro Nilsen, Silje H. Nordgard, Hans Kristian Moen Vollan, Anne-Lise Børresen-Dale, Vessela N. Kristensen et al.
      Pages 57-72

    2. Classification Approaches for Microarray Gene Expression Data Analysis

      • Leo Wang-Kit Cheung
      Pages 73-85

    3. Biclustering of Time Series Microarray Data

      • Jia Meng, Yufei Huang
      Pages 87-100

    4. Using the Bioconductor GeneAnswers Package to Interpret Gene Lists

      • Gang Feng, Pamela Shaw, Steven T. Rosen, Simon M. Lin, Warren A. Kibbe
      Pages 101-112

    5. Analysis of Isoform Expression from Splicing Array Using Multiple Comparisons

      • T. Murlidharan Nair
      Pages 113-121

    6. Functional Comparison of Microarray Data Across Multiple Platforms Using the Method of Percentage of Overlapping Functions

      • Zhiguang Li, Joshua C. Kwekel, Tao Chen
      Pages 123-139

    7. Performance Comparison of Multiple Microarray Platforms for Gene Expression Profiling

      • Fang Liu, Winston P. Kuo, Tor-Kristian Jenssen, Eivind Hovig
      Pages 141-155

    8. Integrative Approaches for Microarray Data Analysis

      • Levi Waldron, Hilary A. Coller, Curtis Huttenhower
      Pages 157-182

  6. Microarray Bioinformatics in Systems Biology (Bottom-Up Approach)

    1. Front Matter

      Pages 183-183
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  7. MICROARRAY BIOINFORMATICS IN SYSTEMS BIOLOGY (BOTTOM UP APPROACH)

    1. Modeling Gene Regulation Networks Using Ordinary Differential Equations

      • Jiguo Cao, Xin Qi, Hongyu Zhao
      Pages 185-197

    2. Nonhomogeneous Dynamic Bayesian Networks in Systems Biology

      • Sophie Lèbre, Frank Dondelinger, Dirk Husmeier
      Pages 199-213

    3. Inference of Regulatory Networks from Microarray Data with R and the Bioconductor Package qpgraph

      • Robert Castelo, Alberto Roverato
      Pages 215-233

    4. Effective Non-linear Methods for Inferring Genetic Regulation from Time-Series Microarray Gene Expression Data

      • Junbai Wang, Tianhai Tian
      Pages 235-246

  8. Next Generation Sequencing Data Analysis

    1. Front Matter

      Pages 247-247
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Keywords

About this book

 Recent improvements in the efficiency, quality, and cost of genome-wide sequencing have prompted biologists and biomedical researchers to move away from microarray-based technology to ultra high-throughput, massively parallel genomic sequencing (Next Generation Sequencing, NGS) technology. In Next Generation Microarray Bioinformatics: Methods and Protocols, expert researchers in the field provide techniques to bring together current computational and statistical methods to analyze and interpreting both microarray and NGS data. These methods and techniques include resources for microarray bioinformatics, microarray data analysis, microarray bioinformatics in systems biology, next generation sequencing data analysis, and emerging applications of microarray and next generation sequencing. Written in the highly successful Methods in Molecular Biology™ series format, the chapters include the kind of detailed description and implementation advice that is crucial for getting optimal results in the laboratory.

 

Authoritative and practical, Next Generation Microarray Bioinformatics: Methods and Protocols seeks to aid scientists in the further study of this crucially important research into the human DNA.

Editors and Affiliations

  • Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway

    Junbai Wang

  • School of Medicine, University of Colorado Denver, Aurora, USA

    Aik Choon Tan

  • School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom

    Tianhai Tian

Bibliographic Information

  • Book Title: Next Generation Microarray Bioinformatics

  • Book Subtitle: Methods and Protocols

  • Editors: Junbai Wang, Aik Choon Tan, Tianhai Tian

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-400-1

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2012

  • Hardcover ISBN: 978-1-61779-399-8Published: 01 December 2011

  • Softcover ISBN: 978-1-4939-5857-3Published: 23 August 2016

  • eBook ISBN: 978-1-61779-400-1Published: 02 December 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 401

  • Topics: Bioinformatics

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