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Bioinformatics for Omics Data

Methods and Protocols

  • Book
  • © 2011

Overview

Editors:
  1. Bernd Mayer

    1. emergentec biodevelopment GmbH, Vienna, Austria

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  • Provides solid practical guidelines as well as inspiration for continuing the study of this complex field
  • Serves scientists with concrete implementation advice for many computational applications
  • Includes expert tips for troubleshooting and avoiding known pitfalls
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 719)

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Table of contents (26 protocols)

  1. Front Matter

    Pages i-xii
    Download chapter PDF

  2. Omics Bioinformatics Fundamentals

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Omics Technologies, Data and Bioinformatics Principles

      • Maria V. Schneider, Sandra Orchard
      Pages 3-30

    3. Data Standards for Omics Data: The Basis of Data Sharing and Reuse

      • Stephen A. Chervitz, Eric W. Deutsch, Dawn Field, Helen Parkinson, John Quackenbush, Phillipe Rocca-Serra et al.
      Pages 31-69

    4. Omics Data Management and Annotation

      • Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran, Doron Lancet
      Pages 71-96

    5. Data and Knowledge Management in Cross-Omics Research Projects

      • Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de Abreu Madeira, Gernot Glöckler, Paul Perco et al.
      Pages 97-111

    6. Statistical Analysis Principles for Omics Data

      • Daniela Dunkler, Fátima Sánchez-Cabo, Georg Heinze
      Pages 113-131

    7. Statistical Methods and Models for Bridging Omics Data Levels

      • Simon Rogers
      Pages 133-151

    8. Analysis of Time Course Omics Datasets

      • Martin G. Grigorov
      Pages 153-172

    9. The Use and Abuse of -Omes

      • Sonja J. Prohaska, Peter F. Stadler
      Pages 173-196

  3. Omics Data and Analysis Tracks

    1. Front Matter

      Pages 197-197
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    2. Computational Analysis of High Throughput Sequencing Data

      • Steve Hoffmann
      Pages 199-217

    3. Analysis of Single Nucleotide Polymorphisms in Case–Control Studies

      • Yonghong Li, Dov Shiffman, Rainer Oberbauer
      Pages 219-234

    4. Bioinformatics for Copy Number Variation Data

      • Melissa Warden, Roger Pique-Regi, Antonio Ortega, Shahab Asgharzadeh
      Pages 235-249

    5. Processing ChIP-Chip Data: From the Scanner to the Browser

      • Pierre Cauchy, Touati Benoukraf, Pierre Ferrier
      Pages 251-268

    6. Insights into Global Mechanisms and Disease by Gene Expression Profiling

      • Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo, Zlatko Trajanoski, Hubert Hackl
      Pages 269-298

    7. Bioinformatics for RNomics

      • Kristin Reiche, Katharina Schutt, Kerstin Boll, Friedemann Horn, Jörg Hackermüller
      Pages 299-330

    8. Bioinformatics for Qualitative and Quantitative Proteomics

      • Chris Bielow, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert
      Pages 331-349

    9. Bioinformatics for Mass Spectrometry-Based Metabolomics

      • David P. Enot, Bernd Haas, Klaus M. Weinberger
      Pages 351-375

  4. Applied Omics Bioinformatics

    1. Front Matter

      Pages 377-377
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Keywords

About this book

Presenting an area of research that intersects with and integrates diverse disciplines, including molecular biology, applied informatics, and statistics, among others, Bioinformatics for Omics Data: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study.  Divided into three convenient sections, this detailed volume covers central analysis strategies, standardization and data-management guidelines, and fundamental statistics for analyzing Omics profiles, followed by a section on bioinformatics approaches for specific Omics tracks, spanning genome, transcriptome, proteome, and metabolome levels, as well as an assortment of examples of integrated Omics bioinformatics applications, complemented by case studies on biomarker and target identification in the context of human disease.  Written in the highly successful Methods in Molecular Biology™ series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

 

Authoritative and accessible, Bioinformatics for Omics Data: Methods and Protocols serves as an ideal guide to scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this research field.

Editors and Affiliations

  • emergentec biodevelopment GmbH, Vienna, Austria

    Bernd Mayer

Bibliographic Information

  • Book Title: Bioinformatics for Omics Data

  • Book Subtitle: Methods and Protocols

  • Editors: Bernd Mayer

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-027-0

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-61779-026-3Published: 03 March 2011

  • Softcover ISBN: 978-1-4939-5780-4Published: 23 August 2016

  • eBook ISBN: 978-1-61779-027-0Published: 03 March 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 584

  • Topics: Bioinformatics, Systems Biology, Computer Appl. in Life Sciences

  • Industry Sectors: Biotechnology

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