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Bioinformatics for Comparative Proteomics

  • Book
  • © 2011

Overview

Editors:
  1. Cathy H. Wu

    1. Delaware Biotechnology Institute, Dept. Computer & Information Sciences, University of Delaware, Newark, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Chuming Chen

    1. Delaware Biotechnology Institute, Dept. Computer & Information Sciences, University of Delaware, Newark, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Contains state-of-the-art bioinformatics databases and tools, novel computational methods and future trends in proteomics data analysis
  • Features comparative proteomics in systems biology
  • Presents material in an interdisciplinary fashion applicable to biotech and pharmaceutical scientists as well as biological, medical, and computational scientists and engineers
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 694)

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Table of contents (22 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Bioinformatics Framework for Comparative Proteomics

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Protein Bioinformatics Databases and Resources

      • Chuming Chen, Hongzhan Huang, Cathy H. Wu
      Pages 3-24

    3. A Guide to UniProt for Protein Scientists

      • Claire O’Donovan, Rolf Apweiler
      Pages 25-35

    4. InterPro Protein Classification

      • Jennifer McDowall, Sarah Hunter
      Pages 37-47

    5. Reactome Knowledgebase of Human Biological Pathways and Processes

      • Peter D’Eustachio
      Pages 49-61

    6. eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature

      • Cecilia N. Arighi, Amy Y. Siu, Catalina O. Tudor, Jules A. Nchoutmboube, Cathy H. Wu, Vijay K. Shanker
      Pages 63-75

    7. A Tutorial on Protein Ontology Resources for Proteomic Studies

      • Cecilia N. Arighi
      Pages 77-90

    8. Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase

      • Sona Vasudevan, C. R. Vinayaka, Darren A. Natale, Hongzhan Huang, Robel Y. Kahsay, Cathy H. Wu
      Pages 91-105

  3. Proteomic Bioinformatics

    1. Front Matter

      Pages 107-107
      Download chapter PDF

    2. Modeling Mass Spectrometry-Based Protein Analysis

      • Jan Eriksson, David Fenyö
      Pages 109-117

    3. Protein Identification from Tandem Mass Spectra by Database Searching

      • Nathan J. Edwards
      Pages 119-138

    4. LC-MS Data Analysis for Differential Protein Expression Detection

      • Rency S. Varghese, Habtom W. Ressom
      Pages 139-150

    5. Protein Identification by Spectral Networks Analysis

      • Nuno Bandeira
      Pages 151-168

    6. Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline

      • Andrew Keller, David Shteynberg
      Pages 169-189

    7. Analysis of High-Throughput ELISA Microarray Data

      • Amanda M. White, Don S. Daly, Richard C. Zangar
      Pages 191-211

    8. Proteomics Databases and Repositories

      • Lennart Martens
      Pages 213-227

    9. Preparing Molecular Interaction Data for Publication

      • Sandra Orchard, Henning Hermjakob
      Pages 229-236

    10. Submitting Proteomics Data to PRIDE Using PRIDE Converter

      • Harald Barsnes, Juan Antonio Vizcaíno, Florian Reisinger, Ingvar Eidhammer, Lennart Martens
      Pages 237-253

    11. Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine

      • Stuart R. Jefferys, Morgan C. Giddings
      Pages 255-290
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Keywords

About this book

With the rapid development of proteomic technologies in the life sciences and in clinical applications, many bioinformatics methodologies, databases, and software tools have been developed to support comparative proteomics study. In Bioinformatics for Comparative Proteomics, experts in the field highlight the current status, challenges, open problems, and future trends for developing bioinformatics tools and resources for comparative proteomics research in order to deliver a definitive reference providing both the breadth and depth needed on the subject. Structured in three major sections, this detailed volume covers basic bioinformatics frameworks relating to comparative proteomics, bioinformatics databases and tools for proteomics data analysis, and integrated bioinformatics systems and approaches for studying comparative proteomics in the systems biology context. Written for the highly successful Methods in Molecular Biology™ series, the contributions in this book provide the meticulous, step-by-step description and implementation advice that is crucial for getting optimal results in the lab. Comprehensive and easy-to-use, Bioinformatics for Comparative Proteomics serves all readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods and future trends in proteomics data analysis, and comparative proteomics in systems biology.

Reviews

From the reviews:

“This book provides comprehensive coverage of the current status, challenges, open problems, and future trends in developing bioinformatics tools and resources for comparative proteomics research. … The audience ranges from graduate students embarking upon a research project to practicing biologists and bioinformaticians. This broad audience working in biotechnology and pharmaceutical companies and in various academic departments … will find this book quite useful. … This well-illustrated book is a comprehensive resource on bioinformatics for comparative proteomics.” (Omer Iqbal, Doody’s Book Reviews, March, 2012)

Editors and Affiliations

  • Delaware Biotechnology Institute, Dept. Computer & Information Sciences, University of Delaware, Newark, USA

    Cathy H. Wu, Chuming Chen

Bibliographic Information

  • Book Title: Bioinformatics for Comparative Proteomics

  • Editors: Cathy H. Wu, Chuming Chen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-60761-977-2

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media LLC 2011

  • Hardcover ISBN: 978-1-60761-976-5Published: 19 November 2010

  • Softcover ISBN: 978-1-4939-5790-3Published: 23 August 2016

  • eBook ISBN: 978-1-60761-977-2Published: 17 November 2010

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 387

  • Topics: Bioinformatics, Proteomics

  • Industry Sectors: Biotechnology

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