Bioinformatics for Comparative Proteomics

ISBN-13: 9781493957903 / Angielski / Miękka / 2016 / 387 str.

Cathy H. Wu; Chuming Chen

Opis

This book covers bioinformatics frameworks relating to comparative proteomics, bioinformatics databases and tools for proteomics data analysis, and integrated systems and approaches to studying comparative proteomics in the systems biology context.

Recenzje

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)

Spis treści

Part I: Bioinformatics Framework for Comparative Proteomics 1. Protein Bioinformatics Databases and Resources Chuming Chen, Hongzhan Huang, and Cathy H. Wu 2. A Guide to UniProt for Protein Scientists Claire O’Donovan and Rolf Apweiler 3. InterPro Protein Classification Jennifer McDowall and Sarah Hunter 4. Reactome Knowledgebase of Human Biological Pathways and Processes Peter D'Eustachio 5. 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, and Vijay K. Shanker 6. A Tutorial on Protein Ontology Resources for Proteomic Studies Cecilia N. Arighi 7. 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, and Cathy H. Wu Part II: Proteomic Bioinformatics 8. Modeling Mass Spectrometry-Based Protein Analysis Jan Eriksson and David Fenyö 9. Protein Identification from Tandem Mass Spectra by Database Searching Nathan J. Edwards 10. LC-MS Data Analysis for Differential Protein Expression Detection Rency S. Varghese and Habtom W. Ressom 11. Protein Identification by Spectral Networks Analysis Nuno Bandeira 12. Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline Andrew Keller and David Shteynberg 13. Analysis of High-Throughput ELISA Microarray Data Amanda M. White, Don S. Daly, and Richard C. Zangar 14. Proteomics Databases and Repositories Lennart Martens 15. Preparing Molecular Interaction Data for Publication Sandra Orchard and Henning Hermjakob 16. Submitting Proteomics Data to PRIDE Using PRIDE Converter Harald Barsnes, Juan Antonio Vizcaíno, Florian Reisinger, Ingvar Eidhammer, and Lennart Martens 17. Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine Stuart R. Jefferys and Morgan C. Giddings 18. An Integrated Top-Down and Bottom-Up Strategy for Broadly Characterizing Protein Isoforms and Modifications Si Wu, Nikola Tolić, Zhixin Tian, Errol W. Robinson, and Ljiljana Paša-Tolić Part III: Comparative Proteomics in Systems Biology 19. Phosphoproteome Resource for Systems Biology Research Bernd Bodenmiller and Ruedi Aebersold 20. Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data Peter B. McGarvey, Jian Zhang, Darren A. Natale, Cathy H. Wu, and Hongzhan Huang 21. Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks Patrick May, Nils Christian, Oliver Ebenhöh, Wolfram Weckwerth, and Dirk Walther 22. Time Series Proteome Profiling Catherine A. Formolo, Michelle Mintz, Asako Takanohashi, Kristy J. Brown, Adeline Vanderver, Brian Halligan, and Yetrib Hathout

Blurb

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.