Bioinformatics for Omics Data: Methods and Protocols

ISBN-13: 9781617790263 / Angielski / Twarda / 2011 / 584 str.

Bernd Mayer

Opis

Presenting an area of research that intersects with and integrates diverse disciplines, 'Bioinformatics for Omics Data' collects contributions from expert researchers in order to provide practical guidelines to this complex study. It serves as an ideal guide to scientists of all backgrounds.

Spis treści

Part I: Omics Bioinformatics Fundamentals

 

1. Omics Technologies, Data, and Bioinformatics Principles

            Maria V. Schneider and Sandra Orchard

 

2. 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, Susanna-Assunta Sansone, Christian J. Stoeckert, Jr., Chris F. Taylor, Ronald Taylor, and Catherine A. Ball

 

3. Omics Data Management and Annotation

            Arye Harel, Irina Dalah, Shmuel Pietrokovski, Marilyn Safran, and Doron Lancet

 

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

            Martin Wiesinger, Martin Haiduk, Marco Behr, Henrique Lopes de Abreu Madeira, Gernot Glöckler, Paul Perco, and Arno Lukas

 

5. Statistical Analysis Principles for Omics Data

            Daniela Dunkler, Fátima Sánchez-Cabo, and Georg Heinze

 

6. Statistical Methods and Models for Bridging Omics Data Levels

            Simon Rogers

 

7. Analysis of Time Course Omics Datasets

            Martin G. Grigorov

 

8. The Use and Abuse of -Omes

            Sonja J. Prohaska and Peter F. Stadler

 

Part II: Omics Data and Analysis Tracks

 

9. Computational Analysis of High Throughput Sequencing Data

            Steve Hoffmann

 

10. Analysis of Single Nucleotide Polymorphisms in Case-Control Studies

            Yonghong Li, Dov Shiffman, and Rainer Oberbauer

 

11. Bioinformatics for Copy Number Variation Data

            Melissa Warden, Roger Pique-Regi, Antonio Ortega, and Shahab Asgharzadeh

 

12. Processing ChIP-chip Data: From the Scanner to the Browser

            Pierre Cauchy, Touati Benoukraf, and Pierre Ferrier

 

13. Insights Into Global Mechanisms and Disease by Gene Expression Profiling

            Fátima Sánchez-Cabo, Johannes Rainer, Ana Dopazo, Zlatko Trajanoski, and Hubert Hackl

 

14. Bioinformatics for RNomics

            Kristin Reiche, Katharina Schutt, Kerstin Ullmann, Friedemann Horn, and Jörg Hackermüller

 

15. Bioinformatics for Qualitative and Quantitative Proteomics

            Chris Bielow, Clemens Gr¨opl, Oliver Kohlbacher, and Knut Reinert

 

16. Bioinformatics for Mass Spectrometry-Based Metabolomics

            David P. Enot, Bernd Haas, and Klaus M. Weinberger

 

Part III: Applied Omics Bioinformatics

 

17. Computational Analysis Workflows for Omics Data Interpretation

            Irmgard Mühlberger, Julia Wilflingseder, Andreas Bernthaler, Raul Fechete, Arno Lukas, and Paul Perco

 

18. Integration, Warehousing, and Analysis Strategies of Omics Data

            Srinubabu Gedela

 

19. Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis

            Paolo Tieri, Alberto de la Fuente, Alberto Termanini, and Claudio Franceschi

 

20. Network Inference from Time-Dependent Omics Data

            Paola Lecca, Thanh-Phuong Nguyen, Corrado Priami, and Paola Quaglia

 

21. Omics and Literature Mining

            Vinod Kumar and Craig Volker

 

22. Omics-Bioinformatics in the Context of Clinical Data

            Gert Mayer, Georg Heinze, Harald Mischak, Merel R. Hellemons, Hiddo J. Lambers Heerspink,  Stephan J.L. Bakker, Dick de Zeeuw, Martin Haiduk, Peter Rossing, and Rainer Oberbauer

 

23. Omics-Based Identification of Pathophysiological Processes

            Hiroshi Tanaka and Soichi Ogishima

 

24. Data Mining Methods in Omics-Based Biomarker Discovery

            Fan Zhang and Jake Y. Chen

 

25. Integrated Bioinformatics Analysis for Cancer Target Identification

            Yongliang Yang, S. James Adelstein, and Amin I. Kassis

 

26. Omics-Based Molecular Target and Biomarker Identification

            Zhang-Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung, Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein

Blurb

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.