Bioinformatics for Omics Data

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.

InhaltsangabePart 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. OmicsBioinformatics 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. OmicsBased 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. OmicsBased Molecular Target and Biomarker Identification             Zhang-Zhi Hu, Hongzhan Huang, Cathy H. Wu, Mira Jung, Anatoly Dritschilo, Anna T. Riegel, and Anton Wellstein