Bioinformatics for Omics Data

by Mayer, Bernd

• ISBN13: 9781617790263
• ISBN10: 1617790265
• Format: Hardcover
• Copyright: 2011-03-03
• Publisher: Humana Pr Inc

Summary

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.

Table of Contents

Preface	p. v
Contributors	p. ix
Omics Bioinformatics Fundamentals
Omics Technologies, Data and Bioinformatics Principles	p. 3
Data Standards for Omics Data: The Basis of Data Sharing and Reuse	p. 31
Omies Data Management and Annotation	p. 71
Data and Knowledge Management in Cross-Omics Research Projects	p. 97
Statistical Analysis Principles for Omics Data	p. 113
Statistical Methods and Models for Bridging Omics Data Levels	p. 133
Analysis of Time Course Omics Datasets	p. 153
The Use and Abuse of -Omes	p. 173
Omics Data And Analysis Tracks
Computational Analysis of High Throughput Sequencing Data	p. 199
Analysis of Single Nucleotide Polymorphisms in Case-Control Studies	p. 219
Bioinformatics for Copy Number Variation Data	p. 235
Processing ChIP-Chip Data: From the Scanner to the Browser	p. 251
Insights Into Global Mechanisms and Disease by Gene Expression Profiling	p. 269
Bioinformatics for RNomics	p. 299
Bioinformatics for Qualitative and Quantitative Proteomics	p. 331
Bioinformatics for Mass Spectrometry-Based Metabolomics	p. 351
Applied Omics Bioinformatics
Computational Analysis Workflows for Omics Data Interpretation	p. 379
Integration, Warehousing, and Analysis Strategies of Omics Data	p. 399
Integrating Omics Data for Signaling Pathways, Interactome Reconstruction, and Functional Analysis	p. 415
Network Inference from Time-Dependent Omics Data	p. 435
Omics and Literature Mining	p. 457
Omics-Bioinformatics in the Context of Clinical Data	p. 479
Omics-Based Identification of Pathophysiological Processes	p. 499
Data Mining Methods in Omics-Based Biomarker Discovery	p. 511
Integrated Biointormatics Analysis for Cancer Target Identification	p. 527
Omics-Based Molecular Target and Biomarker Identification	p. 547
Index	p. 573
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