Fundamentals of Advanced Omics Technologies: From Genes to Metabolites

Contributors to Volume 63Series Editor's PrefacePrefaceChapter 1: DNA Microarrays Technology: Overview and Current StatusAbstract

1 Introduction and Overview

2 Types of DNA Microarrays

3 Applications of Microarrays

4 Microarray Bioinformatics

5 Discussion and Concluding Remarks

Chapter 2: Challenges and Future Trends in DNA Microarray AnalysisAbstract

1 Introduction

2 Toward Microarray POC Devices

3 Validity of Microarray Data

4 Clinical Adoption

5 Future Trends of Microarray

6 Conclusion

Chapter 3: Next-Generation Sequencing: New Tools to Solve Old ChallengesAbstract

1 Introduction

2 Basis for NGS

3 Sample Preparation for NGS

4 Sequencing Techniques

5 NGS Data Analysis

6 Main Applications of NGS

7 Integrating Omics Data

Chapter 4: Omics Tools for the Genome-Wide Analysis of Methylation and Histone ModificationsAbstract

1 Omics Meets Epigenetics

2 Methods in Epigenomics

3 Concluding Remarks

Chapter 5: An Overview of Quantitative Proteomic ApproachesAbstract

1 Introduction

2 Immuno-Based Detection Methods

3 Mass Spectrometry-Based Detection Methods

4 Conclusions

Acknowledgments

Chapter 6: Emerging Nanotechniques in ProteomicsAbstract

1 Introduction

2 Overview of Protein Microarrays

3 Detection Platforms in Nanoproteomics

4 Biomarker Discovery by Nanoproteomics Approaches

5 Conclusions

Acknowledgments

Chapter 7: Mass Spectrometry Imaging in Proteomics and MetabolomicsAbstract

1 The Need for Imaging-Based Proteomics and Metabolomics

2 Mass Spectrometry Imaging

3 Applications of MSI

4 Future Developments

Chapter 8: Advances in NMR-Based MetabolomicsAbstract

1 Introduction

2 NMR Methods

3 Micro-Coil NMR

4 Fast NMR Methods

5 Hyperpolarization in NMR

6 Statistical and Data Analysis Methods

7 Spectral Assignment and Metabolite Quantitation Methods

8 STOCSY and RANSY Methods

9 Applications

10 Conclusions

Acknowledgment

Disclosure of Potential Conflict of Interest

Chapter 9: The Role of Mass Spectrometry in Nontargeted MetabolomicsAbstract

1 Introduction

2 Study Design

3 Sample Preparation

4 Analytical Strategies

5 MS-Based Untargeted Metabolomics

6 Data Analysis

7 Identification of Biomarkers and Biochemical Pathway Visualization

8 Synopsis

Chapter 10: Direct Mass Spectrometry-Based Approaches in MetabolomicsAbstract

1 Introduction

2 Matrix-Assisted and Matrix-Free Laser Desorption/Ionization MS

3 Direct-Infusion MS

4 Ambient-Ionization MS

5 Imaging MS

6 Conclusions

Chapter 11: Functional Glycomics Analysis: Challenges and MethodologiesAbstract

1 Introduction

2 Structural Analysis of Glycans

3 Functional Analysis of Glycans

4 Integrating Structure and Function: A Case Study

5 Conclusions

Acknowledgments

Chapter 12: Applications of Glycan Microarrays to Functional GlycomicsAbstract

1 Introduction

2 Generation of Glycan Microarrays

3 Examples of Reported Glycan Microarrays

4 Identification of Virus Receptors with Glycan Microarrays

5 Conclusions

Acknowledgments

Chapter 13: High-Resolution Analytical Tools for Quantitative PeptidomicsAbstract

1 Introduction

2 Absolute Quantification

3 Relative Quantification

4 Concluding Remarks

Chapter 14: Analysis of Deep Sequencing Data: Insights and ChallengesAbstract

1 Introduction

2 Fundamentals

3 Applications

4 The Computing Side of Deep Sequencing

5 Summary and Future Directions

Acknowledgments

Chapter 15: Gene Expression Analysis and Profiling of Microarrays Data and RNA-Sequencing DataAbstract

1 Human Genome and Transcriptome: From Gene Loci to Gene Products

2 Experimental Technologies for Genome-Wide Expression Analysis

3 Bioinformatic Analysis of Gene Expression Data

Chapter 16: Bioinformatic Approaches to Increase Proteome CoverageAbstract

1 Introduction

2 Increasing the Number of Fragmented Features

3 Reducing the Number of Unassigned Spectra

4 Summary

Acknowledgments

Chapter 17: Transcriptome and Metabolome Data Integration—Technical Perquisites for Successful Data Fusion and VisualizationAbstract

1 Introduction

2 Extraction, Measurement, Raw Data Analysis, and Data Fusion

3 Visualization

4 MassTRIX Reloaded—Combined Analysis and Visualization of Metabolome and Trascriptome Data

5 Conclusions

Chapter 18: Computational Approaches for Visualization and Integration of Omics DataAbstract

1 Introduction

2 Data Overview

3 Data Processing and Analyzing Tools

4 Network and Pathway Databases

5 Visualization of Omics Data

6 Conclusion

Index