Fundamentals of Advanced Omics Technologies: From Genes to Metabolites

Fundamentals of Advanced Omics Technologies: From Genes to Metabolites

1st Edition - November 15, 2008

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  • Editors: Carolina Simó, Alejandro Cifuentes, Virginia García-Cañas
  • eBook ISBN: 9780444626707
  • Hardcover ISBN: 9780444626516

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Description

Fundamentals of Advanced Omics Technologies: From Genes to Metabolites covers the fundamental aspects of the new instrumental and methodological developments in omics technologies, including those related to genomics, transcriptomics, epigenetics, proteomics and metabolomics, as well as other omics approaches such as glycomics, peptidomics and foodomics. The principal applications are presented in the following complementary volume. The chapters discuss in detail omics technologies, DNA microarray analysis, next-generation sequencing technologies, genome-wide analysis of methylation and histone modifications, emerging nanotechniques in proteomics, imaging mass spectrometry in proteomics, recent quantitative proteomics approaches, and advances in high-resolution NMR-based metabolomics, as well as MS-based non-targeted metabolomics and metabolome analysis by CE-MS, global glycomics analyses, foodomics, and high resolution analytical tools for quantitative peptidomics. Key aspects related to chemometrics, bioinformatics, data treatment, data integration and systems biology, deep-sequencing data analysis, statistical approaches for the analysis of microarray data, the integration of transcriptome and metabolome data and computational approaches for visualization and integration of omics data are also covered.

Key Features

  • Covers the latest advances in instrumentation, experimental design, sample preparation, and data analysis
  • Provides thorough explanations and descriptions of specific omics technologies
  • Describes advanced tools and methodologies for data pretreatment, storage, curation and analysis, as well as data integration

Readership

Analytical scientists, PhD students and technicians in control laboratories, universities, hospitals, research laboratories and regulation agencies

Table of Contents

  • Contributors to Volume 63
    Series Editor's Preface
    Preface
    Chapter 1: DNA Microarrays Technology: Overview and Current Status
    Abstract

    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 Analysis
    Abstract

    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 Challenges
    Abstract

    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 Modifications
    Abstract

    1 Omics Meets Epigenetics

    2 Methods in Epigenomics

    3 Concluding Remarks

    Chapter 5: An Overview of Quantitative Proteomic Approaches
    Abstract

    1 Introduction

    2 Immuno-Based Detection Methods

    3 Mass Spectrometry-Based Detection Methods

    4 Conclusions

    Acknowledgments

    Chapter 6: Emerging Nanotechniques in Proteomics
    Abstract

    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 Metabolomics
    Abstract

    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 Metabolomics
    Abstract

    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 Metabolomics
    Abstract

    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 Metabolomics
    Abstract

    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 Methodologies
    Abstract

    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 Glycomics
    Abstract

    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 Peptidomics
    Abstract

    1 Introduction

    2 Absolute Quantification

    3 Relative Quantification

    4 Concluding Remarks

    Chapter 14: Analysis of Deep Sequencing Data: Insights and Challenges
    Abstract

    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 Data
    Abstract

    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 Coverage
    Abstract

    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 Visualization
    Abstract

    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 Data
    Abstract

    1 Introduction

    2 Data Overview

    3 Data Processing and Analyzing Tools

    4 Network and Pathway Databases

    5 Visualization of Omics Data

    6 Conclusion

    Index

Product details

  • No. of pages: 490
  • Language: English
  • Copyright: © Elsevier 2014
  • Published: November 15, 2008
  • Imprint: Elsevier
  • eBook ISBN: 9780444626707
  • Hardcover ISBN: 9780444626516

About the Series Volume Editors

Carolina Simó

Carolina Simó is a Tenured Researcher at the National Research Council of Spain (CSIC) in Madrid, she develops her scientific activities in the Laboratory of Foodomics. Her running research lines include: i) Method development using electrophoretic/chromatographic techniques coupled to mass spectrometry for Proteomics and Metabolomics. ii) Food safety assessment, quality control and other features related to food processing, storage, authenticity; iii) Study of the effect of diet on health/disease and the mechanisms of nutrients and bioactive food components at the molecular level. She has published over 50 SCI papers and 10 book chapters. Her h index is 20 and her works have received over 1000 citations (August-2013).

Affiliations and Expertise

Laboratory of Foodomics, CSIC, Madrid, Spain

Alejandro Cifuentes

Alejandro Cifuentes
Alejandro Cifuentes is a Full Research Professor at the National Research Council of Spain (CSIC) in Madrid, Head of the Laboratory of Foodomics and Director of the Metabolomics Platform (International Excellence Campus CSIC + University Autonoma of Madrid). He has been Founding Director of the Institute of Food Science Research and Deputy Director of the Institute of Industrial Fermentations, both belonging to CSIC. Alejandro's activity includes advanced analytical methods development for Foodomics (including transcriptomics, proteomics and metabolomics), food quality and safety, as well as isolation and characterization of natural bioactive compounds and their effect on human health. He holds different national and international awards, is member of the Editorial Board of 17 international journals (including Journal of Chromatography A, Journal of Separation Science, Food Analytical Methods, International Journal of Molecular Sciences, Heliyon, Journal of Pharmaceutical Analysis, etc.), Editor of TrAC-Trends in Analytical Chemistry and Electrophoresis, and Editor-in-Chief of Open Life Sciences. He has published more than 270 SCI papers, 30 books and book chapters and 9 patents. His h index is 70 (Google scholar, June 2020) and his works have received more than 17000 citations. Alejandro has given more than 200 invited lectures in different national and international meetings in Europe, Asia, Africa, America and Oceania. He has defined for the first time in a SCI journal the new discipline of Foodomics.

Affiliations and Expertise

National Research Council of Spain (CSIC), Madrid, Spain

Virginia García-Cañas

Virginia García-Cañas works in the Laboratory of Foodomics on the development of advanced analytical methods for: Foodomics, including Genomics and Transcriptomics; food quality; food safety; and Nutrigenomic studies. Her research covers: i) development of advanced DNA/RNA-based methods for food analysis (genetically-modified organisms, pathogens, etc.), and ii) Nutrigenomic study of the effect of dietary polyphenols on cancer. She has published over 45 SCI papers and 7 book chapters. Her h index is 19 and her works have received over 900 citations (August-2013).

Affiliations and Expertise

Laboratory of Foodomics, CSIC, Madrid, Spain

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