Data Analysis for Omic Sciences: Methods and Applications - 1st Edition - ISBN: 9780444640444, 9780444640451

Data Analysis for Omic Sciences: Methods and Applications, Volume 82

1st Edition

Serial Volume Editors: Joaquim Jaumot Carmen Bedia Romà Tauler
Hardcover ISBN: 9780444640444
eBook ISBN: 9780444640451
Imprint: Elsevier
Published Date: 28th September 2018
Page Count: 730
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Table of Contents

Volume Editor Preface
Roma Tauler, Carmen Bedia and Joaquim Jaumot
1. Introduction to the data analysis relevance in the omics era
Roma Tauler, Carmen Bedia and Joaquim Jaumot
2. Omics experimental design and data acquisition
Carmen Bedia
3. Microarrays data analysis
Alex Sanchez-Pla
4. Analysis of High-Throughput RNA Sequencing Data
Anna Esteve-Codina
5. Analysis of High-Throughput DNA Bisulfite Sequencing Data
Simon Charles Heath
6. Data quality assessment in untargeted LC-MS metabolomic
Julia Kuligowski, Guillermo Quintas, Angel Sanchez-Illana and Jose David Piñeiro-Ramos
7. Data normalization and scaling: consequences for the analysis in omics sciences
Jan Walach, Peter Filzmoser and Karel Hron, 
8. Metabolomics data preprocessing: From raw data to features for statistical analysis
Ibrahim Karaman and Rui Climaco Pinto,
9. Exploratory data analysis and data decompositions
Ivana Stanimirova and Michal Daszykowski,
10. Chemometric methods for classification and feature selection
Federico Marini and Marina Cocchi
11. Advanced statistical multivariate data analysis
Jasper Engel and Jeroen Jansen,
12. Analysis and interpretation of mass spectrometry imaging datasets
Benjamin Bowen
13. Metabolomics tools for data analysis
Matej Oresic, Alex Dickens, Tuulia Hyötyläinen, Santosh Lamichhane and Partho Sen
14. Metabolite identification and annotation
C. Barbas, Joanna Godzien and Alberto Gil de la Fuente,
15. Multi-omic data integration and analysis via model-driven approaches
Igor Marín de Mas
16. Integration of metabolomic data from multiple analytical platforms: Toward an extensive coverage of the metabolome.
Julien Boccard and Serge Rudaz,
17. Multiomics data integration in time series experiments
Ana Conesa and Sonia Tarazona
18. Metabolomics applications in environmental research
Carmen Bedia
19. Environmental genomics
Carlos Barata and Benjamín Piña, 
20. Transcriptomics and metabolomics systems biology of health and disease
Antonio Checa, Jose Fernández Navarro and Hector Gallart Ayala,
21. Foodomics applications
Alejandro Cifuentes, Alberto Valdés and Carlos León,


Description

Data Analysis for Omic Sciences: Methods and Applications, Volume 82, shows how these types of challenging datasets can be analyzed. Examples of applications in real environmental, clinical and food analysis cases help readers disseminate these approaches. Chapters of note include an Introduction to Data Analysis Relevance in the Omics Era, Omics Experimental Design and Data Acquisition, Microarrays Data, Analysis of High-Throughput RNA Sequencing Data, Analysis of High-Throughput DNA Bisulfite Sequencing Data, Data Quality Assessment in Untargeted LC-MS Metabolomic, Data Normalization and Scaling, Metabolomics Data Preprocessing, and more.

Key Features

  • Presents the best reference book for omics data analysis
  • Provides a review of the latest trends in transcriptomics and metabolomics data analysis tools
  • Includes examples of applications in research fields, such as environmental, biomedical and food analysis

Readership

Academic and non-academic sectors, especially in environmental, biomedical, and food analysis fields. Ph.D. students to senior researchers and scientists who need to update their knowledge regarding data analysis methods


Details

No. of pages:
730
Language:
English
Copyright:
© Elsevier 2018
Published:
28th September 2018
Imprint:
Elsevier
Hardcover ISBN:
9780444640444
eBook ISBN:
9780444640451

Ratings and Reviews


About the Serial Volume Editors

Joaquim Jaumot Serial Volume Editor

Joaquim Jaumot is Research Scientist at the Spanish National Research Council (CSIC) in the Institute of Environmental Assessment and Water Research (IDAEA-CSIC). He graduated in Chemistry in 2001 and received a Ph.D. in Chemistry in 2006 both from the University of Barcelona (Barcelona, Spain). He has published more than 50 scientific papers and participated in several national and international projects. His main research line is focused on the development and application of chemometric data analysis tools to the study of different types of chemical and biological systems. For instance, he has actively participated in the development of the multivariate curve resolution alternating least squares (MCR-ALS) software. In recent years, his research has been focused on the analysis of large –omic data sets. In particular, main efforts have been aimed at the development and application of chemometric tools in the analysis of mass spectrometry metabolomic data evaluating effects of environmental stressors on model organisms.

Affiliations and Expertise

Research Scientist, Spanish National Research Council (CSIC), Institute of Environmental Assessment and Water Research (IDAEA-CSIC)

Carmen Bedia Serial Volume Editor

Carmen Bedia studied Pharmacy at the University of Barcelona (Spain) and obtained her Ph.D. in 2007 in the field of sphingolipid metabolism, in the Spanish National Research Council (CSIC, Barcelona). She moved to the French Institute of Health and Medical Research (INSERM, Toulouse, France) as a postdoctoral researcher where she focused on cell biology of sphingolipid metabolism in the development of melanoma malignancy. After her return to Barcelona in 2010 to the CSIC, she has been working as postdoctoral researcher on medicinal chemistry of sphingolipids and she expanded her knowledge about lipidomics in biological samples using LC-MS. Since 2013 she works in the Institute of Environmental Assessment and Water Research (IDAEA-CSIC) in the frame of an ERC awarded project in which she uses chemometric techniques to extract meaningful information from LC-MS and Mass Spectrometry imaging datasets, in order to investigate the effects of environmental pollutants on human and plant cells.

Affiliations and Expertise

nstitute of Environmental Assessment and Water Research (IDAEA-CSIC)

Romà Tauler Serial Volume Editor

Romà Tauler graduated in Chemistry from the University of Barcelona (1977) and in 1984 obtained his Ph.D. degree in Analytical Chemistry at the University of Barcelona. He was Associate Professor at the University of Barcelona (Analytical Chemistry Dept) from 1987 to 2003. Since July 2003, he is Research Professor at the Institute of Environmental Assessment and Water Research (IDÆA) of the Spanish National Research Council (CSIC). During these years, he carried out postdoc stays at Institut für Anorg. u. Anal. Chemie - Univ. of Innsbruck (Innsbruck, Austria, 1985 and 1989) and a sabbatical leave as a research scientist at the Center for Process Analytical Chemistry (CPAC) - University of Washington (Seattle, US, 1992). Until now, he has published more than 360 papers in ISI journals (WoS gives 11.656 citations and h-index 51 at Sept 7th, 2017). Nowadays, he is the Chief Editor of the Chemometrics and Intelligent Laboratory Systems (Elsevier) journal and Chief Editor of the Major Reference Work: Comprehensive Chemometrics, Chemical and Biochemical Data Analysis (Elsevier). He has been awarded an ERC Advanced Grant (2012) for the project “CHEMometric and High-Throughput Omics Analytical Methods for Assessment of Global Change Effects on Environmental and Biological Systems”. Other academic awards are the Award for Achievements in Chemometrics (Eastern Analytical Symposium, 2009) and the Kowalski Prize (Journal of Chemometrics, 2009). Main research interests are in Chemometrics, especially in the development of multivariate curve resolution methods for the analysis of multiway and multiset data, and for their applications to Omics Sciences, Environmental Chemistry, Analytical and Bioanalytical Chemistry (hyphenated chromatography, spectroscopy, imaging, mass spectrometry, sensor development), and Solution Chemistry (Equilibria and Kinetics).

Affiliations and Expertise

Institute of Chemical and Environmental Research, CSIC, Spain