Table of Contents

Volume Editor PrefaceRoma Tauler, Carmen Bedia and Joaquim Jaumot1. Introduction to the data analysis relevance in the omics eraRoma Tauler, Carmen Bedia and Joaquim Jaumot2. Omics experimental design and data acquisitionCarmen Bedia 3. Microarrays data analysisAlex Sanchez-Pla 4. Analysis of High-Throughput RNA Sequencing DataAnna Esteve-Codina5. Analysis of High-Throughput DNA Bisulfite Sequencing DataSimon Charles Heath 6. Data quality assessment in untargeted LC-MS metabolomicJulia Kuligowski, Guillermo Quintas, Angel Sanchez-Illana and Jose David Piñeiro-Ramos7. Data normalization and scaling: consequences for the analysis in omics sciencesJan Walach, Peter Filzmoser and Karel Hron 8. Metabolomics data preprocessing: From raw data to features for statistical analysisIbrahim Karaman and Rui Climaco Pinto 9. Exploratory data analysis and data decompositionsIvana Stanimirova and Michal Daszykowski 10. Chemometric methods for classification and feature selectionFederico Marini and Marina Cocchi11. Advanced statistical multivariate data analysisJasper Engel and Jeroen Jansen 12. Analysis and interpretation of mass spectrometry imaging datasetsBenjamin Bowen 13. Metabolomics tools for data analysisMatej Oresic, Alex Dickens, Tuulia Hyötyläinen, Santosh Lamichhane and Partho Sen14. Metabolite identification and annotationC. Barbas, Joanna Godzien and Alberto Gil de la Fuente 15. Multi-omic data integration and analysis via model-driven approachesIgor Marín de Mas 16. Integration of metabolomic data from multiple analytical platforms: Toward an extensive coverage of the metabolomeJulien Boccard and Serge Rudaz 17. Multiomics data integration in time series experimentsAna Conesa and Sonia Tarazona18. Metabolomics applications in environmental researchCarmen Bedia 19. Environmental genomicsCarlos Barata and Benjamín Piña 20. Transcriptomics and metabolomics systems biology of health and diseaseAntonio Checa, Jose Fernández Navarro and Hector Gallart Ayala21. Foodomics applicationsAlejandro Cifuentes, Alberto Valdés and Carlos León

About the Author

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. 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. 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).

Main research interests in Chemometrics, especially in the development of multivariate curve resolution methods for the analysis of multiway and muliset data, and for their applications to Omic Sciences, Environmental Chemistry, Analytical and Bioanalytical Chemistry (hyphenated chromatography, spectroscopy, imaging, mass spectrometry, sensor development), and Solution Chemistry (Equilibria and Kinetics). Winner of 2009 Award for Achievements in Chemometrics (Eastern Analytical Symposium) and 2009 Kowalski Prize from the Journal of Chemometrics. Former president of the Catalan Chemistry Society (2008-2013). He has published 354 papers in ISI journals and has an h-index of 53.