Margarida Gama-Carvalho is an Associate Professor in the Department of Chemistry and Biochemistry at the Faculty of Sciences, University of Lisbon. She holds a PhD in Biomedical Sciences and is a Principal Investigator at BioISI, where she leads the RNA Systems Biology laboratory. She currently coordinates GenomePT, the Portuguese national research infrastructure for genome sequencing and analysis. Her research focuses on RNA-dependent regulation of gene expression in health and disease, integrating next-generation sequencing and multi-omics approaches to support the development of RNA-based therapeutic strategies.Andreia Figueiredo is an Associate Professor in the Department of Biology at the Faculty of Sciences, University of Lisbon, and head of the BioISI Grapevine Pathogen Systems (GPS) Lab. She holds a PhD in Cellular and Molecular Biology. Her research addresses plant–pathogen interactions in grapevine using systems biology approaches that integrate multi-omics, functional genomics, and biotechnology, with the aim of elucidating disease regulatory networks and improving crop resilience for sustainable agricultural production.Francisco Rodrigues Pinto is an Assistant Professor in the Department of Chemistry and Biochemistry at the Faculty of Sciences, University of Lisbon and co–Principal Investigator of the RNA Systems Biology laboratory at BioISI. He holds a PhD in Biochemistry and has extensive international research experience. His work focuses on the computational analysis and mathematical modeling of complex biological systems, including gene expression and regulatory networks, host–pathogen interactions, and disease mechanisms, with applications in cancer, microbiology, neurodegeneration, and cystic fibrosis.

• PART I. Capturing the Molecular Universe.- Chapter 1. Microarrays and the Dawn of Omics Data Analysis.- Chapter 2. Advances in Massive Parallel Sequencing: From Genomics to Spatial Transcriptomics.- Chapter 3. Latest Developments in Mass Spectrometry-based Techniques for Metabolomics Analysis.- Chapter 4. Separative Techniques Coupled to Mass Spectrometry for metabolomic analysis.- Chapter 5. Metabolomics: Fundamentals, Methods, Analysis, Limits and Recommendations.- Chapter 6. Interactomics – Dissecting Protein Networks in Living Systems.- Chapter 7. Functional Genomics – Principles and Methods.- PART II. From Large Scale Data to Biological Insights.- Chapter 8. FAIR Omics Data Management: Overview, Challenges and Best Practices.- Chapter 9. Challenges and Opportunities for Statistics in Omics Data Analysis.- Chapter 10. Key Concepts in Transcriptomics Data Analysis in the Era of Next Gen Sequencing.- Chapter 11. Data Analysis in Extreme Resolution Mass Spectrometry Untargeted Metabolomics.- Chapter 12.- A Primer On Modelling Approaches For Omics Data.- Chapter 13. Functional interpretation of omics data: from pathways to networks.- Chapter 14. Multi-omics data integration.- PART III. Applications of Omics approaches.- Chapter 15. Genomics in Health and Biomedicine.- Chapter 16. Genome Sequencing In Infectious Disease Outbreaks.- Chapter 17. A Journey Into Plant-Microbe Interactions: From Lab To Field For A Sustainable Agriculture.- Chapter 18. Decoding Plant Immunity: Proteomics as a Biotechnological tool for crop improvement.- Chapter 19. Clinical Proteomics Applied to Food Allergy.- Chapter 20. Applications of Metabolomics in the Development of Biomedicine and Biotechnology.

Margarida Gama-Carvalho is an Associate Professor in the Department of Chemistry and Biochemistry at the Faculty of Sciences, University of Lisbon. She holds a PhD in Biomedical Sciences and is a Principal Investigator at BioISI, where she leads the RNA Systems Biology laboratory. She currently coordinates GenomePT, the Portuguese national research infrastructure for genome sequencing and analysis. Her research focuses on RNA-dependent regulation of gene expression in health and disease, integrating next-generation sequencing and multi-omics approaches to support the development of RNA-based therapeutic strategies.Andreia Figueiredo is an Associate Professor in the Department of Biology at the Faculty of Sciences, University of Lisbon, and head of the BioISI Grapevine Pathogen Systems (GPS) Lab. She holds a PhD in Cellular and Molecular Biology. Her research addresses plant–pathogen interactions in grapevine using systems biology approaches that integrate multi-omics, functional genomics, and biotechnology, with the aim of elucidating disease regulatory networks and improving crop resilience for sustainable agricultural production.Francisco Rodrigues Pinto is an Assistant Professor in the Department of Chemistry and Biochemistry at the Faculty of Sciences, University of Lisbon and co–Principal Investigator of the RNA Systems Biology laboratory at BioISI. He holds a PhD in Biochemistry and has extensive international research experience. His work focuses on the computational analysis and mathematical modeling of complex biological systems, including gene expression and regulatory networks, host–pathogen interactions, and disease mechanisms, with applications in cancer, microbiology, neurodegeneration, and cystic fibrosis.

• PART I. Capturing the Molecular Universe.- Chapter 1. Microarrays and the Dawn of Omics Data Analysis.- Chapter 2. Advances in Massive Parallel Sequencing: From Genomics to Spatial Transcriptomics.- Chapter 3. Latest Developments in Mass Spectrometry-based Techniques for Metabolomics Analysis.- Chapter 4. Separative Techniques Coupled to Mass Spectrometry for metabolomic analysis.- Chapter 5. Metabolomics: Fundamentals, Methods, Analysis, Limits and Recommendations.- Chapter 6. Interactomics – Dissecting Protein Networks in Living Systems.- Chapter 7. Functional Genomics – Principles and Methods.- PART II. From Large Scale Data to Biological Insights.- Chapter 8. FAIR Omics Data Management: Overview, Challenges and Best Practices.- Chapter 9. Challenges and Opportunities for Statistics in Omics Data Analysis.- Chapter 10. Key Concepts in Transcriptomics Data Analysis in the Era of Next Gen Sequencing.- Chapter 11. Data Analysis in Extreme Resolution Mass Spectrometry Untargeted Metabolomics.- Chapter 12.- A Primer On Modelling Approaches For Omics Data.- Chapter 13. Functional interpretation of omics data: from pathways to networks.- Chapter 14. Multi-omics data integration.- PART III. Applications of Omics approaches.- Chapter 15. Genomics in Health and Biomedicine.- Chapter 16. Genome Sequencing In Infectious Disease Outbreaks.- Chapter 17. A Journey Into Plant-Microbe Interactions: From Lab To Field For A Sustainable Agriculture.- Chapter 18. Decoding Plant Immunity: Proteomics as a Biotechnological tool for crop improvement.- Chapter 19. Clinical Proteomics Applied to Food Allergy.- Chapter 20. Applications of Metabolomics in the Development of Biomedicine and Biotechnology.