This book explores current omics technologies and provides researchers with a comprehensive understanding of them.
In recent years, technological advances have transformed the life sciences, ushering in the era of "omics" approaches. These methods, which emerged in the wake of the Human Genome Project, are driven by the need to systematically understand genomic diversity and gene expression. They have ushered in the age of big data in the life sciences, revolutionising the way biological questions are asked and experimental results are handled.
Omics approaches cover a wide range of applications, from mapping environmental biodiversity to characterising molecular interactions and small molecules. Despite the current accessibility of these technologies, most researchers and students in the life sciences have had limited exposure to the field, preventing them from fully grasping the power and limitations of the technology, or the critical importance of tailored experimental design and data analysis.
The challenges that are posed by omics technologies are addressed in this book. It provides a comprehensive overview and shows how omics approaches can be effectively used to gain innovative insights into specific biological problems.
The book is divided into three main parts:·
Part I Capturing the Molecular Universe, provides an in-depth exploration of the current technologies, highlighting their potential and limitations. Part II From Large Scale Data to Biological Insights, offers a practical introduction to the world of data generated by omics methodologies, emphasizing data sharing, management, and analysis, with a focus on readers in the biological sciences. Part III Application of Omics Approaches, outlines various applications of omics technologies in biomedicine and biotechnology, offering insights into their current use and future potential.
The book is a valuable resource for both seasoned researchers and those entering the field, facilitating a deeper understanding of omics approaches and their transformative impact on the life sciences.
With illustrations by Filipa Santos.
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 plantpathogen 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 coPrincipal 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, hostpathogen interactions, and disease mechanisms, with applications in cancer, microbiology, neurodegeneration, and cystic fibrosis.
