Systems Biology Approaches for Host-Pathogen Interaction Analysis

1st Edition - February 12, 2024
Editors: Mohd. Tashfeen Ashraf, Abdul Arif Khan, Fahad M. Aldakheel
Language: English
Paperback ISBN:
9 7 8 - 0 - 3 2 3 - 9 5 8 9 0 - 5
eBook ISBN:
9 7 8 - 0 - 3 2 3 - 9 5 8 9 1 - 2

Systems Biology Approaches for Host-Pathogen Interaction Analysis aids biological researchers in expanding their research scope using piled up data generated through recent te… Read more

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Systems Biology Approaches for Host-Pathogen Interaction Analysis aids biological researchers in expanding their research scope using piled up data generated through recent technological advancements. In addition, it opens avenues for bioinformatics and computer science researchers to utilize their expertise in biologically meaningful ways. Other areas covered include network biology approaches to decipher complex multiple host-pathogen interactions in addition to valuable coverage of artificial intelligence. This book bridges these gaps through a new paradigm of understanding the consequences of interactions in biological networks.

Host-pathogen interactions are generally considered as highly specific interactions leading to a variety of consequences. The utilization of data science approaches has revolutionized scientific research including host-pathogen interaction analyses. Data science approaches coupled with network biology has taken host-pathogen interaction analysis from specific interaction to a new paradigm of understanding consequences of these interaction in the biological network.

Cover image
Title page
Table of Contents
Copyright
Dedication
List of contributors
Foreword
Preface
Acknowledgments
Chapter 1. Host-pathogen interactions: a general introduction
Abstract
1.1 Introduction
1.2 Methods for prediction of host-pathogen interactions
1.3 Online repositories for host-pathogen interactions
1.4 Conclusion
Acknowledgment
References
Chapter 2. Host-pathogen interactions: databases and approaches for data generation
Abstract
2.1 Introduction
2.2 Databases for host-pathogen interactions
2.3 Bioinformatic methods to discover HPI networking
2.4 Microscopic imaging techniques as stage of the art
2.5 RNA-Seq profiling: tool for determining the HPI network
2.6 Artificial intelligence-driven analysis for HPIs
2.7 Challenges and opportunities
2.8 Conclusion
References
Chapter 3. Generation of host-pathogen interaction data: an overview of recent technological advancements
Abstract
3.1 Introduction
3.2 Introduction of bioinformatics in light of NGS
3.3 A short glimpse of the “integration of omics”
3.4 Why is multiomics study preferred over single omics?
3.5 Advancements in the generation of host-pathogen interaction data
3.6 Bioinformatics resources and web-based databases for host-pathogen interactions
3.7 Challenges in the generation of host-pathogen interaction data
3.8 Discussion and future prospects
3.9 Conclusion
References
Chapter 4. Molecular omics: a promising systems biology approach to unravel host-pathogen interactions
Abstract
4.1 Introduction
4.2 Genomics approaches
4.3 Transcriptomics
4.4 Proteomics of host-pathogen interactions
4.5 Metabolomics approaches
4.6 Future perspectives
References
Chapter 5. Computational methods for detection of host-pathogen interactions
Abstract
5.1 Introduction
5.2 Computational techniques for prediction of host-pathogen interactions
5.3 Case studies
5.4 Discussion
References
Further reading
Chapter 6. Biological interaction networks and their application for microbial pathogenesis
Abstract
6.1 Introduction: biological networks
6.2 Tools for construction and analysis of biological networks
6.3 Functional annotation and biological characterization of host and microbial proteins
6.4 Ontology and pathway analysis to understand microbial pathogenesis
6.5 Case study: host-pathogen interaction networks for CVD pathways in microbial diseases
6.6 Conclusion
References
Chapter 7. Dual transcriptomics data and detection of host-pathogen interactions
Abstract
7.1 Introduction
7.2 Unraveling host-pathogen interactions via genome-wide dual RNA-Seq
7.3 Best practices in dual RNA-Seq: from experimental design to a step-wise guide to performing bioinformatic analysis
7.4 Challenges of dual RNA-Seq experiments and data analysis
7.5 Dual RNA-Seq in the era of third-generation sequencing
7.6 Dissecting the role of noncoding RNA in host-pathogen interactions using dual transcriptomic data
7.7 Future perspectives
Acknowledgments
References
Chapter 8. Functional overrepresentation analysis and their application in microbial pathogenesis
Abstract
8.1 Introduction
8.2 Analysis via different databases
8.3 Application of statistical databases in microbial pathogenesis
References
Chapter 9. Advancements in systems biology-based analysis of microbial pathogenesis
Abstract
9.1 Introduction of microbial pathogenesis
9.2 Systems biology of microbial pathogenesis
9.3 Systems biology techniques to study microbial pathogenesis
9.4 Conclusion
References
Chapter 10. Host-pathogen interactions with special reference to microbiota analysis and integration of systems biology approaches
Abstract
10.1 Introduction
10.2 Methods for identifying the microbiota: a brief account
10.3 Factors to be considered before identifying microbiota
10.4 Role of next-generation sequencing technologies for microbial community analysis in understanding host-pathogen interactions
10.5 Microbial community analysis for understanding the antibiotic resistance phenomenon through 16S sequencing
10.6 Gut microbiota analysis in COVID-19 through 16S metagenomic sequencing
10.7 Challenges and advantages of using systems biology in microbiota analysis
10.8 Pathogen-host interactions in bioinformatics
10.9 Systems biology and omics data
10.10 PHI and systems biology
10.11 Conclusion
Acknowledgment
References
Chapter 11. Role of noncoding RNAs in host-pathogen interactions: a systems biology approach
Abstract
11.1 Introduction
11.2 Exploring different forms of noncoding RNAs
11.3 Comprehending the role of ncRNAs in pathogen-host interplay
11.4 Why is it important to study the function of ncRNAs?
11.5 RNA systems biology
11.6 Computational resources for identifying ncRNAs in host pathogenesis
11.7 How to explore the significance of miRNAs in infection development?
11.8 Why network analysis is important for studying ncRNAs?
References
Chapter 12. Systems biology in food industry: applications in food production, engineering, and pathogen detection
Abstract
12.1 Introduction
12.2 Networks used in systems biology
12.3 Systems biology benefits for food production
12.4 Systems biology in foodborne pathogen detection
12.5 Future scope
12.6 Conclusion
References
Author Index
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Subject Index
A
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Mohd. Tashfeen Ashraf

Dr. Mohd. Tashfeen Ashraf is currently working as Assistant Professor in the School of Biotechnology at Gautam Buddha University (GBU). After securing his master’s degree in Biochemistry, he earned his doctorate in Biotechnology from Aligarh Muslim University during which he characterized the folding intermediates of various proteins. His research area involves the study of folding behavior of proteins, their structure-function relationship and protein-protein interactions under normal and disease conditions.

Affiliations and expertise

Assistant Professor in School of Biotechnology, Gautam Buddha University

Abdul Arif Khan

Abdul Arif Khan is a Microbiologist by training with an interest in the field of host-pathogen interactions, systems biology, and cancer biology. He has received several awards and Fellowships from national and international organizations, including the Royal Society for Public Health and the Federation of European Microbiological Societies. He is a recipient of several grants for his research on artificial Intelligence and host-pathogen interactions. He is credited with several papers and books related to systems biology and host-pathogen interaction analysis.

Affiliations and expertise

College of Pharmacy, King Saud University, Saudi Arabia

Fahad M. Aldakheel

Dr. Fahad Mohammed Aldakheel is an Associate Professor of Clinical Immunology at King Saud University in Riyadh, Saudi Arabia. He obtained his undergraduate degree in Clinical Laboratory Sciences from King Saud University, his master’s degree in Laboratory Medicine from RMIT University, Melbourne, Australia, and his PhD from the University of Melbourne, Australia. He was appointed to the Department of Clinical Laboratory Sciences in the College of Applied Medical Sciences at King Saud University in 2017 as an assistant professor. He was promoted to an associate professor in 2022. Dr. Aldakheel has several research and publications in both local and international scientific journals. He has served as a

(Fahad Aldakheel is an Associate Professor of Clinical Immunology at the Department of Clinical Laboratory Sciences, College of Applied Medical Sciences at King Saud University in Riyadh, Saudi Arabia. He obtained his PhD from the University of Melbourne, Australia. He is a board member of the Saudi Society for Clinical Laboratory Sciences. He has several scientific publications in national and international journals, and is also working as a member and a reviewer in several scientific organizations.

Affiliations and expertise

Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Saudi Arabia