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Systems Biology Approaches for Host-Pathogen Interaction Analysis

  • 1st Edition - February 12, 2024
  • Latest edition
  • Editors: Mohd. Tashfeen Ashraf, Abdul Arif Khan, Fahad M. Aldakheel
  • Language: English

Application and utilization of data science approaches has revolutionized scientific research including host–pathogen interaction analyses. Host–pathogen interactions a… Read more

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Description

Application and utilization of data science approaches has revolutionized scientific research including host–pathogen interaction analyses. Host–pathogen interactions are generally considered highly specific interactions, resulting in a variety of consequences. Data science approaches coupled with network biology has taken host–pathogen interaction analysis from specific interaction to a new paradigm of understanding the consequences of these interactions within a biological network. Unfortunately, basic biological researchers are mostly unaware of these advancements. Conversely, data scientists are not familiar with biological aspects of such data.

Systems Biology Approaches for Host–Pathogen Interaction Analyses benefits biological researchers by expanding the scope of their research and utilization of their accumulated data using recent technological advancements. In addition, the book also opens avenues for bioinformatics and computer science researchers to utilize their expertise in biologically meaningful ways.

Key features

  • Cover approaches to decipher complex multiple host–pathogen interactions
  • Gives biological researcher an insight into the utilization of technological advancements in the field of host–pathogen interaction analyses in their work
  • Provides a new paradigm of understanding the consequences of host–pathogen interaction in biological systems

Readership

Microbiology students and researchers, Biological Data Scientists, Bioinformaticians and Computational Biologists, Pharmaceutical companies dealing with microbes, Libraries of academic institutes dealing with biotechnology, healthcare, data science and bioinformatics

Table of contents

Chapter 1: Host-pathogen interactions: a general introduction
Rabbani Syed, Fahad M. Aldakheel, Shatha A. Alduraywish, Ayesha Mateen, Hadeel Alnajran and Huda Hussain Al-Numan


1.1 Introduction

1.1.1 Role of pathogen

1.1.2 Host-pathogen relationship and mechanisms

1.1.3 Classification of host-pathogen interactions

1.2 Methods for prediction of host-pathogen interactions

1.2.1 Ortholog-based protein interaction detection

1.2.2 Domain-based detection of protein interaction

1.2.3 Biological reasoning-based prediction of host-pathogen interactions

1.2.4 Domain/motif interaction-based predictions

1.2.5 Machine learning-based predictions of host-pathogen interactions

1.3 Online repositories for host-pathogen interactions

1.3.1 Database of fungal virulence factors

1.3.2 E-fungi

1.3.3 Fungi DB

1.3.4 Ensembl genomes

1.3.5 EuPathDB

1.3.6 HPIDB

1.3.7 PLEXdb

1.3.8 VFDB

1.4 Conclusion
Acknowledgment
References

Chapter 2: Host-pathogen interactions: databases and approaches for data generation
Yasmin Bano and Abhinav Shrivastava


2.1 Introduction

2.2 Databases for host-pathogen interactions

2.3 Bioinformatic methods to discover HPI networking

2.3.1 Biological methods

2.3.2 Computational methods

2.4 Microscopic imaging techniques as stage of the art

2.5 RNA-Seq profiling: tool for determining the HPI network

2.5.1 Bacteria-host interactions

2.5.2 Virus-host interactions

2.5.3 Fungus-host interaction and other pathogenic interactions

2.5.4 Technical approach of RNA-seq and data analysis

2.6 Artificial intelligence-driven analysis for HPIs

2.7 Challenges and opportunities

2.7.1 Challenges

2.7.2 Opportunities

2.8 Conclusion
References

Chapter 3: Generation of host-pathogen interaction data: an overview of recent technological advancements
Fatima Noor, Usman Ali Ashfaq, Hafiz Rameez Khalid and Mohsin Khurshid


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

3.5.1 Biological big data and omics

3.5.2 Multiomics approaches to unravel the host-pathogen interactions

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
Samman Munir, Usman Ali Ashfaq, Muhammad Qasim, Tazeem Fatima, Sehar Aslam, Muhammad Hassan Sarfraz, A.K.M. Humayun Kober and Mohsin Khurshid


4.1 Introduction

4.2 Genomics approaches

4.3 Transcriptomics

4.4 Proteomics of host-pathogen interactions

4.4.1 Secretomics of host-pathogen interactions

4.5 Metabolomics approaches

4.5.1 Lipidomics approaches

4.5.2 Multiomics integration for the analysis of host-microbe interactions

4.5.3 Integrated transcriptomicsgenomics approaches

4.5.4 Integrated epigenomics and transcriptomics approaches

4.5.5 Integrated proteomics—genomics, transcriptomics, and metabolomics

4.6 Future perspectives
References

Chapter 5: Computational methods for detection of host-pathogen interactions
Samvedna Singh, Himanshi Gupta and Shakti Sahi


5.1 Introduction

5.2 Computational techniques for prediction of host-pathogen interactions

5.2.1 Protein-protein interaction methods

5.2.2 RNA-mediated interaction-based method

5.2.3 Computational approaches using integrated pipelines

5.3 Case studies

5.3.1 Case study based on host-parasite interaction

5.3.2 Case study based on host-virus interaction

5.3.3 Case study based on host-bacteria interactions

5.3.4 Case study based on host-fungus interactions

5.4 Discussion
References
Further reading

Chapter 6: Biological interaction networks and their application for microbial pathogenesis
Nirupma Singh and Sonika Bhatnagar


6.1 Introduction: biological networks

6.1.1 What is a network?

6.1.2 Types of networks

6.1.3 Biological networks

6.1.4 Properties of biological networks

6.1.5 Host-pathogen interaction networks

6.2 Tools for construction and analysis of biological networks

6.2.1 Cytoscape

6.2.2 R studio

6.2.3 Important plugins and functions

6.3 Functional annotation and biological characterization of host and microbial proteins

6.3.1 DAVID

6.3.2 KOBAS 3.0 server

6.3.3 Biocyc

6.4 Ontology and pathway analysis to understand microbial pathogenesis

6.4.1 KEGG pathways

6.4.2 Wiki pathways

6.4.3 NCBI biosystems

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
Vahap Eldem, Yusuf Ula¸s C¸ınar, Selahattin Barı¸s C¸ ay, Selim Can Kuralay, O¨zgecan Kayalar, Go¨kmen Zararsız, Yakup Bakır and Fatih Dikmen


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
Shilpa Kumari, Neha Verma, Anil Kumar, Sunita Dalal and Kanu Priya


8.1 Introduction

8.2 Analysis via different databases

8.2.1 GO enrichment analysis/GO functional overrepresentation analysis

8.2.2 Functional overrepresentation analysis using DOSE (Disease Ontology Semantic and Enrichment Analysis)

8.2.3 Functional overrepresentation analysis using MeSH

8.2.4 Functional overrepresentation analysis using Reactome pathway (ReactomePA)

8.3 Application of statistical databases in microbial pathogenesis
References

Chapter 9: Advancements in systems biology-based analysis of microbial pathogenesis
Neha Verma, Shilpa Kumari, Anil Kumar and Kanu Priya


9.1 Introduction of microbial pathogenesis

9.1.1 Mechanism of microbial pathogenesis

9.2 Systems biology of microbial pathogenesis

9.2.1 Host-pathogen interaction

9.2.2 Pathogen’s molecular interaction network

9.2.3 Host’s reaction to a microbial infection

9.3 Systems biology techniques to study microbial pathogenesis

9.3.1 OMICS data contributing to microbial pathogenesis (including genomics, transcriptomics, metabolomics, and proteomics)

9.3.2 Computational biology of host-pathogen interaction in microbial pathogenesis

9.3.3 High-throughput techniques

9.4 Conclusion
References

Chapter 10: Host-pathogen interactions with special reference to microbiota analysis and integration of systems biology approaches
Fahad M. Aldakheel, Dalia Mohsen and Barkha Singhal


10.1 Introduction

10.2 Methods for identifying the microbiota: a brief account

10.3 Factors to be considered before identifying microbiota

10.3.1 Geographical factors and diet

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
Kartavya Mathur, Ananya Gupta, Varun Rawat, Vineet Sharma and Shailendra Shakya


11.1 Introduction

11.2 Exploring different forms of noncoding RNAs

11.2.1 microRNAs

11.2.2 Long noncoding RNAs

11.2.3 Piwi-like RNAs

11.2.4 Small interfering RNA

11.2.5 Small nuclear RNA

11.2.6 Small nucleolar RNA

11.2.7 Ribonucleic acid enzymes (or ribozymes)

11.2.8 Circular RNAs

11.2.9 Competing endogenous RNA

11.3 Comprehending the role of ncRNAs in pathogen-host interplay

11.3.1 Role of ncRNAs in bacterial pathogenesis

11.3.2 Function of noncoding RNAs in viral infection

11.3.3 Role of ncRNAs in fungal pathogenesis

11.3.4 Role of ncRNAs in protozoan pathogenesis

11.3.5 Role of ncRNAs in helminth pathogenesis

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

11.6.1 ncRNA expression profiling

11.6.2 Functional annotation and interpretation of ncRNA transcriptome

11.6.3 ncRNA web resources

11.6.4 Predicting ncRNA function

11.6.5 Methods for predicting and investigating microRNA targets

11.6.6 Estimating interaction events of ncRNAs

11.6.7 Predicting ncRNA structure

11.6.8 Graph-based approaches for ncRNA structure and function prediction

11.7 How to explore the significance of miRNAs in infection development?

11.7.1 Mathematical modeling for comprehending host-pathogen interaction

11.8 Why network analysis is important for studying ncRNAs?

11.8.1 Network analysis to study the regulation of host-pathogen interaction

11.8.2 Predicting ncRNA-disease association and tripartite network

11.8.3 Corelational network analysis for ncRNAs

11.8.4 Competing endogenous RNA network analysis
References

Chapter 12: Systems biology in food industry: applications in food production, engineering, and pathogen detection
Ananya Srivastava and Anuradha Mishra


12.1 Introduction

12.2 Networks used in systems biology

12.2.1 Gene regulatory networks

12.2.2 Signal transduction networks

12.2.3 Protein-protein interaction networks

12.2.4 Metabolic networks

12.3 Systems biology benefits for food production

12.3.1 Applied systems biology in nutrition and health

12.3.2 Systems biology in food production and processing

12.3.3 Biofortification and development of nutraceuticals

12.3.4 Systems biology in food safety and quality

12.4 Systems biology in foodborne pathogen detection

12.4.1 Pathogen detection techniques used in food sectors

12.4.2 Limitations

12.5 Future scope

12.6 Conclusion
References

Product details

  • Edition: 1
  • Latest edition
  • Published: February 16, 2024
  • Language: English

About the editors

MA

Mohd. Tashfeen Ashraf

Mohd. Tashfeen Ashraf is currently working as Assistant Professor in the School of Biotechnology, Gautam Buddha University (GBU). After securing his Master’s degree in biochemistry, he earned his Doctorate in Biotechnology from Aligarh Muslim University, India, 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

AK

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

FA

Fahad M. Aldakheel

Fahad M. 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, Riyadh, KSA

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