At the intersection of experimental and computational sciences, the second edition of Immunoinformatics provides biological insights as well as a simpler way to implement approaches and algorithms in the immunoinformatics research domain. After an introductory section, this extensive volume moves on to cover topics such as databases, tools for prediction, systems biology approaches, as well as a variety of immunoinformatics applications. As part of the highly successful Methods in Molecular Biology series, chapters include the type of detailed information and implementation advice to ensure successful results.
Comprehensive and practical, Immunoinformatics, Second Edition aims at students and researchers from diverse backgrounds and levels interested in working with immunological problems.
TOC:
Part I: Immunoinformatics: Transition from Basic Biology to Informatics
1. A Brief Outline of the Immune System
Namrata Tomar and Rajat K. De
2. Crosstalk Between the Metabolic and Immune Systems
Namrata Tomar and Rajat K. De
3. Immunoinformatics: A Brief Review
Namrata Tomar and Rajat K. De
Part II: Databases
4. Immunoinformatics of the V, C and G Domains: IMGT® Definitive System for IG, TR and IgSF, MH and MhSF
Marie-Paule Lefranc
5. IMGT/HLA and the Immuno Polymorphism Database
James Robinson, Jason A. Halliwell, and Steven G.E. Marsh
6. Databases for T-Cell Epitopes
Chun-Wei Tung
7. Databases for B-Cell Epitopes
Juan Liu and Wen Zhang
8. Antigen-Antibody Interaction Database (AgAbDb): A Compendium of Antigen-Antibody Interactions
Urmila Kulkarni-Kale, Snehal Raskar-Renuse, Girija Natekar-Kalantre, and Smita A. Saxena
9. Allergen Databases
Gaurab Sircar, Debasree Sarkar, Swati Gupta Bhattacharya, and Sudipto Saha
Part III: Tools for Prediction
10. Prediction of Conformational B-Cell Epitopes
Wen Zhang, Yanqing Niu, Yi Xiong, and Meng Ke
11. Computational Prediction of B Cell Epitopes from Antigen Sequences
Jianzhao Gao and Lukasz Kurgan
12. Machine Learning Based Methods for Prediction of Linear B-Cell Epitopes
Hsin-Wei Wang and Tun-Wen Pai
13. Mimotope-Based Prediction of B-Cell Epitopes
Jian Huang and Peng Zhou
14. Hybrid Methods for B-Cell Epitope Prediction: Approaches to the Development and Utilization of Computational Tools for Practical Applications
Salvador Eugenio C. Caoili
15. Building Hybrid Classifiers for B-Cell Epitopes Prediction
Yasser EL-Manzalawy and Vasant Honavar
16. Multiplex Peptide-Based B-Cell Epitope Mapping
Sanne M.M. Hensen, Merel Derksen, and Ger J.M. Pruijn
17. Classification of Human Leukocyte Antigen (HLA) Supertypes
Mingjun Wang and Mogens H. Claesson
18. Customized Predictions of Peptide-MHC Binding and T-Cell Epitopes Using EPIMHC
Magdalena Molero-Abraham, Esther M. Lafuente, and Pedro Reche
19. T-Cell Epitope Prediction Methods: An Overview
Dattatraya V. Desai and Urmila Kulkarni-Kale
20. Computational Antigenic Epitope Prediction by Calculating Electrostatic Desolvation Penalties of Protein Surfaces
Sébastien Fiorucci and Martin Zacharias
21. In Silico Prediction of Allergenic Proteins
Gaurab Sircar, Bodhisattwa Saha, Swati Gupta Bhattacharya, and Sudipto Saha
22. Prediction of Virulence Factors Using Bioinformatics Approaches
Rupanjali Chaudhuri and Srinivasan Ramachandran
Part IV: Systems Biology Approaches in Immunoinformatics
23. A Systems Biology Approach to Study Systemic Inflammation
Bor-Sen Chen and Chia-Chou Wu
24. Procedures for Mucosal Immunization and Analyses of Cellular Immune Response to Candidate HIV Vaccines in Murine and Nonhuman Primate Models
Shailbala Singh, Pramod Nehete, Patrick Hanley, Bharti Nehete, Guojun Yang, Hong He, Scott M. Anthony, Kimberly Schluns, and K. Jagannadha Sastry
25. Immunoinformatics and Systems Biology in Personalized Medicine
Guillermo Lopez-Campos, Jesús F. Bermejo-Martin, Raquel Almansa, and Fernando Martin-Sanchez
Part V: Applications of Immunoinformatics
26. The Role of Small RNAs in Vaccination
Ajeet Chaudhary and Sunil Kumar Mukherjee
27. Structure-Based Clustering of Major Histocompatibility Complex (MHC) Proteins for Broad-Based T-Cell Vaccine Design
Joo Chuan Tong, Tin Wee Tan, and Shoba Ranganathan
28. Immunoinformatics, Molecular Modeling, and Cancer Vaccines
Seema Mishra and Subrata Sinha
29. Investigating Host Pathogen Behavior and Their Interaction Using Genome-Scale Metabolic Network Models
Priyanka P. Sadhukhan and Anu Raghunathan
30. Mathematical Models of HIV Replication and Pathogenesis
Dominik Wodarz