Methods in Molecular Biology

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(R) 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 Sebastien 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, Jesus 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