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9780262122801

Immunological Bioinformatics

by ; ; ; ;
  • ISBN13:

    9780262122801

  • ISBN10:

    0262122804

  • Format: Hardcover
  • Copyright: 2005-06-17
  • Publisher: The MIT Press

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

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Summary

Despite the fact that advanced bioinformatics methodologies have not been used as extensively in immunology as in other subdisciplines within biology, research in immunological bioinformatics has already developed models of components of the immune system that can be combined and that may help develop therapies, vaccines, and diagnostic tools for such diseases as AIDS, malaria, and cancer. In a broader perspective, specialized bioinformatics methods in immunology make possible for the first time a systems-level understanding of the immune system. The traditional approaches to immunology are reductionist, avoiding complexity but providing detailed knowledge of a single event, cell, or molecular entity. Today, a variety of experimental bioinformatics techniques connected to the sequencing of the human genome provides a sound scientific basis for a comprehensive description of the complex immunological processes. This book offers a description of bioinformatics techniques as they are applied to immunology, including a succinct account of the main biological concepts for students and researchers with backgrounds in mathematics, statistics, and computer science as well as explanations of the new data-driven algorithms in the context of biological data that will be useful for immunologists, biologists, and biochemists working on vaccine design. In each chapter the authors show interesting biological insights gained from the bioinformatics approach. The book concludes by explaining how all the methods presented in the book can be integrated to identify immunogenic regions in microorganisms and host genomes.

Author Biography

Ole Lund is Associate Professor and leader of the Immunological Bioinformatics group at the Center for Biological Sequence Analysis at Technical University of Denmark Morten Nielsen and Claus Lundegaard are Associate Professors, and Soren Brunak is Professor and Center Director Can Kesmir is Assistant Professor at the Department of Theoretical Biology at Utrecht University

Table of Contents

Preface ix
1 Immune Systems and Systems Biology
1(16)
1.1 Innate and Adaptive Immunity in Vertebrates
10(1)
1.2 Antigen Processing and Presentation
11(3)
1.3 Individualized Immune Reactivity
14(3)
2 Contemporary Challenges to the Immune System
17(18)
2.1 Infectious Diseases in the New Millennium
17(1)
2.2 Major Killers in the World
17(4)
2.3 Childhood Diseases
21(1)
2.4 Clustering of Infectious Disease Organisms
22(2)
2.5 Biodefense Targets
24(6)
2.6 Cancer
30(1)
2.7 Allergy
31(1)
2.8 Autoimmune Diseases
32(3)
3 Sequence Analysis in Immunology
35(34)
3.1 Sequence Analysis
35(1)
3.2 Alignments
36(16)
3.3 Multiple Alignments
52(2)
3.4 DNA Alignments
54(1)
3.5 Molecular Evolution and Phylogeny
55(2)
3.6 Viral Evolution and Escape: Sequence Variation
57(4)
3.7 Prediction of Functional Features of Biological Sequences
61(8)
4 Methods Applied in Immunological Bioinformatics
69(34)
4.1 Simple Motifs, Motifs and Matrices
69(3)
4.2 Information Carried by Immunogenic Sequences
72(3)
4.3 Sequence Weighting Methods
75(2)
4.4 Pseudocount Correction Methods
77(2)
4.5 Weight on Pseudocount Correction
79(1)
4.6 Position Specific Weighting
79(1)
4.7 Gibbs Sampling
80(4)
4.8 Hidden Markov Models
84(7)
4.9 Artificial Neural Networks
91(8)
4.10 Performance Measures for Prediction Methods
99(3)
4.11 Clustering and Generation of Representative Sets
102(1)
5 DNA Microarrays in Immunology
103(8)
5.1 DNA Microarray Analysis
103(3)
5.2 Clustering
106(2)
5.3 Immunological Applications
108(3)
6 Prediction of Cytotoxic T Cell (MHC Class I) Epitopes
111(24)
6.1 Background and Historical Overview of Methods for Pep-tide MHC Binding Prediction
112(2)
6.2 MHC Class I Epitope Binding Prediction Trained on Small Data Sets
114(6)
6.3 Prediction of CTL Epitopes by Neural Network Methods
120(13)
6.4 Summary of the Prediction Approach
133(2)
7 Antigen Processing in the MHC Class I Pathway
135(22)
7.1 The Proteasome
135(2)
7.2 Evolution of the Immunosubunits
137(2)
7.3 Specificity of the (Immuno)Proteasome
139(4)
7.4 Predicting Proteasome Specificity
143(4)
7.5 Comparison of Proteasomal Prediction Performance
147(2)
7.6 Escape from Proteasomal Cleavage
149(1)
7.7 Post-Proteasomal Processing of Epitopes
150(3)
7.8 Predicting the Specificity of TAP
153(1)
7.9 Proteasome and TAP Evolution
154(3)
8 Prediction of Helper T Cell (MHC Class II) Epitopes
157(18)
8.1 Prediction Methods
158(1)
8.2 The Gibbs Sampler Method
159(13)
8.3 Further Improvements of the Approach
172(3)
9 Processing of MHC Class II Epitopes
175(12)
9.1 Enzymes Involved in Generating MHC Class II Ligands
176(3)
9.2 Selective Loading of Peptides to MHC Class II Molecules
179(1)
9.3 Phylogenetic Analysis of the Lysosomal Proteases
180(2)
9.4 Signs of the Specificities of Lysosomal Proteases on MHC Class II Epitopes
182(1)
9.5 Predicting the Specificity of Lysosomal Enzymes
182(5)
10 B Cell Epitopes 187(16)
10.1 Affinity Maturation
188(3)
10.2 Recognition of Antigen by B cells
191(10)
10.3 Neutralizing Antibodies
201(2)
11 Vaccine Design 203(12)
11.1 Categories of Vaccines
204(3)
11.2 Polytope Vaccine: Optimizing Plasmid Design
207(2)
11.3 Therapeutic Vaccines
209(4)
11.4 Vaccine Market
213(2)
12 Web-Based Tools for Vaccine Design 215(8)
12.1 Databases of MHC Ligands
215(2)
12.2 Prediction Servers
217(6)
13 MHC Polymorphism 223(20)
13.1 What Causes MHC Polymorphism?
223(2)
13.2 MHC Supertypes
225(18)
14 Predicting Immunogenicity: An Integrative Approach 243(11)
14.1 Combination of MHC and Proteasome Predictions
244(1)
14.2 Independent Contributions from TAP and Proteasome Predictions
245(2)
14.3 Combinations of MHC, TAP, and Proteasome Predictions
247(4)
14.4 Validation on HIV Data Set
251(1)
14.5 Perspectives on Data Integration
252(2)
References 254(37)
Index 291

Supplemental Materials

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The New copy of this book will include any supplemental materials advertised. Please check the title of the book to determine if it should include any access cards, study guides, lab manuals, CDs, etc.

The Used, Rental and eBook copies of this book are not guaranteed to include any supplemental materials. Typically, only the book itself is included. This is true even if the title states it includes any access cards, study guides, lab manuals, CDs, etc.

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