"... this book was written from start to finish by one
extremely dedicated and erudite individual. The author has done an
excellent job of covering the many topics that fall under the
umbrella of computational biology for vaccine design, demonstrating
an admirable command of subject matter in fields as disparate as
object-oriented databases and regulation of T cell response. Simply
put, it has just the right breadth and depth, and it reads well. In
fact, readability is one of its virtues--making the book
enticing and useful, all at once..." Human Vaccines,
2010

"... This book has several strong points. Although there are
many textbooks that deal with vaccinology, few attempts have been
made to bring together descriptions of vaccines in history, basic
bioinformatics, various computational solutions and challenges in
vaccinology, detailed experimental methodologies, and cutting-edge
technologies... This book may well serve as a first line of
reference for all biologists and computer scientists..."
-Virology Journal, 2009

Vaccines have probably saved more lives and reduced suffering in a
greater number of people than any other medical intervention in
human history, succeeding in eradicating smallpox and significantly
reducing the mortality and incidence of other diseases. However,
with the emergence of diseases such as SARS and the threat of
biological warfare, vaccination has once again become a topic of
major interest in public health.

Vaccinology now has at its disposal an array of post-genomic
approaches of great power. None has a more persuasive potential
impact than the application of computational informatics to vaccine
discovery; the recent expansion in genome data and the parallel
increase in cheap computing power have placed the bioinformatics
exploration of pathogen genomes centre stage for vaccine
researchers.

This is the first book to address the area of bioinformatics as
applied to rational vaccine design, discussing the ways in which
bioinformatics can contribute to improved vaccine development
by

* introducing the subject of harnessing the mathematical and
computing power inherent in bioinformatics to the study of
vaccinology

* putting it into a historical and societal context,
and

* exploring the scope of its methods and applications.

Bioinformatics for Vaccinology is a one-stop
introduction to computational vaccinology. It will be of particular
interest to bioinformaticians with an interest in immunology, as
well as to immunologists, and other biologists who need to
understand how advances in theoretical and computational
immunobiology can transform their working practices.

Dr Darren R Flower, Reader in Pharmacy, School of Life and Health Sciences, University of Aston, Birmingham, UK.

"... This book has several strong points. Although there are many textbooks that deal with vaccinology, few attempts have been made to bring together descriptions of vaccines in history, basic bioinformatics, various computational solutions and challenges in vaccinology, detailed experimental methodologies, and cutting-edge technologies... This book may well serve as a first line of reference for all biologists and computer scientists..." Virology Journal, 2009

Vaccines have probably saved more lives and reduced suffering in a greater number of people than any other medical intervention in human history, succeeding in eradicating smallpox and significantly reducing the mortality and incidence of other diseases. However, with the emergence of diseases such as SARS and the threat of biological warfare, vaccination has once again become a topic of major interest in public health.

Vaccinology now has at its disposal an array of post-genomic approaches of great power. None has a more persuasive potential impact than the application of computational informatics to vaccine discovery; the recent expansion in genome data and the parallel increase in cheap computing power have placed the bioinformatics exploration of pathogen genomes centre stage for vaccine researchers.

This is the first book to address the area of bioinformatics as applied to rational vaccine design, discussing the ways in which bioinformatics can contribute to improved vaccine development by

• introducing the subject of harnessing the mathematical and computing power inherent in bioinformatics to the study of vaccinology
• putting it into a historical and societal context, and
• exploring the scope of its methods and applications.

Bioinformatics for Vaccinology is a one-stop introduction to computational vaccinology. It will be of particular interest to bioinformaticians with an interest in immunology, as well as to immunologists, and other biologists who need to understand how advances in theoretical and computational immunobiology can transform their working practices.

Preface xiii

Acknowledgements xv

Exordium xvii

1 Vaccines: Their place in history 1

Smallpox in history 1

Variolation 3

Variolation in history 5

Variolation comes to Britain 6

Lady Mary Wortley Montagu 9

Variolation and the Sublime Porte 11

The royal experiment 13

The boston connection 14

Variolation takes hold 17

The Suttonian method 18

Variolation in Europe 19

The coming of vaccination 21

Edward Jenner 23

Cowpox 26

Vaccination vindicated 28

Louis Pasteur 29

Vaccination becomes a science 30

Meister, Pasteur and rabies 31

A vaccine for every disease 33

In the time of cholera 34

Haffkine and cholera 36

Bubonic plague 37

The changing face of disease 39

Almroth wright and typhoid 40

Tuberculosis, Koch, and Calmette 43

Vaccine BCG 44

Poliomyelitis 46

Salk and Sabin 47

Diphtheria 49

Whooping cough 50

Many diseases, many vaccines 51

Smallpox: Endgame 53

Further reading 54

2 Vaccines: Need and opportunity 55

Eradication and reservoirs 55

The ongoing burden of disease 57

Lifespans 57

The evolving nature of disease 59

Economics, climate and disease 60

Three threats 60

Tuberculosis in the 21st century 61

HIV and AIDS 62

Malaria: Then and now 63

Influenza 64

Bioterrorism 65

Vaccines as medicines 67

Vaccines and the pharmaceutical industry 68

Making vaccines 70

The coming of the vaccine industry 70

3 Vaccines: How they work 73

Challenging the immune system 73

The threat from bacteria: Robust, diverse, and endemic 74

Microbes, diversity and metagenomics 75

The intrinsic complexity of the bacterial threat 76

Microbes and humankind 77

The nature of vaccines 78

Types of vaccine 80

Carbohydrate vaccines 82

Epitopic vaccines 82

Vaccine delivery 83

Emerging immunovaccinology 84

The immune system 85

Innate immunit…