Using bioinformatics methods to generate a systems-level view of the immune system; description of the main biological concepts and the new data-driven algorithms. 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.

The astounding diversity of the immune system and the complexity of its regulatory pathways makes immunology a combinatorial science. Computational analysis has therefore become an essential element of immunology research and this has led to the creation of the emerging field of immunoinformatics. This book is the first to feature thorough coverage of this new field. Immunoinformatics facilitates the understanding of immune function by modelling the interactions among immunological components. Biological research provides ever deeper insights into the complexity of living organisms while computer science provides an effective means to store and analyse large volumes of complex data. Combining the two fields increases the efficiency of biological research and offers the potential for major advances in the study of biological systems. This book encompasses key developments in immunoinformatics, including immunological databases, sequence analysis, structure modelling, mathematical modelling of the immune system, simulation of laboratory experiments, statistical support for immunological experimentation and immunogenomics. The difficulties in effective application of bioinformatic tools in immunology arise at both ends of the spectrum: most immunologists have only a limited comprehension of sophisticated data analysis and applicability and limitations, while the average computer scientist lacks knowledge of the depth and complexity of biological data. The purpose of this book, therefore, is to present contributions from a multidisciplinary team of biologists and computer scientists to explore the issues related to better understanding of immune function and, in particular, to help apply new computer science methods to immunological research. Related Novartis Foundation symposia: 247 In Silico Simulation of Biological Processes Chair: Denis Noble 252 Generation and effector functions of regulatory lymphocytes Chair: Jean-François Bach

Like many words, the term “immunomics” equates to different ideas contingent on context. For a brief span, immunomics meant the study of the Immunome, of which there were, in turn, several different definitions. A now largely defunct meaning rendered the Immunome as the set of antigenic peptides or immunogenic proteins within a single microorganism – be that virus, bacteria, fungus, or parasite – or microbial population, or antigenic or allergenic proteins and peptides derived from the environment as a whole, containing also proteins from eukaryotic sources. However, times have changed and the meaning of immunomics has also changed. Other newer definitions of the Immunome have come to focus on the plethora of immunological receptors and accessory molecules that comprise the host immune arsenal. Today, Immunomics or immunogenomics is now most often used as a synonym for high-throughput genome-based immunology. This is the study of aspects of the immune system using high-throughput techniques within a conc- tual landscape borne of both clinical and biophysical thinking.

In contrast to existing books on immunoinformatics, this volume presents a cross-section of immunoinformatics research. The contributions highlight the interdisciplinary nature of the field and how collaborative efforts among bioinformaticians and bench scientists result in innovative strategies for understanding the immune system. Immunoinformatics is ideal for scientists and students in immunology, bioinformatics, microbiology, and many other disciplines.

Structural Biology in Immunology, Structure/Function of Novel Molecules of Immunologic Importance delivers important information on the structure and functional relationships in novel molecules of immunologic interest. Due to an increasingly sophisticated understanding of the immune system, the approach to the treatment of many immune-mediated diseases, including multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis, and inflammatory bowel disease has been dramatically altered. Furthermore, there is an increasing awareness of the critical role of the immune system in cancer biology. The improved central structure function relationships presented in this book will further enhance our ability to understand what defects in normal individuals can lead to disease. Describes novel/recently discovered immunomodulatory proteins, including antibodies and co-stimulatory or co-inhibitory molecules Emphasizes new biologic and small molecule drug design through the exploration of structure-function relationship Features a collaborative editorial effort, involving clinical immunologists and structural biologists Provides useful and practical insights on developing the necessary links between basic science and clinical therapy in immunology Gives interested parties a bridge to learn about computer modeling and structure based design principles