Preface to the Second Edition

Overview and aims. This book is intended as a self-contained guide to the entire field

of bioinformatics, interpreted as the application of information science to biology.

There is strong underlying belief that information is a profound concept underlying

biology, and familiarity with the concepts of information should make it possible

to gain many important new insights into biology. In other words, the vision under-

pinning this book goes beyond the narrow interpretation of bioinformatics some-

times encountered, which may confine itself to specific tasks such as the attempted

identification of genes in a DNA sequence.

Organization and features. The chapters are grouped into three parts, respec-

tively covering the relevant fundamentals of information science; overviewing all of

biology; and surveying applications. Thus Part I (fundamentals) carefully explains

what information is, and discusses attributes such as value and quality, and its multiple

meanings of accuracy, meaning, and effect. The transmission of information through

channels is described. Brief summaries of the necessary elements of set theory,

combinatorics, probability, likelihood, clustering, and pattern recognition are given.

Concepts such as randomness, complexity, systems, and networks, needed for the

understanding of biological organization, are also discussed. Part II (biology) covers

both organismal (ontogeny and phylogeny, as well as genome structure) and molec-

ular aspects. Part III (applications) is devoted to the most important practical appli-

cations of bioinformatics, notably gene identification, transcriptomics, proteomics,

interactomics (dealing with networks of interactions), and metabolomics. These

chapters start with a discussion of the experimental aspects (such as DNA sequencing

in the genomics chapter), and then move on to a thorough discussion of how the data

is analysed. Specifically medical applications are grouped in a separate chapter. A

number of problems are suggested, many of which are open-ended and intended to

stimulate further thinking. The bibliography points to specialized monographs and

review articles expanding on material in the text, and includes guide references to

very recently reported research not yet to be found in reviews.

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