PLAN OF THE SECOND EDITION

Chapter 1, Introduction to Genomics, sets the stage, and introduces all of the major players: DNA and protein sequences and structures, genomes and proteomes, databases and information retrieval, and bioinformatics and the World Wide Web. Subsequent chapters develop these topics in detail. Chapter 1 briefly provides the framework of how they fit together and sets them in their context of biomedical, physical, and computational sciences.

Chapter 2 demonstrates that Genomes are the Hub of Biology. Whereas genome sequences are determined from individuals, to appreciate life as a whole requires extending our point of view spatially, to populations and interacting populations; and temporally, to consider life as a phenomenon with a history. We can study the characteristics of life in the present, we can determine what came before, and we can – at least to some extent – extrapolate to the future. The ‘central dogma’ and the genetic code underly the implementation of the genome, in terms of the synthesis of RNAs and proteins. Absent from Crick’s original statement of the central dogma is the crucial role of regulation in making cells stable and robust, two characteristics essential for survival.

Chapter 3, Mapping, Sequencing, Annotation, and Databases, describes how genomics has emerged from classical genetics and molecular biology. The first nucleic acid sequencing, by groups led by F. Sanger and W. Gilbert, in the 1970s, were a breakthrough comparable to the discovery of the double helix of DNA. The challenges of sequencing stimulated spectacular improvements in technology. The first was the automation of the Sanger method. The original sequences of the human genome were accomplished by batteries of automated Sanger sequencers. Subsquently a series of ‘new generations’ of novel approaches have brought the landmark goal, the $US1000 human genome, within reach. Where do all the data go? Chapter 3 also introduces the databanks that archive, curate, and distribute the data, and some of the information-retrieval tools that make them accessible to scientific enquiry.

Chapter 4, Comparative Genomics, begins with a general survey of the different modes of genome organization with which living things have experimented. With complete sequences of genomes of many different species, we can confront and compare them. But, of course, different individuals of a species do not necessarily have identical genomes. What is the nature and extent of the variability? With intraspecies variability as a baseline, what are the similarities and differences between genomes of different species? Comparative genomics thereby allows us to address a question central not only to this book but to the field as a whole: what does it mean to be human?

Chapter 5, Evolution and Genomic Change, relates genomics to evolution, a major unifying principle of biology. (Arguably the laws of thermodynamics are another.) T. Dobzhansky famously said: ‘Nothing in biology makes sense except in the light of evolution.’ Description of some of the important ideas and tools – of taxonomy and phylogeny, on the classical species level and on the molecular level – will be useful in organizing the material in subsequent chapters.

Chapter 6, Genomes of Prokaryotes, surveys the genomes of bacteria and archaea in more detail. Taxonomy and phylogeny of prokaryotes present problems because of extensive horizontal gene transfer. This challenges the whole idea of a hierarchy of biological classification. Many bacteria have been cloned and studied in isolation, especially those responsible for disease. However, a new field, metagenomics, deals with the entire complement of living things in an environmental sample, allowing us to address questions about interspecies interaction in the ‘real world’. Sources include ocean water, soil, and the human gut.

Chapter 7 surveys Genomes of Eukaryotes. It starts with yeast, which is about as simple as a eukaryote can get. Selected plant, invertebrate, and chordate genomes illuminate the many profound common features of eukaryotic genomes; and the very great variety of structures, biochemistry, and lifestyles that are compatible with the underlying similarities.

Chapter 8, Genomics and Human Biology, develops applications to the study of our own species. Although clinical applications are undoubtedly the most important, genomics has important contributions to make to human palaeontology, anthropology, and the law. The ability to extract DNA from extinct

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Introduction to Genomics
Table of contents

Table of contents

  • Title Page iii
  • Preface to the First Edition vii
  • Preface to the Second Edition ix
  • Plan of the Second Edition x
  • New to This Edition xii
  • Contents xv
  • Chapter 1 - Introduction to Genomics 3
  • Chapter 2 - Genomes Are the Hub of Biology 41
  • Chapter 3 - Mapping, Sequencing, Annotation, and Databases 79
  • Chapter 4 - Comparative Genomics 115
  • Chapter 5 - Evolution and Genomic Change 161
  • Chapter 6 - Genomes of Prokaryotes 191
  • Chapter 7 - Genomes of Eukaryotes 215
  • Chapter 8 - Genomics and Human Biology 237
  • Chapter 9 - Microarrays and Transcriptomics 265
  • Chapter 10 - Proteomics 297
  • Chapter 11 - Systems Biology 341
  • Epilogue 389
  • Index 390
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