Computing for Comparative Microbial Genomics

1. Front Matter

   Pages I-XIV

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2. Introductions

   1. Front Matter

      Pages 1-1

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   2. Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 3-17

   3. Bioinformatics for Microbiologists: An Introduction

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 19-35

   4. Microbial Genome Sequences: A New Era in Microbiology

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 37-51

   5. An Overview of Genome Databases

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 53-67

   6. The Challenges of Programming: A Brief Introduction

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 69-91

3. Comparative Genomics

   1. Front Matter

      Pages 93-93

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   2. Methods to Compare Genomes The First Examples

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 95-109

   3. Genomic Properties: Length, Base Composition and DNA Structures

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 111-135

   4. Word Frequencies and Repeats

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 137-150

4. Transcriptomics and Proteomics

   1. Front Matter

      Pages 151-151

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   2. Transcriptomics: Translated and Untranslated RNA

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 153-166

   3. Expression of Genes and Proteins

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 167-187

   4. Of Proteins, Genomes, and Proteomes

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 189-210

5. Microbial Communities

   1. Front Matter

      Pages 211-211

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   2. Microbial Communities: Core and Pan-Genomics

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 213-228

   3. Metagenomics of Microbial Communities

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 229-242

   4. Evolution of Microbial Communities; or, On the Origins of Bacterial Species

      • David W. Ussery, Trudy M. Wassenaar, Stefano Borini

      Pages 243-256

6. Back Matter

   Pages 257-270

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Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.

• Chromosome
• DNA
• Metagenomics
• RNA
• bioinformatics
• databases
• evolution
• gene expression
• genome
• heat map
• metagenomes
• microbiology

From the reviews:

"It is a very well-written review of genomics and proteomics of microbes, and makes convincing arguments for the practicality of applying bioinformatics to the study of communities of these species. The references are well chosen. The writing style is superb. … There is an amazing amount of interesting material, in fewer than 275 pages. … The book is probably more suitable as an introduction to contemporary applications of bioinformatics and microbiology for computational scientists." (Anthony J. Duben, ACM Computing Reviews, June, 2009)

• Department of Systems Biology, The Technical University of Denmark, Lyngby, Denmark

  David W. Ussery

• Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany

  Trudy M. Wassenaar

• Laboratory of Physical Chemistry Swiss Federal Institute of Technology (ETH), Zurich, Switzerland

  Stefano Borini

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