Microbial Genomes

by Fraser, Claire M.; Read, Timothy D., Ph.D.; Nelson, Karen E., Ph.D.; Venter, J. Craig

• ISBN13: 9781588291899
• ISBN10: 1588291898
• Format: Hardcover
• Copyright: 2004-04-01
• Publisher: Humana Pr Inc

Summary

This collection of diverse articles by the pioneers of modern genomics takes stock of the current state of the field and elucidates the contribution that sequencing genomes has made to our understanding of microbial metabolism and evolution. Through twenty-eight thought-provoking chapters, the authors describe some of the most common computational methods and their applications to studying pathogenic microorganisms, show how genomics can be used to reconstruct the history and dynamism of the microbial world, and discuss issues as diverse as reconstruction of metabolic pathways, cell cycle processes, microbial evolution, metagenomics, and vaccine development. Additional chapters deal with microarrays and expression analysis and the role of genomic in drug discovery.

Table of Contents

Foreword by J. Craig Venter	v
Preface	vii
Contributors	xiii
PART I: INTRODUCTION
1 History of Microbial Genomics
Hamilton O. Smith	3	(16)
PART II: BIOINFORMATICS As w TOOL IN GENOMICS
2 Tools for Gene Finding and Whole Genome Comparison
Steven L. Salzberg and Arthur L. Delcher	19	(14)
3 Bacterial Genome Annotation at TIGR
Owen White	33	(14)
4 Bioinformatics and Microbial Pathogenesis
Fiona S.L. Brinkman and Joanna L. Fuego	47	(24)
5 Bacteriophage Bioinformatics
Derrick E. Fouts	71	(24)
PART III: CORE FUNCTIONS
6 Comparative Microbial Metabolism
Karen E. Nelson	95	(18)
7 Genomic Analysis of Membrane Transport
Ian T. Paulsen, Katherine H. Kang, Mark E. Hance, and Qinghu Ren	113	(14)
8 Genomics-Based Analysis of the Bacterial Cell Cycle
Michael T. Laub, Harley H. McAdams, and Lucy Shapiro	127	(16)
PART IV: THE EVOLUTION OF MICROBIAL GENOMES
9 A Brief History of Views of Prokaryotic Evolution and Taxonomy
Lorraine Olendzenski, Olga Zhaxybayeva, and J. Peter Gogarten	143	(12)
10 How Bacterial Genomes Change
Timothy D. Read and Garry S.A. Myers	155	(20)
11 Concepts of Bacterial Biodiversity for the Age of Genomics
Frederick M. Cohan	175	(20)
12 Coevolution of Symbionts and Pathogens With Their Hosts
Robert A. Feldman	195	(18)
PART V: A SURVEY OF MICROBIAL GENOMES
13 A Survey of Plant Pathogen Genomes
C. Robin Buell	213	(12)
14 Anoxygenic Phototrophic Bacteria
F. Robert Tabita and Thomas E. Hanson	225	(20)
15 Genomics of Thermophiles
Frank T. Robb	245	(24)
16 The Genomes of Pathogenic Enterobacteria
Julian Parkhill and Nicholas R. Thomson	269	(22)
17 Obligate Intracellular Pathogens
Siv G.E. Andersson	291	(18)
18 Low G+C Gram-Positive Genomes
Steven R. Gill	309	(24)
19 Genomics of Actinobacteria, the High G+C Gram-Positive Bacteria
Stephen D. Bentley, Roland Brosch, Stephen V. Gordon, David A. Hopwood, and Stewart T. Cole	333	(28)
20 Parasite Genomics
Malcolm J. Gardner	361	(22)
21 Genome Sequence of an Extremely Halophilic Archaeon
Shiladitya DasSarma	383	(20)
PART VI: APPLICATIONS OF GENOMIC DATA
22 Microarrays, Expression Analysis, and Bacterial Genomes
Carsten Rosenow and Brian Tjaden	403	(16)
23 Microbial Population Genomics and Ecology: A New Frontier
Edward F. Delong	419	(24)
24 Application of Genomics to Biocatalysts and Biodegradation
Lawrence P. Wackett	443	(18)
25 Enzyme Discovery and Microbial Genomics
Robert M. Kelly and Keith R. Shockley	461	(24)
26 Integration of Genomics in the Drug Discovery Process
Jacques Ravel	485	(20)
27 A Genomic Approach to Vaccine Development
Rino Rappuoli, Vega Masignani, Mariagrazia Pizza, Guido Grandi, and John L. Telford	505	(12)
28 Microbial Proteomics
Svend Birkelund, Brian B. Vandahl, Allan C. Shaw, and Gunna Christiansen	517	(14)
Index	531