Part I: Genome Sequencing

1. Helicos Single Molecule Sequencing of Bacterial Genomes

Kathleen E. Steinmann, Christopher E. Hart, John F. Thompson, and Patrice M. Milos

2. Whole Genome Sequencing of Unculturable Bacterium Using Whole Genome Amplification

Yuichi Hongoh and Atsushi Toyoda

Part II: Gene Expression Analysis

3. RNA Sequencing and Quantitation Using the Helicos Genetic Analysis System

Tal Raz, Marie Causey, Daniel R. Jones, Alix Kieu, Stan Letovsky, Doron Lipson, Edward Thayer, John F. Thompson, and Patrice M. Milos

4. Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing

Fatih Ozsolak and Patrice M. Milos

5. Discovery of Bacterial sRNAs by High-Throughput Sequencing

Jane M. Liu and Andrew Camilli

6. Identification of Virus Encoding MicroRNAs Using 454 FLX Sequencing Platform

Byung-Whi Kong

7. Ribosomal RNA Depletion for Massively Parallel Bacterial RNA-Sequencing Applications

Zhoutao Chen and Xiaoping Duan

Part III: Microbial Diversity

8. Integrating High-Throughput Pyrosequencing and Quantitative Real-Time PCR to Analyze Complex Microbial Communities

Husen Zhang, Prathap Parameswaran, Jonathan Badalamenti, Bruce E. Rittmann, and Rosa Krajmalnik-Brown

9. Tag-Encoded FLX Amplicon Pyrosequencing for the Elucidation of Microbial and Functional Gene Diversity in Any Environment

Yan Sun, Randall D. Wolcott, and Scot E. Dowd

10. Pyrosequencing of Chaperonin-60 (cpn60) Amplicons as a Means of Determining Microbial Community Composition

John Schellenberg, Matthew G. Links, Janet E. Hill, Sean M. Hemmingsen, Geoffrey A. Peters, and Tim J. Dumonceaux

11. Prescreening of Microbial Populations for the Assessment of Sequencing Potential

Irene B. Hanning and Steven C. Ricke

Part IV: Metagenomics

12. Metagenomics

Jack A Gilbert, Bonnie Laverock, Ben Temperton, Simon Thomas, Martin Muhling, and Margaret Hughes

13. Metagenomic Analysis of Intestinal Microbiomes in Chickens

Taejoong Kim and Egbert Mundt

14. Gene Expression Profiling: Metatranscriptomics

Jack A. Gilbert and Margaret Hughes

Part V: Sequence Profiling for Functional Analysis

15. High-Throughput Insertion Tracking by Deep Sequencing for the Analysis of Bacterial Pathogens

Sandy M.S. Wong, Jeffrey D. Gawronski, David Lapointe, and Brian J. Akerley

16. Determining DNA Methylation Profiles Using Sequencing

Suhua Feng, Liudmilla Rubbi, Steven E. Jacobsen, and Matteo Pellegrini

Part VI: Sequencing Library Preparation

17. Preparation of Next-Generation Sequencing Libraries Using Nextera(TM) Technology: Simultaneous DNA Fragmentation and Adaptor Tagging by In Vitro Transposition

Nicholas Caruccio

18. Amplification-Free Library Preparation for Paired-End Illumina Sequencing

Iwanka Kozarewa and Daniel J. Turner

19. Target-Enrichment through Amplification of Hairpin-Ligated Universal Targets for Next-Generation Sequencing Analysis

Pallavi Singh, Rajesh Nayak, and Young Min Kwon