Part 1. E. coli

1. Bacterial Genome Reengineering

Jindan Zhou and Kenneth E. Rudd

2. Targeted Chromosomal Gene Knockout using PCR Fragments

Kenan C. Murphy

3. Scarless Chromosomal Gene Knockout Methods

Bong Hyun Sung, Jun Hyoung Lee, and Sun Chang Kim

4. Random Chromosomal Gene Disruption In vivo using Transposomes

Les M. Hoffman

5. Genome Engineering using Targeted Oligonucleotide Libraries and Functional Selection

Elie J. Diner, Fernando Garza-Sánchez, and Christopher S. Hayes

6. Microarray-based Genetic Footprinting Strategy to Identify Strain Improvement Genes after Competitive Selection of Transposon Libraries

Alison K. Hottes and Saeed Tavazoie

7. Optimization of Synthetic Operons using Libraries of Post-Transciptional Regulatory Elements

Daniel E. Agnew and Brian F. Pfleger

8. Marker Free Chromosomal Expression of Foreign and Native Genes in E. coli

Chung-Jen Chiang, Po Ting Chen, Shan-Yu Chen, and Yun-Peng Chao

9. Array-based Synthetic Genetic Screens to Map Bacterial Pathways and Functional Networks in Escherichia coli

Mohan Babu, Alla Gagarinova, and Andrew Emili

10. Assembling New E. coli Strains by Transduction using Phage P1

Sean D. Moore

Part II. Saccharomyces cerevisiae

11. Yeast Bioinformatics and Strain Engineering Resources

Audrey L. Atkin

12. Delete and Repeat: A Comprehensive Toolkit for Sequential Gene Knock-out in the Budding Yeast Saccharomyces cerevisiae

Johannes H. Hegemann and Sven Boris Heick

13. Genome-wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans

Tao Xu, Nikë Bharucha, and Anuj Kumar

14. Signature-tagged Mutagenesis to Characterize Genes Through Competitive Selection of Barcoded Genome Libraries

Julia Oh and Corey Nislow

15. Global Strain Engineering by Mutant Transcription Factors

Amanda M. Lanza and Hal S. Alper

16. Genomic Promoter Replacement Cassettes to Alter Gene Expression in the Yeast Saccharomyces cerevisiae

Andreas Kaufmann and Michael Knop

Part III. Strain Engineering Other Industrially Important Microbes

17. Microbial Genome Analysis and Comparisons: Web-based Protocols and Resources

Medha Bhagwat and Arvind A. Bhagwat

18. Plasmid Artificial Modification: A Novel Method for Efficient DNA Transfer into Bacteria

Tohru Suzuki and Kazumasa Yasui

19. Broad-host-range Plasmid Vectors for Gene Expression in Bacteria

Rahmi Lale, Trygve Brautaset, and Svein Valla

20. Simple Method for Introducing Marker-free Deletions in the Bacillus subtilis Genome

Takuya Morimoto, Katsutoshi Ara, Katsuya Ozaki, and Naotake Ogasawara

21. Transposon-mediated Random Mutagenesis of Bacillus subtilis

Adam C. Wilson and Hendrik Szurmant

22. Integrative Food Grade Expression System for Lactic Acid Bacteria

Grace L. Douglas, Yong Jun Goh and Todd R. Klaenhammer

23. ClosTron-mediated Engineering of Clostridium

Sarah A. Kuehne, John T. Heap, Clare M. Cooksley, Stephen T. Cartman, and Nigel P. Minton

24. High Throughput Transposon Mutagenesis of Corynebacterium glutamicum

Nobuaki Suzuki, Masayuki Inui, and Hideaki Yukawa

25. Mini-Mu Transposon Mutagenesis of Ethanologenic Zymomonas mobilis

Katherine M. Pappas

26. Engineering Thermoacidop