Part I: Modeling and Simulation Tools
1. Genome-Scale Model Management and Comparison
Stephan Pabinger and Zlatko Trajanoski
2. Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED
Scott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A. Best, and Christopher Henry
3. Metabolic Model Refinement Using Phenotypic Microarray Data
Pratish Gawand, Laurence Yang, William R. Cluett, and Radhakrishnan Mahadevan
4. Linking Genome-Scale Metabolic Modeling and Genome Annotation
Edik M. Blais, Arvind K. Chavali, and Jason A. Papin
5. Resolving Cell Composition through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm
Ryan S. Senger and Hadi Nazem-Bokaee
6. A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)
Evangelos Simeonidis, Sriram Chandrasekaran, and Nathan D. Price
7. Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis
Kieran Smallbone and Natalie J. Stanford
8. Computational Tools for Guided Discovery and Engineering of Metabolic Pathways
Matthew Moura, Linda Broadbelt, and Keith Tyo
9. Retrosynthetic Design of Heterologous Pathways
Pablo Carbonell, Anne-Gaëlle Planson, and Jean-Loup Faulon
Part II: Genome Engineering Tools
10. Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering
Yongbo Yuan, Jing Du, and Huimin Zhao
11. Adaptive Laboratory Evolution for Strain Engineering
James Winkler, Luis H. Reyes, and Katy C. Kao
12. Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli
Thomas J. Mansell, Joseph R. Warner, and Ryan T. Gill
Part III: Systems-Level 'Omics Tools
13. Identification of Mutations in Evolved Bacterial Genomes
Liam Royce, Erin Boggess, Tao Jin, Julie Dickerson, and Laura Jarboe
14. Discovery of Post-Transcriptional Regulatory RNAs Using Next Generation Sequencing Technologies
Grant Gelderman and Lydia M. Contreras
15. 13C-based Metabolic Flux Analysis: Fundamentals and Practice
Tae Hoon Yang
16. Nuclear Magnetic Resonance Methods for Metabolic Fluxomics
Shilpa Nargund, Max E. Joffe, Dennis Tran, Vitali Tugarinov, and Ganesh Sriram
17. Using Multiple Tracers for 13C Metabolic Flux Analysis
Maciek R. Antoniewicz
18. Isotopically Nonstationary 13C Metabolic Flux Analysis
Lara J. Jazmin and Jamey D. Young
19. Sample Preparation and Biostatistics for Integrated Genomics Approaches
Hein Stam, Michiel Akeroyd, Hilly Menke, Renger H. Jellema, Fredoen Valianpour, Wilbert H.M. Heijne, Maurien M.A. Olsthoorn, Sabine Metzelaar, Viktor M. Boer, Carlos M.F.M. Ribeiro, Philippe Gaudin, and Cees M.J. Sagt
Part IV: Integrating Large Datasets for Modeling and Engineering Applications
20. Targeted Metabolic Engineering Guided by Computational Analysis of
