Systems Metabolic Engineering: Methods and Protocols. Book + Online Access

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 Single Nucleotide Polymorphisms (SNPs)

D.B.R.K. Gupta Udatha, Simon Rasmussen, Thomas Sicheritz-Pontén, and Gianni Panagiotou

21. Linking RNA Measurements and Proteomics with Genome-Scale Models

Christopher M. Gowen and Stephen S. Fong

22. Comparative Transcriptome Analysis for Metabolic Engineering

Shuobo Shi, Tao Chen, and Xueming Zhao

23. Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation

Kazuharu Arakawa and Masaru Tomita