Systems Metabolic Engineering

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-Gaelle 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-Ponten, 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 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-Gaelle 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-Ponten, 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 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-Gaelle 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-Ponten, 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 Matthew Moura, Linda Broadbelt, and Keith Tyo 9. Retrosynthetic Design of Heterologous Pathways Pablo Carbonell, Anne-Gaelle 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 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-Ponten, 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 D.B.R.K. Gupta Udatha, Simon Rasmussen, Thomas Sicheritz-Ponten, 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 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 Shuobo Shi, Tao Chen, and Xueming Zhao 23. Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation Kazuharu Arakawa and Masaru Tomita Kazuharu Arakawa and Masaru Tomita