Genome-Scale Model Management and Comparison -- Automated Genome Annotation and Metabolic Model Reconstruction in the SEED and Model SEED -- Metabolic Model Refinement Using Phenotypic Microarray Data -- Linking Genome-Scale Metabolic Modeling and Genome Annotation -- Resolving Cell Composition through Simple Measurements, Genome-Scale Modeling, and a Genetic Algorithm -- A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism) -- Kinetic Modeling of Metabolic Pathways: Application to Serine Biosynthesis -- Computational Tools for Guided Discovery and Engineering of Metabolic Pathways -- Retrosynthetic Design of Heterologous Pathways -- Customized Optimization of Metabolic Pathways by Combinatorial Transcriptional Engineering -- Adaptive Laboratory Evolution for Strain Engineering -- Trackable Multiplex Recombineering for Gene-Trait Mapping in E. coli -- Identification of Mutations in Evolved Bacterial Genomes -- Discovery of Post-Transcriptional Regulatory RNAs Using Next Generation Sequencing Technologies -- 13C-based Metabolic Flux Analysis: Fundamentals and Practice -- Nuclear Magnetic Resonance Methods for Metabolic Fluxomics -- Using Multiple Tracers for 13C Metabolic Flux Analysis -- Isotopically Nonstationary 13C Metabolic Flux Analysis -- Sample Preparation and Biostatistics for Integrated Genomics Approaches -- Targeted Metabolic Engineering Guided by Computational Analysis of Single Nucleotide Polymorphisms (SNPs) -- Linking RNA Measurements and Proteomics with Genome-Scale Models -- Comparative Transcriptome Analysis for Metabolic Engineering -- Merging Multiple Omics Datasets In Silico: Statistical Analyses and Data Interpretation.

With the ultimate goal of systematically and robustly defining the specific perturbations necessary to alter a cellular phenotype, systems metabolic engineering has the potential to lead to a complete cell model capable of simulating cell and metabolic function as well as predicting phenotypic response to changes in media, gene knockouts/overexpressions, or the incorporation of heterologous pathways.  In Systems Metabolic Engineering: Methods and Protocols, experts in the field describe the methodologies and approaches in the area of systems metabolic engineering and provide a step-by-step guide for their implementation. Four major tenants of this approach are addressed, including modeling and simulation, multiplexed genome engineering, ‘omics technologies, and large data-set incorporation and synthesis, all elucidated through the use of model host organisms.  Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions on their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.   Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Protocols serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.