Metabolic Engineering

  1. Modeling and Analysis of Metabolic Networks
    1. Stoichiometric Modeling
      1. Construction of Stoichiometric Matrices
        1. Reaction Listing
          1. Mass Balance Equations
            1. Matrix Representation
            2. Network Reconstruction
              1. Pathway Mapping
                1. Database Integration
                  1. Gap Filling
                    1. Model Curation
                  2. Flux Balance Analysis
                    1. Linear Programming Formulation
                      1. Objective Functions
                        1. Biomass Maximization
                          1. Product Yield Optimization
                            1. ATP Maintenance
                            2. Constraints
                              1. Stoichiometric Constraints
                                1. Thermodynamic Constraints
                                  1. Capacity Constraints
                                  2. Predicting Growth and Production Rates
                                    1. Sensitivity Analysis
                                      1. Gene Deletion Studies
                                        1. Single Knockouts
                                          1. Multiple Knockouts
                                            1. Synthetic Lethality
                                          2. Advanced Modeling Techniques
                                            1. Minimization of Metabolic Adjustment
                                              1. MOMA Algorithm
                                                1. Quadratic Programming
                                                2. Regulatory On/Off Minimization
                                                  1. ROOM Algorithm
                                                    1. Binary Variables
                                                    2. Elementary Flux Modes
                                                      1. Definition and Properties
                                                        1. Calculation Methods
                                                          1. Pathway Analysis
                                                          2. Extreme Pathways
                                                            1. Convex Analysis
                                                              1. Pathway Enumeration
                                                            2. Kinetic Modeling
                                                              1. Rate Law Selection
                                                                1. Mass Action Kinetics
                                                                  1. Michaelis-Menten Kinetics
                                                                    1. Allosteric Rate Laws
                                                                    2. Model Construction
                                                                      1. Parameter Estimation
                                                                        1. Model Validation
                                                                        2. Metabolic Control Analysis
                                                                          1. Flux Control Coefficients
                                                                            1. Concentration Control Coefficients
                                                                              1. Elasticity Coefficients
                                                                                1. Control Summation Theorems

                                                                            Previous

                                                                            4. Analytical Methods for Metabolic Engineering

                                                                            Go to top

                                                                            Next

                                                                            6. Strategies for Pathway Optimization