Engineering Genetic Circuits: Table of Contents

  • Forward – by Adam Arkin
  • Preface
  • 1. An Engineer’s Guide to Genetic Circuits
    • 1.1 Chemical Reactions
    • 1.2 Macromolecules
    • 1.3 Genomes
    • 1.4 Cells and Their Structure
    • 1.5 Genetic Circuits
    • 1.6 Viruses
    • 1.7 Phage lambda: A Simple Genetic Circuit
    • 1.8 Sources
    • Problems
    • Appendix
  • 2 Learning Models
    • 2.1 Experimental Methods
    • 2.2 Experimental Data
    • 2.3 Cluster Analysis
    • 2.4 Learning Bayesian Networks
    • 2.5 Learning Causal Networks
    • 2.6 Experimental Design
    • 2.7 Sources
    • Problems
  • 3 Differential Equation Analysis
    • 3.1 A Classical Chemical Kinetic Model
    • 3.2 Differential Equation Simulation
    • 3.3 Qualitative ODE Analysis
    • 3.4 Spatial Methods
    • 3.5 Sources
    • Problems
  • 4 Stochastic Analysis
    • 4.1 A Stochastic Chemical Kinetic Model
    • 4.2 The Chemical Master Equation
    • 4.3 Gillespie’s Stochastic Simulation Algorithm
    • 4.4 Gibson/Bruck’s Next Reaction Method
    • 4.5 Tau-Leaping
    • 4.6 Relationship to Reaction Rate Equations
    • 4.7 Stochastic Petri-Nets
    • 4.8 Phage lambda Decision Circuit Example
    • 4.9 Spatial Gillespie
    • 4.10 Sources
    • Problems
  • 5 Reaction-Based Abstraction
    • 5.1 Irrelevant Node Elimination
    • 5.2 Enzymatic Approximations
    • 5.3 Operator Site Reduction
    • 5.4 Statistical Thermodynamical Model
    • 5.5 Dimerization Reduction
    • 5.6 Phage lambda Decision Circuit Example
    • 5.7 Stoichiometry Amplification
    • 5.8 Sources
    • Problems
  • 6 Logical Abstraction
    • 6.1 Logical Encoding
    • 6.2 Piecewise Models
    • 6.3 Stochastic Finite-State Machines
    • 6.4 Markov Chain Analysis
    • 6.5 Qualitative Logical Models
    • 6.6 Sources
    • Problems
  • 7 Genetic Circuit Design
    • 7.1 Assembly of Genetic Circuits
    • 7.2 Combinational Logic Gates
    • 7.3 PoPS Gates
    • 7.4 Sequential Logic Circuits
    • 7.5 Future Challenges
    • 7.6 Sources
    • Problems
  • Solutions to Selected Problems
  • References
  • Glossary
  • Index