An Engineer’s Guide to Genetic Circuits
Chemical Reactions
Macromolecules
Genomes
Cells and Their Structure
Genetic Circuits
Viruses
Phage lambda: A Simple Genetic Circuit
Learning Models
Experimental Methods
Experimental Data
Cluster Analysis
Learning Bayesian Networks
Learning Causal Networks
Experimental Design
Differential Equation Analysis
A Classical Chemical Kinetic Model
Differential Equation Simulation
Qualitative ODE Analysis
Spatial Methods
Stochastic Analysis
A Stochastic Chemical Kinetic Model
The Chemical Master Equation
Gillespie’s Stochastic Simulation Algorithm
Gibson/Bruck’s Next Reaction Method
Tau-Leaping
Relationship to Reaction Rate Equations
Stochastic Petri-Nets
Phage lambda Decision Circuit Example
Spatial Gillespie
Reaction-Based Abstraction
Irrelevant Node Elimination
Enzymatic Approximations
Operator Site Reduction
Statistical Thermodynamical Model
Dimerization Reduction
Phage lambda Decision Circuit Example
Stoichiometry Amplification
Logical Abstraction
Logical Encoding
Piecewise Models
Stochastic Finite-State Machines
Markov Chain Analysis
Qualitative Logical Models
Genetic Circuit Design
Assembly of Genetic Circuits
Combinational Logic Gates
PoPS Gates
Sequential Logic Circuits
Future Challenges
Solutions to Selected Problems
References
Glossary
Index
Sources and Problems appear at the end of each chapter.
Biography
Chris J. Myers is a professor in the Department of Electrical and Computer Engineering at the University of Utah. A co-inventor on four patents and author of more than 80 technical papers and the textbook Asynchronous Circuit Design, Dr. Myers received an NSF Fellowship in 1991 and an NSF CAREER award in 1996. His research interests include formal verification, asynchronous circuit design, and the analysis and design of genetic regulatory circuits.
"This book by Professor Myers is one of the few texts in the area that gently brings the uninitiated to these edges. I congratulate him for his achievement—Engineering Genetic Circuits admirably touches on much of the ‘required’ knowledge while creating a minimal toolset with which beginning students can confidently venture into this exciting new territory of systems biology."
—From the Foreword, Adam Arkin, University of California, Berkeley, USA"Prof. Myers’ book will be an excellent reference for any course in systems biology … . I find the many illustrations (worked-out examples and ample number of figures) and exercises at the end of each chapter quite useful and important."
—Baltazar Aguda, The Ohio State University, Columbus, USA
