1st Edition

Engineering Genetic Circuits

By Chris J. Myers Copyright 2010
    306 Pages 128 B/W Illustrations
    by Chapman & Hall

    306 Pages 128 B/W Illustrations
    by Chapman & Hall

    An Introduction to Systems Bioengineering
    Takes a Clear and Systematic Engineering Approach to Systems Biology

    Focusing on genetic regulatory networks, Engineering Genetic Circuits presents the modeling, analysis, and design methods for systems biology. It discusses how to examine experimental data to learn about mathematical models, develop efficient abstraction and simulation methods to analyze these models, and use analytical methods to guide the design of new circuits.

    After reviewing the basic molecular biology and biochemistry principles needed to understand genetic circuits, the book describes modern experimental techniques and methods for discovering genetic circuit models from the data generated by experiments. The next four chapters present state-of-the-art methods for analyzing these genetic circuit models. The final chapter explores how researchers are beginning to use analytical methods to design synthetic genetic circuits.

    This text clearly shows how the success of systems biology depends on collaborations between engineers and biologists. From biomolecular observations to mathematical models to circuit design, it provides essential information on genetic circuits and engineering techniques that can be used to study biological systems.

    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