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Engineering Genetic Circuits





ISBN 9781138372733
Published September 10, 2018 by Chapman and Hall/CRC
306 Pages 128 B/W Illustrations

 
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Book Description

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.

Table of Contents

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.

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Author(s)

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.

Reviews

"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