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Engineering Genetic Circuits

Edition:
1st
Author(s):
Chris J. Myers
ISBN:
9781420083248
Format:
Hardback
Publication Date:
July 14, 2009
Content Details:
306 pages
Language:
English

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List Price:   $91.95

  
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  • About the Book

    Book Summary

    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.

    Features

        • Introduces relevant biology and biochemistry for readers with an engineering background
        • Covers key methods for modeling and analyzing genetic circuits, such as differential equations and stochastic analysis
        • Describes abstraction methods, which can substantially improve the efficiency of analyses
        • Uses the lysis/lysogeny decision circuit of phage lambda as an example throughout to help illustrate the various methods
        • Presents an introduction to the emerging area of synthetic biology
        • Includes exercises and self-study problem sets in every chapter
        • Offers iBioSim software, lecture slides, and a password-protected solutions manual on the author’s website

      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

    • 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.