Myers Engineering Genetic Circuits

1. Auflage 2011
ISBN: 978-1-4200-8325-5
Verlag: Taylor & Francis
Format: PDF
Kopierschutz: Adobe DRM (»Systemvoraussetzungen)

E-Book, Englisch, 306 Seiten

Reihe: Chapman & Hall/CRC Mathematical & Computational Biology

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.

Zielgruppe

Advanced undergraduate and graduate students in bioengineering, systems biology, and bioinformatics; biologists, computer scientists, and engineers involved in the modeling, analysis, and design of genetic circuits.

Autoren/Hrsg.

Myers, Chris J.

Fachgebiete

• Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Medizin, Gesundheitswesen Medizintechnik, Biomedizintechnik, Medizinische Werkstoffe

Inhaltsverzeichnis

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.

Über Autor(innen)

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.