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An Introduction to Systems Biology: Design Principles of Biological Circuits (Chapman & Hall/CRC Mathematical & Computational Biology) [Paperback]

Uri Alon
4.0 out of 5 stars  See all reviews (1 customer review)
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Book Description

7 July 2006 1584886420 978-1584886426 1
Thorough and accessible, this book presents the design principles of biological systems, and highlights the recurring circuit elements that make up biological networks. It provides a simple mathematical framework which can be used to understand and even design biological circuits. The textavoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles.

An Introduction to Systems Biology: Design Principles of Biological Circuits builds a solid foundation for the intuitive understanding of general principles. It encourages the reader to ask why a system is designed in a particular way and then proceeds to answer with simplified models.

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Product details

  • Paperback: 320 pages
  • Publisher: Chapman and Hall/CRC; 1 edition (7 July 2006)
  • Language: English
  • ISBN-10: 1584886420
  • ISBN-13: 978-1584886426
  • Product Dimensions: 1.8 x 17.7 x 25.1 cm
  • Average Customer Review: 4.0 out of 5 stars  See all reviews (1 customer review)
  • Amazon Bestsellers Rank: 293,928 in Books (See Top 100 in Books)
  • See Complete Table of Contents

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"[This text deserves] serious attention from any quantitative scientist or physicist who hopes to learn about modern biology. [It is] well written. … Alon’s book is the better place for physicists to start. It assumes no prior knowledge of or even interest in biology. Yet right from chapter 1, the author succeeds in explaining in an intellectually exciting way what the cell does and what degrees of freedom enable it to function. … The book proceeds with detailed discussions of some of the key network motifs, circuit-element designs … [and] focuses on concrete examples such as chemotaxis and developmental pattern formation. … He draws the detailed strands together into an appealing and inspiring overview of biology. … One final aspect that must be mentioned is the wonderful set of exercises that accompany each chapter. … Alon’s book should become a standard part of the training of graduate students in biological physics… ."
—Nigel Goldenfeld, University of Illinois at Urbana-Champaign, Physics Today, June 2007

"…a superb, beautifully written and organized work that takes an engineering approach to systems biology. Alon provides nicely written appendices to explain the basic mathematical and biological concepts clearly and succinctly without interfering with the main text. He starts with a mathematical description of transcriptional activation and then describes some basic transcription-network motifs (patterns) that can be combined to form larger networks. … Alon investigates networks at a higher level, including genomic regulatory networks. He does an excellent job of explaining and motivating a useful toolbox of engineering models and methods using network-based controls. … will be a valuable and non-overlapping addition to a systems-biology curriculum."
—Eric Werner, Department of Physiology, Anatomy and Genetics, University of Oxford, Nature, Vol. 446, No. 29, March 2007

"I read Uri Alon’s elegant book almost without stopping for breath. He perceives and explains so many simple regularities, so clearly, that the novice reading this book can move on immediately to research literature, armed with a grasp of the many connections between diverse phenomena."
—Philip Nelson, Professor of Physics, University of Pennsylvania, Philadelphia, USA

"… Beyond simply recounting recent results, Alon boldly articulates the basic principles underlying biological circuitry at different levels and shows how powerful they can be in understanding the complexity of living cells. For anyone who wants to understand how a living cell works, but thought they never would, this book is essential."
—Michael B. Elowitz, California Institute of Technology, Pasadena, USA

"Uri Alon offers a highly original perspective on systems biology, emphasizing the function of certain simple networks that appear as ubiquitous building blocks of living matter. The quest for simplicity — without losing contact with complex reality — is the only way to uncover the principles organizing biological systems. Alon writes with uncommon lucidity…"
—Boris Shraiman, University of California, Santa Barbara, USA

"This is a remarkable book that introduces not only a field but a way of thinking. Uri Alon describes in an elegant, simple way how principles such as stability, robustness and optimal design can be used to analyze and understand the evolution and behavior of living organisms. Alon’s clear intuitive language and helpful examples offer — even to a mathematically naive reader — deep mathematical insights into biology. The community has been waiting for this book; it was worth the wait."
—Galit Lahav, Harvard Medical School, Boston, Massachusetts, USA

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Front Cover | Copyright | Table of Contents | Excerpt | Index | Back Cover
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Most Helpful Customer Reviews
4.0 out of 5 stars Nice 10 Feb 2013
Format:Paperback|Verified Purchase
Nice book, but it could have better descriptions and more figures. A perfect book is a book that have short and concise texts which provides the reader all the needed information to understand a given issue as fast as possible and have informative figures visualizing what is described.
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Amazon.com: 4.1 out of 5 stars  28 reviews
43 of 49 people found the following review helpful
5.0 out of 5 stars Excellent serious book about biology -- no chemistry needed. 23 July 2008
By George Stanton - Published on Amazon.com
This is a great book for learning about how biology works. I've been wanting to learn a bit more about biology, and I've read many of the popularized science books on the subject. Most serious biology books require a pretty good understanding of organic chemistry. (At first that didn't seem like a problem, after all organic chemistry is just regular chemistry with a bunch of carbon atoms lying around, but the jargon gets so dense that you lose track of what's going on.) This book offers an entirely different perspective on biology that is much more accessible to someone with a general interest in science.

This book looks at biology from the perspective of how genes and proteins interact at a network level, rather than a chemical level. It's a lot like learning electronics -- you can understand a lot about a transistor without knowing how semiconductors work. After explaining the operation of some of the most common network "motifs" the author talks about why those motifs were favored by evolution, in particular what makes them robust and how can they act to minimize errors. The book leaves you with the very interesting question of what characteristics might be different between an engineered system and an evolved one?

The language of the book is very clear, this is a technical book you could easily read for fun. The math is simple, just a little calculus, and if you don't care about the math you can just look at the diagrams.
39 of 46 people found the following review helpful
5.0 out of 5 stars Clear, rigorous, fascinating 20 Jan 2007
By student scientist - Published on Amazon.com
I'm a Ph.D. student in biophysics. This is the best treatment of systems biology that I've encountered. It treats both the math and the biology with clarity, rigor, and respect. It simplifies without dumbing down. It's beautifully written. If you doubt that systems biology is a real scientific discipline, this book will change your mind.
16 of 19 people found the following review helpful
5.0 out of 5 stars Wow! This book elicits such a strong response! 8 Jan 2010
By D. Chen - Published on Amazon.com
I have never seen a book, especially a science one, with such a bimodal response. IMO, the people with one star were trained as biologists. They present a valid viewpoint--I'll get back to that later.

When I first read this book at the end of my undergrad days, I was simply amazed. I never realized biology could be so fun, if we asked questions about robustness, optimality, design principles, etc. Now that I'm in this field in my day job (as a grad student), I realize this book does have some issues.

First, the book does make some strong claims, ie. the idea of inherent design principles. This is what most of the one-star reviews here are angry about. Alon doesn't really discuss the philosophy behind systems biology, but jumps straight to the physicists' view that the system is understandable and our job is to understand it.

Also, the book pretty much only covers work done by people in Leibler's lab. The works presented in the book are considered hallmarks in the field of systems biology, but people familiar with the field might be sad to see some areas not presented here.

Finally, it should be noted that the book doesn't really teach you that much. It does a wonderful job telling the story of the papers that it does discuss, but it hides away the details. Thus, you don't learn the biology of what's going on nor will you learn common mathematical techniques used in this field (eg, bifurcation analysis).

Nonetheless, I give this book five stars enthusiastically. This is the most enjoyable book I have read, and I highly recommend it to everyone who has any interest in this field. The problems included in the chapters are not bad for use in a class, although I recommend Strogatz's Nonliner Dynamics for a class focused on the modeling.
11 of 13 people found the following review helpful
5.0 out of 5 stars Elegant and thorough introduction to systems biology 5 Aug 2009
By O. Shoval - Published on Amazon.com
This is a great book! It manages to convey the new ideas of systems biology with clarity and without sacrificing scientific rigor.
Whether you're a biologist, physicist or engineer this book will be perfect for you as it encompasses the many disciplines that make up systems biology.
Many universities (including Harvard) are using this book as their textbook for introductory courses to systems biology. This is a testament to its clearness and thoroughness. There are also excellent homework type problems at the end of each chapter, and a solution manual is available from the author for class instructors.
As a graduate student of systems biology I found this book very useful and I highly recommend it!

Disregard the 4 reviews that give this book a low rating! I wonder if they are related, as they all are from July 09, and argue the exact same thing: that the modeling of biology described in the book is not representative of biology. This is a philosophical argument that by no means reduces the importance, relevance and scientific depth of this book. Discussions as to what is systems biology should not be conducted using Amazon book reviews.
31 of 41 people found the following review helpful
5.0 out of 5 stars Great Job 9 Sep 2006
By Jake Keenan - Published on Amazon.com
A superb intro to the field. The math is moderate and helpful. Network concepts and their ties to examples and theory are clearly and succinctly presented. This is a textbook but reads easily like a book. Covers key elements while connecting them by at least mention to up-to-date further research. The basics and the grandeur of systems biology. I am trying to remember now anything on the negative side and cannot.
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