An Introduction to Systems Biology - Design Principles of Biological Circuits

Movies of Systems Biology course:

Book Stores:


  • New! Second edition is now available
  • Full solutions Manual for excercises, and powerpoint versions of figures, available or instructors, please contact Uri Alon
  • Third printing available from April 2007, about 100 typos corrected
  • To report typos, please contact Uri Alon
  • All book figures are available online here !

Book Description:

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.

  • Explains the basic circuitry in transcription regulation, signal transduction, and developmental networks
  • Includes examples ranging from bacterial chemotaxis through developmental patterning and neuronal circuits to immune recognition
  • Examines the principle of robustness
  • Details how constrained evolutionary optimization can be used to understand optimal circuit design
  • Considers how kinetic proofreading and other mechanisms can minimize errors made in biological information-processing
  • Includes solved problems after each chapter that detail topics not discussed in the main text

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 text avoids specialist terms, focusing instead on several well-studied biological systems that concisely demonstrate key principles.

Book Reviews:

Editorial Reviews:

"[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 [a good] 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 … Alon ends his book with an epilogue of simplicity in biology. He draws the detailed strands together into an appealing and inspiring overview of biology. One final aspect of the An Introduction to Systems Biology 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, Physics Today, June 2007

"Uri Alon's An Introduction to Systems Biology is 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."
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

"...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, 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, UCSB, 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



On page 81 ("Solved Example 5.1" regarding the toggle switch) the nullclines are switched, in the text and in the figure.