An Introduction to Systems Biology Design Principles of Biological Circuits
Praise for the first edition:
… 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. – Nature
[This text deserves] serious attention from any quantitative scientist who hopes to learn about modern biology … It assumes no prior knowledge of or even interest in 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. – Physics Today
Written for students and researchers, the second edition of this best-selling textbook continues to offer a clear presentation of design principles that govern the structure and behavior of biological systems. It highlights simple, recurring circuit elements that make up the regulation of cells and tissues. Rigorously classroom-tested, this edition includes new chapters on exciting advances made in the last decade.
- Includes seven new chapters
- The new edition has 189 exercises, the previous edition had 66
- Offers new examples relevant to human physiology and disease
The book website including course videos can be found here: https://www.weizmann.ac.il/mcb/UriAlon/introduction-systems-biology-design-principles-biological-circuits.
Part One: Network Motifs
Chapter 1. Transcription Networks basic concepts
Chapter 2. Autoregulation
Chapter 3. The Feed Forward Loop
Chapter 4. Temporal Programs and the Global Structure of Transcription Networks
Chapter 5. Positive Feedback, Bistability and Memory
Chapter 6. How to Build a Biological Oscillator
Part Two: Robustness
Chapter 7. Kinetic Proofreading and Conformational Proofreading
Chapter 8. Robust Signalling
Chapter 9. Chemotaxis
Chapter 10. Fold-change Detection
Chapter 11. Dynamical Compensation and Mutal Resistance in Tissues
Chapter 12. Robust Spatial Patterning in Development.
Part Three: Optimality
Chapter 13. Optimal Gene Circuit Design
Chapter14. Multi-objective Optimality in Biology
Chapter 15. Modularity
"Systems biology is based on the idea that engineered and evolved systems share common principles. Here, Alon (Weizmann Inst. of Science, Rehovot) elucidates three of the major principles... This book is a compendium of many different experiments. Together, they show that biological systems do obey these design principles." --P. Cull, Oregon State University, CHOICE connect (57:5, Jan 2020)
"A very good book. Very well written, everything is clearly illustrated and presented. It makes a tough subject easy to follow." --Radu Angelescu, Senior Programmer at Ubisoft
"Alon’s book is the ideal counterargument to the idea that organisms are inherently human-opaque: it directly demonstrates the human-understandable structures which comprise real biological systems." --LessWrong.com
Praise for the First Edition
"[This text deserves] serious attention from any quantitative scientist or physicist who hopes to learn about modern biology. … the author succeeds in explaining in an intellectually exciting way what the cell does and what degrees of freedom enable it to function. … He draws the detailed strands together into an appealing and inspiring overview of biology. … 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. … He does an excellent job of explaining and motivating a useful toolbox of engineering models and methods using network-based controls. … a valuable and non-overlapping addition to a systems-biology curriculum."
—Eric Werner, 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, 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. …"
—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