[BioEdu] New textbook on Systems Biology

[Uri Alon]

Hi,

I'm happy to say that my new textbook, "An Introduction to Systems
Biology: Design Principles of Biological Circuits" 
has just been published by Chapman & Hall/CRC.
This book was a pleasure to write and to teach with. 

Yours,
Uri.

For details, please see 
http://www.crcpress.co.uk/shopping_cart/products/product_reviews.asp?id=&parent_id=&sku=C6420&pc=

Contents 
INTRODUCTION

TRANSCRIPTION NETWORKS, BASIC CONCEPTS
Introduction
The Cognitive Problem of the Cell
Elements of Transcription Networks
Dynamics and Response Time of Simple Gene Circuits

AUTO-REGULATION, A NETWORK MOTIF
Introduction
Patterns, Randomized Networks and Network Motifs
Autoregulation is a Network Motif
Negative Auto-Regulation Speeds the Response Time of Gene 
Circuits
Negative Auto-Regulation Promotes Robustness to Fluctuations 
in Production 
Positive auto-regulation speeds responses and widens cell-cell
variability
Summary

THE FEEDFORWARD LOOP NETWORK MOTIF
Introduction
The Number of Appearances of a Subgraph in Random 
Networks
The Feedforward Loop (FFL) is a Network Motif
The Structure of the Feedforward Loop Circuit
Dynamics of the Coherent FFL with AND-Logic
The C1-FFL is a Sign-Sensitive Delay Element
The Incoherent FFL: a pulse generator and response accelerator
Why Are Some FFL Types Rare?
Convergent Evolution of FFLs
Summary

TEMPORAL PROGRAMS AND THE GLOBAL STRUCTURE OF TRANSCRIPTION NETWORKS
Introduction
The Single-Input Module (SIM) Network Motif
SIMs Can Generate Temporal Expression Programs
Topological Generalizations of Network Motifs
The Multi-Output FFL Can Generate FIFO Temporal Order
Signal Integration and Combinatorial Control: Bi-Fans and 
Dense-Overlapping Regulons
Network Motifs and the Global Structure of Sensory 
Transcription Networks

NETWORK MOTIFS IN DEVELOPMENTAL, SIGNAL-TRANSDUCTION AND NEURONAL
NETWORKS
Introduction
Network Motifs in Developmental Transcription Networks:
Positive feedback loops and bistability
Motifs in Signal Transduction Networks
Information Processing Using Multi-Layer Perceptrons
Composite Network Motifs: Negative Feedback and Oscillator 
Motifs
Network Motifs in the Neuronal Network of C. Elegans
Summary

ROBUSTNESS OF PROTEIN CIRCUITS, THE EXAMPLE OF BACTERIAL CHEMOTAXIS
The Robustness Principle
Bacterial Chemotaxis, or How Bacteria 'Think'
The Chemotaxis Protein Circuit of E. coli
Two Models Can Explain Exact Adaptation, One is Robust and 
the Other Fine Tuned
The Barkai-Leibler model
Individuality and Robustness in Bacterial Chemotaxis

ROBUST PATTERNING IN DEVELOPMENT
Introduction to Morphogen Gradients
Exponential Gradients Are Not Robust
Increased Robustness by Self-Enhanced Morphogen 
Degradation
Network Motifs That Provide Robust Patterning
The Robustness Principle Can Distinguish Between 
Mechanisms of Fruit Fly Patterning

KINETIC PROOFREADING
Introduction
Kinetic Proofreading of the Genetic Code Can Reduce Error 
Rates of Molecular Recognition
Recognition of Self and Non-Self by the Immune System
Kinetic Proofreading May Occur in Diverse Recognition 
Processes in the Cell

OPTIMAL GENE CIRCUIT DESIGN
Introduction
Cost and Benefit Analysis of Gene circuits
Optimal Expression Level of a Protein Under Constant 
Conditions
To Regulate or Not to Regulate: Optimal Regulation in Variable 
Environments
Environmental Selection of the Feedforward Loop Network Motif
Summary

DEMAND RULES FOR GENE REGULATION 
Introduction
The Savageau Demand Rules
Rules for Gene Regulation Based on Minimal Error Load
Demand Rules for Genes with Multiple Regulators
Summary

EPILOGUE: Simplicity in Biology

APPENDIX A: The Input-Function of a Gene, Michaelis-Menten and Hill
Equations

APPENDIX B: Multi-Dimensional Input-Functions

APPENDIX C: Graph Properties of Transcription Networks

APPENDIX D: Cell-Cell Variability in Gene Expression

GLOSSARY


-----------------------------------------------------------
Uri Alon
Depts. Molecular Cell Biology and Physics of Complex Systems
Weizmann Institute of Science
Rehovot Israel 76100
www.weizmann.ac.il/mcb/UriAlon
FAX: 972-8-934-4125   Tel: 972-8-934-4448

NEW BOOK: An Introduction to Systems Biology  (CRC press,2006)

See:  www.weizmann.ac.il/mcb/UriAlon