This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work. Chapters organized around broader themes of Organelles and Organisms, Systems Properties of Biological Processes, Cellular Networks, and Systems Biology and Disease discuss the development of concepts, the current applications, and the future prospects. Emphasis is placed on concepts and insights into the multi-disciplinary nature of the field as well as the importance of systems biology in human biological research. Technology, being an extremely important aspect of scientific progress overall, and in the creation of new fields in particular, is discussed in 'boxes' within each chapter to relate to appropriate topics.

Key Features

  • 2013 Honorable Mention for Single Volume Reference in Science from the Association of American Publishers' PROSE Awards
  • Emphasizes the interdisciplinary nature of systems biology with contributions from leaders in a variety of disciplines
  • Includes the latest research developments in human and animal models to assist with translational research
  • Presents biological and computational aspects of the science side-by-side to facilitate collaboration between computational and biological researchers


Current researchers and recent graduates in genetics, molecular biology, cell biology, biomedical science, and systems engineering who can integrate systems biology concepts into their work

Table of Contents

List of Contributors



Section I: Components of Biological Systems

Chapter 1. Proteomic Analysis of Cellular Systems


MS-Based Proteomics Workflow

Computational Proteomics

Deep Expression Proteomics

Interaction Proteomics

Large-Scale Determination of Post-Translational Modifications

Outlook and Future Challenges


Chapter 2. The Coding and the Non-coding Transcriptome


The Pathway from DNA to Protein Sequences

Methods to Determine the Reference Transcriptome

The Human Transcriptome

Conclusions and Future Challenges


Section II: Network Properties of Biological Systems

Chapter 3. Interactome Networks


Towards a Reference Protein–Protein Interactome Map

Drawing Inferences from Interactome Networks

Towards Dynamic Interactomes

Concluding Remarks



Chapter 4. Gene Regulatory Networks

Cells are Computers

Gene Regulation


Gene Regulatory Networks (GRNs)

Future Challenges



Chapter 5. Analyzing the Structure, Function and Information Flow in Signaling Networks using Quantitative Cellular Signatures

The Concept of Linear Cassettes and Modularity in Signal Transduction

Genetic Dissection of Signal Transduction Pathways

Systems Approaches to Identify the ‘Parts’ of Cellular Signaling Networks

Quantitative RNAi Signatures or Phenoprints to Infer Context Dependent Information Flow Through Cellular Signaling Networks

Concluding Remarks


Chapter 6. Genetic Networks


Defining Genetic Interactions

Experimental Approaches to Map Genetic I


No. of pages:
© 2013
Academic Press
Print ISBN:
Electronic ISBN:


2013 PROSE Awards - Honorable Mention, Single Volume Reference Works: Association of American Publishers, Handbook of Systems Biology PROSE Award 2013, Reference Work, Single Volume /Science, Honorable Mention, American Association of Publishers


"Systems biology is a field concerned with the interactions of biomolecules, tissues, and organs amongst each other. This work is essentially an introductory textbook for this field as well as a reference for scientists working in it. Editors Walhout and Dekker are systems biologists, while Vidal is a geneticist. They bring together numerous contributors with backgrounds ranging from physics to various biological specialties."--Reference & Research Book News, December 2013
"This book provides an entry point into Systems Biology for researchers in genetics, molecular biology, cell biology, microbiology and biomedical science to understand the key concepts to expanding their work.", April 24, 2013