Methods in Systems Biology

Systems biology is a term used to describe a number of trends in bioscience research and a movement that draws on those trends. This volume in the Methods in Enzymology series comprehensively covers the methods in systems biology. With an international board of authors, this volume is split into sections that cover subjects such as machines for systems biology, protein production and quantification for systems biology, and enzymatic assays in systems biology research.
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Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists


Book information

  • Published: September 2011
  • ISBN: 978-0-12-385118-5

Table of Contents

Section 1 - Strategies in systems biology. top down, middle-out and bottom-up strategies - Hans V. Westerhoff

Hans V. Westerhoff; OK

Section 2 - Machines for systems biology - Roy Goodacre

4 chapters explaining the workings of four of the most important measurement techniques for systems biology:

Mass spectrometry



Section 3 - Nucleic acids and systems biology - James Adaye

4 Chapters on DNA sequencing, Arrays studies, PCR, deep sequencing

Section 4 - Protein production and quantification for Systems Biology -Naglis Malys and Kathleen Carroll

Chapter 1: Quantification of proteins and their modifications using QconCAT technology

Kathleen Carroll, Francesco Lanucara and Claire E. Eyers


Chapter 2: Mass spectrometric based quantitative proteomics using SILAC

Francesco Lanucara and Claire E. Eyers

Chapter 3: Nucleic Acid Programmable Protein Array (NAPPA) - a just-in-time multiplexed protein expression and purification platform

Joshua LaBaer

Chapter 4: Economical high throughput protein production and purification in prokaryotic and eukaryotic systems

Ron Seidel and James Love

Chapter 5: Systems biology of recombinant protein production using Bacillus megaterium

Rebekka Biedendieck and Dieter Jahn

Chapter 6: Protein production in S. cerevisiae for systems biology studies

Naglis Malys

Section 5 - Enzymatic Assays in Systems Biology Research Farid Khan, Hanan Messiha and Malgorzata Adamczyk

Chapter 1: Enzymatic Assays in Systems Biology Research: Strategies and


Farid Khan

Chapter 2: Real-time kinetic assay technologies for characterising

enzymes in metabolic pathways.

Farid Khan

Chapter 3: A bottom-up approach towards a full quantitative description

of yeast energy metabolism: A systematic approach for estimating the

kinetic parameters of isoenzymes under in vivo like conditions

Hanan Messiha

Chapter 4: A top-down approach for measuring enzyme kinetics in cell

lysates: mimicking an in vivo environment.

Malgorzata Adamczyk

Section 6 - Sample preparation in Metabolomics Studies -Warwick Dunn & Catherine Winder


Chapter 1 - The use of continuous culture in systems biology investigations

Dr Catherine Winder and Dr Karin Lanthaler, University of Manchester

Chapter 2 - Metabolomic studies of yeast - methods for sample collection in profiling and quantitation studies

Dr Catherine Winder and Dr Warwick Dunn, University of Manchester

Chapter 3 - The role of metabolomics in plant studies - views on sampling and data acquisition

Dr William Allwood, University of Manchester

Chapter 4 - The study of mammaliam metabolism - how, when and why

Dr Jules Griffin and Dr Helen Atherton

Chapter 5 - The study of the environment from a metabolomic perspective

Dr Jake Bundy


Section 7 - Mathematical modelling in Systems Biology -Kieran Smallbone & Evangelos Simeonidis

Chapter 1: Building a kinetic model of a metabolic pathway

E. Simeonidis, K. Smallbone

Chapter 2: Making systems biology models reusable: the role of standards and biological semantics

F. Krause, M. Schulz, N. Swainston, W. Liebermeister

Chapter 3: From reaction networks to information flow - using modular response analysis to track the routes of information in large signalling networks

P. Schulthess, N. Bluthgen

Chapter 4: The mathematics of Metabolic Control Analysis

M. Muldoon

Chapter 5: Constraint-based analysis of biochemical networks

J. Papin


Section 8 - Understanding systems biology (Hans Westerhoff)

1. Elementary mode analysis

2. Flux analysis

3. Flux balance analysis

4. Metabolic control analysis

5. Supply-demand analysis

6. Modular kinetic analysis

7. Regulation Analysis

8. Noise and heterogeneity

Section 9 - Dealing with Systems Biology Research: - Neil W. Hayes

Chapter 1 - Crossing the Boundaries; Delivering Interdisciplinary Science in a Disciplinary World

Neil. W. Hayes and Elizabeth Elliot