Methods in Systems Biology

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

Microscopy

Spectroscopy

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

challenges.

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