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.

This volume in the Methods in Enzymology series comprehensively covers the methods in systems biologyWith 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

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

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  Chapter 2: Mass spectrometric based quantitative proteomics using SILAC Chapter 3: Nucleic Acid Programmable Protein Array (NAPPA) - a just-in-time multiplexed protein expression and purification platform Chapter 4: Economical high throughput protein production and purification in prokaryotic and eukaryotic systems Chapter 5: Systems biology of recombinant protein production using Bacillus megaterium Chapter 6: Protein production in S. cerevisiae for systems biology studies

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.  Chapter 2: Real-time kinetic assay technologies for characterising enzymes in metabolic pathways.  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  Chapter 4: A top-down approach for measuring enzyme kinetics in cell lysates: mimicking an in vivo environment. 

Section 6 – Sample preparation in Metabolomics Studies –Warwick Dunn & Catherine Winder Chapter 1 - The use of continuous culture in systems biology investigations  Chapter 2 - Metabolomic studies of yeast – methods for sample collection in profiling and quantitation studies  Chapter 3 - The role of metabolomics in plant studies – views on sampling and data acquisition  Chapter 4 - The study of mammaliam metabolism – how, when and why  Chapter 5 - The study of the environment from a metabolomic perspective 

Section 7 – Mathematical modelling in Systems Biology –Kieran Smallbone & Evangelos Simeonidis Chapter 1: Building a kinetic model of a metabolic pathway  Chapter 2: Making systems biology models reusable: the role of standards and biological semantics  Chapter 3: From reaction networks to information flow - using modular response analysis to track the routes of information in large signalling networks  Chapter 4: The mathematics of Metabolic Control Analysis  Chapter 5: Constraint-based analysis of biochemical networks  

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