Methods in Systems Biology

<p>Section 1 – Strategies in systems biology. top down, middle-out and bottom-up strategies – Hans V. Westerhoff</p> <p>Section 2 – Machines for systems biology – Roy Goodacre<br>4 chapters explaining the workings of four of the most important measurement techniques for systems biology:<br>Mass spectrometry <br>Microscopy <br>Spectroscopy </p> <p>Section 3 – Nucleic acids and systems biology – James Adaye <br>4 Chapters on DNA sequencing, Arrays studies, PCR, deep sequencing </p> <p>Section 4 - Protein production and quantification for Systems Biology –Naglis Malys and Kathleen Carroll <br>Chapter 1: Quantification of proteins and their modifications using QconCAT technology <br>Chapter 2: Mass spectrometric based quantitative proteomics using SILAC<br>Chapter 3: Nucleic Acid Programmable Protein Array (NAPPA) - a just-in-time multiplexed protein expression and purification platform<br>Chapter 4: Economical high throughput protein production and purification in prokaryotic and eukaryotic systems<br>Chapter 5: Systems biology of recombinant protein production using Bacillus megaterium<br>Chapter 6: Protein production in S. cerevisiae for systems biology studies</p> <p>Section 5 – Enzymatic Assays in Systems Biology Research Farid Khan, Hanan Messiha and Malgorzata Adamczyk<br>Chapter 1: Enzymatic Assays in Systems Biology Research: Strategies and challenges. <br>Chapter 2: Real-time kinetic assay technologies for characterising enzymes in metabolic pathways. <br>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 <br>Chapter 4: A top-down approach for measuring enzyme kinetics in cell lysates: mimicking an in vivo environment. </p> <p>Section 6 – Sample preparation in Metabolomics Studies –Warwick Dunn & Catherine Winder<br>Chapter 1 - The use of continuous culture in systems biology investigations <br>Chapter 2 - Metabolomic studies of yeast – methods for sample collection in profiling and quantitation studies <br>Chapter 3 - The role of metabolomics in plant studies – views on sampling and data acquisition <br>Chapter 4 - The study of mammaliam metabolism – how, when and why <br>Chapter 5 - The study of the environment from a metabolomic perspective </p> <p>Section 7 – Mathematical modelling in Systems Biology –Kieran Smallbone & Evangelos Simeonidis <br>Chapter 1: Building a kinetic model of a metabolic pathway <br>Chapter 2: Making systems biology models reusable: the role of standards and biological semantics <br>Chapter 3: From reaction networks to information flow - using modular response analysis to track the routes of information in large signalling networks <br>Chapter 4: The mathematics of Metabolic Control Analysis <br>Chapter 5: Constraint-based analysis of biochemical networks  </p> <p>Section 8 – Understanding systems biology (Hans Westerhoff)<br>1. Elementary mode analysis <br>2. Flux analysis<br>3. Flux balance analysis<br>4. Metabolic control analysis <br>5. Supply-demand analysis <br>6. Modular kinetic analysis <br>7. Regulation Analysis <br>8. Noise and heterogeneity </p> <p>Section 9 – Dealing with Systems Biology Research: – Neil W. Hayes <br>Chapter 1 - Crossing the Boundaries; Delivering Interdisciplinary Science in a Disciplinary World </p>