Methods in Systems Biology

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