Methods in Systems Biology book cover

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.

Audience
Biochemists, biophysicists, molecular biologists, analytical chemists, and physiologists

Included in series
Methods in Enzymology

Hardbound, 668 Pages

Published: September 2011

Imprint: Academic Press

ISBN: 978-0-12-385118-5

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

    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

     

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