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Yeast Systems Biology

Methods and Protocols

  • Book
  • © 2011

Overview

Editors:
  1. Juan I. Castrillo

    1. , Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

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    You can also search for this editor in PubMed   Google Scholar

  2. Stephen G. Oliver

    1. , Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Presents an up-to-date view of yeast as a model eukaryote for systems biology studies
  • Provides practical, easy to use methodologies
  • Includes key tips and vital implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 759)

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Table of contents (28 protocols)

  1. Front Matter

    Pages i-xiv
    Download chapter PDF

  2. Yeast Systems Biology

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Yeast Systems Biology: The Challenge of Eukaryotic Complexity

      • Juan I. Castrillo, Stephen G. Oliver
      Pages 3-28

  3. Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies

    1. Front Matter

      Pages 29-29
      Download chapter PDF

  4. Experimental Systems Biology: High-Throughput Genome-Wide And Molecular Studies

    1. Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State of the Art Through Comparative Genomics

      • Ed Louis
      Pages 31-40

    2. Genome-Wide Measurement of Histone H3 Replacement Dynamics in Yeast

      • Oliver J. Rando
      Pages 41-60

    3. Genome-Wide Approaches to Studying Yeast Chromatin Modifications

      • Dustin E. Schones, Kairong Cui, Suresh Cuddapah
      Pages 61-71

    4. Absolute and Relative Quantification of mRNA Expression (Transcript Analysis)

      • Andrew Hayes, Bharat M. Rash, Leo A.H. Zeef
      Pages 73-86

    5. Enrichment of Unstable Non-coding RNAs and Their Genome-Wide Identification

      • Helen Neil, Alain Jacquier
      Pages 87-106

    6. Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays

      • Lior David, Sandra Clauder-Münster, Lars M. Steinmetz
      Pages 107-123

    7. RNA Sequencing

      • Karl Waern, Ugrappa Nagalakshmi, Michael Snyder
      Pages 125-132

    8. Polyadenylation State Microarray (PASTA) Analysis

      • Traude H. Beilharz, Thomas Preiss
      Pages 133-148

    9. Enabling Technologies for Yeast Proteome Analysis

      • Johanna Rees, Kathryn Lilley
      Pages 149-178

    10. Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC

      • Amy J. Claydon, Robert J. Beynon
      Pages 179-195

    11. Protein–Protein Interactions and Networks: Forward and Reverse Edgetics

      • Benoit Charloteaux, Quan Zhong, Matija Dreze, Michael E. Cusick, David E. Hill, Marc Vidal
      Pages 197-213

    12. Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases

      • Avinash Persaud, Daniela Rotin
      Pages 215-224

    13. Fit-for-Purpose Quenching and Extraction Protocols for Metabolic Profiling of Yeast Using Chromatography-Mass Spectrometry Platforms

      • Catherine L. Winder, Warwick B. Dunn
      Pages 225-238

    14. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening

      • Michael Proctor, Malene L. Urbanus, Eula L. Fung, Daniel F. Jaramillo, Ronald W. Davis, Corey Nislow et al.
      Pages 239-269

    15. Competition Experiments Coupled with High-Throughput Analyses for Functional Genomics Studies in Yeast

      • Daniela Delneri
      Pages 271-282

    16. Fluorescence Fluctuation Spectroscopy and Imaging Methods for Examination of Dynamic Protein Interactions in Yeast

      • Brian D. Slaughter, Jay R. Unruh, Rong Li
      Pages 283-306
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Keywords

About this book

Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems.  Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques  for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine.  These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases.  Written for the highly successful Methods in Molecular Biology™ series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results.

 

Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all ‘omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.

Editors and Affiliations

  • , Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom

    Juan I. Castrillo, Stephen G. Oliver

Bibliographic Information

  • Book Title: Yeast Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Juan I. Castrillo, Stephen G. Oliver

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-61779-173-4

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC 2011

  • Hardcover ISBN: 978-1-61779-172-7Published: 23 August 2011

  • Softcover ISBN: 978-1-4939-6135-1Published: 23 August 2016

  • eBook ISBN: 978-1-61779-173-4Published: 23 August 2011

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIV, 535

  • Number of Illustrations: 83 b/w illustrations, 2 illustrations in colour

  • Topics: Microbiology, Gene Expression

  • Industry Sectors: Biotechnology, Chemical Manufacturing, Consumer Packaged Goods, Pharma

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