Yeast Systems Biology

1. Front Matter

   Pages i-xiv

   PDF

2. Yeast Systems Biology

   1. Front Matter

      Pages 1-1

      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

      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

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.

• Biological networks
• Biotechnology
• Budding yeast
• Computational systems biology
• Eukaryotic systems
• Experimental 'omics techniques
• Experimental systems biology
• High-throughput genome-wide studies
• Medicine
• Model eukaryote
• Modeling
• Network Biology
• Next Generation Sequencing (NGS)
• Saccharomyces cerevisiae
• gene expression

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

  Juan I. Castrillo, Stephen G. Oliver

Policies and ethics