Yeast Functional Genomics and Proteomics

1. Front Matter

   Pages i-xiii

   PDF

2. Comparative Genome Hybridization on Tiling Microarrays to Detect Aneuploidies in Yeast

   • Barry Dion, Grant W. Brown

   Pages 1-18

3. Identification of Transcription Factor Targets by Phenotypic Activation and Microarray Expression Profiling in Yeast

   • Gordon Chua

   Pages 19-35

4. SGAM: An Array-Based Approach for High-Resolution Genetic Mapping in Saccharomyces cerevisiae

   • Michael Costanzo, Charles Boone

   Pages 37-53

5. Reporter-Based Synthetic Genetic Array Analysis: A Functional Genomics Approach for Investigating the Cell Cycle in Saccharomyces cerevisiae

   • Holly E. Sassi, Nazareth Bastajian, Pinay Kainth, Brenda J. Andrews

   Pages 55-73

6. The Fidgety Yeast: Focus on High-Resolution Live Yeast Cell Microscopy

   • Heimo Wolinski, Klaus Natter, Sepp D. Kohlwein

   Pages 75-99

7. A Genomic Approach to Yeast Chronological Aging

   • Christopher R. Burtner, Christopher J. Murakami, Matt Kaeberlein

   Pages 101-114

8. Chemogenomic Approaches to Elucidation of Gene Function and Genetic Pathways

   • Sarah E. Pierce, Ronald W. Davis, Corey Nislow, Guri Giaever

   Pages 115-143

9. Identification of Inhibitors of Chromatin Modifying Enzymes Using the Yeast Phenotypic Screens

   • Benjamin Newcomb, Antonio Bedalov

   Pages 145-160

10. Exploiting Yeast Genetics to Inform Therapeutic Strategies for Huntington’s Disease

    • Flaviano Giorgini, Paul J. Muchowski

    Pages 161-174

11. Global Proteomic Analysis of Saccharomyces cerevisiae Identifies Molecular Pathways of Histone Modifications

    • Jessica Jackson, Ali Shilatifard

    Pages 175-186

12. Systematic Characterization of the Protein Interaction Network and Protein Complexes in Saccharomyces cerevisiae Using Tandem Affinity Purification and Mass Spectrometry

    • Mohan Babu, Nevan J. Krogan, Donald E. Awrey, Andrew Emili, Jack F. Greenblatt

    Pages 187-207

13. Protein Microarrays

    • Joseph Fasolo, Michael Snyder

    Pages 209-222

14. Analysis of Protein–Protein Interactions Using Array-Based Yeast Two-Hybrid Screens

    • Seesandra V. Rajagopala, Peter Uetz

    Pages 223-245

15. Analysis of Membrane Protein Complexes Using the Split-Ubiquitin Membrane Yeast Two-Hybrid System

    • Saranya Kittanakom*, Matthew Chuk*, Victoria Wong, Jamie Snyder, Dawn Edmonds, Apostolos Lydakis et al.

    Pages 247-271

16. Computational Analysis of the Yeast Proteome: Understanding and Exploiting Functional Specificity in Genomic Data

    • Curtis Huttenhower, Chad L. Myers, Matthew A. Hibbs, Olga G. Troyanskaya

    Pages 273-293

17. Back Matter

    Pages 295-300

    PDF

Given the popularity and utility of Saccharomyces cerevisiae, yeast-based functional genomics and proteomics technologies, developed over the past decade, have contributed greatly to our understanding of bacterial, yeast, fly, worm and human gene functions. In Yeast Functional Genomics and Proteomics: Methods and Protocols, experts in the field contribute stand-alone protocols suitable for daily use in research laboratories. The volume examines methods from the most major and fundamental techniques to more cutting-edge, advanced concepts. As part of the highly successful Methods in Molecular Biology™ series, the chapters are clearly formatted with introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easy to use, Yeast Functional Genomics and Proteomics: Methods and Protocols is an ideal reference for both yeast researchers and those who wish to use yeast as a model system for the further study of functional genomics and proteomics.

• Chemical genomics
• DNA microarrays
• Microarray
• Model system
• Proteomics
• Saccharomyces cerevisiae
• Synthetic Genetic Array (SGA)
• enzymes
• genes
• genetics
• hybridization
• molecular biology
• transcription

From the reviews: “This volume takes a snapshot of the questions which can be asked with a genome … . A major value of this book may be in helping to overcome the fear factor. Most of the approaches are feasible in a moderately resourced laboratory, and as the tools for S. cerevisiae spread to other organisms, so will the potential usefulness of this collection.” (John Armstrong, Microbiology Today, January, 2010)

Policies and ethics