Guide to Yeast Genetics: Functional Genomics, Proteomics and Other Systems Analysis

PART I - Functional Genomics
1.Analysis of Gene Function using DNA Microarrays
Andrew P. Capaldi
2.An introduction to microarray data analysis and visualization
Gregg B. Whitworth
3. Genome-wide approaches to monitor pre-mRNA splicing
Maki Inada and Jeff Pleiss
4. ChIP-Seq: Using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites
Philippe Lefrançois, Wei Zheng and Michael Snyder
5. Genome-wide mapping of nucleosomes in yeast
Oliver J. Rando
6. Genome-wide translational profiling by ribosome footprinting
Nicholas T. Ingolia

PART II - Systematic Genetic Analysis
7. Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe
Anastasia Baryshnikova, Michael Costanzo, Scott Dixon, Franco J. Vizeacoumar, Chad L. Myers, Brenda Andrews and Charles Boone
8. Making temperature-sensitive mutants
Shay Ben-Aroya, Xuewen Pan, Jef D. Boeke and Philip Hieter
9. Quantitative Genetic Interaction Mapping using the E-MAP Approach
Sean R. Collins, Assen Roguev and Nevan J. Krogan
10. Exploring gene function and drug action using chemogenomic dosage assays
Elke Ericson, Shawn Hoon, Robert P. St. Onge, Guri Giaever and Corey Nislow

PART III - Proteomics
11. Yeast Expression Proteomics by High-Resolution Mass Spectrometry
Tobias C. Walther, Jesper V. Olsen and Matthias Mann
12. High-quality binary interactome mapping
Matija Dreze, Dario Monachello, Claire Lurin, Michael E. Cusick, David E. Hill, March Vidal, and Pascal Braun
13. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry based proteomics
Bernd Bodenmiller and Rudi Aebersold
14. A Toolkit of Protein-fragment Complementation Assays for Studying and Dissecting Large-scale and Dynamic Protein-Protein Interactions in Living Cells
Stephen W. Michnick, Po-Hien Ear, Christian Landry, Mohan K. Malleshaiah and Vincent Messier
15. Yeast Lipid Analysis and Quantification by Mass Spectrometry
Xue Li Guan, Isabelle Riezman, Markus R. Wenk and Howard Riezman
16. Mass Spectrometry-Based Metabolomics of Yeast
Christopher A. Crutchfield, Wenyun Lu, Eugene Melamud, and Joshua D. Rabinowitz

PART IV - Systems Analysis
17. Imaging single mRNA molecules in yeast
Hyun Youk, Arjun Raj and Alexander van Oudenaarden
18. Reconstructing gene histories in Ascomycota fungi
IlanWapinski and Aviv Regev
19. Experimental evolution in yeast: a practical guide
Maitreya J. Dunham

PART V - Synthetic Biology
20. Enhancing stress resistance and production phenotypes through transcriptome engineering
Felix H. Lam, Franz S. Hartner, Gerald R. Fink, and Gregory Stephanopoulos

PART VI - Advances in Cytology/Biochemistry
21. Visualizing yeast chromosomes and nuclear architecture
Peter Meister, Lutz R. Gehlen, Elisa Varela, Veronique Kalck and Susan M. Gasser
22. Quantitative localization of chromosomal loci by immunofluorescence
Donna Garvey Brickner, William Light and Jason H. Brickner
23. Spinning Disk Confocal Microscopy of Yeast
Kurt Thorn
24. Correlative GFP-immunoelectron microscopy in yeast
Christopher Buser and Kent McDonald
25. Analyzing P-bodies and stress granules in Saccharomyces cerevisiae
J Ross Buchan, Tracy Nissan and Roy Parker
26. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridization
Daniel Zenklusen and Robert H Singer
27. The Use of In Vitro Assays to Measure Endoplasmic Reticulum Associated Degradation (ERAD)
Jeffrey L. Brodsky
28. A protein transformation protocol for introducing yeast prion particles into yeast
Motomasa Tanaka
29. Overexpression and Purification of Integral Membrane Proteins in Yeast
Franklin A. Hays, Zygy Roe-Zurz, and Robert M. Stroud
30. Biochemical, cell biological and genetic assays to analyze amyloid and prion aggregation in yeast
Simon Alberti, Randal Halfmann and Susan Lindquist

PART VII - Other Fungi
31. Genetics and Molecular Biology in Candida albicans
Hernday, A.D., Noble, S. M., Mitrovich, Q.M., and Johnson, A.D.
32. Molecular Genetics of Schizosaccharomyces pombe
Sarah A. Sabatinos and Susan L. Forsburg
33. Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans
Cheryl D. Chun and Hiten D. Madhani
34. The Fungal Genome Initiative and lessons learned from genome sequencing
Christina A. Cuomo and Bruce W. Birren
35. Ultradian metabolic cycles in yeast
Benjamin Tu