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

PART I - Functional Genomics<br>1.Analysis of Gene Function using DNA Microarrays<br>Andrew P. Capaldi<br>2.An introduction to microarray data analysis and visualization<br>Gregg B. Whitworth<br>3. Genome-wide approaches to monitor pre-mRNA splicing<br>Maki Inada and Jeff Pleiss<br>4. ChIP-Seq: Using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites<br>Philippe Lefrançois, Wei Zheng and Michael Snyder<br>5. Genome-wide mapping of nucleosomes in yeast<br>Oliver J. Rando<br>6. Genome-wide translational profiling by ribosome footprinting<br>Nicholas T. Ingolia<br><br>PART II - Systematic Genetic Analysis<br>7. Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe<br>Anastasia Baryshnikova, Michael Costanzo, Scott Dixon, Franco J. Vizeacoumar, Chad L. Myers, Brenda Andrews and Charles Boone<br>8. Making temperature-sensitive mutants<br>Shay Ben-Aroya, Xuewen Pan, Jef D. Boeke and Philip Hieter<br>9. Quantitative Genetic Interaction Mapping using the E-MAP Approach<br>Sean R. Collins, Assen Roguev and Nevan J. Krogan<br>10. Exploring gene function and drug action using chemogenomic dosage assays<br>Elke Ericson, Shawn Hoon, Robert P. St. Onge, Guri Giaever and Corey Nislow<br><br>PART III - Proteomics<br>11. Yeast Expression Proteomics by High-Resolution Mass Spectrometry<br>Tobias C. Walther, Jesper V. Olsen and Matthias Mann<br>12. High-quality binary interactome mapping<br>Matija Dreze, Dario Monachello, Claire Lurin, Michael E. Cusick, David E. Hill, March Vidal, and Pascal Braun<br>13. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry based proteomics<br>Bernd Bodenmiller and Rudi Aebersold<br>14. A Toolkit of Protein-fragment Complementation Assays for Studying and Dissecting Large-scale and Dynamic Protein-Protein Interactions in Living Cells<br>Stephen W. Michnick, Po-Hien Ear, Christian Landry, Mohan K. Malleshaiah and Vincent Messier<br>15. Yeast Lipid Analysis and Quantification by Mass Spectrometry<br>Xue Li Guan, Isabelle Riezman, Markus R. Wenk and Howard Riezman<br>16. Mass Spectrometry-Based Metabolomics of Yeast<br>Christopher A. Crutchfield, Wenyun Lu, Eugene Melamud, and Joshua D. Rabinowitz<br><br>PART IV - Systems Analysis<br>17. Imaging single mRNA molecules in yeast<br>Hyun Youk, Arjun Raj and Alexander van Oudenaarden<br>18. Reconstructing gene histories in Ascomycota fungi<br>IlanWapinski and Aviv Regev<br>19. Experimental evolution in yeast: a practical guide<br>Maitreya J. Dunham<br><br>PART V - Synthetic Biology<br>20. Enhancing stress resistance and production phenotypes through transcriptome engineering<br>Felix H. Lam, Franz S. Hartner, Gerald R. Fink, and Gregory Stephanopoulos<br><br>PART VI - Advances in Cytology/Biochemistry<br>21. Visualizing yeast chromosomes and nuclear architecture<br>Peter Meister, Lutz R. Gehlen, Elisa Varela, Veronique Kalck and Susan M. Gasser<br>22. Quantitative localization of chromosomal loci by immunofluorescence<br>Donna Garvey Brickner, William Light and Jason H. Brickner<br>23. Spinning Disk Confocal Microscopy of Yeast<br>Kurt Thorn<br>24. Correlative GFP-immunoelectron microscopy in yeast<br>Christopher Buser and Kent McDonald<br>25. Analyzing P-bodies and stress granules in Saccharomyces cerevisiae<br>J Ross Buchan, Tracy Nissan and Roy Parker<br>26. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridization<br>Daniel Zenklusen and Robert H Singer<br>27. The Use of In Vitro Assays to Measure Endoplasmic Reticulum Associated Degradation (ERAD)<br>Jeffrey L. Brodsky<br>28. A protein transformation protocol for introducing yeast prion particles into yeast<br>Motomasa Tanaka<br>29. Overexpression and Purification of Integral Membrane Proteins in Yeast<br>Franklin A. Hays, Zygy Roe-Zurz, and Robert M. Stroud<br>30. Biochemical, cell biological and genetic assays to analyze amyloid and prion aggregation in yeast<br>Simon Alberti, Randal Halfmann and Susan Lindquist<br><br>PART VII - Other Fungi<br>31. Genetics and Molecular Biology in Candida albicans<br>Hernday, A.D., Noble, S. M., Mitrovich, Q.M., and Johnson, A.D.<br>32. Molecular Genetics of Schizosaccharomyces pombe<br>Sarah A. Sabatinos and Susan L. Forsburg<br>33. Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans<br>Cheryl D. Chun and Hiten D. Madhani<br>34. The Fungal Genome Initiative and lessons learned from genome sequencing<br>Christina A. Cuomo and Bruce W. Birren<br>35. Ultradian metabolic cycles in yeast<br>Benjamin Tu