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 Giaeverand 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 |
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