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

PART I - Functional Genomics1. Analysis of Gene Function using DNA Microarrays2. An introduction to microarray data analysis and visualization3. Genome-wide approaches to monitor pre-mRNA splicing4. ChIP-Seq: Using high-throughput DNA sequencing for genome-wide identification of transcription factor binding sites5. Genome-wide mapping of nucleosomes in yeast6. Genome-wide translational profiling by ribosome footprintingPART II - Systematic Genetic Analysis7. Synthetic Genetic Array (SGA) Analysis in Saccharomyces cerevisiae and Schizosaccharomyces pombe8. Making temperature-sensitive mutants9. Quantitative Genetic Interaction Mapping using the E-MAP Approach10. Exploring gene function and drug action using chemogenomic dosage assaysPART III - Proteomics11. Yeast Expression Proteomics by High-Resolution Mass Spectrometry12. High-quality binary interactome mapping13. Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry based proteomics14. A Toolkit of Protein-fragment Complementation Assays for Studying and Dissecting Large-scale and Dynamic Protein-Protein Interactions in Living Cells15. Yeast Lipid Analysis and Quantification by Mass Spectrometry16. Mass Spectrometry-Based Metabolomics of YeastPART IV - Systems Analysis17. Imaging single mRNA molecules in yeast18. Reconstructing gene histories in Ascomycota fungi19. Experimental evolution in yeast: a practical guidePART V - Synthetic Biology20. Enhancing stress resistance and production phenotypes through transcriptome engineeringPART VI - Advances in Cytology/Biochemistry21. Visualizing yeast chromosomes and nuclear architecture22. Quantitative localization of chromosomal loci by immunofluorescence23. Spinning Disk Confocal Microscopy of Yeast24. Correlative GFP-immunoelectron microscopy in yeast25. Analyzing P-bodies and stress granules in Saccharomyces cerevisiae26. Analyzing mRNA expression using single mRNA resolution fluorescent in situ hybridization27. The Use of In Vitro Assays to Measure Endoplasmic Reticulum Associated Degradation (ERAD)28. A protein transformation protocol for introducing yeast prion particles into yeast29. Overexpression and Purification of Integral Membrane Proteins in Yeast30. Biochemical, cell biological and genetic assays to analyze amyloid and prion aggregation in yeastPART VII - Other Fungi31. Genetics and Molecular Biology in Candida albicans32. Molecular Genetics of Schizosaccharomyces pombe33. Applying Genetics and Molecular Biology to the Study of the Human Pathogen Cryptococcus neoformans34. The Fungal Genome Initiative and lessons learned from genome sequencing35. Ultradian metabolic cycles in yeast