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