Part I: Yeast Systems Biology 1. Yeast Systems Biology: The Challenge of Eukaryotic Complexity Juan I. Castrillo and Stephen G. Oliver Part II: Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies 2. Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State-of-the-Art Through Comparative Genomics Ed Louis 3. Genome-Wide Measurement of Histone H3 Replacement Dynamics in Yeast Oliver J. Rando 4. Genome-Wide Approaches to Studying Yeast Chromatin Modifications Dustin E. Schones, Kairong Cui, and Suresh Cuddapah 5. Absolute and Relative Quantification of mRNA Expression (Transcript Analysis) Andrew Hayes, Bharat M. Rash, and Leo A.H. Zeef 6. Enrichment of Unstable Non-Coding RNAs and Their Genome-Wide Identification Helen Neil and Alain Jacquier 7. Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays Lior David, Sandra Clauder-Münster, and Lars M. Steinmetz 8. RNA Sequencing Karl Waern, Ugrappa Nagalakshmi, and Michael Snyder 9. Polyadenylation State Microarray (PASTA) Analysis Traude H Beilharz and Thomas Preiss 10. Enabling Technologies for Yeast Proteome Analysis Johanna Rees and Kathryn Lilley 11. Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC Amy J. Claydon and Robert J. Beynon 12. Protein-Protein Interactions and Networks: Forward and Reverse Edgetics Benoit Charloteaux, Quan Zhong, Matija Dreze, Michael E. Cusick, David E. Hill, and Marc Vidal 13. Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases Avinash Persaud and Daniela Rotin 14. Fit for Purpose Quenching and Extraction Protocols for Metabolic Profiling of Yeast Using Chromatography-Mass Spectrometry Platforms Catherine L. Winder and Warwick B. Dunn 15. The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening Michael Proctor, Malene L. Urbanus, Eula L. Fung, Daniel F. Jaramillo, Ronald W. Davis, Corey Nislow, and Guri Giaever 16. Competition Experiments Coupled with High-Throughput Analyses for Functional Genomics Studies in Yeast Daniela Delneri 17. Fluorescence Fluctuation Spectroscopy and Imaging Methods for Examination of Dynamic Protein Interactions in Yeast Brian D. Slaughter, Jay R. Unruh, and Rong Li 18. Nutritional Control of Cell Growth Via TOR Signaling in Budding Yeast Yuehua Wei and X.F. Steven Zheng Part III: Computational Systems Biology: Computational Studies and Analyses 19. Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade Edda Klipp 20. Standards, Tools, and Databases for the Analysis of Yeast 'Omics Data Axel Kowald and Christoph Wierling 21. A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements Stephen C.J. Parker, Aaron Harlap, and Thomas D. Tullius 22. High Throughput Analyses and Curation of Protein Interactions in Yeast Shoshana J. Wodak, Jim Vl