Chapter 1 Yeast systems biology: the challenge of eukaryotic complexity.

Chapter 2 Saccharomyces cerevisiae: Gene Annotation and Genome Variability, State of the Art Through Comparative Genomics

Chapter 3 Genome-Wide Measurement of Histone H3 Replacement Dynamics in Yeast

Chapter 4 Genome-Wide Approaches to Studying Yeast Chromatin Modifications

Chapter 5 Absolute and relative quantification of mRNA expression (transcript analysis).

Chapter 6 Enrichment of Unstable Non-coding RNAs and Their Genome-Wide Identification

Chapter 7 Genome-Wide Transcriptome Analysis in Yeast Using High-Density Tiling Arrays

Chapter 8 RNA Sequencing

Chapter 9 Polyadenylation State Microarray (PASTA) Analysis

Chapter 10 Enabling technologies for yeast proteome analysis.

Chapter 11 Protein Turnover Methods in Single-Celled Organisms: Dynamic SILAC

Chapter 12 Protein-protein interactions and networks: forward and reverse edgetics.

Chapter 13 Use of Proteome Arrays to Globally Identify Substrates for E3 Ubiquitin Ligases

Chapter 14 Fit-for-Purpose Quenching and Extraction Protocols for Metabolic Profiling of Yeast Using Chromatography-Mass Spectrometry Platforms

Chapter 15 The Automated Cell: Compound and Environment Screening System (ACCESS) for Chemogenomic Screening

Chapter 16 Competition experiments coupled with high-throughput analyses for functional genomics studies in yeast.

Chapter 17 Fluorescence Fluctuation Spectroscopy and Imaging Methods for Examination of Dynamic Protein Interactions in Yeast

Chapter 18 Nutritional Control of Cell Growth via TOR Signaling in Budding Yeast

Chapter 19 Computational Yeast Systems Biology: A Case Study for the MAP Kinase Cascade

Chapter 20 Standards, Tools, and Databases for the Analysis of Yeast ‘Omics Data

Chapter 21 A Computational Method to Search for DNA Structural Motifs in Functional Genomic Elements

Chapter 22 High-Throughput Analyses and Curation of Protein Interactions in Yeast

Chapter 23 Noise in Biological Systems: Pros, Cons, and Mechanisms of Control

Chapter 24 Genome-scale integrative data analysis and modeling of dynamic processes in yeast.

Chapter 25 Genome-Scale Metabolic Models of Saccharomyces cerevisiae

Chapter 26 Representation, Simulation, and Hypothesis Generation in Graph and Logical Models of Biological Networks

Chapter 27 Use of Genome-Scale Metabolic Models in Evolutionary Systems Biology

Chapter 28 Contributions of Saccharomyces cerevisiae to understanding mammalian gene function and therapy.