Main description:

Systems Biology aims at deciphering the genotype-phenotype relationships at the levels of genes, transcripts (RNAs), peptides, proteins, metabolites, and environmental factors participating in complex cellular networks in order to reveal the mechanisms and principles governing the behavior of complex biological systems. Yeast Systems Biology: Methods and Protocols presents an up-to-date view of the optimal characteristics of the yeast Saccharomyces cerevisiae as a model eukaryote, perspective on the latest experimental and computational techniques for systems biology studies, most of which were first designed for and validated in yeast, and selected examples of yeast systems biology studies and their applications in biotechnology and medicine. These experiments under controlled conditions can uncover the complexity and interplay of biological networks with their dynamics, basic principles of internal organization, and balanced orchestrated functions between organelles in direct interaction with the environment as well as the characterization of short and long-term effects of perturbations and dysregulation of networks that may illuminate the origin of complex human diseases. Written for the highly successful Methods in Molecular Biology (TM) series, this volume contains the kind of detailed description and implementation advice that is crucial for getting optimal results.

Practical and cutting-edge, Yeast Systems Biology: Methods and Protocols serves researchers interested in comprehensive systems biology strategies in well-defined model systems with specific objectives as well as a better knowledge of the latest post-genomic strategies at all 'omic levels and computational approaches towards analysis, integration, and modeling of biological systems, from single-celled organisms to higher eukaryotes.

Contents:

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-Munster, 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 Vlasblom, and Shuye Pu

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

Yitzhak Pilpel

24. Genome-Scale Integrative Data Analysis and Modeling of Dynamic Processes in Yeast

Jean-Marc Schwartz and Claire Gaugain

25. Genome-Scale Metabolic Models of Saccharomyces cerevisiae

Intawat Nookaew, Roberto Olivares-Hernandez, Sakarindr Bhumiratana, and Jens Nielsen

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

Ken Whelan, Oliver Ray, and Ross King

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

Balazs Papp, Balazs Szappanos, and Richard A. Notebaart

Part IV: Yeast Systems Biology in Practice: Saccharomyces cerevisiae as a Tool for Mammalian Studies

28. Saccharomyces cerevisiae Contributions Towards Understanding Mammalian Gene Function and Therapy

Nianshu Zhang and Elizabeth Bilsland