Yeast Systems Biology

This second edition volume expands on the previous edition with a look at the latest advances in techniques to study yeast and its core set of interactions, modules, architectures, and network dynamics that are common in all eukaryotes. The chapters in this book are organized into Four Parts: Part One provides readers with an update on the development of novel experimental and computational approaches to yeast systems biology; Part Two explores high-throughput methods used to study yeast epigenome, transcriptome, proteome, and metabolome; Part Three talks about computational systems biology, and focuses on data management, dynamic modeling, constraint-based models of metabolic networks, and multi-level 'omics data; while Part Four looks at experimental platforms that utilize yeast to model systemic human diseases such as Alzheimer's and Parkinson's diseases. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics; lists of the necessary materials and reagents; step-by-step, readily reproducible laboratory protocols; and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and comprehensive, Yeast System Biology: Methods and Protocols, Second Edition is a valuable tool for graduate students, post-doctoral researchers, and experts who are interested in learning about the latest developments in the study of yeast.

Includes cutting-edge methods and protocols Provides step-by-step detail essential for reproducible results Contains key notes and implementation advice from the experts

Contenu
Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity.- Capture of Ribonucleotides in Yeast Genomic DNA using Ribose-Seq.- Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9.- Ultra-High-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate.- Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode ChIP-Seq.- Transcript Profiling Analysis through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Revealing Transcriptome Complexity in Yeast.- RNA Sequencing Best Practices: Experimental Protocol and Data Analysis.- Advanced Methods for the Analysis of Altered Pre-mRNA Splicing in Yeast and Disease.- PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A) Length-Distribution in Yeast Transcriptomes.- Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolutionusing hyperLOPIT.- Data-Independent Acquisition for Yeast Glycoproteomics.- Protein-Protein Interaction Profiling in Candida albicans Revealed by Biochemical Purification-Mass Spectrometry (BP/MS).- Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges.- Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges.- Measuring the Activity of Plasma Membrane and Vacuolar Transporters in Yeast.- Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic Cells.- Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.- Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic Systems.- Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and Challenges.- Next-Generation Genome-Scale Models Incorporating Multilevel 'omics Data: From Yeast to Human.- Advanced Modeling of Cellular Proliferation: Towards a Multi-Scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based Models.- Yeast Genome Screening and Methods for the Discovery of Metabolism Pathways Involved in a Phenotypic Response to Anti-Cancer Agents.- Advanced Yeast Models of Familial Alzheimer Disease Expressing FAD-Linked Presenilin to Screen Mutations and g-Secretase Modulators.- From Yeast-to-Humans: Leveraging New Approaches in Yeast to Accelerate Discovery of Therapeutic Targets for Synucleinopathies.