Yeast systems biology : methods and protocols
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Bibliographic Information
Yeast systems biology : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2049）（Springer protocols）
Humana Press, c2019
2nd ed
- : [hardback]
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Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
Dedication...Preface...Table of Contents...Contributing Authors...
Part I Yeast Systems Biology
1. Yeast Systems Biology: The Continuing Challenge of Eukaryotic ComplexityStephen G. Oliver
Part II Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies
2. Capture of Ribonucleotides in Yeast Genomic DNA using Ribose-SeqSathya Balachander, Taehwan Yang, Gary Newnam, Waleed M. M. El-Sayed, Kyung Duk Koh, and Francesca Storici
3. Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9Jessica M. Walter, Max G. Schubert, Stephanie H. Kung, Kristy Hawkins, Darren M. Platt, Aaron D. Hernday, Tina Mahatdejkul-Meadows, Wayne Szeto, Sunil S. Chandran, Jack D. Newman, and Andrew A. Horwitz
4. Ultra-High-Density Screens for Genome-Wide Yeast EMAPs in a Single PlateKatherine Licon, John Paul Shen, Brenton P. Munson, Manuel Michaca, Cole Fassino, Luke Fassino, Jason F. Kreisberg, and Trey Ideker
5. Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode ChIP-SeqDeepani W. Poramba-Liyanage, Tessy Korthout, and Fred van Leeuwen
6. Transcript Profiling Analysis through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Revealing Transcriptome Complexity in YeastYani Kang, Hong Sain Ooi, and Xiaodong Zhao
7. RNA Sequencing Best Practices: Experimental Protocol and Data AnalysisAndy Hesketh
8. Advanced Methods for the Analysis of Altered Pre-mRNA Splicing in Yeast and DiseaseHuw B. Thomas and Raymond T. O'Keefe
9. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A) Length-Distribution in Yeast TranscriptomesAngavai Swaminathan, Paul F. Harrison, Thomas Preiss, and Traude H. Beilharz
10. Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution using hyperLOPITDaniel J. H. Nightingale, Stephen G. Oliver, and Kathryn S. Lilley
11. Data-Independent Acquisition for Yeast GlycoproteomicsLucia F. Zacchi and, Benjamin L. Schulz
12. Protein-Protein Interaction Profiling in Candida albicans Revealed by Biochemical Purification-Mass Spectrometry (BP/MS)Reza Pourhaghighi, Teresa R. O'Meara, Leah E. Cowen, and Andrew Emili
13. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and ChallengesBenedikt M. Beckmann and SanderGranneman
14. Metabolomic Analysis of Yeast and Human Cells: Latest Advances and ChallengesRomanas Chaleckis , Kazuto Ohashi, Isabel Meister, Shama Naz, and Craig E. Wheelock
15. Measuring the Activity of Plasma Membrane and Vacuolar Transporters in YeastMelody Cools, Maria Rompf, Andreas Mayer, and Bruno Andre
16. Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic CellsKate Campbell, Clara Correia-Melo, and Markus Ralser
Part III Computational System Biology: Data Management and Modeling the Cell
17. Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best PracticesNatalie J. Stanford, Martin Scharm, Paul D. Dobson, Martin Golebiewski, Mike Hucka, Varun B. Kothamachu, David Nickerson, Stuart Owen, Jurgen Pahle, Ulrike Wittig, Dagmar Waltemath, Carole Goble, Pedro Mendes, and Jacky Snoep
18. Rational Design and Methods of Analysis for the Study of Short- and Long-Term Dynamic Responses of Eukaryotic SystemsDuygu Dikicioglu
19. Genome-Scale Metabolic Modeling from Yeast to Human Cell Models of Complex Diseases: Latest Advances and ChallengesYu Chen, Gang Li, and Jens Nielsen
20. Next-Generation Genome-Scale Models Incorporating Multilevel 'omics Data: From Yeast to HumanTunahan Cakir, Emel Koekrek, Gulben Avsar, Ecehan Abdik, and Pinar Pir
21. Advanced Modeling of Cellular Proliferation: Towards a Multi-Scale Framework Coupling Cell Cycle to Metabolism by Integrating Logical and Constraint-Based ModelsLucas van der Zee and Matteo Barberis
Part IV Using Yeast to Model Human Diseases
22. Yeast Genome Screening and Methods for the Discovery of Metabolism Pathways Involved in a Phenotypic Response to Anti-Cancer Agents Magdalena Cal, Irwin Matyjaszczyk, and Stanislaw Ulaszewski
23. Advanced Yeast Models of Familial Alzheimer Disease Expressing FAD-Linked Presenilin to Screen Mutations and g-Secretase ModulatorsEugene Futai
24. From Yeast-to-Humans: Leveraging New Approaches in Yeast to Accelerate Discovery of Therapeutic Targets for SynucleinopathiesJeff S. Piotrowski and Daniel F. Tardiff
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