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Yeast Systems Biology

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Stephen G. Oliver

    1. Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK

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    You can also search for this editor in PubMed   Google Scholar

  2. Juan I. Castrillo

    1. Genetadi Biotech, Parque Tecnológico de Bizkaia, Biscay, Spain

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2049)

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Table of contents (24 protocols)

  1. Front Matter

    Pages i-xviii
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  2. Yeast Systems Biology

    1. Front Matter

      Pages 1-1
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    2. Yeast Systems Biology: The Continuing Challenge of Eukaryotic Complexity

      • Stephen G. Oliver
      Pages 3-13

  3. Experimental Systems Biology: High-Throughput Genome-Wide and Molecular Studies

    1. Front Matter

      Pages 15-15
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    2. Capture of Ribonucleotides in Yeast Genomic DNA Using Ribose-Seq

      • Sathya Balachander, Taehwan Yang, Gary Newnam, Waleed M. M. El-Sayed, Kyung Duk Koh, Francesca Storici
      Pages 17-37

    3. Method for Multiplexed Integration of Synergistic Alleles and Metabolic Pathways in Yeasts via CRISPR-Cas9

      • Jessica M. Walter, Max G. Schubert, Stephanie H. Kung, Kristy Hawkins, Darren M. Platt, Aaron D. Hernday et al.
      Pages 39-72

    4. Ultrahigh-Density Screens for Genome-Wide Yeast EMAPs in a Single Plate

      • Katherine Licon, John Paul Shen, Brenton P. Munson, Manuel Michaca, Cole Fassino, Luke Fassino et al.
      Pages 73-85

    5. Epi-ID: Systematic and Direct Screening for Chromatin Regulators in Yeast by Barcode-ChIP-Seq

      • Deepani W. Poramba-Liyanage, Tessy Korthout, Fred van Leeuwen
      Pages 87-103

    6. Transcript Profiling Analysis Through Paired-End Ditag (PET) Approach Coupled with Deep Sequencing Reveals Transcriptome Complexity in Yeast

      • Yani Kang, Hong Sain Ooi, Xiaodong Zhao
      Pages 105-112

    7. RNA Sequencing Best Practices: Experimental Protocol and Data Analysis

      • Andrew R. Hesketh
      Pages 113-129

    8. Advanced Methods for the Analysis of Altered Pre-mRNA Splicing in Yeast and Disease

      • Huw B. Thomas, Raymond T. O’Keefe
      Pages 131-140

    9. PAT-Seq: A Method for Simultaneous Quantitation of Gene Expression, Poly(A)-Site Selection and Poly(A)-Length Distribution in Yeast Transcriptomes

      • Angavai Swaminathan, Paul F. Harrison, Thomas Preiss, Traude H. Beilharz
      Pages 141-164

    10. Mapping the Saccharomyces cerevisiae Spatial Proteome with High Resolution Using hyperLOPIT

      • Daniel J. H. Nightingale, Stephen G. Oliver, Kathryn S. Lilley
      Pages 165-190

    11. Data-Independent Acquisition for Yeast Glycoproteomics

      • Lucía F. Zacchi, Benjamin L. Schulz
      Pages 191-202

    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, Andrew Emili
      Pages 203-211

    13. Probing the RNA-Binding Proteome from Yeast to Man: Major Advances and Challenges

      • Benedikt M. Beckmann, Sander Granneman
      Pages 213-231

    14. Metabolomic Analysis of Yeast and Human Cells: Latest Advances and Challenges

      • Romanas Chaleckis, Kazuto Ohashi, Isabel Meister, Shama Naz, Craig E. Wheelock
      Pages 233-245

    15. Measuring the Activity of Plasma Membrane and Vacuolar Transporters in Yeast

      • Melody Cools, Maria Rompf, Andreas Mayer, Bruno André
      Pages 247-261

    16. Self-Establishing Communities: A Yeast Model to Study the Physiological Impact of Metabolic Cooperation in Eukaryotic Cells

      • Kate Campbell, Clara Correia-Melo, Markus Ralser
      Pages 263-282

  4. Computational Systems Biology: Data Management and Modeling the Cell

    1. Front Matter

      Pages 283-283
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Keywords

About this book

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.



Editors and Affiliations

  • Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK

    Stephen G. Oliver

  • Genetadi Biotech, Parque Tecnológico de Bizkaia, Biscay, Spain

    Juan I. Castrillo

Bibliographic Information

  • Book Title: Yeast Systems Biology

  • Book Subtitle: Methods and Protocols

  • Editors: Stephen G. Oliver, Juan I. Castrillo

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9736-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9735-0Published: 11 October 2019

  • Softcover ISBN: 978-1-4939-9738-1Published: 12 October 2020

  • eBook ISBN: 978-1-4939-9736-7Published: 10 October 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XVIII, 447

  • Number of Illustrations: 25 b/w illustrations, 48 illustrations in colour

  • Topics: Systems Biology, Microbiology

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