Skip to main content
SpringerLink
Log in

Ribosome Profiling

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Vyacheslav M. Labunskyy

    1. Department of Dermatology, Boston University School of Medicine, Boston, USA

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2252)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

Table of contents (16 protocols)

  1. Front Matter

    Pages i-xi
    Download chapter PDF

  2. Experimental Protocols

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Monitoring Bacterial Translation Rates Genome-Wide

      • Eugene Oh
      Pages 3-26

    3. Identification of Translation Start Sites in Bacterial Genomes

      • Sezen Meydan, Dorota Klepacki, Alexander S. Mankin, Nora Vázquez-Laslop
      Pages 27-55

    4. Genome-Wide Ribosome Profiling of the Plasmodium falciparum Intraerythrocytic Developmental Cycle

      • Florence Caro, Joseph L. DeRisi
      Pages 57-87

    5. Performing Ribosome Profiling to Assess Translation in Vegetative and Meiotic Yeast Cells

      • Emily Nicole Powers, Gloria Ann Brar
      Pages 89-125

    6. Quantitative Comparisons of Translation Activity by Ribosome Profiling with Internal Standards

      • Yinuo J. Wang, Wendy V. Gilbert
      Pages 127-149

    7. Genome-Wide Analysis of Translation in Replicatively Aged Yeast

      • Hanna Barlit, Manish K. Rai, Sara I. Shoushtari, Carine Beaupere, Vyacheslav M. Labunskyy
      Pages 151-173

    8. Tissue-Specific Ribosome Profiling in Drosophila

      • Xun Chen, Dion Dickman
      Pages 175-188

    9. Measuring Organ-Specific Translation Elongation Rate in Mice

      • Maxim V. Gerashchenko, Vadim N. Gladyshev
      Pages 189-200

    10. Active Ribosome Profiling with RiboLace: From Bench to Data Analysis

      • Massimiliano Clamer, Fabio Lauria, Toma Tebaldi, Gabriella Viero
      Pages 201-220

    11. Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction

      • Jingfan Qiu, Shu-Bing Qian
      Pages 221-237

    12. Choice of Ribonucleases for Ribosome Profiling Experiments

      • Maxim V. Gerashchenko
      Pages 239-248

  3. Bioinformatics and Statistical Analysis

    1. Front Matter

      Pages 249-249
      Download chapter PDF

    2. Codon Resolution Analysis of Ribosome Profiling Data

      • Alexander Bartholomäus, Zoya Ignatova
      Pages 251-268

    3. Assessing Ribosome Distribution Along Transcripts with Polarity Scores and Regression Slope Estimates

      • Ilya E. Vorontsov, Artyom A. Egorov, Aleksandra S. Anisimova, Irina A. Eliseeva, Vsevolod J. Makeev, Vadim N. Gladyshev et al.
      Pages 269-294

    4. Unsupervised Bayesian Prediction of RNA Translation from Ribosome Profiling Data

      • Etienne Boileau, Christoph Dieterich
      Pages 295-312

    5. uORF-seqr: A Machine Learning-Based Approach to the Identification of Upstream Open Reading Frames in Yeast

      • Pieter Spealman, Armaghan Naik, Joel McManus
      Pages 313-329

    6. Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant

      • Dermot Harnett, Eelco Meerdink, Lorenzo Calviello, Dominique Sydow, Uwe Ohler
      Pages 331-346

  4. Back Matter

    Pages 347-348
    Download chapter PDF
Back to top

Keywords

About this book

This book provides a single-source reference on the current state of the ribosome profiling method by describing experimental protocols for the quantitative analysis of translation in a variety of model organisms. In addition, the volume presents a detailed overview of the existing software tools and includes detailed description of methods for statistical analysis, data processing, and visualization of ribosome profiling data. Written for the highly successful Methods in Molecular Biology series, 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. 

Authoritative and practical, Ribosome Profiling: Methods and Protocols aims to provide the type of standardized protocols that have previously been unavailable in an effort to bypass the major barriers to wide use of ribosome profiling-based approaches.

Editors and Affiliations

  • Department of Dermatology, Boston University School of Medicine, Boston, USA

    Vyacheslav M. Labunskyy

Bibliographic Information

  • Book Title: Ribosome Profiling

  • Book Subtitle: Methods and Protocols

  • Editors: Vyacheslav M. Labunskyy

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1150-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1149-4Published: 26 March 2021

  • Softcover ISBN: 978-1-0716-1152-4Published: 26 March 2021

  • eBook ISBN: 978-1-0716-1150-0Published: 25 March 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 348

  • Number of Illustrations: 19 b/w illustrations, 53 illustrations in colour

  • Topics: Biochemistry, general, Protein Science, Bioinformatics

Publish with us

Policies and ethics

Back to top

Search

Navigation