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  • © 2021

RNA Bioinformatics

Editors:

  1. Ernesto Picardi

    1. Dipartimento Di Bioscienze Biotecnologie E Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Bari, Italy

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  • Includes cutting-edge techniques

  • Provides step-by-step detail essential for reproducible results

  • Contains key implementation from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2284)

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  • ISBN: 978-1-0716-1307-8
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Table of contents (32 protocols)

  1. Front Matter

    Pages i-xiv
    PDF

  2. Advanced Design of Structural RNAs Using RNARedPrint

    • Yann Ponty, Stefan Hammer, Hua-Ting Yao, Sebastian Will
    Pages 1-15

  3. Modeling and Predicting RNA Three-Dimensional Structures

    • Vladimir Reinharz, Roman Sarrazin-Gendron, Jérôme Waldispühl
    Pages 17-42

  4. Motif Discovery from CLIP Experiments

    • Marco Pietrosanto, Gabriele Ausiello, Manuela Helmer-Citterich
    Pages 43-50

  5. Profiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS

    • Uciel Chorostecki, Jesse R. Willis, Ester Saus, Toni Gabaldon
    Pages 51-62Open Access

  9. QuickIsoSeq for Isoform Quantification in Large-Scale RNA Sequencing

    • Ramya Gamini, Reiko Nakashima, Wen He, Chi Zhang, Ying Huang, Ying Zhang et al.
    Pages 135-145

  11. Computational Analysis of circRNA Expression Data

    • Giulio Ferrero, Nicola Licheri, Michele De Bortoli, Raffaele A. Calogero, Marco Beccuti, Francesca Cordero
    Pages 181-192

  12. Differential Expression Analysis of Long Noncoding RNAs

    • Qian Li, Xuefeng Wang
    Pages 193-205

  14. In Silico Analysis of Micro-RNA Sequencing Data

    • Ernesto Aparicio-Puerta, Bastian Fromm, Michael Hackenberg, Marc K. Halushka
    Pages 231-251

  15. RNA Editing Detection in HPC Infrastructures

    • Claudio Lo Giudice, Luigi Mansi, Tiziano Flati, Silvia Gioiosa, Giovanni Chillemi, Pietro Libro et al.
    Pages 253-270

  17. Computational Analysis of Single-Cell RNA-Seq Data

    • Luca Alessandrì, Francesca Cordero, Marco Beccuti, Maddalena Arigoni, Raffaele A. Calogero
    Pages 289-301

  18. Normalization of Single-Cell RNA-Seq Data

    • Davide Risso
    Pages 303-329

  19. Dimensionality Reduction of Single-Cell RNA-Seq Data

    • George C. Linderman
    Pages 331-342

  20. Single-Cell RNA Sequencing Analysis: A Step-by-Step Overview

    • Shaked Slovin, Annamaria Carissimo, Francesco Panariello, Antonio Grimaldi, Valentina Bouché, Gennaro Gambardella et al.
    Pages 343-365
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About this book

This detailed book aims to provide an overview of novel bioinformatics resources for exploring diverse aspects of RNA biology. This edition focuses on methods dealing with non-coding RNA (miRNAs, circRNAs or lncRNAs), RNA modifications (m6A or RNA editing), single cell RNA-seq and statistical models to handle count data from RNA-seq experiments. The book also includes chapters based on the classical RNA bioinformatics methods, such as those for deciphering secondary and tertiary RNA structures; however, they are revised to take into account deep sequencing data. Finally, chapters describing methods to analyze RNA sequencing data from emerging third generation sequencing technologies that could provide interesting insights into the transcriptional process and its regulation are also included. 

Written for the highly successful Methods in Molecular Biology series, chapters include the kind of expert implementation advice that encourages quality results. Comprehensive and up-to-date, RNA Bioinformatics, Second Edition serves as an ideal guide for researchers digging ever-deeper into the depths of the study of RNAs.

The chapter 'RNA-Seq Data Analysis in Galaxy' is open access under a CC BY 4.0 license.
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Keywords

  • Computational biology
  • RNA biology
  • RNA-Seq data
  • Database resources
  • Non-coding RNAs
  • RNA modifications
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Editors and Affiliations

  • Dipartimento Di Bioscienze Biotecnologie E Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Bari, Italy

    Ernesto Picardi

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Bibliographic Information

  • Book Title: RNA Bioinformatics

  • Editors: Ernesto Picardi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1307-8

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

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

  • Hardcover ISBN: 978-1-0716-1306-1Published: 10 April 2021

  • Softcover ISBN: 978-1-0716-1309-2Published: 10 April 2022

  • eBook ISBN: 978-1-0716-1307-8Published: 09 April 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: XIV, 581

  • Number of Illustrations: 25 b/w illustrations, 178 illustrations in colour

  • Topics: Biochemistry, Bioinformatics

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Access via your institution
eBook USD 149.00
Price excludes VAT (USA)
  • ISBN: 978-1-0716-1307-8
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book USD 199.99
Price excludes VAT (USA)
Hardcover Book USD 279.99
Price excludes VAT (USA)
Learn about institutional subscriptions