RNA Bioinformatics

  • Ernesto Picardi

Part of the Methods in Molecular Biology book series (MIMB, volume 1269)

Table of contents

  1. Front Matter
    Pages i-xii
  2. RNA Secondary and Tertiary Structures

    1. Front Matter
      Pages 1-1
    2. Alexander Churkin, Lina Weinbrand, Danny Barash
      Pages 3-16
    3. Eugenio Mattei, Manuela Helmer-Citterich, Fabrizio Ferrè
      Pages 39-47
    4. Federico Zambelli, Giulio Pavesi
      Pages 49-62
    5. Yann Ponty, Fabrice Leclerc
      Pages 63-100
    6. Jérôme Waldispühl, Vladimir Reinharz
      Pages 101-121
  3. Analysis of High-Throughput RNA Sequencing Data

    1. Front Matter
      Pages 135-135
    2. Xing Li, Asha Nair, Shengqin Wang, Liguo Wang
      Pages 137-146
    3. Kin Fai Au
      Pages 147-161
    4. Raffaele A. Calogero, Francesca Zolezzi
      Pages 163-172
    5. Paola Bonizzoni, Gianluca Della Vedova, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi
      Pages 173-188
    6. Ernesto Picardi, Anna Maria D’Erchia, Angela Gallo, Graziano Pesole
      Pages 189-205
    7. Anastasis Oulas, Nestoras Karathanasis, Annita Louloupi, Georgios A. Pavlopoulos, Panayiota Poirazi, Kriton Kalantidis et al.
      Pages 207-229
    8. Ilenia Boria, Lara Boatti, Igor Saggese, Flavio Mignone
      Pages 243-256
    9. Fosso Bruno, Marzano Marinella, Monica Santamaria
      Pages 257-278
    10. Evguenia Kopylova, Laurent Noé, Corinne Da Silva, Jean-Frédéric Berthelot, Adriana Alberti, Jean-Marc Aury et al.
      Pages 279-291
    11. Federico Zambelli, Giulio Pavesi
      Pages 293-303
  4. Web Resources for RNA Data Analysis

    1. Front Matter
      Pages 305-305
    2. Andreas R. Gruber, Stephan H. Bernhart, Ronny Lorenz
      Pages 307-326
    3. Mattia D’Antonio, Ernesto Picardi, Tiziana Castrignanò, Anna Maria D’Erchia, Graziano Pesole
      Pages 327-338
    4. Matteo Giulietti, Giorgio Grillo, Sabino Liuni, Graziano Pesole
      Pages 339-348
    5. Jennifer Daub, Ruth Y. Eberhardt, John G. Tate, Sarah W. Burge
      Pages 349-363
    6. Mattia D’Antonio, Tiziana Castrgnanò, Matteo Pallocca, Anna Maria D’Erchia, Ernesto Picardi, Graziano Pesole
      Pages 365-378
    7. Alessandro Laganà, Dario Veneziano, Francesco Russo, Alfredo Pulvirenti, Rosalba Giugno, Carlo Maria Croce et al.
      Pages 393-412
  5. Back Matter
    Pages 413-415

About this book


This volume provides an overview of RNA bioinformatics methodologies, including basic strategies to predict secondary and tertiary structures, and novel algorithms based on massive RNA sequencing. Interest in RNA bioinformatics has rapidly increased thanks to the recent high-throughput sequencing technologies allowing scientists to investigate complete transcriptomes at single nucleotide resolution. Adopting advanced computational technics, scientists are now able to conduct more in-depth studies and present them to you in this book. Written in the highly successful Methods of Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and equipment, step-by-step, readily reproducible bioinformatics protocols, and key tips to avoid known pitfalls.

Authoritative and practical, RNA Bioinformatics seeks to aid scientists in the further study of bioinformatics and computational biology of RNA.


DNA Non-coding RNAs RNA bioinformatics RNA data analysis RNA molecules RNA sequence mapping RNA-RNA interactions eukaryotic transcriptomes high-throughput RNA sequencing

Editors and affiliations

  • Ernesto Picardi
    • 1
  1. 1.Department of Biosciences, Biotechnology and Biopharmaceutics, and National Research CouncilUniversity of Bari; Institute of Biomembranes and Bioenergetics, Bari, Italy, and National Institute of Biostructures and Biosystems (INBB)RomeItaly

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media New York 2015
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-2290-1
  • Online ISBN 978-1-4939-2291-8
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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