© 2015

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

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

About the editors

Ernesto Picardi Dipartimento di Biochimica e Biologia Molecolare E. Quagliariello, Università di Bari, Bari, Italy

Bibliographic information

  • Book Title RNA Bioinformatics
  • Editors Ernesto Picardi
  • Series Title Methods in Molecular Biology
  • Series Abbreviated Title Methods Molecular Biology
  • DOI
  • Copyright Information Springer Science+Business Media New York 2015
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-1-4939-2290-1
  • Softcover ISBN 978-1-4939-4644-0
  • eBook ISBN 978-1-4939-2291-8
  • Series ISSN 1064-3745
  • Series E-ISSN 1940-6029
  • Edition Number 1
  • Number of Pages XII, 415
  • Number of Illustrations 29 b/w illustrations, 73 illustrations in colour
  • Topics Bioinformatics
    Protein Structure
  • Buy this book on publisher's site


“This text is a timely book that overviews the state of art of methodological approaches for the analysis of RNA data … . the authors often provide sufficient description of the fields and state of the art, combined with numerous references. The major advantage of the book is that it encompasses elements that attract both bioinformaticians seeking an applicability of their proposed methods and biologists seeking for answers to particular biological questions.” (Irina Ioana Mohorianu, zbMATH 1318.92003, 2015)