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Computational Biology of Non-Coding RNA

Methods and Protocols

  • Xin Lai
  • Shailendra K. Gupta
  • Julio Vera

Part of the Methods in Molecular Biology book series (MIMB, volume 1912)

Table of contents

  1. Front Matter
    Pages i-xii
  2. Overview of Disease-Specific ncRNAs

    1. Front Matter
      Pages 1-1
    2. Leon N. Schulte, Wilhelm Bertrams, Christina Stielow, Bernd Schmeck
      Pages 3-32
  3. Computational Methods and Workflows for ncRNA Discovery and Annotation Based on High-Throughput Sequencing Data

    1. Front Matter
      Pages 53-53
    2. Disha Sharma, Paras Sehgal, Judith Hariprakash, Sridhar Sivasubbu, Vinod Scaria
      Pages 55-76
    3. Samatha Mathew, Ambily Sivadas, Paras Sehgal, Kriti Kaushik, Shamsudheen K. Vellarikkal, Vinod Scaria et al.
      Pages 77-110
    4. Markus Wolfien, David Leon Brauer, Andrea Bagnacani, Olaf Wolkenhauer
      Pages 111-132
    5. Giovanni Nigita, Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Federica Calore, Dario Veneziano et al.
      Pages 133-174
    6. Müşerref Duygu Saçar Demirci, Malik Yousef, Jens Allmer
      Pages 175-196
  4. Bioinformatics Tools and Databases for ncRNA Analyses

    1. Front Matter
      Pages 197-197
    2. Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer
      Pages 199-214
    3. Vinicius Maracaja-Coutinho, Alexandre Rossi Paschoal, José Carlos Caris-Maldonado, Pedro Vinícius Borges, Almir José Ferreira, Alan Mitchell Durham
      Pages 251-285
  5. Network-Based Methods for Characterizing ncRNA Function

  6. Kinetic Modeling of ncRNA-Mediated Gene Regulation

    1. Front Matter
      Pages 339-339
    2. Federico Bocci, Mohit Kumar Jolly, Herbert Levine, José Nelson Onuchic
      Pages 341-366
    3. Araks Martirosyan, Marco Del Giudice, Chiara Enrico Bena, Andrea Pagnani, Carla Bosia, Andrea De Martino
      Pages 367-409
    4. Xiao-Jun Tian, Manuela Vanegas Ferro, Hanah Goetz
      Pages 411-426
    5. Jomar F. Rabajante, Ricardo C. H. del Rosario
      Pages 427-445
  7. Back Matter
    Pages 447-451

About this book

Introduction

This volume details a collection of state-of-art methods including identification of novel ncRNAs and their targets, functional annotation and disease association in different biological contexts. Chapters guide readers through an overview of disease-specific ncRNAs, computational methods and workflows for ncRNA discovery, annotation based on high-throughput sequencing data, bioinformatics tools and databases for ncRNA analyses, network-based methods, and kinetic modelling of ncRNA-mediated gene regulation. 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.

Authoritative and cutting-edge, Computational Biology of Non-Coding RNA: Methods and Protocols aims to provide a state-of-the-art collection of computational methods and approaches that will be of value to researchers interested in ncRNA field.

Keywords

ncRNAs deep sequencing data miRNA-mRNA interactome ncRNA databases regulatory networks

Editors and affiliations

  • Xin Lai
    • 1
  • Shailendra K. Gupta
    • 2
  • Julio Vera
    • 3
  1. 1.Department of DermatologyErlangen University HospitalErlangenGermany
  2. 2.Department of Systems Biology and BioinformaticsUniversity of RostockRostockGermany
  3. 3.Department of DermatologyErlangen University HospitalErlangenGermany

Bibliographic information

  • DOI https://doi.org/10.1007/978-1-4939-8982-9
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-8981-2
  • Online ISBN 978-1-4939-8982-9
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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