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Computational Biology of Non-Coding RNA

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Xin Lai

    1. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

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    You can also search for this editor in PubMed   Google Scholar

  2. Shailendra K. Gupta

    1. Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

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    You can also search for this editor in PubMed   Google Scholar

  3. Julio Vera

    1. Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

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

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Table of contents (17 protocols)

  1. Front Matter

    Pages i-xii
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  2. Overview of Disease-Specific ncRNAs

    1. Front Matter

      Pages 1-1
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    2. ncRNAs in Inflammatory and Infectious Diseases

      • Leon N. Schulte, Wilhelm Bertrams, Christina Stielow, Bernd Schmeck
      Pages 3-32

    3. p73-Governed miRNA Networks: Translating Bioinformatics Approaches to Therapeutic Solutions for Cancer Metastasis

      • Stella Logotheti, Stephan Marquardt, Brigitte M. Pützer
      Pages 33-52

  3. Computational Methods and Workflows for ncRNA Discovery and Annotation Based on High-Throughput Sequencing Data

    1. Front Matter

      Pages 53-53
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    2. Methods for Annotation and Validation of Circular RNAs from RNAseq Data

      • Disha Sharma, Paras Sehgal, Judith Hariprakash, Sridhar Sivasubbu, Vinod Scaria
      Pages 55-76

    3. Methods to Study Long Noncoding RNA Expression and Dynamics in Zebrafish Using RNA Sequencing

      • Samatha Mathew, Ambily Sivadas, Paras Sehgal, Kriti Kaushik, Shamsudheen K. Vellarikkal, Vinod Scaria et al.
      Pages 77-110

    4. Workflow Development for the Functional Characterization of ncRNAs

      • Markus Wolfien, David Leon Brauer, Andrea Bagnacani, Olaf Wolkenhauer
      Pages 111-132

    5. ncRNA Editing: Functional Characterization and Computational Resources

      • Giovanni Nigita, Gioacchino P. Marceca, Luisa Tomasello, Rosario Distefano, Federica Calore, Dario Veneziano et al.
      Pages 133-174

    6. Computational Prediction of Functional MicroRNA–mRNA Interactions

      • 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
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    2. Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis

      • Andrea Bagnacani, Markus Wolfien, Olaf Wolkenhauer
      Pages 199-214

    3. Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome

      • Isha Monga, Manoj Kumar
      Pages 215-250

    4. Noncoding RNAs Databases: Current Status and Trends

      • 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

    1. Front Matter

      Pages 287-287
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    2. Controllability Methods for Identifying Associations Between Critical Control ncRNAs and Human Diseases

      • Jose C. Nacher, Tatsuya Akutsu
      Pages 289-300

    3. Network-Based Methods and Other Approaches for Predicting lncRNA Functions and Disease Associations

      • Rosario Michael Piro, Annalisa Marsico
      Pages 301-321

    4. Integration of miRNA and mRNA Expression Data for Understanding Etiology of Gynecologic Cancers

      • Sushmita Paul
      Pages 323-338

  6. Kinetic Modeling of ncRNA-Mediated Gene Regulation

    1. Front Matter

      Pages 339-339
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    2. Quantitative Characteristic of ncRNA Regulation in Gene Regulatory Networks

      • Federico Bocci, Mohit Kumar Jolly, Herbert Levine, José Nelson Onuchic
      Pages 341-366
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Keywords

About this book

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 methodsand approaches that will be of value to researchers interested in ncRNA field.


Editors and Affiliations

  • Department of Dermatology, Erlangen University Hospital, Erlangen, Germany

    Xin Lai, Julio Vera

  • Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany

    Shailendra K. Gupta

Bibliographic Information

  • Book Title: Computational Biology of Non-Coding RNA

  • Book Subtitle: Methods and Protocols

  • Editors: Xin Lai, Shailendra K. Gupta, Julio Vera

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-8982-9

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-8981-2Published: 12 January 2019

  • eBook ISBN: 978-1-4939-8982-9Published: 11 January 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XII, 451

  • Number of Illustrations: 13 b/w illustrations, 65 illustrations in colour

  • Topics: Bioinformatics, Human Genetics, Computational Biology/Bioinformatics

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