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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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  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

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    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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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.


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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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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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