Workflow Development for the Functional Characterization of ncRNAs

  • Markus WolfienEmail author
  • David Leon Brauer
  • Andrea Bagnacani
  • Olaf Wolkenhauer
Part of the Methods in Molecular Biology book series (MIMB, volume 1912)


During the last decade, ncRNAs have been investigated intensively and revealed their regulatory role in various biological processes. Worldwide research efforts have identified numerous ncRNAs and multiple RNA subtypes, which are attributed to diverse functionalities known to interact with different functional layers, from DNA and RNA to proteins. This makes the prediction of functions for newly identified ncRNAs challenging. Current bioinformatics and systems biology approaches show promising results to facilitate an identification of these diverse ncRNA functionalities. Here, we review (a) current experimental protocols, i.e., for Next Generation Sequencing, for a successful identification of ncRNAs; (b) sequencing data analysis workflows as well as available computational environments; and (c) state-of-the-art approaches to functionally characterize ncRNAs, e.g., by means of transcriptome-wide association studies, molecular network analyses, or artificial intelligence guided prediction. In addition, we present a strategy to cover the identification and functional characterization of unknown transcripts by using connective workflows.

Key words

Workflow ncRNA Transcript identification Experimental RNA discovery Data analysis Next Generation Sequencing Network analysis Co-expression analysis Machine learning 



We acknowledge the partners and management of the German Network for Bioinformatics Infrastructure (de.NBI) for continuous support and guidance. Financial support for this work by the German Federal Ministry for Education and Research (BMBF) and European Social Fund (ESF) is greatly acknowledged (Grant 031L0106C, 02NUK043C, ESF/14-BM-A55-0027/18).


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Markus Wolfien
    • 1
    Email author
  • David Leon Brauer
    • 1
  • Andrea Bagnacani
    • 1
  • Olaf Wolkenhauer
    • 1
    • 2
  1. 1.Department of Systems Biology and Bioinformatics, Institute of Computer ScienceUniversity of RostockRostockGermany
  2. 2.Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research CentreStellenbosch UniversityStellenboschSouth Africa

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