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Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis

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Computational Biology of Non-Coding RNA

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

Abstract

MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. The use of RNA data in gene expression analysis has become increasingly important to gain insights into the regulatory mechanisms behind miRNA–mRNA interactions. As a result, we are confronted with a growing landscape of tools, while standards for reproducibility and benchmarking lag behind. This work identifies the challenges for reproducible RNA analysis, and highlights best practices on the processing and dissemination of scientific results. We found that the success of a tool does not solely depend on its performances: equally important is how a tool is received, and then supported within a community. This leads us to a detailed presentation of the RNA workbench, a community effort for sharing workflows and processing tools, built on top of the Galaxy framework. Here, we follow the community guidelines to extend its portfolio of RNA tools with the integration of the TriplexRNA (https://triplexrna.org). Our findings provide the basis for the development of a recommendation system, to guide users in the choice of tools and workflows.

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Acknowledgments

The authors would like to thank the de.NBI and ELIXIR initiatives, for their support in the bioinformatics infrastructure. Thanks also to the Galaxy community, for developing, maintaining, and providing guidance on the use of this comprehensive framework. A warm thank you goes to the RBC Freiburg group, in particular to Anup Kumar, Björn Grüning, and Rolf Backofen for their efforts and commitment in improving the Galaxy framework.

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Authors and Affiliations

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

    Andrea Bagnacani, Markus Wolfien & Olaf Wolkenhauer

  2. Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre, Stellenbosch University, Stellenbosch, South Africa

    Olaf Wolkenhauer

Authors
  1. Andrea Bagnacani
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  2. Markus Wolfien
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  3. Olaf Wolkenhauer
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Corresponding author

Correspondence to Andrea Bagnacani .

Editor information

Editors and Affiliations

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

    Xin Lai

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

    Shailendra K. Gupta

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

    Julio Vera

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Bagnacani, A., Wolfien, M., Wolkenhauer, O. (2019). Tools for Understanding miRNA–mRNA Interactions for Reproducible RNA Analysis. In: Lai, X., Gupta, S., Vera, J. (eds) Computational Biology of Non-Coding RNA. Methods in Molecular Biology, vol 1912. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8982-9_8

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  • DOI: https://doi.org/10.1007/978-1-4939-8982-9_8

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8981-2

  • Online ISBN: 978-1-4939-8982-9

  • eBook Packages: Springer Protocols

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