Special Issue "Bioinformatics Resource and Protocols for Small RNA Research"

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: 31 May 2020.

Special Issue Editor

Assoc. Prof. Michael Hackenberg
E-Mail Website
Guest Editor
Computational Epigenomics Lab, Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
Interests: Computational Genomics, Bioinformatics, small RNA detection and prediction, miRNA targets, small RNAs at the interface between parasites and hosts, NGS data analysis, Epigenomics, Epitranscriptomics

Special Issue Information

Dear colleagues,

Small RNA-based research has experienced a strong increase over the last 15 years. An important event that caused this boost was certainly the advent of high-throughput sequencing methods which facilitate the profiling of known small RNAs, its functional characterization, and the detection of novel sequences.

MicroRNAs were discovered over 25 years ago, and initially, the research focus was on its molecular functions in cell homeostasis through the negative regulation of target genes or by stabilizing gene expression programs during development. Since then, small RNAs have made their way into other research fields like biomedicine as putative therapeutic targets or diagnostic and predictive biomarkers, or in parasitology given their importance at the interface between parasites and hosts. Finally, small RNA research is no longer limited to microRNAs, as other small RNAs like tRNA, snoRNAs or yRNAs seem to produce fragments that might be functional as well.

Bioinformatics methods play an important role in small RNA research; however, frequently, the data analysis or the in silico functional analysis of RNAs are highly parametrized processes, and it is not always easy for the user to select the correct settings. Therefore, in this Special Issue, we seek both original research papers on bioinformatics resources for small RNA research and protocols for already published, well established tools, methods or databases. The protocol papers should be addressed to a non-bioinformatics readership with a clear focus on how to resolve clearly defined biological or biomedical problems. The protocol papers should contain (i) a very brief introduction including the mention of other, similar resources, (ii) discussion of the hardware requirements (if applicable) and instructions on the installation process, and (iii) a clear outline of the biological questions or problems that can be addressed including a discussion of the required input data, main parameters, and output files together with the biological interpretation of the results. The protocol papers should not contain a detailed description of the resource nor a comparison to others, as this should be contained in the original publications.

Assoc. Prof. Michael Hackenberg
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


  • Small RNA data analysis microRNA target prediction and analysis microRNA networks de novo annotation of small RNAs in silico functional analysis of small RNAs

Published Papers

This special issue is now open for submission, see below for planned papers.

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Type: Article
Authors: Wenjing Kang, Bastian Fromm, Marc Friedländer, et al
Affiliation: Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
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