Special Issue "Bioinformatics Softwares and Databases for Non-coding RNA Research 2.0"

A special issue of Non-Coding RNA (ISSN 2311-553X).

Deadline for manuscript submissions: 15 March 2021.

Special Issue Editor

Prof. Dr. Y-h. Taguchi
Website
Guest Editor
Department of Physics, Chuo University, Tokyo 112-8551, Japan
Interests: bioinformatics; gene expression analysis; feature selection; tensor decomposition
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, non-coding RNAs have attracted more and more attention from researchers, as they have been found to affect a wider range of biological processes than previously believed. Other than miRNAs that are already known to contribute to many biological processes, including disease and developments, more recently identified non-coding RNAs, e.g., lncRNAs and circRNAs, have begun to serve as the focus of various scientific studies, especially the interaction between these newly identified non-coding RNAs and others, e.g., mRNAs, proteins, and miRNAs, which has been discovered to play critical roles on various biological aspects. Since it is very difficult to confirm the interaction between them because of the large number of potential combinations, computational approaches are more desirable. However, and in spite of the urgency of this need, not a large enough number of bioinformatics tools as well as databases of these non-coding RNAs is available.

In this Special Issue, we encourage researchers to submit papers on the following topics, but not limited to them:

  • Bioinformatics tools and databases of interaction between non-coding RNAs and others;
  • Bioinformatics tools and databases for biomarker identification for diseases with non-coding RNAs;
  • Bioinformatics tools and databases for non-coding RNAs as therapy and drug targets;
  • Bioinformatics tools and databases for regulation of transcription by non-coding RNA;
  • Bioinformatics tools and databases epigenetics affected by non-coding RNAs.

Prof. Dr. Y-h. Taguchi
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. Non-Coding RNA is an international peer-reviewed open access quarterly 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 1600 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.

Published Papers (1 paper)

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Research

Open AccessArticle
FuncPEP: A Database of Functional Peptides Encoded by Non-Coding RNAs
Non-Coding RNA 2020, 6(4), 41; https://doi.org/10.3390/ncrna6040041 - 23 Sep 2020
Cited by 1 | Viewed by 1186
Abstract
Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less [...] Read more.
Non-coding RNAs (ncRNAs) are essential players in many cellular processes, from normal development to oncogenic transformation. Initially, ncRNAs were defined as transcripts that lacked an open reading frame (ORF). However, multiple lines of evidence suggest that certain ncRNAs encode small peptides of less than 100 amino acids. The sequences encoding these peptides are known as small open reading frames (smORFs), many initiating with the traditional AUG start codon but terminating with atypical stop codons, suggesting a different biogenesis. The ncRNA-encoded peptides (ncPEPs) are gradually becoming appreciated as a new class of functional molecules that contribute to diverse cellular processes, and are deregulated in different diseases contributing to pathogenesis. As multiple publications have identified unique ncPEPs, we appreciated the need for assembling a new web resource that could gather information about these functional ncPEPs. We developed FuncPEP, a new database of functional ncRNA encoded peptides, containing all experimentally validated and functionally characterized ncPEPs. Currently, FuncPEP includes a comprehensive annotation of 112 functional ncPEPs and specific details regarding the ncRNA transcripts that encode these peptides. We believe that FuncPEP will serve as a platform for further deciphering the biologic significance and medical use of ncPEPs. The link for FuncPEP database can be found at the end of the Introduction Section. Full article
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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.

Title: CRISPR ncRNA bioinformatics
Authors: Chris M. Brown; David Chyou
Affiliation: Biochemistry and Genetics Otago, University of Otago, Dunedin 9054, New Zealand

Title: miRNA profiling and its role in multi-omics regulatory networks connected with somaclonal variation in cucumber (Cucumis sativus L.)
Authors: Wojciech Pląder
Affiliation: Szkoła Główna Gospodarstwa Wiejskiego, Warsaw, Poland

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