ijms-logo

Journal Browser

Journal Browser

Harnessing Bioinformatics for miRNA Research: Methods, Insights and Applications

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Informatics".

Deadline for manuscript submissions: 20 February 2026 | Viewed by 966

Special Issue Editors


E-Mail Website
Guest Editor
1. Department of Biological & Environmental Sciences & Technology, University of Salento, 73100 Lecce, Italy
2. National Research Council, Institute of Clinical Physiology, Lecce, Italy
Interests: micro RNA; non-coding RNA; human health; public health
Special Issues, Collections and Topics in MDPI journals

E-Mail Website
Guest Editor
National Research Council, Institute of Clinical Physiology, Lecce, Italy
Interests: bioinformatics; microRNA; SNP; public health; exercise physiology

Special Issue Information

Dear Colleagues,

MicroRNAs (miRNAs) are small, non-coding RNAs that play crucial roles in gene regulation and are involved in a wide range of biological and pathological processes. The rapid advancement of high-throughput sequencing technologies and computational approaches has significantly expanded our ability to identify, annotate, and analyze miRNAs, providing deeper insights into their functional roles and regulatory mechanisms.

The aim of this Special Issue is to highlight novel discoveries and breakthroughs in miRNA research, emphasizing the innovative bioinformatics methods, tools, and databases that enable these discoveries. We welcome contributions on a variety of topics, including, but not limited to, the following:

  • Computational miRNA prediction and annotation.
  • miRNA target identification and validation.
  • Integrative multi-omics approaches for miRNA studies.
  • Artificial intelligence applications in miRNA research.
  • Network-based analysis of miRNA regulatory circuits.
  • Clinical and translational bioinformatics in miRNA-based diagnostics and therapeutics.

By integrating cutting-edge bioinformatics research on miRNAs with a special focus on studies revealing novel insights into their physiological and pathological roles, this Special Issue aims to provide a comprehensive perspective on current challenges and future directions in the field. We invite researchers to submit original research articles, reviews, and methodological papers that leverage computational and bioinformatics approaches to advance our understanding of miRNAs from both physiological and pathological viewpoints.

Dr. Maria Rosaria Tumolo
Dr. Saverio Sabina
Guest Editors

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 submissions that pass pre-check are 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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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.

Keywords

  • microRNA
  • bioinformatics
  • hub genes
  • miRNA target prediction
  • miRNA regulatory networks
  • miRNA-based biomarkers
  • artificial intelligence in miRNA research
  • multi-omics approaches

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

25 pages, 7428 KB  
Article
In Silico Analysis of MiRNA Regulatory Networks to Identify Potential Biomarkers for the Clinical Course of Viral Infections
by Elena V. Mikheeva, Kseniya S. Aulova, Georgy A. Nevinsky and Anna M. Timofeeva
Int. J. Mol. Sci. 2025, 26(20), 10100; https://doi.org/10.3390/ijms262010100 - 16 Oct 2025
Viewed by 444
Abstract
MiRNA expression profiles exhibit notable alterations in numerous diseases, particularly viral infections. Consequently, miRNAs may be regarded as both therapeutic targets and markers for the development of complications. MiRNAs can significantly influence the modulation of immune responses, offering an extra layer of regulation [...] Read more.
MiRNA expression profiles exhibit notable alterations in numerous diseases, particularly viral infections. Consequently, miRNAs may be regarded as both therapeutic targets and markers for the development of complications. MiRNAs can significantly influence the modulation of immune responses, offering an extra layer of regulation during viral infections. In this study, miRNAs associated with viral infections were analyzed using an in silico approach. Computer modeling predicted a number of miRNAs capable of influencing the functionality of specific components of the immune system. As a result, 242 miRNAs common to the three types of infections were identified. A network of miRNA-gene regulatory interactions, encompassing 502 nodes (224 miRNAs and 278 genes) and 2236 interactions, was developed. Within this network, subnetworks were identified that are involved in the operation of specific connections in the immune response to viruses. For each step of the immune response, the miRNAs involved in governing these processes were examined. These predicted miRNAs are of particular interest for further analysis aimed at establishing the relationship between their differential expression and disease symptom severity. The obtained data lay the foundation for identifying the most promising molecules as predictive biomarkers and the subsequent development of a diagnostic system. Full article
Show Figures

Figure 1

13 pages, 6985 KB  
Article
Investigation of the Role of miR-1236-3p in Heat Tolerance of American Shad (Alosa sapidissima) by Targeted Regulation of hsp90b1
by Mingkun Luo, Ying Liu, Wenbin Zhu, Bingbing Feng, Wei Xu and Zaijie Dong
Int. J. Mol. Sci. 2025, 26(20), 9908; https://doi.org/10.3390/ijms26209908 - 11 Oct 2025
Viewed by 300
Abstract
High temperatures are one of the most important abiotic stressors affecting the survival and growth of American shad (Alosa sapidissima). Building on previous omics sequencing studies of A. sapidissima liver and gills under high temperature stress, this study focused on investigating [...] Read more.
High temperatures are one of the most important abiotic stressors affecting the survival and growth of American shad (Alosa sapidissima). Building on previous omics sequencing studies of A. sapidissima liver and gills under high temperature stress, this study focused on investigating the regulatory role of miR-1236-3p and its target gene hsp90b1. The results indicate that the full-length cDNA of the hsp90b1 gene is 2023 bp and comprises a 5’ end of 58 bp, a 3’ end of 84 bp, and a coding region of 1881 bp, encoding 626 amino acids. Sequence alignment and phylogenetic tree analysis reveal that the hsp90b1 sequence is highly conserved across species. In situ hybridization showed that hsp90b1 is mainly localized in the cytoplasm. Software prediction identified a potential binding site between miR-1236-3p and hsp90b1. Through the construction of wild-type and mutant 3’UTR hsp90b1 dual luciferase reporter plasmids, the targeted relationship between the two was confirmed. In addition, the spatiotemporal expression levels of the hsp90b1 was found to be highest in the multicellular stage and liver tissue at a cultivation temperature of 27 °C; miR-1236-3P was highly expressed in the hatching stage and heart tissue at 30 °C. These findings provide a theoretical foundation for further investigating the regulatory role of non-coding RNA in A. sapidissima heat stress and offer data for subsequent molecular breeding studies. Full article
Show Figures

Figure 1

Back to TopTop