Frontiers in Bioinformatics | RNA Bioinformatics section | New and Recent Articles https://www.frontiersin.org/journals/bioinformatics/sections/rna-bioinformatics RSS Feed for RNA Bioinformatics section in the Frontiers in Bioinformatics journal | New and Recent Articles en-us Frontiers Feed Generator,version:1 2026-05-14T18:26:37.465+00:00 60 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1794098 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1794098 <![CDATA[Machine learning-based determination of sex-related bladder cancer biomarkers]]> 2026-04-29T00:00:00Z Original Research Joseph R. PizziImage AdhikariPrakyat PrakashHangchuan ShiHiroshi MiyamotoFeng Cui https://www.frontiersin.org/articles/10.3389/fbinf.2026.1719535 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1719535 <![CDATA[Characterizing miRNA editing patterns in 5 types of cells using single-cell small RNA sequencing data]]> 2026-04-09T00:00:00Z Original Research Chunyi MaoHao GuoWenping XieYue XuHongjia ZhangKang LuoJun YangYun Zheng https://www.frontiersin.org/articles/10.3389/fbinf.2026.1760987 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1760987 <![CDATA[An explainable-AI framework reveals novel lncRNAs specific for breast cancer subtypes]]> 2026-03-10T00:00:00Z Original Research Jai Chand PatelAvinash VeerappaChittibabu Guda https://www.frontiersin.org/articles/10.3389/fbinf.2026.1758257 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1758257 <![CDATA[A clustering method for single-cell RNA sequencing data based on denoising and masking learning]]> 2026-03-03T00:00:00Z Original Research Shuang XuWen YanBin ZhangHong QiKai Wang https://www.frontiersin.org/articles/10.3389/fbinf.2026.1787360 https://www.frontiersin.org/articles/10.3389/fbinf.2026.1787360 <![CDATA[From clinical phenotypes to genomic signatures: machine learning integration for precision tuberculosis treatment prediction ]]> 2026-03-03T00:00:00Z Original Research Liping LiHuanqing LiuQian LeiTingting Li https://www.frontiersin.org/articles/10.3389/fbinf.2025.1676149 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1676149 <![CDATA[TRANSAID: a hybrid deep learning framework for translation site prediction with integrated biological feature scoring]]> 2026-01-19T00:00:00Z Technology and Code Yan LiBoran WangZhen LiuWei WeiCaiyi FeiShi XuTiyun HanWei GengZengding Wu https://www.frontiersin.org/articles/10.3389/fbinf.2025.1690932 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1690932 <![CDATA[Altered circRNAs: a novel potential mechanism for the functions of extracellular vesicles derived from platelet-rich plasma]]> 2026-01-08T00:00:00Z Original Research Lifeng NiuYanli WangYao GaoJun Zhang https://www.frontiersin.org/articles/10.3389/fbinf.2025.1696823 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1696823 <![CDATA[inDAGO: a user-friendly interface for seamless dual and bulk RNA-Seq analysis]]> 2025-11-21T00:00:00Z Technology and Code Gaetano AufieroCarmine FruggieroNunzio D’Agostino https://www.frontiersin.org/articles/10.3389/fbinf.2025.1629526 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1629526 <![CDATA[Unveiling the impact of interferon genes on the immune microenvironment of triple-negative breast cancer: identification of therapeutic targets]]> 2025-10-08T00:00:00Z Original Research Ying LiuJiayi CaiAamir FahiraKai ZhuangJiaojiao WangZhi ZhangLin YanYong LiuDefang OuyangZunnan Huang https://www.frontiersin.org/articles/10.3389/fbinf.2025.1633494 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1633494 <![CDATA[Association between dysregulated expression of Ca2+ and ROS-related genes and breast cancer patient survival]]> 2025-09-22T00:00:00Z Brief Research Report Sofia RamosJoão GregórioAna Sofia FernandesNuno Saraiva https://www.frontiersin.org/articles/10.3389/fbinf.2025.1605681 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1605681 <![CDATA[Bioinformatics analysis of lncRNA and mRNA differentially expressed in patients with cervical cancer]]> 2025-08-01T00:00:00Z Original Research Xiaohua AnXiaoxue HuangQiujie YuYiyue TangYan WangHuasu ChenYafei ZhangQianhao HuangYudi RaoGuomei HuHe Zha 2 and P < 0.05). Additionally, 3,666 mRNAs were significantly upregulated, while 2,220 mRNAs were significantly downregulated (Fold change >2 and P < 0.05). GO/KEGG enrichment analysis showed that differentially expressed mRNA played a significant role in cell cycle and cell senescence, and was related to signal pathways such as cAMP and MAPK, forming a complex network among the proteins encoded by these mRNAs. Further analysis indicated that the 20 antisense lncRNAs with the most remarkable differences might exert biological functions by influencing their corresponding mRNAs. The results of RT-qPCR revealed that CDKN2B-AS1, HAGLROS and GATA6-AS1 were potentially regulated by HPV16 E6/E7, which were in accordance with those obtained from chip detection. In this study, differentially expressed lncRNAs associated with HPV16 infection were screened and explored their transcriptional molecular functions and biological pathways, providing a molecular basis for predicting diagnostic markers of cervical cancer.]]> https://www.frontiersin.org/articles/10.3389/fbinf.2025.1625145 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1625145 <![CDATA[Comparative transcriptome analysis of different tissues of Hylomecon japonica provides new insights into the biosynthesis pathway of triterpenoid saponins]]> 2025-07-07T00:00:00Z Original Research Bing HeTeng XuShaowei XuHuqiang FangQingshan Yang https://www.frontiersin.org/articles/10.3389/fbinf.2025.1585794 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1585794 <![CDATA[CytoLNCpred-a computational method for predicting cytoplasm associated long non-coding RNAs in 15 cell-lines]]> 2025-05-26T00:00:00Z Original Research Shubham ChoudhuryNaman Kumar MehtaGajendra P. S. Raghava https://www.frontiersin.org/articles/10.3389/fbinf.2025.1575346 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1575346 <![CDATA[MORE-RNAseq: a pipeline for quantifying retrotransposition-capable LINE1 expression based on RNA-seq data]]> 2025-05-22T00:00:00Z Brief Research Report Yutaka NakachiJianbin DuRisa WatanabeYutaro YanagidaMiki BundoKazuya Iwamoto https://www.frontiersin.org/articles/10.3389/fbinf.2025.1571476 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1571476 <![CDATA[Tumor tissue-of-origin classification using miRNA-mRNA-lncRNA interaction networks and machine learning methods]]> 2025-05-06T00:00:00Z Original Research Ankita LawardeMasuma KhatunPrakash LingasamyAndres SalumetsVijayachitra Modhukur https://www.frontiersin.org/articles/10.3389/fbinf.2025.1545680 https://www.frontiersin.org/articles/10.3389/fbinf.2025.1545680 <![CDATA[An extended miRNA repertoire in Rattus norvegicus]]> 2025-03-10T00:00:00Z Data Report Julienne LehmannAli YazbeckJörg HackermüllerSebastian Canzler https://www.frontiersin.org/articles/10.3389/fbinf.2024.1487292 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1487292 <![CDATA[hsa-miR-548d-3p: a potential microRNA to target nucleocapsid and/or capsid genes in multiple members of the Flaviviridae family ]]> 2025-01-14T00:00:00Z Original Research H. W. CayatinetoS. T. Hakim https://www.frontiersin.org/articles/10.3389/fbinf.2024.1493712 https://www.frontiersin.org/articles/10.3389/fbinf.2024.1493712 <![CDATA[In silico identification of chilli genome encoded MicroRNAs targeting the 16S rRNA and secA genes of “Candidatus phytoplasma trifolii”]]> 2025-01-06T00:00:00Z Original Research Vineeta PandeyAarshi SrivastavaRamwant GuptaHaitham E. M. ZakiMuhammad Shafiq ShahidRajarshi K. Gaur