Empowering bioinformatics communities with Nextflow and nf-core by Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen, Peter W. Harrison, Matthias Hörtenhuber, Cyril Kurylo, Christa Kühn, Sandrine Lagarrigue, Delphine Lallias, Daniel J. Macqueen, Edmund Miller, Júlia Mir-Pedrol, Gabriel Costa Monteiro Moreira, Sven Nahnsen, Harshil Patel, Alexander Peltzer, Frederique Pitel, Yuliaxis Ramayo-Caldas, Marcel da Câmara Ribeiro-Dantas, Dominique Rocha, Mazdak Salavati, Alexey Sokolov, Jose Espinosa-Carrasco, Cedric Notredame, the nf-core community

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Identification of core noncoding RNA-associated competing endogenous RNA networks in renal fibrosis via whole-transcriptome sequencing by Yizhen Chen, Meng Cheng, Rong Dai, Weili Wang, Yonghao Sang, Liuting Wei, Yilin Gao, Wei Zhang, Yiping Wang, Lei Zhang

“…Enrichment analysis showed significant pathways including Rap1 signaling, extracellular matrix–receptor interaction, and PI3K-Akt signaling, with RBPs enriched in RNA binding and ferroptosis.Conclusion By integrating data from three distinct models, we identified conserved ceRNA axis—TCONS_00008870/circRNA_3140–miR-466b-3p–Adamts2—potentially modulating fibrotic progression in renal tissue.…”
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Mir-199a-3p aggravates neuroinflammation in an Alzheimer’s disease transgenic mouse model by promoting M1-polarization microglia by Chenyang Wang, Xiaolu Bu, Mengyao Cao, Yunyu Lian, Haocong Ling, Mo You, Junfei Yi, Xiaoya Gao, Duobin Wu, Yang Li

“…Transcriptome sequencing was performed on miR-199a-3p-modulated BV2 cells, and the sequencing data were cross-analyzed with public databases to predict miR-199a-3p-mediated pathways. …”
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Hsa_Circ_0105596/FTO inhibits progression of Parkinson's disease by sponging miR-187-3p and regulating eEF2 by Jiahao Feng, Jin Zhao, Yong Kuang, Yuheng Zhou, Ziheng Ye, Yutong He, Dandan Chen, Li Zhang, Tingying Zhang, Qingqing Zhu, Shumin Cheng, Taoli Liu

“…Result: CircFTO is upregulated and miR-187-3p is downregulated in SN of PD. EEF2 was the core of neural repair related modules in both SN and striatum using Weighted Correlation Network Analysis (WGCNA) and protein-protein interaction (PPI). …”
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The miR-183/96/182 cluster regulates sensory innervation, resident myeloid cells and functions of the cornea through cell type-specific target genes by Naman Gupta, Mallika Somayajulu, Katherine Gurdziel, Giovanni LoGrasso, Haidy Aziz, Rita Rosati, Sharon McClellan, Ahalya Pitchaikannu, Manoranjan Santra, Muhammed Farooq Abdul Shukkur, Paul Stemmer, Linda D. Hazlett, Shunbin Xu

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MicroRNA-mediated repression of the seed maturation program during vegetative development in Arabidopsis. by Xurong Tang, Shaomin Bian, Mingjuan Tang, Qing Lu, Shengben Li, Xigang Liu, Gang Tian, Vi Nguyen, Edward W T Tsang, Aiming Wang, Steven J Rothstein, Xuemei Chen, Yuhai Cui

“…Therefore, this study establishes a core module composed of a miRNA, its target genes (PHB and PHV), and the direct target of PHB (LEC2) as an underlying mechanism that keeps the seed maturation program off during vegetative development.…”
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miRNAs-19b, -29b-2* and -339-5p show an early and sustained up-regulation in ischemic models of stroke. by Dalbir K Dhiraj, Elvina Chrysanthou, Giovanna R Mallucci, Martin Bushell

“…Understanding molecular events occurring in the apoptotic ischemic penumbra may give greater insight into mechanisms controlling this salvageable tissue. miRNAs are known to have key roles in the regulation of gene expression in numerous pathological conditions, including the modulation of distinct pathways in stroke. However, previous studies have profiled miRNAs in the whole ischemic infarct, and do not differentiate between miRNA regulation in the necrotic core versus the apoptotic penumbra. …”
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Integrated bioinformatics and network pharmacology to identify and validate macrophage polarization related hub genes in the treatment of osteoarthritis with Astragalus membranaceu... by Hui Zang, Liuyan Wang, Yang Wu, Junfei Chang, Wanjun Liu

“…We identified that CREBBP and PIM3 were regulated by 6 miRNAs (e.g., hsa-mir-942-5p) and 79 transcription factors (TFs) (e.g., IRF1). …”
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Alternative polyadenylation and metabolic profiling in young panicle development of hybrid rice and its parents by Guangliang Wu, Shangwei Yu, Junru Fu, Linjuan Ouyang, Lifang Hu, Jianmin Bian, Xiaorong Chen, Jie Xu, Dahu Zhou, Haohua He, Haihui Fu

“…Notably, transcripts with a shortened 3’-untranslated region (3’UTR) exhibited elevated expression levels of their corresponding genes, suggesting that APA plays an important role in modulating gene expression. Furthermore, the variable 3’UTR of the 25% differentially expressed APA genes contained numerous miRNA binding sites, including osa-miR1848 and osa-miR5075, which are known to influence spikelet development. …”
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Research progress of deubiquitinating enzymes in cerebral ischemia-reperfusion injury by XiaoHong Qin, JiangRui Zhu, HaoRan Lu, MaoRui Yi, ZiLong Zhao, WenFei Zhang, Jing Cheng

“…This review systematically elucidates the core regulatory mechanisms of DUBs in CIRI: (i) suppression of neuroinflammation via modulation of NLRP6/NF-κB pathways; (ii) mitigation of oxidative stress through the KEAP1-NRF2 axis and mitochondrial quality control; and (iii) neuroprotection by intercepting necroptosis, ferroptosis, and other PCD pathways. …”
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Identification Exploring the Mechanism and Clinical Validation of Mitochondrial Dynamics-Related Genes in Membranous Nephropathy Based on Mendelian Randomization Study and Bioinfor... by Qiuyuan Shao, Nan Li, Huimin Qiu, Min Zhao, Chunming Jiang, Cheng Wan

“…Regulatory network analyses revealed ATF2 co-regulation mediated by RTTN and MYO9A, along with RTTN-driven modulation of ELOA-AS1 via hsa-mir-431-5p. scRNA-seq analysis identified mesenchymal–epithelial transitioning cells as key contributors, with pseudotime trajectory mapping indicating distinct temporal expression profiles: NFKBIZ (initial upregulation followed by decline), USP40 (gradual fluctuation), and RTTN (persistently low expression). …”
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