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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...is well established that miRNAs can repress the expression of their targets, at both the RNA and the protein level (Baek et al. 2008; Selbach et al. 2008). However, alternative functions for miRNAs have also been proposed, including buffering of gene expression variation (noise) (Hornstein and Shomron...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...by expression analysis of host genes. Genome Res 19: 481–490. doi:10.1101/gr.084129.108 ↵Gennarino VA, D'Angelo G, Dharmalingam G, Fernandez S, Russolillo G, Sanges R, Mutarelli M, Belcastro V, Ballabio A, Verde P, et al. 2012. Identification of microRNA-regulated gene networks by expression analysis of target...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...).Dysregulation of APA could be associated with human diseases, including cancer. It has been shown that APA-mediated 3′ UTR shortening could activate oncogene expression via escaping from microRNA regulation, whereas RNA transcripts with shortened 3′ UTRs could also inhibit other transcripts from tumor...
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Method: Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks
- Hua-Sheng Chiu,
- David Llobet-Navas,
- Xuerui Yang,
- Wei-Jen Chung,
- Alberto Ambesi-Impiombato,
- Archana Iyer,
- Hyunjae Ryan Kim,
- Elena G. Seviour,
- Zijun Luo,
- Vasudha Sehgal,
- Tyler Moss,
- Yiling Lu,
- Prahlad Ram,
- José Silva,
- Gordon B. Mills,
- Andrea Califano,
- and Pavel Sumazin
Genome Res. February 2015 25: 257-267; Published in Advance November 5, 2014, doi:10.1101/gr.178194.114
...inferred targets compete for their predicted miRNA regulators. In the following sections, we discuss results from Cupid-inferred miRNA targets based on gene expression profile data of TCGA breast cancer samples (The Cancer Genome Atlas Network 2012). Step I (miRNA binding-site analysis) miRNA binding sites...
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Research: microRNA target prediction programs predict many false positives
- Natalia Pinzón,
- Blaise Li,
- Laura Martinez,
- Anna Sergeeva,
- Jessy Presumey,
- Florence Apparailly,
- and Hervé Seitz
Genome Res. February 2017 27: 234-245; Published in Advance November 15, 2016, doi:10.1101/gr.205146.116
...of Medicine, 34060 Montpellier, France; 4Clinical Department for Osteoarticular Diseases, University Hospital Lapeyronie, 34295 Montpellier, France According to the current view, each microRNA regulates hundreds of genes. Computational tools aim at identifying microRNA targets, usually selecting...
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Research: Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma
- Swati Venkat,
- Arwen A. Tisdale,
- Johann R. Schwarz,
- Abdulrahman A. Alahmari,
- H. Carlo Maurer,
- Kenneth P. Olive,
- Kevin H. Eng,
- and Michael E. Feigin
Genome Res. March 2020 30: 347-360; Published in Advance February 6, 2020, doi:10.1101/gr.257550.119
..., TP53, SMAD4, CDKN2A) and dysregulated pathways (axon guidance, cell adhesion, small GTPase signaling, protein metabolism) driving disease initiation and progression (Jones et al. 2008; Waddell et al. 2015; The Cancer Genome Atlas Research Network 2017). Gene expression profiles from hundreds...
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Method: Inhibition of microRNA 128 promotes excitability of cultured cortical neuronal networks
- K. Melodi McSweeney,
- Ayal B. Gussow,
- Shelton S. Bradrick,
- Sarah A. Dugger,
- Sahar Gelfman,
- Quanli Wang,
- Slavé Petrovski,
- Wayne N. Frankel,
- Michael J. Boland,
- and David B. Goldstein
Genome Res. October 2016 26: 1411-1416; Published in Advance August 11, 2016, doi:10.1101/gr.199828.115
..., Tuebing F, Nigh EA, Kane CG, Sabatini ME, Kiebler M, Greenberg ME. 2006. A brain-specific microRNA regulates dendritic spine development. Nature 439: 283–289. Sombati S, Delorenzo RJ. 1995. Recurrent spontaneous seizure activity in hippocampal neuronal networks in culture. J Neurophysiol 73: 1706...
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Research: Impact of microRNA regulation on variation in human gene expression
- Jian Lu and
- Andrew G. Clark
Genome Res. July 2012 22: 1243-1254; Published in Advance March 28, 2012, doi:10.1101/gr.132514.111
...Impact of microRNA regulation on variation in human gene expression Jian Lu 1 and Andrew G. Clark 1 Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA Abstract MicroRNAs (miRNAs) are endogenously...
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Research: Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations
- Irene Mei,
- Susanne Nichterwitz,
- Melanie Leboeuf,
- Jik Nijssen,
- Isadora Lenoel,
- Dirk Repsilber,
- Christian S. Lobsiger,
- and Eva Hedlund
Genome Res. September 2025 35: 1975-1991; Published in Advance July 17, 2025, doi:10.1101/gr.279501.124
...interactions, genetic interaction profile similarity, gene regulation, mRNA coexpression, microRNA regulation, protein coexpression, phylogenetic profile similarity, physical interaction, subcellular localization, and transcription factor binding profile. (E) PCA plot illustrates the clustering pattern...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...et al. 2019; Teets et al. 2023). Neural events also control the production and release of prothoracicotropic hormone (PTTH), as well as the production of ecdysone (Ahmadi et al. 2021). Additionally, downstream genes, such as microRNAs regulated by ecdysone titers (e.g., let-7, miR-252, and miR-8–3p...

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