ArticlePLoS computational biology2011
Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
29 citing papers in PubMed, 84 citations in OpenAlex.
- Features of Complementary Interactions of BmiRNAs with mRNAs of Human Genes.International journal of molecular sciences · 2026Article
- Exploring the role of food-source microRNAs as potential nutritional bioactives in humans.NPJ science of food · 2026Article
- Beyond the heat shock pathway: Heat stress responses in Drosophila development.Developmental biology · 2025Review
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- Opening new frontiers with catalytic nucleic acids in miRNA inhibition.Frontiers in pharmacology · 2025Review
- Bulge-Forming miRNases Cleave Oncogenic miRNAs at the Central Loop Region in a Sequence-Specific Manner.International journal of molecular sciences · 2022Article
- Identification of putative microRNAs in the complete genome of Mycobacterium avium and their possible interaction with human transcripts.Journal of applied genetics · 2022Article
- Differential expression of miRNAs in a human developing neuronal cell line chronically infected with Zika virus.The Libyan journal of medicine · 2021Article
- MicroRNAs are minor constituents of extracellular vesicles that are rarely delivered to target cells.PLoS genetics · 2021Article
- Evaluating the Effect of 3'-UTR Variants inCurrent issues in molecular biology · 2021Article
- First passage time in post-transcriptional regulation by multiple small RNAs.The European physical journal. E, Soft matter · 2021Article
- Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers.3 Biotech · 2019Review
- Article
- Unraveling multifaceted contributions of small regulatory RNAs to photomorphogenic development in Arabidopsis.BMC genomics · 2017Article
- Analysis of alternative splicing events for cancer diagnosis using a multiplexing nanophotonic biosensor.Scientific reports · 2017Article
- Identification of MicroRNA Targets ofFrontiers in plant science · 2017Article
- Gene-microRNA network module analysis for ovarian cancer.BMC systems biology · 2016Article
- Pilocarpine-induced seizures trigger differential regulation of microRNA-stability related genes in rat hippocampal neurons.Scientific reports · 2016Article
- Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential.BMC systems biology · 2015Review
- FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts.Nucleic acids research · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 3 institutions in 2 countries.
Funding
Abstract
MicroRNAs (miRNAs) suppress gene expression by forming a duplex with a target messenger RNA (mRNA), blocking translation or initiating cleavage. Computational approaches have proven valuable for predicting which mRNAs can be targeted by a given miRNA, but currently available prediction methods do not address the extent of duplex formation under physiological conditions. Some miRNAs can at low concentrations bind to target mRNAs, whereas others are unlikely to bind within a physiologically relevant concentration range. Here we present a novel approach in which we find potential target sites on mRNA that minimize the calculated free energy of duplex formation, compute the free energy change involved in unfolding these sites, and use these energies to estimate the extent of duplex formation at specified initial concentrations of both species. We compare our predictions to experimentally confirmed miRNA-mRNA interactions (and non-interactions) in Drosophila melanogaster and in human. Although our method does not predict whether the targeted mRNA is degraded and/or its translation to protein inhibited, our quantitative estimates generally track experimentally supported results, indicating that this approach can be used to predict whether an interaction occurs at specified concentrations. Our approach offers a more-quantitative understanding of post-translational regulation in different cell types, tissues, and developmental conditions.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.