ArticlePloS one2018
SeedVicious: Analysis of microRNA target and near-target sites.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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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
17 citing papers in PubMed, 30 citations in OpenAlex.
- The AGO2 adaptor LIMD1 expands the functional and evolutionary reach of microRNA targeting.Science advances · 2026Article
- Analysis of coding gene expression from small RNA sequencing.Genome research · 2026Article
- Decoding microRNA arm switching: a key to evolutionary innovation and gene regulation.Cellular and molecular life sciences : CMLS · 2025Review
- High-throughput microRNA sequencing in the developing branchial arches suggests miR-92b-3p regulation of a cardiovascular gene network.Frontiers in genetics · 2025Article
- Predictive modeling of oocyte maternal mRNA features for five mammalian species reveals potential shared and species-restricted regulators during maturation.Physiological genomics · 2024Article
- Exon-intron split analysis reveals posttranscriptional regulatory signals induced by high and low n-6/n-3 polyunsaturated fatty acid ratio diets in piglets.Journal of animal science · 2023Article
- miR-9a regulates levels of both rhomboid mRNA and protein in the early Drosophila melanogaster embryo.G3 (Bethesda, Md.) · 2022Article
- Differences in PLAToxins · 2022Article
- Urinary microRNAome in healthy cats and cats with pyelonephritis or other urological conditions.PloS one · 2022Article
- Resources and Methods for the Analysis of MicroRNA Function in Drosophila.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Computational Detection of MicroRNA Targets.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Pervasive Selection against MicroRNA Target Sites in Human Populations.Molecular biology and evolution · 2020Article
- Article
- A High-Content Screen Identifies MicroRNAs That Regulate Liver Repopulation After Injury in Mice.Gastroenterology · 2020Article
- The Impact of Population Variation in the Analysis of microRNA Target Sites.Non-coding RNA · 2019Article
- PopTargs: a database for studying population evolutionary genetics of human microRNA target sites.Database : the journal of biological databases and curation · 2019Article
- Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Some analyses suggest that near-target sites may also be functional sites, although there is no conclusive evidence for that, and they may actually be target alleles segregating in a population. SeedVicious does not aim to outperform but to complement existing microRNA prediction tools. For instance, the precision of TargetScan is almost doubled (from 11% to ~20%) when we filter predictions by the distance between target sites using this program. Interestingly, two adjacent canonical target sites are more likely to be present in bona fide target transcripts than pairs of target sites at slightly longer distances. The software is written in Perl and runs on 64-bit Unix computers (Linux and MacOS X). Users with no computing experience can also run the program in a dedicated web-server by uploading custom data, or browse pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license.
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What OpenQuestion holds
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.