ArticleNucleic acids research2014
TargetRNA2: identifying targets of small regulatory RNAs in bacteria.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 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
106 citing papers in PubMed, 203 citations in OpenAlex.
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- Benchmarking the methods for predicting base pairs in RNA-RNA interactions.Bioinformatics (Oxford, England) · 2025Article
- Improving prediction of bacterial sRNA regulatory targets with expression data.NAR genomics and bioinformatics · 2025Article
- GNNs and ensemble models enhance the prediction of new sRNA-mRNA interactions in unseen conditions.BMC bioinformatics · 2025Article
- Sequencing-based analysis of microbiomes.Nature reviews. Genetics · 2024Review
- The Small RNA MicF Represses ObgE and SeqA inMicroorganisms · 2024Article
- Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis.Functional & integrative genomics · 2024Article
- Beyond membrane permeability: A role for the small RNA MicF in regulation of chromosome replication and partitioning.bioRxiv : the preprint server for biology · 2024Article
- Identification and Characterization of Non-protein Coding RNA Homologs inIndian journal of microbiology · 2024Article
- CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.GigaScience · 2024Article
- Devising Isolation Forest-Based Method to Investigate the sRNAome ofBioinformatics and biology insights · 2024Article
- How to do RNA-RNA Interaction Prediction? A Use-Case Driven Handbook Using IntaRNA.Methods in molecular biology (Clifton, N.J.) · 2024Review
- A novel small RNA regulates Locus of Enterocyte Effacement and site-specific colonization of enterohemorrhagicFrontiers in cellular and infection microbiology · 2024Article
- Identification ofVirulence · 2023Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- σeLife · 2023Article
- Small regulatory RNAs are mediators of theJournal of bacteriology · 2023Article
- A thermo-resistant and RNase-sensitive cargo fromJournal of extracellular biology · 2023Article
- Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection.Applied microbiology and biotechnology · 2023Article
46 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Many small, noncoding RNAs (sRNAs) in bacteria act as posttranscriptional regulators of messenger RNAs. TargetRNA2 is a web server that identifies mRNA targets of sRNA regulatory action in bacteria. As input, TargetRNA2 takes the sequence of an sRNA and the name of a sequenced bacterial replicon. When searching for targets of RNA regulation, TargetRNA2 uses a variety of features, including conservation of the sRNA in other bacteria, the secondary structure of the sRNA, the secondary structure of each candidate mRNA target and the hybridization energy between the sRNA and each candidate mRNA target. TargetRNA2 outputs a ranked list of likely regulatory targets for the input sRNA. When evaluated on a comprehensive set of sRNA-target interactions, TargetRNA2 was found to be both accurate and efficient in identifying targets of sRNA regulatory action. Furthermore, TargetRNA2 has the ability to integrate RNA-seq data, if available. If an sRNA is differentially expressed in two or more RNA-seq experiments, TargetRNA2 considers co-differential gene expression when searching for regulatory targets, significantly improving the accuracy of target identifications. The TargetRNA2 web server is freely available for use at http://cs.wellesley.edu/∼btjaden/TargetRNA2.
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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.