ArticleGenome biology2023
TargetRNA3: predicting prokaryotic RNA regulatory targets with machine learning.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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.
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Who cites it
22 citing papers in PubMed, 22 citations in OpenAlex.
- Inducible Protein Knockdown via Engineered Small RNAs in Chlamydia.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Two coinfecting archaeal viruses provide insights into virus-virus interactions.Communications biology · 2026Article
- CRISPRi and beyond: studying essential gene function in the obligate intracellular bacteriumJournal of bacteriology · 2026Review
- PhuS conformational dynamics are essential for DNA binding and heme-responsive control of the prrF operon in Pseudomonas aeruginosa.The Journal of biological chemistry · 2026Article
- Analysis of Human miRNA Derived From Bladder Epithelial Cells Infected With Uropathogenic Escherichia coli.APMIS : acta pathologica, microbiologica, et immunologica Scandinavica · 2026Article
- Machine Learning Approaches for Predicting RNA-RNA/DNA Interactions.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Assessing the conservation and targets of putative sRNAs inMicrobiology spectrum · 2025Article
- Article
- What makes a small RNA work?Nucleic acids research · 2025Review
- 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
- Tiny but Mighty: Small RNAs-The Micromanagers of Bacterial Survival, Virulence, and Host-Pathogen Interactions.Non-coding RNA · 2025Review
- Article
- Article
- Comparative Transcriptomics Reveal Differential Expression of Coding and Non-Coding RNAs in Clinical Strains ofInternational journal of molecular sciences · 2024Article
- RNA Metabolism and the Role of Small RNAs in Regulating Multiple Aspects of RNA Metabolism.Non-coding RNA · 2024Review
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
- Quantitative mapping of pseudouridines in bacteria RNA.bioRxiv : the preprint server for biology · 2024Article
- sRNAdeep: a novel tool for bacterial sRNA prediction based on DistilBERT encoding mode and deep learning algorithms.BMC genomics · 2024Article
- Strain ofPlants (Basel, Switzerland) · 2024Article
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Small regulatory RNAs pervade prokaryotes, with the best-studied family of these non-coding genes corresponding to trans-acting regulators that bind via base pairing to their message targets. Given the increasing frequency with which these genes are being identified, it is important that methods for illuminating their regulatory targets keep pace. Using a machine learning approach, we investigate thousands of interactions between small RNAs and their targets, and we interrogate more than a hundred features indicative of these interactions. We present a new method, TargetRNA3, for predicting targets of small RNA regulators and show that it outperforms existing approaches. TargetRNA3 is available at https://cs.wellesley.edu/~btjaden/TargetRNA3 .
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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.