ArticleNucleic acids research2011
RNIE: genome-wide prediction of bacterial intrinsic terminators.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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Who cites it
54 citing papers in PubMed, 97 citations in OpenAlex.
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- TerminatorNet: comprehensive identification of intrinsic transcription terminators in bacteria.Bioinformatics (Oxford, England) · 2026Article
- Exploring the regulatory potential of RNA structures in 202 cyanobacterial genomes.Nucleic acids research · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT.Nucleic acids research · 2025Article
- Canonical transcription termination mechanisms explain a minority of operons in cyanobacteria.bioRxiv : the preprint server for biology · 2025Article
- Analysis of 3'-seq data from multiplebioRxiv : the preprint server for biology · 2025Article
- BacTermFinder: a comprehensive and general bacterial terminator finder using a CNN ensemble.NAR genomics and bioinformatics · 2025Article
- Disparate mechanisms counteract extraneous CRISPR RNA production in type II-C CRISPR-Cas systems.microLife · 2025Article
- 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
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.bioRxiv : the preprint server for biology · 2024Article
- CoCas9 is a compact nuclease from the human microbiome for efficient and precise genome editing.Nature communications · 2024Article
- Improved RNA stability estimation through Bayesian modeling reveals mostProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- CryptKeeper: a negative design tool for reducing unintentional gene expression in bacteria.Synthetic biology (Oxford, England) · 2024Article
- Article
- Identification of over ten thousand candidate structured RNAs in viruses and phages.Computational and structural biotechnology journal · 2023Article
- Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data.Nature communications · 2022Article
- Inverse folding based pre-training for the reliable identification of intrinsic transcription terminators.PLoS computational biology · 2022Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.
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