ArticleLife (Basel, Switzerland)2021
RiboNT: A Noise-Tolerant Predictor of Open Reading Frames from Ribosome-Protected Footprints.
Article in Life (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 13 citations in OpenAlex.
- Text mining reveals the increasing importance of genomic approaches in crop research and breeding.Molecular breeding : new strategies in plant improvement · 2025Review
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Review
- slORFfinder: a tool to detect open reading frames resulting from trans-splicing of spliced leader sequences.Briefings in bioinformatics · 2023Article
- Discovering microproteins: making the most of ribosome profiling data.RNA biology · 2023Review
- Identification of short open reading frames in plant genomes.Frontiers in plant science · 2023Review
- Peptidomics Methods Applied to the Study of Flower Development.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Three-nucleotide periodicity of nucleotide diversity in a population enables the identification of open reading frames.Briefings in bioinformatics · 2022Article
- Small open reading frames in plant research: from prediction to functional characterization.3 Biotech · 2022Review
- Life: Computational Genomics Applications in Life Sciences.Life (Basel, Switzerland) · 2021Article
- Small Open Reading Frames, How to Find Them and Determine Their Function.Frontiers in genetics · 2021Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Ribo-seq, also known as ribosome profiling, refers to the sequencing of ribosome-protected mRNA fragments (RPFs). This technique has greatly advanced our understanding of translation and facilitated the identification of novel open reading frames (ORFs) within untranslated regions or non-coding sequences as well as the identification of non-canonical start codons. However, the widespread application of Ribo-seq has been hindered because obtaining periodic RPFs requires a highly optimized protocol, which may be difficult to achieve, particularly in non-model organisms. Furthermore, the periodic RPFs are too short (28 nt) for accurate mapping to polyploid genomes, but longer RPFs are usually produced with a compromise in periodicity. Here we present RiboNT, a noise-tolerant ORF predictor that can utilize RPFs with poor periodicity. It evaluates RPF periodicity and automatically weighs the support from RPFs and codon usage before combining their contributions to identify translated ORFs. The results demonstrate the utility of RiboNT for identifying both long and small ORFs using RPFs with either good or poor periodicity. We implemented the pipeline on a dataset of RPFs with poor periodicity derived from membrane-bound polysomes of
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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.