ArticleNature methods2016
Detecting actively translated open reading frames in ribosome profiling data.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 276 papers.
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Who cites it
276 citing papers in PubMed.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue.Nature communications · 2026Article
- Overlapping upstream ORFs repress translation and expand proteome diversity in Arabidopsis.bioRxiv : the preprint server for biology · 2026Article
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 2026Article
- Inferring translational efficiency from transcriptomes improves noncanonical neoantigen prioritization and cancer patient stratification.NPJ precision oncology · 2026Article
- Computational identification and characterization of noncoding RNA-encoded peptides: tools, databases, and in silico strategies.Amino acids · 2026Review
- seq2ribo: Structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.bioRxiv : the preprint server for biology · 2026Article
- Maize Anther Development Involves Translated Open Reading Frames From 3' Untranslated Regions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- An expanded reference catalog of translated open reading frames for biomedical research.Nucleic acids research · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- cncFinder: A graph-attention-network-based interpretable learning model to identify bifunctional long non-coding RNAs.Molecular therapy. Nucleic acids · 2026Article
- NLRSeek: A reannotation-based pipeline for mining missing NLR genes in sequenced genomes.aBIOTECH · 2026Article
- Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).Genome biology and evolution · 2026Article
- A Global Assessment of the Transcription-Dependent Single Nucleotide Variants Relies on the Characteristics of RNA-Sequencing Technologies.Biomolecules · 2026Article
- Translation Signature Scores: Data-Driven Approach to Assess Evidence for Active Translation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Identification and Characterization of Microproteins/ MicroORFs.Methods in molecular biology (Clifton, N.J.) · 2026Article
- InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data.Bioinformatics advances · 2026Article
- Identifying and Visualizing Novel Small Open Reading Frames (sORFs) Via Ribo-Seq, Transcriptome Assembly, and ggRibo.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Codon deoptimization of multispecific biologics reduces mispairing during transient mammalian protein expression.Frontiers in bioengineering and biotechnology · 2026Article
- eIF3d and eIF3e mediate selective translational control of hypoxia that can be inhibited by small molecules.Cell reports · 2025Article
216 more citing papers are in PubMed but not listed here.
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Funding
Abstract
RNA-sequencing protocols can quantify gene expression regulation from transcription to protein synthesis. Ribosome profiling (Ribo-seq) maps the positions of translating ribosomes over the entire transcriptome. We have developed RiboTaper (available at https://ohlerlab.mdc-berlin.de/software/), a rigorous statistical approach that identifies translated regions on the basis of the characteristic three-nucleotide periodicity of Ribo-seq data. We used RiboTaper with deep Ribo-seq data from HEK293 cells to derive an extensive map of translation that covered open reading frame (ORF) annotations for more than 11,000 protein-coding genes. We also found distinct ribosomal signatures for several hundred upstream ORFs and ORFs in annotated noncoding genes (ncORFs). Mass spectrometry data confirmed that RiboTaper achieved excellent coverage of the cellular proteome. Although dozens of novel peptide products were validated in this manner, few of the currently annotated long noncoding RNAs appeared to encode stable polypeptides. RiboTaper is a powerful method for comprehensive de novo identification of actively used ORFs from Ribo-seq data.
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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.