ArticleNature structural & molecular biology2020
Quantification of translation uncovers the functions of the alternative transcriptome.
Article in Nature structural & molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 71 citations in OpenAlex.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- Unbiased profiling of translational landscape reveals TNFR2 as a translation-dependent vulnerability in colorectal cancer.Journal of experimental & clinical cancer research : CR · 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
- InspectorORF: a tool for visualizing Ribo-Seq and additional genomic or transcriptomic data.Bioinformatics advances · 2026Article
- Translation Signature Scores: Data-Driven Approach to Assess Evidence for Active Translation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Decoding the Cryptic Proteome Between Antigens and Novel Functional Proteins.European journal of immunology · 2025Review
- Proteogenomic Discovery of Novel Open Reading Frames With HLA Immune Presentation on Human β-Cells.Diabetes · 2025Article
- TheGenome research · 2025Article
- Upstream open reading frame translation enhances immunogenic peptide presentation in mitotically arrested cancer cells.Nature communications · 2025Article
- Proteogenomics Reveals Microproteins in Activated T Cells.Molecular & cellular proteomics : MCP · 2025Article
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Deep learning to decode sites of RNA translation in normal and cancerous tissues.Nature communications · 2025Article
- Micropeptides Encoded by Noncoding RNAs: Biological Functions and Roles in Diseases.Research (Washington, D.C.) · 2025Review
- Steering research on mRNA splicing in cancer towards clinical translation.Nature reviews. Cancer · 2024Review
- Interpreting deep neural networks for the prediction of translation rates.BMC genomics · 2024Article
- Evolution of translational control and the emergence of genes and open reading frames in human and non-human primate hearts.Nature cardiovascular research · 2024Article
- Comparison of software packages for detecting unannotated translated small open reading frames by Ribo-seq.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation has a fundamental function in defining the fate of the transcribed genome. RNA-sequencing (RNA-seq) data enable the quantification of complex transcript mixtures, often detecting several transcript isoforms of unknown functions for one gene. Here, we describe ORFquant, a method to annotate and quantify translation at the level of single open reading frames (ORFs), using information from Ribo-seq data. By developing an approach for transcript filtering, we quantify translation transcriptome-wide, revealing translated ORFs on multiple isoforms per gene. For most genes, one ORF represents the dominant translation product, but we also detect genes with translated ORFs on multiple transcript isoforms, including targets of RNA surveillance mechanisms. Measuring translation across human cell lines reveals the extent of gene-specific differences in protein production, supported by steady-state protein abundance estimates. Computational analysis of Ribo-seq data with ORFquant (https://github.com/lcalviell/ORFquant) provides insights into the heterogeneous functions of complex transcriptomes.
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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.