ArticleNucleic acids research2018
De novo annotation and characterization of the translatome with ribosome profiling data.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 103 papers.
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Who cites it
103 citing papers in PubMed.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Protocol for ribosome-protected fragment isolation from rare leukemia cell populations.STAR protocols · 2026Article
- FERONIA Modulates Translational Buffering Capacity of Ribosome-Associated Gene Module in Salt-Stressed Tomato Roots.Plants (Basel, Switzerland) · 2026Article
- Translational resistance to amino acid starvation in breast cancer cells revealed by ribosome profiling.iScience · 2026Article
- The translation landscape of ovarian clear cell carcinoma indicates that RBM4 plays a pro-oncogenic role in tumor progression.Oncogene · 2026Article
- RNA helicase DHX29 controls the translation of transcription factors involved in germinal center response and plasma cell differentiation in mice.The EMBO journal · 2026Article
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 2026Article
- A Proteogenomic Approach to Discover Novel lncRNA-Derived Microproteins and Their Potential Clinical Utility in Hepatocellular Carcinoma.Molecular & cellular proteomics : MCP · 2026Article
- Article
- Single-oocyte full-length isoform sequencing unveils the impact of transposable elements on RNA diversity and stability.Nature communications · 2026Article
- 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
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The birth, death, and evolutionary compensation of uORFs in Drosophila.Nucleic acids research · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Eukaryote initiation factor 6 modulates small-cell lung carcinoma plasticity via the integrin-FAK signaling axis.Nature communications · 2026Article
- Integrative profiling of condensation-prone RNAs during early development.Cell genomics · 2026Article
- EIF5A Couples Translational Control With Transcriptional Reprogramming Through Chromocenter Reorganization During Spermiogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- AI-powered mapping of tumor immunity for optimized mRNA vaccine engineering.Frontiers in oncology · 2026Review
- Translation Signature Scores: Data-Driven Approach to Assess Evidence for Active Translation.Methods in molecular biology (Clifton, N.J.) · 2026Article
43 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
By capturing and sequencing the RNA fragments protected by translating ribosomes, ribosome profiling provides snapshots of translation at subcodon resolution. The growing needs for comprehensive annotation and characterization of the context-dependent translatomes are calling for an efficient and unbiased method to accurately recover the signal of active translation from the ribosome profiling data. Here we present our new method, RiboCode, for such purpose. Being tested with simulated and real ribosome profiling data, and validated with cell type-specific QTI-seq and mass spectrometry data, RiboCode exhibits superior efficiency, sensitivity, and accuracy for de novo annotation of the translatome, which covers various types of ORFs in the previously annotated coding and non-coding regions. As an example, RiboCode was applied to assemble the context-specific translatomes of yeast under normal and stress conditions. Comparisons among these translatomes revealed stress-activated novel upstream and downstream ORFs, some of which are associated with translational dysregulations of the annotated main ORFs under the stress conditions.
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