ArticleNature communications2016
Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
74 citing papers in PubMed.
- Ribo-seq rRNA reads reveal co-predicted signatures of ribosome heterogeneity and collisions.Briefings in bioinformatics · 2026Article
- RPL41 stabilizes ribosome dynamics and supports long-protein homeostasis in mammals.Nucleic acids research · 2026Article
- Approaches for Studying Context Specificity of Translation Inhibitor Action.International journal of molecular sciences · 2026Review
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 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
- Conditional deep learning model reveals translation elongation determinants during amino acid deprivation.Communications biology · 2025Article
- Capturing Translation in Action with Protein Synthesis Profiling.bioRxiv : the preprint server for biology · 2025Article
- Ageing-related decline of translation as a consequence of transcription dysregulation.Journal of the Royal Society, Interface · 2025Article
- Sequencing technologies to measure translation in single cells.Nature reviews. Molecular cell biology · 2025Review
- Ribosome profiling reveals differences in global translational vs transcriptional gene expression changes during earlyMicrobiology spectrum · 2025Article
- Evaluation of Eukaryotic mRNA Coding Potential.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer.Nucleic acids research · 2024Article
- Riboformer: a deep learning framework for predicting context-dependent translation dynamics.Nature communications · 2024Article
- Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control.Wellcome open research · 2024Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.Nature communications · 2023Article
- choros: correction of sequence-based biases for accurate quantification of ribosome profiling data.bioRxiv : the preprint server for biology · 2023Article
- A critical period of translational control during brain development at codon resolution.Nature structural & molecular biology · 2022Article
- Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles.Nucleic acids research · 2022Article
- Review
14 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Ribosome profiling (Ribo-seq), a promising technology for exploring ribosome decoding rates, is characterized by the presence of infrequent high peaks in ribosome footprint density and by long alignment gaps. Here, to reduce the impact of data heterogeneity we introduce a simple normalization method, Ribo-seq Unit Step Transformation (RUST). RUST is robust and outperforms other normalization techniques in the presence of heterogeneous noise. We illustrate how RUST can be used for identifying mRNA sequence features that affect ribosome footprint densities globally. We show that a few parameters extracted with RUST are sufficient for predicting experimental densities with high accuracy. Importantly the application of RUST to 30 publicly available Ribo-seq data sets revealed a substantial variation in sequence determinants of ribosome footprint frequencies, questioning the reliability of Ribo-seq as an accurate representation of local ribosome densities without prior quality control. This emphasizes our incomplete understanding of how protocol parameters affect ribosome footprint densities.
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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.