ArticleBioinformatics (Oxford, England)2016
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
27 citing papers in PubMed.
- 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
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data.bioRxiv : the preprint server for biology · 2025Article
- RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling.Briefings in bioinformatics · 2025Article
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Long-read sequencing for 29 immune cell subsets reveals disease-linked isoforms.Nature communications · 2024Article
- Uncovering the impacts of alternative splicing on the proteome with current omics techniques.Wiley interdisciplinary reviews. RNA · 2022Review
- A tool for analyzing and visualizing ribo-seq data at the isoform level.BMC bioinformatics · 2021Article
- Control of translation by eukaryotic mRNA transcript leaders-Insights from high-throughput assays and computational modeling.Wiley interdisciplinary reviews. RNA · 2021Review
- RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.Nucleic acids research · 2020Article
- Quantification of translation uncovers the functions of the alternative transcriptome.Nature structural & molecular biology · 2020Article
- Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome.Nature communications · 2020Article
- Accurate annotation of human protein-coding small open reading frames.Nature chemical biology · 2020Article
- XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.PLoS computational biology · 2020Article
- Multimapping confounds ribosome profiling analysis: A case-study of the Hsp90 molecular chaperone.Proteins · 2020Article
- DeepShape: estimating isoform-level ribosome abundance and distribution with Ribo-seq data.BMC bioinformatics · 2019Article
- CDK12 phosphorylates 4E-BP1 to enable mTORC1-dependent translation and mitotic genome stability.Genes & development · 2019Article
- Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.Journal of proteome research · 2018Article
- The exon-intron gene structure upstream of the initiation codon predicts translation efficiency.Nucleic acids research · 2018Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
unlabelled: Ribosome profiling is a recently developed high-throughput sequencing technique that captures approximately 30 bp long ribosome-protected mRNA fragments during translation. Because of alternative splicing and repetitive sequences, a ribosome-protected read may map to many places in the transcriptome, leading to discarded or arbitrary mappings when standard approaches are used. We present a technique and software that addresses this problem by assigning reads to potential origins proportional to estimated transcript abundance. This yields a more accurate estimate of ribosome profiles compared with a naïve mapping. AVAILABILITY AND IMPLEMENTATION: Ribomap is available as open source at http://www.cs.cmu.edu/∼ckingsf/software/ribomap CONTACT: carlk@cs.cmu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.