ArticleNucleic acids research2020
RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed.
- PIWIL1 activates the R2TP-TELO2-mTORC1 axis independently of piRNA to promote TOP mRNA translation in gastric cancer.Oncogene · 2026Article
- Deciphering tRNA repertoires and translation coordination during mouse early embryogenesis by ORACLE-tRNAseq.Nature communications · 2026Article
- Ribosome Molecular Aging Shapes Translation Dynamics.bioRxiv : the preprint server for biology · 2026Article
- Targeting tRNA-Arg-TCT-4-1 suppresses cancer cell growth and tumorigenesis.bioRxiv : the preprint server for biology · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The tRNA Editing Complex ADAT2/3 Promotes Cancer Cell Growth and Codon-biased mRNA Translation.Journal of molecular biology · 2025Article
- ribofootPrinter: A precision python toolbox for analysis of ribosome profiling data.bioRxiv : the preprint server for biology · 2025Article
- Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.Molecular cancer · 2025Review
- Extensive location bias of the GPCR-dependent translatome via site-selective activation of mTOR.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.International journal of molecular sciences · 2025Article
- The transcriptional and translational landscape of HCoV-OC43 infection.PLoS pathogens · 2025Article
- Phosphorylation of P-stalk proteins defines the ribosomal state for interaction with auxiliary protein factors.EMBO reports · 2024Article
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- Article
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Disruption of tRNA biogenesis enhances proteostatic resilience, improves later-life health, and promotes longevity.PLoS biology · 2024Article
- Metabolic rewiring during bone development underlies tRNA m7G-associated primordial dwarfism.The Journal of clinical investigation · 2024Article
- The tRNA Gm18 methyltransferase TARBP1 promotes hepatocellular carcinoma progression via metabolic reprogramming of glutamine.Cell death and differentiation · 2024Article
- mNature communications · 2024Article
- Extensive location bias of the GPCR-dependent translatome via site-selective activation of mTOR.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Ribosome profiling (Ribo-seq) is a powerful technology for globally monitoring RNA translation; ranging from codon occupancy profiling, identification of actively translated open reading frames (ORFs), to the quantification of translational efficiency under various physiological or experimental conditions. However, analyzing and decoding translation information from Ribo-seq data is not trivial. Although there are many existing tools to analyze Ribo-seq data, most of these tools are designed for specific or limited functionalities and an easy-to-use integrated tool to analyze Ribo-seq data is lacking. Fortunately, the small size (26-34 nt) of ribosome protected fragments (RPFs) in Ribo-seq and the relatively small amount of sequencing data greatly facilitates the development of such a web platform, which is easy to manipulate for users with or without bioinformatic expertise. Thus, we developed RiboToolkit (http://rnabioinfor.tch.harvard.edu/RiboToolkit), a convenient, freely available, web-based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs. Besides, easy-to-use web interfaces were developed to facilitate data analysis and intuitively visualize results. Thus, RiboToolkit will greatly facilitate the study of mRNA translation based on ribosome profiling.
Indexed as
Identifiers
What OpenQuestion holds
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.