ArticleNucleic acids research2016
RPFdb: a database for genome wide information of translated mRNA generated from ribosome profiling.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 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
29 citing papers in PubMed, 70 citations in OpenAlex.
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- riboCIRC v2.0: an expanded resource for translatable CircRNAs.Nucleic acids research · 2026Article
- AUGcontext DB: a comprehensive catalog of the mRNA AUG initiator codon context across eukaryotes.RNA biology · 2025Review
- Deep generative optimization of mRNA codon sequences for enhanced mRNA translation and therapeutic efficacy.Nature communications · 2025Article
- Translatomics to explore dynamic differences in immunocytes in the tumor microenvironment.Molecular therapy. Nucleic acids · 2023Review
- What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?Molecular & cellular proteomics : MCP · 2023Article
- What can Ribo-seq and proteomics tell us about the non-canonical proteome?bioRxiv : the preprint server for biology · 2023Article
- Micropeptides translated from putative long non-coding RNAs.Acta biochimica et biophysica Sinica · 2022Review
- Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.BMC biology · 2021Article
- OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes.Nucleic acids research · 2021Article
- Unveiling a Ghost Proteome in the Glioblastoma Non-Coding RNAs.Frontiers in cell and developmental biology · 2021Review
- Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast.Scientific reports · 2019Article
- RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling.Nucleic acids research · 2019Article
- Trips-Viz: a transcriptome browser for exploring Ribo-Seq data.Nucleic acids research · 2019Article
- PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data.RNA (New York, N.Y.) · 2018Article
- Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship.Genome research · 2018Review
- An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.Nucleic acids research · 2018Article
- TranslatomeDB: a comprehensive database and cloud-based analysis platform for translatome sequencing data.Nucleic acids research · 2018Article
- HRPDviewer: human ribosome profiling data viewer.Database : the journal of biological databases and curation · 2018Article
- An RNA structure-mediated, posttranscriptional model of human α-1-antitrypsin expression.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
Abstract
Translational control is crucial in the regulation of gene expression and deregulation of translation is associated with a wide range of cancers and human diseases. Ribosome profiling is a technique that provides genome wide information of mRNA in translation based on deep sequencing of ribosome protected mRNA fragments (RPF). RPFdb is a comprehensive resource for hosting, analyzing and visualizing RPF data, available at www.rpfdb.org or http://sysbio.sysu.edu.cn/rpfdb/index.html. The current version of database contains 777 samples from 82 studies in 8 species, processed and reanalyzed by a unified pipeline. There are two ways to query the database: by keywords of studies or by genes. The outputs are presented in three levels. (i) Study level: including meta information of studies and reprocessed data for gene expression of translated mRNAs; (ii) Sample level: including global perspective of translated mRNA and a list of the most translated mRNA of each sample from a study; (iii) Gene level: including normalized sequence counts of translated mRNA on different genomic location of a gene from multiple samples and studies. To explore rich information provided by RPF, RPFdb also provides a genome browser to query and visualize context-specific translated mRNA. Overall our database provides a simple way to search, analyze, compare, visualize and download RPF data sets.
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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.