ArticleF1000Research2016
RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing.
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 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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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
42 citing papers in PubMed.
- NAT10 maintains stem cell homeostasis by mitigating mRNA decay through an acNature cell biology · 2026Article
- Unbiased profiling of translational landscape reveals TNFR2 as a translation-dependent vulnerability in colorectal cancer.Journal of experimental & clinical cancer research : CR · 2026Article
- Micropeptides in the oncological dark matter: decoding their roles in tumor progression and therapy resistance.Journal of translational medicine · 2025Review
- RNA-seq and Ribosome Profiling Reveal the Translational Landscape of Rice in Response to Rice Stripe Virus Infection.Viruses · 2024Article
- Deciphering the Functional Long Non-Coding RNAs Derived from MicroRNA Loci.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- The translation initiation factor homolog eif4e1c regulates cardiomyocyte metabolism and proliferation during heart regeneration.Development (Cambridge, England) · 2023Article
- Tumor suppressor mediated ubiquitylation of hnRNPK is a barrier to oncogenic translation.Nature communications · 2022Article
- Review
- Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.EMBO reports · 2022Article
- The effects of NCBP3 on METTL3-mediated m6A RNA methylation to enhance translation process in hypoxic cardiomyocytes.Journal of cellular and molecular medicine · 2021Article
- Genome-Scale Analysis of Acetobacterium woodii Identifies Translational Regulation of Acetogenesis.mSystems · 2021Article
- Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.Nucleic acids research · 2021Article
- ORFik: a comprehensive R toolkit for the analysis of translation.BMC bioinformatics · 2021Article
- A tool for analyzing and visualizing ribo-seq data at the isoform level.BMC bioinformatics · 2021Article
- RiboA: a web application to identify ribosome A-site locations in ribosome profiling data.BMC bioinformatics · 2021Article
- Translational landscape and protein biogenesis demands of the early secretory pathway in Komagataella phaffii.Microbial cell factories · 2021Article
- Codon Resolution Analysis of Ribosome Profiling Data.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes.Molecular therapy. Nucleic acids · 2020Article
- RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.Nucleic acids research · 2020Article
- What determines eukaryotic translation elongation: recent molecular and quantitative analyses of protein synthesis.Open biology · 2020Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially translated transcripts under different experimental conditions, and/or ribosome pausing on codon motifs. In the context of the ever-growing need for tools analyzing Ribo-seq reads, we have developed 'RiboProfiling', a new Bioconductor open-source package. 'RiboProfiling' provides a full pipeline to cover all key steps for the analysis of ribosome footprints. This pipeline has been implemented in a single R workflow. The package takes an alignment (BAM) file as input and performs ribosome footprint quantification at a transcript level. It also identifies footprint accumulation on particular amino acids or multi amino-acids motifs. Report summary graphs and data quantification are generated automatically. The package facilitates quality assessment and quantification of Ribo-seq experiments. Its implementation in Bioconductor enables the modeling and statistical analysis of its output through the vast choice of packages available in R. This article illustrates how to identify codon-motifs accumulating ribosome footprints, based on data from Escherichia coli.
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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.