ArticleBMC bioinformatics2020
RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.
Article in BMC bioinformatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Translational resistance to amino acid starvation in breast cancer cells revealed by ribosome profiling.iScience · 2026Article
- RNA helicase DHX29 controls the translation of transcription factors involved in germinal center response and plasma cell differentiation in mice.The EMBO journal · 2026Article
- Mechanism of RACK1-dependent ZAKα activation at stalled and collided ribosomes.Molecular cell · 2026Article
- Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.RNA (New York, N.Y.) · 2026Article
- Eukaryote initiation factor 6 modulates small-cell lung carcinoma plasticity via the integrin-FAK signaling axis.Nature communications · 2026Article
- EIF5A Couples Translational Control With Transcriptional Reprogramming Through Chromocenter Reorganization During Spermiogenesis.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Degradation factor 1, Def1, regulates mRNA translation and decay through Ccr4-Not-dependent ubiquitylation of the ribosome.bioRxiv : the preprint server for biology · 2025Article
- Serine tRNAs compete to regulate the mRNA translation of serine-sensitive codons.Science advances · 2025Article
- Codon-specific ribosome stalling reshapes translational dynamics during branched-chain amino acid starvation.Genome biology · 2025Article
- A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay.Nature communications · 2025Article
- Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review.Briefings in bioinformatics · 2024Review
- Alternative translation initiation produces synaptic organizer proteoforms with distinct localization and functions.Molecular cell · 2024Article
- SMYD5 is a ribosomal methyltransferase that catalyzes RPL40 lysine methylation to enhance translation output and promote hepatocellular carcinoma.Cell research · 2024Article
- Next generation sequencing technologies to address aberrant mRNA translation in cancer.NAR cancer · 2024Review
- MetageneCluster: a Python package for filtering conflicting signal trends in metagene plots.BMC bioinformatics · 2024Article
- Article
- Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development.Nature cell biology · 2022Article
- Cellular responses to halofuginone reveal a vulnerability of the GCN2 branch of the integrated stress response.The EMBO journal · 2022Article
- Pan-cancer analyses of synonymous mutations based on tissue-specific codon optimality.Computational and structural biotechnology journal · 2022Article
- HRIBO: high-throughput analysis of bacterial ribosome profiling data.Bioinformatics (Oxford, England) · 2021Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundRibosome profiling has been widely used for studies of translation under a large variety of cellular and physiological contexts. Many of these studies have greatly benefitted from a series of data-mining tools designed for dissection of the translatome from different aspects. However, as the studies of translation advance quickly, the current toolbox still falls in short, and more specialized tools are in urgent need for deeper and more efficient mining of the important and new features of the translation landscapes.
resultsHere, we present RiboMiner, a bioinformatics toolset for mining of multi-dimensional features of the translatome with ribosome profiling data. RiboMiner performs extensive quality assessment of the data and integrates a spectrum of tools for various metagene analyses of the ribosome footprints and for detailed analyses of multiple features related to translation regulation. Visualizations of all the results are available. Many of these analyses have not been provided by previous methods. RiboMiner is highly flexible, as the pipeline could be easily adapted and customized for different scopes and targets of the studies.
conclusionsApplications of RiboMiner on two published datasets did not only reproduced the main results reported before, but also generated novel insights into the translation regulation processes. Therefore, being complementary to the current tools, RiboMiner could be a valuable resource for dissections of the translation landscapes and the translation regulations by mining the ribosome profiling data more comprehensively and with higher resolution. RiboMiner is freely available at https://github.com/xryanglab/RiboMiner and https://pypi.org/project/RiboMiner .
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