ArticleBioinformatics (Oxford, England)2017
Riborex: fast and flexible identification of differential translation from Ribo-seq data.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
- Posttranscriptional reprogramming controls MASLD progression through chronic ER stress adaptation.Science advances · 2026Article
- RBM15B recognizes H3K79me2 to guide selective mThe EMBO journal · 2026Article
- Mammalian tRNA acetylation determines translation efficiency and tRNA quality control.Nature communications · 2025Article
- Species-specific circular RNA circDS-1 enhances adaptive evolution in Talaromyces marneffei through regulation of dimorphic transition.PLoS genetics · 2025Article
- G3BP isoforms differentially affect stress granule assembly and gene expression during cellular stress.Molecular biology of the cell · 2024Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Article
- Next generation sequencing technologies to address aberrant mRNA translation in cancer.NAR cancer · 2024Review
- Translation initiation factor eIF1.2 promotes Toxoplasma stage conversion by regulating levels of key differentiation factors.Nature communications · 2024Article
- Promoter recruitment drives the emergence of proto-genes in a long-term evolution experiment with Escherichia coli.PLoS biology · 2024Article
- A hidden translatome in tumors-the coding lncRNAs.Science China. Life sciences · 2023Review
- Genome-wide translational response ofMicrobiology spectrum · 2023Article
- Kaposi's sarcoma-associated herpesvirus induces specialised ribosomes to efficiently translate viral lytic mRNAs.Nature communications · 2023Article
- The landscape of transcriptional and translational changes over 22 years of bacterial adaptation.eLife · 2022Article
- Review
- Introduction to Bioinformatics Resources for Post-transcriptional Regulation of Gene Expression.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Microtubule integrity regulates budding yeast RAM pathway gene expression.Frontiers in cell and developmental biology · 2022Article
- Differential translation elongation directs protein synthesis in response to acute glucose deprivation in yeast.RNA biology · 2022Article
- Ribosome profiling analysis of human skeletal muscle identifies reduced translation of mitochondrial proteins with age.RNA biology · 2021Article
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5 authors.
Funding
Abstract
motivationGlobal analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample. Measurements of translation efficiency are generated when Ribo-seq data is analyzed in combination with matched RNA-seq gene expression profiles. Existing computational methods for identifying genes with differential translation across samples are based on sound principles, but require users to choose between accuracy and speed.
resultsWe present Riborex, a computational tool for mapping genome-wide differences in translation efficiency. Riborex shares a similar mathematical structure with existing methods, but has a simplified implementation. Riborex directly leverages established RNA-seq analysis frameworks for all parameter estimation, providing users with a choice among robust engines for these computations. The result is a method that is dramatically faster than available methods without sacrificing accuracy. AVAILABILITY AND IMPLEMENTATION: https://github.com/smithlabcode/riborex. CONTACT: andrewds@usc.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.