ArticleBioinformatics (Oxford, England)2017
RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
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 115 papers.
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Who cites it
115 citing papers in PubMed.
- RPL41 stabilizes ribosome dynamics and supports long-protein homeostasis in mammals.Nucleic acids research · 2026Article
- Mutant KRAS-driven selective mRNA translation reveals mechanisms and therapeutic vulnerabilities in cancer.Cell reports · 2026Article
- Targeting eIF4A-dependent translation in genetically complex sarcoma.JCI insight · 2026Article
- 2'-O-Methylation maintains ribosome structural and translation integrity.Molecular cell · 2026Article
- Translational buffering tunes gene expression in mice and humans.Genome biology · 2026Article
- Coronaviruses reprogram the tRNA epitranscriptome to favor viral protein expression.Nature communications · 2026Article
- KnockRBP: an integrated multi-omics database of functional perturbation profiles for RNA-binding proteins.Nucleic acids research · 2026Article
- eIF2D promotes 40S ribosomal subunit recycling during intrinsic ribosome destabilization.Nucleic acids research · 2025Article
- Translational regulation plasticity shapes wheat grain adaptation to heat stress.Genome biology · 2025Article
- Article
- Optimised Ribosome Profiling Reveals New Insights Into Translational Regulation in Synchronised Chlamydomonas reinhardtii Cultures.Plant, cell & environment · 2025Article
- Ribo-Seq Analysis-Based Elucidation of the Dynamic Translation Landscape of Yak Ovarian Tissues in Different Reproductive Stages.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Comparative Analysis of Testicular Transcriptional and Translational Landscapes in Yak and Cattle-Yak: Implications for Hybrid Male Sterility.Biomolecules · 2025Article
- Lysyl-tRNA synthetase orchestrates translation and hormone signaling during reproduction in Aedes aegypti mosquitoes.Communications biology · 2025Article
- The m6A demethylase FTO promotes C/EBPβ-LIP translation to perform oncogenic functions in breast cancer cells.The FEBS journal · 2025Article
- Chloroplast precursor protein preClpD overaccumulation triggers multilevel reprogramming of gene expression and a heat shock-like response.Nature communications · 2025Article
- Article
- Ribosome profiling and single-cell RNA sequencing identify the unfolded protein response as a key regulator of pigeon lactation.Zoological research · 2025Article
- NAC regulates metabolism and cell fate in intestinal stem cells.Science advances · 2025Article
- New insights into the efficient secretion of foreign protein in Bacillus subtilis via Ribo-seq and RNA-seq integrative analyses.BMC microbiology · 2024Article
55 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
motivationDeep sequencing based ribosome footprint profiling can provide novel insights into the regulatory mechanisms of protein translation. However, the observed ribosome profile is fundamentally confounded by transcriptional activity. In order to decipher principles of translation regulation, tools that can reliably detect changes in translation efficiency in case-control studies are needed.
resultsWe present a statistical framework and an analysis tool, RiboDiff, to detect genes with changes in translation efficiency across experimental treatments. RiboDiff uses generalized linear models to estimate the over-dispersion of RNA-Seq and ribosome profiling measurements separately, and performs a statistical test for differential translation efficiency using both mRNA abundance and ribosome occupancy. AVAILABILITY AND IMPLEMENTATION: RiboDiff webpage http://bioweb.me/ribodiff Source code including scripts for preprocessing the FASTQ data are available at http://github.com/ratschlab/ribodiff CONTACTS: zhongy@cbio.mskcc.org or raetsch@inf.ethz.chSupplementary 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.