ArticlePLoS computational biology2018
riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.
Article in PLoS computational biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 136 papers.
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Who cites it
136 citing papers in PubMed, 224 citations in OpenAlex.
- RiboBA: a bias-aware probabilistic framework for robust ORF identification across diverse ribosome profiling protocols.Nucleic acids research · 2026Article
- Protocol for ribosome-protected fragment isolation from rare leukemia cell populations.STAR protocols · 2026Article
- Translation fidelity mechanisms and their changes in aging.bioRxiv : the preprint server for biology · 2026Article
- Hepatic translational rewiring in insulin deficiency identifies Reg3α as an insulin-independent glucoregulatory factor.Endocrinology · 2026Article
- Regulation of mRNA poly(A) tail length governs mammalian body plan formation in gastruloids.Nature communications · 2026Article
- Asymmetric RBBP7 regulates the first cell fate decision of early mammalian embryos.Cell discovery · 2026Article
- Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.RNA (New York, N.Y.) · 2026Article
- NNature · 2026Article
- FERONIA Modulates Translational Buffering Capacity of Ribosome-Associated Gene Module in Salt-Stressed Tomato Roots.Plants (Basel, Switzerland) · 2026Article
- SLC15A3-mediated dipeptide metabolism confers antimetabolite resistance in lymphoma via mTORC1 activation.The Journal of clinical investigation · 2026Article
- A plastoglobuli-localized enzyme links phenylalanine biosynthesis to translational homeostasis in maize.Nature communications · 2026Article
- Ribo-Tweezer: Rapid removal of ribosomal proteins reveals additional layers of post-transcriptional gene regulation.Molecular cell · 2026Article
- PIWIL1 activates the R2TP-TELO2-mTORC1 axis independently of piRNA to promote TOP mRNA translation in gastric cancer.Oncogene · 2026Article
- Article
- 2'-O-Methylation maintains ribosome structural and translation integrity.Molecular cell · 2026Article
- Unfolding of RNA secondary structure impairs RNA stability to fine-tune phosphate starvation responses in rice roots.Plant communications · 2026Article
- Genome-wide ribosome profiling reveals a dynamic translational landscape in Arabidopsis seedling roots under simulated microgravity.Communications biology · 2026Article
- Crosstalk between the ribosome quality control-associated E3 ubiquitin ligases LTN1 and RNF10.FEBS letters · 2026Article
- Multi-Tissue Omics Analysis Uncovers Translational Regulation Underlying Complex Traits in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Article
76 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Ribosome profiling is a powerful technique used to study translation at the genome-wide level, generating unique information concerning ribosome positions along RNAs. Optimal localization of ribosomes requires the proper identification of the ribosome P-site in each ribosome protected fragment, a crucial step to determine the trinucleotide periodicity of translating ribosomes, and draw correct conclusions concerning where ribosomes are located. To determine the P-site within ribosome footprints at nucleotide resolution, the precise estimation of its offset with respect to the protected fragment is necessary. Here we present riboWaltz, an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Compared to existing tools, riboWaltz shows improved accuracies for P-site estimation and neat ribosome positioning in multiple case studies. riboWaltz was implemented in R and is available as an R package at https://github.com/LabTranslationalArchitectomics/RiboWaltz.
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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.