ArticleNucleic acids research2021
Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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The trial behind it
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
26 citing papers in PubMed.
- 5PSeq Explorer: interactive analysis of co-translational mRNA decay and ribosome dynamics.RNA biology · 2026Article
- Article
- Human SRD5A1 as a case of gene expression indel-resistance in triple-coding region.Genome biology · 2026Article
- TEDD: a comprehensive database for translation efficiency dynamics.Nucleic acids research · 2026Article
- Translation Signature Scores: Data-Driven Approach to Assess Evidence for Active Translation.Methods in molecular biology (Clifton, N.J.) · 2026Article
- RiboMicrobe: An Integrated Translatome Atlas for Microorganism.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Ribosome association inhibits stress-induced gene mRNA localization to stress granules.Genes & development · 2025Article
- Guidelines for minimal reporting requirements, design and interpretation of experiments involving the use of eukaryotic dual gene expression reporters (MINDR).Nature structural & molecular biology · 2025Review
- Ribosome pausing in amylase producing Bacillus subtilis during long fermentation.Microbial cell factories · 2025Article
- Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis.Computational and structural biotechnology journal · 2025Article
- A universal pipeline MosaicProt enables large-scale modeling and detection of chimeric protein sequences for studies on programmed ribosomal frameshifting.Computational and structural biotechnology journal · 2025Article
- Functional Activity of Isoform 2 of Human eRF1.International journal of molecular sciences · 2024Article
- Ribosome decision graphs for the representation of eukaryotic RNA translation complexity.Genome research · 2024Article
- Impact of eIF2α phosphorylation on the translational landscape of mouse embryonic stem cells.Cell reports · 2024Article
- Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity.bioRxiv : the preprint server for biology · 2023Article
- RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.Journal of molecular biology · 2023Article
- The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome.Nucleic acids research · 2023Article
- Ribo-uORF: a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling.Nucleic acids research · 2023Article
- Discovering microproteins: making the most of ribosome profiling data.RNA biology · 2023Review
- Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals.Nature communications · 2022Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Trips-Viz (https://trips.ucc.ie/) is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data. This includes publicly available and user generated data, hence Trips-Viz can be classified as a database and as a server. As a database it provides access to many processed Ribo-Seq and RNA-seq data aligned to reference transcriptomes which has been expanded considerably since its inception. Here, we focus on the server functionality of Trips-viz which also has been greatly improved. Trips-viz now enables visualisation of proteomics data from a large number of processed mass spectrometry datasets. It can be used to support translation inferred from Ribo-Seq data. Users are now able to upload a custom reference transcriptome as well as data types other than Ribo-Seq/RNA-Seq. Incorporating custom data has been streamlined with RiboGalaxy (https://ribogalaxy.ucc.ie/) integration. The other new functionality is the rapid detection of translated open reading frames (ORFs) through a simple easy to use interface. The analysis of differential expression has been also improved via integration of DESeq2 and Anota2seq in addition to a number of other improvements of existing Trips-viz features.
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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.