ArticleNature communications2023
grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Drug-induced metabolic remodeling promotes antimicrobial activity in macrophages and extends longevity in vivo.Life science alliance · 2026Article
- Spatial mapping of RNA turnover kinetics in the mouse brain.Nature neuroscience · 2026Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Ageing alters cysteine oxidation-regulated redox signalling in skeletal muscle: Integrative omics and AI-based structural predictions.Experimental physiology · 2026Article
- Nascent transcriptome of embryonic genome activation reveals a regulatory axis linking transcriptional priming to early lineage specification in mouse embryos.Nucleic acids research · 2026Article
- thematicGO: A Keyword-Based Framework for Interpreting Gene Ontology Enrichment via Biological Themes.bioRxiv : the preprint server for biology · 2026Article
- Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain.bioRxiv : the preprint server for biology · 2026Article
- Exonuclease ISG20 inhibits human cytomegalovirus replication by inducing an innate immune defense signature.PLoS pathogens · 2026Article
- Article
- TDP-43 loss induces cryptic polyadenylation in ALS/FTD.Nature neuroscience · 2025Article
- mRNA turnover dynamics are affected by cell differentiation and loss of the cytosine methyltransferase Nsun2.Nucleic acids research · 2025Article
- RNA-mediated condensation of TFE3 oncofusions facilitates transcriptional hub formation to promote translocation renal cell carcinoma.Nature communications · 2025Article
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Drug-induced metabolic remodeling of immune cell repertoire generates an effective broad-range antimicrobial effect.Research square · 2025Article
- mCell · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- SLAM-seq reveals independent contributions of RNA processing and stability to gene expression in African trypanosomes.Nucleic acids research · 2025Article
- Non-redundant roles for the human mRNA decapping cofactor paralogs DCP1a and DCP1b.Life science alliance · 2024Article
- Metabolic RNA Labeling and Translating Ribosome Affinity Purification for Measurement of Nascent RNA Translation.Bio-protocol · 2024Article
- Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data.Nucleic acids research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metabolic labeling of RNA is a powerful technique for studying the temporal dynamics of gene expression. Nucleotide conversion approaches greatly facilitate the generation of data but introduce challenges for their analysis. Here we present grandR, a comprehensive package for quality control, differential gene expression analysis, kinetic modeling, and visualization of such data. We compare several existing methods for inference of RNA synthesis rates and half-lives using progressive labeling time courses. We demonstrate the need for recalibration of effective labeling times and introduce a Bayesian approach to study the temporal dynamics of RNA using snapshot experiments.
Indexed as
Identifiers
What OpenQuestion holds
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.