ArticleRNA (New York, N.Y.)2023
bakR: uncovering differential RNA synthesis and degradation kinetics transcriptome-wide with Bayesian hierarchical modeling.
Article in RNA (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Article
- Uncovering the isoform-resolution kinetic landscape of nonsense-mediated mRNA decay with EZbakR.Genome biology · 2026Article
- Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation.Nucleic acids research · 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
- Investigation of TRMT61B methyltransferase activity on mRNA and its effects on translation.bioRxiv : the preprint server for biology · 2025Article
- RBM15-MKL1 fusion protein promotes leukemia via m6A methylation and Wnt pathway activation.Blood · 2025Article
- RNADecayCafe, a uniformly processed atlas of RNA half-life estimates across multiple human cell lines.bioRxiv : the preprint server for biology · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- Rapid folding of nascent RNA regulates eukaryotic RNA biogenesis.Molecular cell · 2025Article
- Profiling transcriptome composition and dynamics within nuclear compartments using SLAM-RT&Tag.Molecular cell · 2025Article
- Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.Molecular cell · 2025Article
- Translation elongation inhibitors stabilize select short-lived transcripts.RNA (New York, N.Y.) · 2024Article
- Transcription elongation factor ELOF1 is required for efficient somatic hypermutation and class switch recombination.bioRxiv : the preprint server for biology · 2024Article
- Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide.ACS chemical biology · 2024Article
- Phosphorylation of the nuclear poly(A) binding protein (PABPN1) during mitosis protects mRNA from hyperadenylation and maintains transcriptome dynamics.Nucleic acids research · 2024Article
- Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq.Cell reports · 2024Article
- Article
- grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis.Nature communications · 2023Article
- Improving the study of RNA dynamics through advances in RNA-seq with metabolic labeling and nucleotide-recoding chemistry.bioRxiv : the preprint server for biology · 2023Article
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2 authors.
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Abstract
Differential expression analysis of RNA sequencing (RNA-seq) data can identify changes in cellular RNA levels, but provides limited information about the kinetic mechanisms underlying such changes. Nucleotide recoding RNA-seq methods (NR-seq; e.g., TimeLapse-seq, SLAM-seq, etc.) address this shortcoming and are widely used approaches to identify changes in RNA synthesis and degradation kinetics. While advanced statistical models implemented in user-friendly software (e.g., DESeq2) have ensured the statistical rigor of differential expression analyses, no such tools that facilitate differential kinetic analysis with NR-seq exist. Here, we report the development of Bayesian analysis of the kinetics of RNA (bakR; https:// github.com/simonlabcode/bakR), an R package to address this need. bakR relies on Bayesian hierarchical modeling of NR-seq data to increase statistical power by sharing information across transcripts. Analyses of simulated data confirmed that bakR implementations of the hierarchical model outperform attempts to analyze differential kinetics with existing models. bakR also uncovers biological signals in real NR-seq data sets and provides improved analyses of existing data sets. This work establishes bakR as an important tool for identifying differential RNA synthesis and degradation kinetics.
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