ArticleF1000Research2016
DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics.
Article in F1000Research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers, 3 of them syntheses that pooled it.
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Who cites it
144 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- FSHD muscle shows perturbation in fibroadipogenic progenitor cells, mitochondrial function and alternative splicing independently of inflammation.Human molecular genetics · 2024Pooled it
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- A signaling pathway-driven bioinformatics pipeline for predicting therapeutics against emerging infectious diseases.F1000Research · 2021Pooled it
- Review
- LRP2: A proteogenomics pipeline for long-read informed protein isoform analysis and discovery.bioRxiv : the preprint server for biology · 2026Article
- A Real-Data-Driven Framework for Evaluating Differential Transcript Usage Methods Across Long-Read Bulk, Single-Cell, and Spatial Transcriptomics.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Single-cell splice isoform usage reveals distinct axes of cellular identity and senescence.bioRxiv : the preprint server for biology · 2026Article
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- Multimodal Framework of Left Heart-Pulmonary Vascular Remodeling Underlying Right Ventricular Failure in PH-HFpEF.Circulation. Heart failure · 2026Article
- Long-Read RNA Sequencing Reveals an Isoform Switching Pattern in Healthy Microglial Cell Lines Exposed to Radiotherapy.Non-coding RNA · 2026Article
- Distinct 5' and 3' coverage biases shape transcriptome interpretation in Nanopore direct RNA versus PCR-cDNA sequencing.BMC genomics · 2026Article
- Retina-specific long non-coding RNAs associated with inherited retinal disease genes.Cellular and molecular life sciences : CMLS · 2026Article
- Gene Expression and Alternative Splicing Throughout the Reproductive Cycle of a Viviparous Lizard Reveal Novel Genes for Pregnancy and Convergence With Squamates and Mammals.Molecular ecology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Large-scale analysis of temporal gene expression variation in peripheral blood.Nature communications · 2026Article
- Article
- Peritoneal macrophages regulate distal wound healing via endocrine release of plasma fibronectin.The Journal of clinical investigation · 2026Article
- Humanized Klotho haplotypes cause widespread transcriptomic changes in mouse brain.bioRxiv : the preprint server for biology · 2026Article
- Relationship between the distribution of LEDGF along genes and positions of HIV-1 DNA integration.mBio · 2026Article
- Multi-platform profiling reveals host- and cell -type-specific pseudorabies virus gene expression.Scientific reports · 2026Article
84 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There are many instances in genomics data analyses where measurements are made on a multivariate response. For example, alternative splicing can lead to multiple expressed isoforms from the same primary transcript. There are situations where differences (e.g. between normal and disease state) in the relative ratio of expressed isoforms may have significant phenotypic consequences or lead to prognostic capabilities. Similarly, knowledge of single nucleotide polymorphisms (SNPs) that affect splicing, so-called splicing quantitative trait loci (sQTL) will help to characterize the effects of genetic variation on gene expression. RNA sequencing (RNA-seq) has provided an attractive toolbox to carefully unravel alternative splicing outcomes and recently, fast and accurate methods for transcript quantification have become available. We propose a statistical framework based on the Dirichlet-multinomial distribution that can discover changes in isoform usage between conditions and SNPs that affect relative expression of transcripts using these quantifications. The Dirichlet-multinomial model naturally accounts for the differential gene expression without losing information about overall gene abundance and by joint modeling of isoform expression, it has the capability to account for their correlated nature. The main challenge in this approach is to get robust estimates of model parameters with limited numbers of replicates. We approach this by sharing information and show that our method improves on existing approaches in terms of standard statistical performance metrics. The framework is applicable to other multivariate scenarios, such as Poly-A-seq or where beta-binomial models have been applied (e.g., differential DNA methylation). Our method is available as a Bioconductor R package called DRIMSeq.
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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.