ArticleNature biotechnology2023
Accurate isoform discovery with IsoQuant using long reads.
Article in Nature biotechnology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 192 papers.
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Who cites it
192 citing papers in PubMed.
- Molecular histomorphometry and the emerging role of transcriptomics in celiac disease diagnosis and therapeutic trials.Annals of medicine · 2026Review
- A hybrid transcriptome assembly reveals coding and noncoding landscapes in Drosophila hemocytes.Genetics · 2026Article
- Review
- Conserved and Tissue-Specific RNA and Protein Cargos of Small Extracellular Vesicles From 120 Tissue Sites Across 34 Organs in a Single Pig.Journal of extracellular vesicles · 2026Article
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- The insulin/IGF axis is critically important for controlling gene transcription in the podocyte.eLife · 2026Article
- Long-read transcriptome analysis using IsoRanker for identifying pathogenic variants in Mendelian conditions.American journal of human genetics · 2026Article
- Spatial isoform sequencing at single-cell resolution reveals cell-type-specific spatial isoform variability in multiple brain cell types.Nature methods · 2026Article
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Long-Read Single-Cell RNA Sequencing Reveals Dynamic Isoform Changes During Corneal Epithelial Wound Healing in Cynomolgus Monkeys.Investigative ophthalmology & visual science · 2026Article
- IsoformSwitchAnalyzeR v2: analysis of functional isoform changes in long-read and single-cell sequencing data.NAR genomics and bioinformatics · 2026Article
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Single-cell multi-omics dissects transcript isoform and immune repertoire dynamics in human immunosenescence.Science China. Life sciences · 2026Article
- Leveraging long read RNA-seq to decipher neuronal regulation of alternative polyadenylation.Nature communications · 2026Article
- Multimodal Framework of Left Heart-Pulmonary Vascular Remodeling Underlying Right Ventricular Failure in PH-HFpEF.Circulation. Heart failure · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- A complete genome for the common marmoset.Cell · 2026Article
- NextLongIso: a comprehensive Nextflow pipeline for multi-dimensional long-read RNA-seq analysis.Bioinformatics (Oxford, England) · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- Long-read RNA-seq maps the isoform landscape of the trigeminal ganglion in an allergic rhinitis mouse model.BMC genomics · 2026Article
132 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant-a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data.
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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.