ArticleNature biotechnology2026
Improving gene isoform quantification with miniQuant.
Article in Nature biotechnology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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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
8 citing papers in PubMed.
- Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencing.Nature communications · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Improving gene isoform quantification with miniQuant.Nature biotechnology · 2026Article
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Article
- Cell-type-resolvedbioRxiv : the preprint server for biology · 2025Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
RNA sequencing has been widely applied for gene isoform quantification, but limitations exist in quantifying isoforms of complex genes accurately, especially for short reads. Here we identify genes that are difficult to quantify accurately with short reads and illustrate the information benefit of using long reads to quantify these regions. We present miniQuant, which ranks genes with quantification errors caused by the ambiguity of read alignments and integrates the complementary strengths of long reads and short reads with optimal combination in a gene- and data-specific manner to achieve more accurate quantification. These results are supported by rigorous mathematical proofs, validated with a wide range of simulation data, experimental validations and more than 17,000 public datasets from GTEx, TCGA and ENCODE consortia. We demonstrate miniQuant can uncover isoform switches during the differentiation of human embryonic stem cells to pharyngeal endoderm and primordial germ cell-like cells.
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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.