ArticleGenome biology2021
LIQA: long-read isoform quantification and analysis.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Review
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- 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
- TNRSim - a simulator of truncated oxford nanopore direct RNA long reads for isoform analysis.Frontiers in bioinformatics · 2026Article
- Oxford Nanopore Sequencing in pediatric emergency infectious diseases: from rapid diagnosis to precision medicine.Frontiers in cellular and infection microbiology · 2026Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain.Genome biology · 2025Article
- Article
- Splicing QTL mapping in stimulated macrophages associates low-usage splice junctions with immune-mediated disease risk.Nature communications · 2025Article
- Combining panel-based and whole-transcriptome-based gene fusion detection by long-read sequencing.Cell reports methods · 2025Article
- A comparative evaluation of computational models for RNA modification detection using nanopore sequencing with RNA004 chemistry.Briefings in bioinformatics · 2025Article
- A Comparative Evaluation of Computational Models for RNA modification detection using Nanopore sequencing with RNA004 Chemistry.bioRxiv : the preprint server for biology · 2025Article
- Mitochondrial transcriptome of Candida albicans in flagranti - direct RNA sequencing reveals a new layer of information.BMC genomics · 2024Article
- Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with Isosceles.Nature communications · 2024Article
- Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.Nature methods · 2024Article
- Article
- Oarfish: Enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Long-read RNA sequencing (RNA-seq) technologies can sequence full-length transcripts, facilitating the exploration of isoform-specific gene expression over short-read RNA-seq. We present LIQA to quantify isoform expression and detect differential alternative splicing (DAS) events using long-read direct mRNA sequencing or cDNA sequencing data. LIQA incorporates base pair quality score and isoform-specific read length information in a survival model to assign different weights across reads, and uses an expectation-maximization algorithm for parameter estimation. We apply LIQA to long-read RNA-seq data from the Universal Human Reference, acute myeloid leukemia, and esophageal squamous epithelial cells and demonstrate its high accuracy in profiling alternative splicing events.
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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.