ArticleScience advances2023
ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data.
Article in Science advances, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed, 86 citations in OpenAlex.
- Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- Exploring the role of differential splicing of Pekin ducks resistant to DHAV-3 based on full-length transcriptome.Poultry science · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- The splice of life: an isoform-centric view of disease, technology, and therapeutics.The Journal of clinical investigation · 2026Review
- PASSpedia: A Polyadenylation Site Database Across Different Species at Single-cell Resolution.Genomics, proteomics & bioinformatics · 2026Article
- Chromosome-level assembly and annotation of the Jaguar (Panthera onca) genome.BMC genomic data · 2026Article
- Long-read cDNA sequencing reveals novel isoforms and spliceosome-mutant-enriched transcripts in AML and MDS.bioRxiv : the preprint server for biology · 2026Article
- Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.Science China. Life sciences · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Role of alternative splicing in cancer progression.Irish journal of medical science · 2026Review
- Annotating genomes at increased scale and resolution.Nature reviews. Genetics · 2026Review
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Non-destructive transcriptomics via vesicular export.Nature communications · 2026Article
- Variant-resolved prediction of context-specific isoform variation with a graph-based attention model.Cell genomics · 2026Article
- Long-read assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function.Nature communications · 2026Article
- DeepISO: deep learning-powered prediction of protein-protein interaction rewiring generated by alternative splicing.Genome biology · 2026Article
- Improving isoform-level eQTL and integrative genetic analyses of breast cancer risk with long-read RNA transcript assemblies.bioRxiv : the preprint server for biology · 2026Article
- Natural variation in transplacental transfer efficiency exposes distinct transcriptional network architectures of PFAS effects on birth weight and gestational age.bioRxiv : the preprint server for biology · 2026Article
- Population-scale interpretation of RNA isoform diversity enabled by Isopedia.bioRxiv : the preprint server for biology · 2026Article
11 more citing papers are in PubMed but not listed here.
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing platforms poses a major challenge. We present ESPRESSO, a computational tool for robust discovery and quantification of transcript isoforms from error-prone long reads. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. On both a synthetic spike-in RNA sample and human RNA samples, ESPRESSO outperforms multiple contemporary tools in not only transcript isoform discovery but also transcript isoform quantification. In total, we generated and analyzed ~1.1 billion nanopore RNA-seq reads covering 30 human tissue samples and three human cell lines. ESPRESSO and its companion dataset provide a useful resource for studying the RNA repertoire of eukaryotic transcriptomes.
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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.