ArticlePLoS computational biology2025
Long-read sequencing transcriptome quantification with lr-kallisto.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Review
- Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification.bioRxiv : the preprint server for biology · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- BenchDrop-seq: a microfluidics-free platform for benchtop single-cell long-read RNA sequencing.bioRxiv : the preprint server for biology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Dogme: a nextflow pipeline for reprocessing nanopore RNA and DNA modifications.Bioinformatics (Oxford, England) · 2026Article
- A systematic benchmark of high-accuracy PacBio long-read RNA sequencing for transcript-level quantification.Genome biology · 2026Article
- A comprehensive evaluation of long-read de novo transcriptome assembly.Genome biology · 2026Article
- Review
- Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation.Nature communications · 2025Article
- Long-read sequencing transcriptome quantification with lr-kallisto.PLoS computational biology · 2025Article
- Bioinformatics frameworks for single-cell long-read sequencing: unlocking isoform-level resolution.Briefings in bioinformatics · 2025Review
- scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.Bioinformatics (Oxford, England) · 2025Article
- Oarfish: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification.Bioinformatics (Oxford, England) · 2025Article
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18 authors.
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Abstract
RNA abundance quantification has become routine and affordable thanks to high-throughput "short-read" technologies that provide accurate molecule counts at the gene level. Similarly accurate and affordable quantification of definitive full-length, transcript isoforms has remained a stubborn challenge, despite its obvious biological significance across a wide range of problems. "Long-read" sequencing platforms now produce data-types that can, in principle, drive routine definitive isoform quantification. However some particulars of contemporary long-read datatypes, together with isoform complexity and genetic variation, present bioinformatic challenges. We show here, using ONT data, that fast and accurate quantification of long-read data is possible and that it is improved by exome capture. To perform quantifications we developed lr-kallisto, which adapts the kallisto bulk and single-cell RNA-seq quantification methods for long-read technologies.
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