ArticleGenome biology2023
Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
29 citing papers in PubMed.
- Review
- Handling biological replicates in long-read RNA sequencing data by joining or not joining.Nature communications · 2026Article
- Beyond the gene: isoform diversity as a key contributor to human brain disorders.Current opinion in genetics & development · 2026Review
- The circadian isoform landscape of mouse livers.NAR genomics and bioinformatics · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.Briefings in bioinformatics · 2026Review
- Efficient reconstruction of full-length RNA isoforms using ISAtools and large-scale PacBio circular consensus sequencing data.Briefings in bioinformatics · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution.bioRxiv : the preprint server for biology · 2026Article
- Review
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- Single cell and spatial alternative splicing analysis with Nanopore long read sequencing.Nature communications · 2025Article
- CRISPRware: a software package for contextual gRNA library design.BMC genomics · 2025Article
- Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation.Genome research · 2025Review
- Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq.Genome research · 2025Article
- Discovery of Novel Protein-Coding and Long Non-coding Transcripts in Distinct Regions of the Human Brain.Journal of molecular neuroscience : MN · 2025Article
- Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation.Genome research · 2024Article
- Generation and analysis of a mouse multitissue genome annotation atlas.Genome research · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
In this manuscript, we introduce and benchmark Mandalorion v4.1 for the identification and quantification of full-length transcriptome sequencing reads. It further improves upon the already strong performance of Mandalorion v3.6 used in the LRGASP consortium challenge. By processing real and simulated data, we show three main features of Mandalorion: first, Mandalorion-based isoform identification has very high precision and maintains high recall even in the absence of any genome annotation. Second, isoform read counts as quantified by Mandalorion show a high correlation with simulated read counts. Third, isoforms identified by Mandalorion closely reflect the full-length transcriptome sequencing data sets they are based on.
Indexed as
Identifiers
What OpenQuestion holds
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.