ArticleNature methods2023
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
- Review
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Signatures of nonsense-mediated mRNA decay but no evidence for transcriptional adaptation associated with protein-truncating variants in wild yeast diploids.Molecular biology and evolution · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq.Plant methods · 2026Article
- Skin metatranscriptomics reveals a landscape of variation in microbial activity and gene expression across the human body.Nature biotechnology · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
- Lossless pangenome indexing using tag arrays.Algorithms for molecular biology : AMB · 2026Article
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- A Super-Pangenome for Cultivated Citrus Reveals Evolutive Features During the Allopatric Phase of Their Reticulate Evolution.Plant biotechnology journal · 2026Article
- From structural pangenomes to functional panomics in plants.Molecular biology and evolution · 2026Review
- Accessing crop genetic diversity via pangenomics.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- Lossless Pangenome Indexing Using Tag Arrays.Research square · 2026Article
- GFSeeker: a splicing-graph-based approach for accurate gene fusion detection from long-read RNA sequencing data.Briefings in bioinformatics · 2026Article
- Long-read transcriptomics of a diverse human cohort reveals ancestry bias in gene annotation.Nature communications · 2025Article
- SAFARI: pangenome alignment of ancient DNA using purine/pyrimidine encodings.NAR genomics and bioinformatics · 2025Article
- Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid.Genome biology · 2025Article
- Transcriptomics in the era of long-read sequencing.Nature reviews. Genetics · 2025Review
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
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7 authors.
Funding
Abstract
Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our toolchain, which consists of additions to the VG toolkit and a standalone tool, RPVG, can construct spliced pangenome graphs, map RNA sequencing data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. We show that this workflow improves accuracy over state-of-the-art RNA sequencing mapping methods, and that it can efficiently quantify haplotype-specific transcript expression without needing to characterize the haplotypes of a sample beforehand.
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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.