ArticleBioinformatics (Oxford, England)2024
Exploring gene content with pangene graphs.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Defining and cataloging variants in pangenome graphs.Cell genomics · 2026Article
- COSIGT: population-scalable genotyping of complex loci from low-coverage sequencing data using pangenome graphs.Genome biology · 2026Article
- Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber.Nature genetics · 2026Article
- Scalable computation of ultrabubbles in pangenomes by orienting bidirected graphs.Bioinformatics (Oxford, England) · 2026Article
- Article
- A repeat expansion in GOLGA8A is a major risk factor for atypical frontotemporal lobar degeneration with ubiquitin-positive inclusions.Nature genetics · 2026Article
- High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.Cell genomics · 2026Article
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Transposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.The Plant journal : for cell and molecular biology · 2025Article
- Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.Scientific data · 2025Article
- A survey of sequence-to-graph mapping algorithms in the pangenome era.Genome biology · 2025Review
- Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.Bioinformatics (Oxford, England) · 2025Article
- Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.bioRxiv : the preprint server for biology · 2025Article
- Small variant benchmark from a complete assembly of X and Y chromosomes.Nature communications · 2025Article
- Complexity welcome: Pangenome graphs for comprehensive population genomics.Quantitative plant biology · 2025Review
- BWT construction and search at the terabase scale.Bioinformatics (Oxford, England) · 2024Article
- Fitness consequences of structural variation inferred from a House Finch pangenome.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Haplotype-aware sequence alignment to pangenome graphs.Genome research · 2024Article
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3 authors.
Funding
Abstract
motivationThe gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.
resultsWe developed pangene, a computational tool to identify gene orientation, gene order, and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented as a walk in the graph. It additionally finds subgraphs, which we call bibubbles, that capture gene content changes. Applied to the human pangenome, pangene identifies known gene-level variations and reveals complex haplotypes that are not well studied before. Pangene also works with high-quality bacterial pangenome and reports similar numbers of core and accessory genes in comparison to existing tools. AVAILABILITY AND IMPLEMENTATION: Source code at https://github.com/lh3/pangene; prebuilt pangene graphs can be downloaded from https://zenodo.org/records/8118576 and visualized at https://pangene.bioinweb.org.
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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.