ArticleNature methods2024
Building pangenome graphs.
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Article in Nature methods, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
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151citing papers in PubMed
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Who cites it
151 citing papers in PubMed.
- Insights into goatpox virus and sheeppox virus genomes from pangenome graphs.Archives of virology · 2026Article
- Translating functional molecular knowledge into crop-breeding success.Nature reviews. Genetics · 2026Review
- An Icelandic pangenome reference.Nature · 2026Article
- Privacy-preserving pangenome graphs.Nature communications · 2026Article
- 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
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa.Scientific data · 2026Article
- gaftools: a toolkit for analyzing and manipulating pangenome alignments.Bioinformatics (Oxford, England) · 2026Article
- PangyPlot: multi-scale interactive visualization of pangenome variation graphs.Bioinformatics (Oxford, England) · 2026Article
- A T2T Genome of the Lobed-Lip Iguazu Joana (Crenicichla tuca) Reveals Intrachromosomal Rearrangements and Trans-species Polymorphism in Cichlid Fishes.Genome biology and evolution · 2026Article
- VN1K is a pangenome-informed multi-omics and phenomics resource for the Vietnamese population.Nature communications · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Bacterial DNA invasion triggers transposable element proliferation and genome expansion.bioRxiv : the preprint server for biology · 2026Article
- Navigating the pangenome coordinate system with Shredtools.bioRxiv : the preprint server for biology · 2026Article
- De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping.Briefings in bioinformatics · 2026Article
- Phylogeny-driven pangenome analysis uncovers the genomic landscape of domesticated and wild Armeniaca species.Horticulture research · 2026Article
- PanGraphRNA: An efficient and flexible bioinformatics platform for graph pangenome-based RNA-seq data analysis.Journal of integrative plant biology · 2026Article
- Scalable computation of ultrabubbles in pangenomes by orienting bidirected graphs.Bioinformatics (Oxford, England) · 2026Article
- Building and applying pangenome references to capture genetic diversity.Nature reviews. Genetics · 2026Review
91 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
30 authors.
Erik Garrison *Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA. egarris5@uthsc.edu.ORCID http://orcid.org/0000-0003-3821-631X
Andrea Guarracino *Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0001-9744-131X
Simon HeumosQuantitative Biology Center (QBiC) Tübingen, University of Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0003-3326-817X
Flavia VillaniDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0003-3633-0610
Zhigui BaoDepartment of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0003-3601-460X
Lorenzo TattiniUniversité Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
Jörg HagmannComputomics, Tübingen, Germany.ORCID http://orcid.org/0000-0002-7232-3103
Sebastian VorbruggDepartment of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
Santiago Marco-SolaComputer Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.ORCID http://orcid.org/0000-0001-7951-3914
Christian KubicaDepartment of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
David G AshbrookDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-7397-8910
Kaisa ThorellChemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden.ORCID http://orcid.org/0000-0002-4447-8968
Rachel L Rusholme-PilcherEarlham Institute, Norwich Research Park, Norwich, UK.ORCID http://orcid.org/0000-0003-0000-0038
Gianni LitiUniversité Côte d'Azur, CNRS, INSERM, IRCAN, Nice, France.
Emilio RudbeckClinical Genomics Gothenburg, Bioinformatics and Data Centre, University of Gothenburg, Gothenburg, Sweden.
Agnieszka A GoliczDepartment of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.ORCID http://orcid.org/0000-0002-9711-4826
Sven NahnsenQuantitative Biology Center (QBiC) Tübingen, University of Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0002-4375-0691
Zuyu YangThe Institute of Environmental Science and Research, Wellington, New Zealand.ORCID http://orcid.org/0000-0002-0651-848X
Moses Njagi MwanikiDepartment of Computer Science, University of Pisa, Pisa, Italy.
Franklin L NobregaSchool of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.ORCID http://orcid.org/0000-0002-8238-1083
Yi WuSchool of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, UK.
Hao ChenDepartment of Pharmacology, Addiction Science and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Joep de LigtHartwig Medical Foundation, Amsterdam, the Netherlands.ORCID http://orcid.org/0000-0002-0348-419X
Peter H SudmantDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-9573-8248
Sanwen HuangShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.ORCID http://orcid.org/0000-0002-8547-5309
Detlef WeigelDepartment of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.ORCID http://orcid.org/0000-0002-2114-7963
Nicole SoranzoHuman Technopole, Milan, Italy.
Vincenza ColonnaDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-3966-0474
Robert W WilliamsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.
Pjotr PrinsDepartment of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA.ORCID http://orcid.org/0000-0002-8021-9162
Funding
A Unified High Performance Web Service for Systems Genetics and Precision MedicineR01GM123489 · NIGMS · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI PRINS, PJOTR, SEN, SAUNAK · 2017 to 2024
$3.7MSystem genetics of menthol and nicotine addictionU01DA047638 · NIDA · UNIVERSITY OF TENNESSEE HEALTH SCI CTR · PI CHEN, HAO, WILLIAMS, ROBERT W. · 2019 to 2023
$3.1MThe evolution and diversity of mutation, molecular fidelity, and genome structureR35GM142916 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI Peter Heshedahl Sudmant · 2021 to 2026
$2.5MNational Science Foundation (NSF) 2118709University of Tennessee (UT) Center for Integrative and Translational GenomicsU.S. Department of Health & Human Services | National Institutes of Health (NIH) R01GM123489U.S. Department of Health & Human Services | National Institutes of Health (NIH) U01DA047638
Abstract
Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.
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PhylogenySoftwareAlgorithmsComputational BiologyGenomeGenomicsHumans
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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.