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The Human Pangenome Project: a global resource to map genomic diversity.
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D; Human Pangenome Reference Consortium. Wang T, et al. Nature. 2022 Apr;604(7906):437-446. doi: 10.1038/s41586-022-04601-8. Epub 2022 Apr 20. Nature. 2022. PMID: 35444317 Free PMC article. Review.
Pangenome graph construction from genome alignments with Minigraph-Cactus.
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y; Human Pangenome Reference Consortium; Marschall T, Li H, Paten B. Hickey G, et al. Nat Biotechnol. 2024 Apr;42(4):663-673. doi: 10.1038/s41587-023-01793-w. Epub 2023 May 10. Nat Biotechnol. 2024. PMID: 37165083 Free PMC article.
Recombination between heterologous human acrocentric chromosomes.
Guarracino A, Buonaiuto S, de Lima LG, Potapova T, Rhie A, Koren S, Rubinstein B, Fischer C; Human Pangenome Reference Consortium; Gerton JL, Phillippy AM, Colonna V, Garrison E. Guarracino A, et al. Nature. 2023 May;617(7960):335-343. doi: 10.1038/s41586-023-05976-y. Epub 2023 May 10. Nature. 2023. PMID: 37165241 Free PMC article.
Semi-automated assembly of high-quality diploid human reference genomes.
Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH; Human Pangenome Reference Consortium. Jarvis ED, et al. Nature. 2022 Nov;611(7936):519-531. doi: 10.1038/s41586-022-05325-5. Epub 2022 Oct 19. Nature. 2022. PMID: 36261518 Free PMC article.
Inversion polymorphism in a complete human genome assembly.
Porubsky D, Harvey WT, Rozanski AN, Ebler J, Höps W, Ashraf H, Hasenfeld P; Human Pangenome Reference Consortium (HPRC); Human Genome Structural Variation Consortium (HGSVC); Paten B, Sanders AD, Marschall T, Korbel JO, Eichler EE. Porubsky D, et al. Genome Biol. 2023 Apr 30;24(1):100. doi: 10.1186/s13059-023-02919-8. Genome Biol. 2023. PMID: 37122002 Free PMC article.
Increased mutation and gene conversion within human segmental duplications.
Vollger MR, Dishuck PC, Harvey WT, DeWitt WS, Guitart X, Goldberg ME, Rozanski AN, Lucas J, Asri M; Human Pangenome Reference Consortium; Munson KM, Lewis AP, Hoekzema K, Logsdon GA, Porubsky D, Paten B, Harris K, Hsieh P, Eichler EE. Vollger MR, et al. Nature. 2023 May;617(7960):325-334. doi: 10.1038/s41586-023-05895-y. Epub 2023 May 10. Nature. 2023. PMID: 37165237 Free PMC article.
Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C; Human Pangenome Reference Consortium; Korbel JO, Paten B, Marschall T, Eichler EE. Porubsky D, et al. Genome Res. 2023 Apr;33(4):496-510. doi: 10.1101/gr.277334.122. Epub 2023 May 10. Genome Res. 2023. PMID: 37164484 Free PMC article.