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Page 1
A strategy for building and using a human reference pangenome.
Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B. Llamas B, et al. Among authors: regier a. F1000Res. 2019 Oct 14;8:1751. doi: 10.12688/f1000research.19630.2. eCollection 2019. F1000Res. 2019. PMID: 34386196 Free PMC article.
Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Ebert P, et al. Among authors: regier aa. Science. 2021 Apr 2;372(6537):eabf7117. doi: 10.1126/science.abf7117. Epub 2021 Feb 25. Science. 2021. PMID: 33632895 Free PMC article.
Mako: A Graph-based Pattern Growth Approach to Detect Complex Structural Variants.
Lin J, Yang X, Kosters W, Xu T, Jia Y, Wang S, Zhu Q, Ryan M, Guo L, Zhang C; Human Genome Structural Variation Consortium; Lee C, Devine SE, Eichler EE, Ye K. Lin J, et al. Genomics Proteomics Bioinformatics. 2022 Feb;20(1):205-218. doi: 10.1016/j.gpb.2021.03.007. Epub 2021 Jul 3. Genomics Proteomics Bioinformatics. 2022. PMID: 34224879 Free PMC article.
High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios.
Byrska-Bishop M, Evani US, Zhao X, Basile AO, Abel HJ, Regier AA, Corvelo A, Clarke WE, Musunuri R, Nagulapalli K, Fairley S, Runnels A, Winterkorn L, Lowy E; Human Genome Structural Variation Consortium; Paul Flicek, Germer S, Brand H, Hall IM, Talkowski ME, Narzisi G, Zody MC. Byrska-Bishop M, et al. Among authors: regier aa. Cell. 2022 Sep 1;185(18):3426-3440.e19. doi: 10.1016/j.cell.2022.08.004. Cell. 2022. PMID: 36055201 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. Among authors: regier a. 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.
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.
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.
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.
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.
A draft human pangenome reference.
Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichl… See abstract for full author list ➔ Liao WW, et al. Among authors: regier aa. Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10. Nature. 2023. PMID: 37165242 Free PMC article.
26 results