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Pangenome Graphs.
Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E. Eizenga JM, et al. Among authors: chang x. Annu Rev Genomics Hum Genet. 2020 Aug 31;21:139-162. doi: 10.1146/annurev-genom-120219-080406. Epub 2020 May 26. Annu Rev Genomics Hum Genet. 2020. PMID: 32453966 Free PMC article. Review.
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: chang xh. 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.
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. Among authors: chang x. 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.
Personalized Pangenome References.
Sirén J, Eskandar P, Ungaro MT, Hickey G, Eizenga JM, Novak AM, Chang X, Chang PC, Kolmogorov M, Carroll A, Monlong J, Paten B. Sirén J, et al. Among authors: chang x. bioRxiv [Preprint]. 2023 Dec 15:2023.12.13.571553. doi: 10.1101/2023.12.13.571553. bioRxiv. 2023. PMID: 38168361 Free PMC article. Preprint.
Distance indexing and seed clustering in sequence graphs.
Chang X, Eizenga J, Novak AM, Sirén J, Paten B. Chang X, et al. Bioinformatics. 2020 Jul 1;36(Suppl_1):i146-i153. doi: 10.1093/bioinformatics/btaa446. Bioinformatics. 2020. PMID: 32657356 Free PMC article.
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: chang x. F1000Res. 2019 Oct 14;8:1751. doi: 10.12688/f1000research.19630.2. eCollection 2019. F1000Res. 2019. PMID: 34386196 Free PMC article.
28 results