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2000 1
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2023 10
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Page 1
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: guarracino a. 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 complete sequence of a human Y chromosome.
Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. Rhie A, et al. Among authors: guarracino a. Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23. Nature. 2023. PMID: 37612512
Unbiased pangenome graphs.
Garrison E, Guarracino A. Garrison E, et al. Among authors: guarracino a. Bioinformatics. 2023 Jan 1;39(1):btac743. doi: 10.1093/bioinformatics/btac743. Bioinformatics. 2023. PMID: 36448683 Free PMC article.
Type I IFNs promote cancer cell stemness by triggering the epigenetic regulator KDM1B.
Musella M, Guarracino A, Manduca N, Galassi C, Ruggiero E, Potenza A, Maccafeo E, Manic G, Mattiello L, Soliman Abdel Rehim S, Signore M, Pietrosanto M, Helmer-Citterich M, Pallocca M, Fanciulli M, Bruno T, De Nicola F, Corleone G, Di Benedetto A, Ercolani C, Pescarmona E, Pizzuti L, Guidi F, Sperati F, Vitale S, Macchia D, Spada M, Schiavoni G, Mattei F, De Ninno A, Businaro L, Lucarini V, Bracci L, Aricò E, Ziccheddu G, Facchiano F, Rossi S, Sanchez M, Boe A, Biffoni M, De Maria R, Vitale I, Sistigu A. Musella M, et al. Among authors: guarracino a. Nat Immunol. 2022 Sep;23(9):1379-1392. doi: 10.1038/s41590-022-01290-3. Epub 2022 Aug 24. Nat Immunol. 2022. PMID: 36002648 Free PMC article.
Building pangenome graphs.
Garrison E, Guarracino A, Heumos S, Villani F, Bao Z, Tattini L, Hagmann J, Vorbrugg S, Marco-Sola S, Kubica C, Ashbrook DG, Thorell K, Rusholme-Pilcher RL, Liti G, Rudbeck E, Nahnsen S, Yang Z, Moses MN, Nobrega FL, Wu Y, Chen H, de Ligt J, Sudmant PH, Soranzo N, Colonna V, Williams RW, Prins P. Garrison E, et al. Among authors: guarracino a. bioRxiv [Preprint]. 2023 Apr 6:2023.04.05.535718. doi: 10.1101/2023.04.05.535718. bioRxiv. 2023. PMID: 37066137 Free PMC article. Preprint.
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: guarracino 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.
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.
ODGI: understanding pangenome graphs.
Guarracino A, Heumos S, Nahnsen S, Prins P, Garrison E. Guarracino A, et al. Bioinformatics. 2022 Jun 27;38(13):3319-3326. doi: 10.1093/bioinformatics/btac308. Bioinformatics. 2022. PMID: 35552372 Free PMC article.
Optimal gap-affine alignment in O(s) space.
Marco-Sola S, Eizenga JM, Guarracino A, Paten B, Garrison E, Moreto M. Marco-Sola S, et al. Among authors: guarracino a. Bioinformatics. 2023 Feb 3;39(2):btad074. doi: 10.1093/bioinformatics/btad074. Bioinformatics. 2023. PMID: 36749013 Free PMC article.
Pangenome graph layout by Path-Guided Stochastic Gradient Descent.
Heumos S, Guarracino A, Schmelzle JM, Li J, Zhang Z, Hagmann J, Nahnsen S, Prins P, Garrison E. Heumos S, et al. Among authors: guarracino a. bioRxiv [Preprint]. 2023 Oct 17:2023.09.22.558964. doi: 10.1101/2023.09.22.558964. bioRxiv. 2023. PMID: 37790531 Free PMC article. Preprint.
28 results