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Page 1
Epigenetic patterns in a complete human genome.
Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Gershman A, et al. Among authors: shumate a. Science. 2022 Apr;376(6588):eabj5089. doi: 10.1126/science.abj5089. Epub 2022 Apr 1. Science. 2022. PMID: 35357915 Free PMC article.
Assembly and annotation of an Ashkenazi human reference genome.
Shumate A, Zimin AV, Sherman RM, Puiu D, Wagner JM, Olson ND, Pertea M, Salit ML, Zook JM, Salzberg SL. Shumate A, et al. Genome Biol. 2020 Jun 2;21(1):129. doi: 10.1186/s13059-020-02047-7. Genome Biol. 2020. PMID: 32487205 Free PMC article.
Curated variation benchmarks for challenging medically relevant autosomal genes.
Wagner J, Olson ND, Harris L, McDaniel J, Cheng H, Fungtammasan A, Hwang YC, Gupta R, Wenger AM, Rowell WJ, Khan ZM, Farek J, Zhu Y, Pisupati A, Mahmoud M, Xiao C, Yoo B, Sahraeian SME, Miller DE, Jáspez D, Lorenzo-Salazar JM, Muñoz-Barrera A, Rubio-Rodríguez LA, Flores C, Narzisi G, Evani US, Clarke WE, Lee J, Mason CE, Lincoln SE, Miga KH, Ebbert MTW, Shumate A, Li H, Chin CS, Zook JM, Sedlazeck FJ. Wagner J, et al. Among authors: shumate a. Nat Biotechnol. 2022 May;40(5):672-680. doi: 10.1038/s41587-021-01158-1. Epub 2022 Feb 7. Nat Biotechnol. 2022. PMID: 35132260 Free PMC article.
The complete sequence of a human genome.
Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. Nurk S, et al. Among authors: shumate a. Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31. Science. 2022. PMID: 35357919 Free PMC article.
A complete reference genome improves analysis of human genetic variation.
Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. Aganezov S, et al. Among authors: shumate a. Science. 2022 Apr;376(6588):eabl3533. doi: 10.1126/science.abl3533. Epub 2022 Apr 1. Science. 2022. PMID: 35357935 Free PMC article.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JMD, Zook JM, Phillippy AM, Rhie A. Mc Cartney AM, et al. Among authors: shumate a. Nat Methods. 2022 Jun;19(6):687-695. doi: 10.1038/s41592-022-01440-3. Epub 2022 Mar 31. Nat Methods. 2022. PMID: 35361931 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: shumate 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.
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: shumate a. Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23. Nature. 2023. PMID: 37612512 Free PMC article.
47 results