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Page 1
A chromosome-level reference genome and pangenome for barn swallow population genomics.
Secomandi S, Gallo GR, Sozzoni M, Iannucci A, Galati E, Abueg L, Balacco J, Caprioli M, Chow W, Ciofi C, Collins J, Fedrigo O, Ferretti L, Fungtammasan A, Haase B, Howe K, Kwak W, Lombardo G, Masterson P, Messina G, Møller AP, Mountcastle J, Mousseau TA, Ferrer Obiol J, Olivieri A, Rhie A, Rubolini D, Saclier M, Stanyon R, Stucki D, Thibaud-Nissen F, Torrance J, Torroni A, Weber K, Ambrosini R, Bonisoli-Alquati A, Jarvis ED, Gianfranceschi L, Formenti G. Secomandi S, et al. Among authors: rhie a. Cell Rep. 2023 Jan 31;42(1):111992. doi: 10.1016/j.celrep.2023.111992. Epub 2023 Jan 19. Cell Rep. 2023. PMID: 36662619 Free PMC article.
The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content.
Smith T, Olagunju T, Rosen B, Neibergs H, Becker G, Davenport K, Elsik C, Hadfield T, Koren S, Kuhn K, Rhie A, Shira K, Skibiel A, Stegemiller M, Thorne J, Villamediana P, Cockett N, Murdoch B. Smith T, et al. Among authors: rhie a. Res Sq [Preprint]. 2024 Apr 3:rs.3.rs-4033388. doi: 10.21203/rs.3.rs-4033388/v1. Res Sq. 2024. Update in: Nat Commun. 2024 Sep 27;15(1):8277. doi: 10.1038/s41467-024-52384-5 PMID: 38712074 Free PMC article. Updated. Preprint.
FX: an RNA-Seq analysis tool on the cloud.
Hong D, Rhie A, Park SS, Lee J, Ju YS, Kim S, Yu SB, Bleazard T, Park HS, Rhee H, Chong H, Yang KS, Lee YS, Kim IH, Lee JS, Kim JI, Seo JS. Hong D, et al. Among authors: rhie a. Bioinformatics. 2012 Mar 1;28(5):721-3. doi: 10.1093/bioinformatics/bts023. Epub 2012 Jan 17. Bioinformatics. 2012. PMID: 22257667
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing.
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM. Koren S, et al. Among authors: rhie a. bioRxiv [Preprint]. 2024 Mar 19:2024.03.15.585294. doi: 10.1101/2024.03.15.585294. bioRxiv. 2024. Update in: Genome Res. 2024 Nov 20;34(11):1919-1930. doi: 10.1101/gr.279334.124 PMID: 38529488 Free PMC article. Updated. Preprint.
De novo assembly of the cattle reference genome with single-molecule sequencing.
Rosen BD, Bickhart DM, Schnabel RD, Koren S, Elsik CG, Tseng E, Rowan TN, Low WY, Zimin A, Couldrey C, Hall R, Li W, Rhie A, Ghurye J, McKay SD, Thibaud-Nissen F, Hoffman J, Murdoch BM, Snelling WM, McDaneld TG, Hammond JA, Schwartz JC, Nandolo W, Hagen DE, Dreischer C, Schultheiss SJ, Schroeder SG, Phillippy AM, Cole JB, Van Tassell CP, Liu G, Smith TPL, Medrano JF. Rosen BD, et al. Among authors: rhie a. Gigascience. 2020 Mar 1;9(3):giaa021. doi: 10.1093/gigascience/giaa021. Gigascience. 2020. PMID: 32191811 Free PMC article.
Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle.
Low WY, Tearle R, Liu R, Koren S, Rhie A, Bickhart DM, Rosen BD, Kronenberg ZN, Kingan SB, Tseng E, Thibaud-Nissen F, Martin FJ, Billis K, Ghurye J, Hastie AR, Lee J, Pang AWC, Heaton MP, Phillippy AM, Hiendleder S, Smith TPL, Williams JL. Low WY, et al. Among authors: rhie a. Nat Commun. 2020 Apr 29;11(1):2071. doi: 10.1038/s41467-020-15848-y. Nat Commun. 2020. PMID: 32350247 Free PMC article.
Telomere-to-telomere assembly of a complete human X chromosome.
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM. Miga KH, et al. Among authors: rhie a. Nature. 2020 Sep;585(7823):79-84. doi: 10.1038/s41586-020-2547-7. Epub 2020 Jul 14. Nature. 2020. PMID: 32663838 Free PMC article.
Improved reference genome of the arboviral vector Aedes albopictus.
Palatini U, Masri RA, Cosme LV, Koren S, Thibaud-Nissen F, Biedler JK, Krsticevic F, Johnston JS, Halbach R, Crawford JE, Antoshechkin I, Failloux AB, Pischedda E, Marconcini M, Ghurye J, Rhie A, Sharma A, Karagodin DA, Jenrette J, Gamez S, Miesen P, Masterson P, Caccone A, Sharakhova MV, Tu Z, Papathanos PA, Van Rij RP, Akbari OS, Powell J, Phillippy AM, Bonizzoni M. Palatini U, et al. Among authors: rhie a. Genome Biol. 2020 Aug 26;21(1):215. doi: 10.1186/s13059-020-02141-w. Genome Biol. 2020. PMID: 32847630 Free PMC article.
78 results