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Page 1
From telomere to telomere: The transcriptional and epigenetic state of human repeat elements.
Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O'Neill RJ. Hoyt SJ, et al. Among authors: rhie a. Science. 2022 Apr;376(6588):eabk3112. doi: 10.1126/science.abk3112. Epub 2022 Apr 1. Science. 2022. PMID: 35357925 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.
Nanopore sequencing and assembly of a human genome with ultra-long reads.
Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M. Jain M, et al. Among authors: rhie a. Nat Biotechnol. 2018 Apr;36(4):338-345. doi: 10.1038/nbt.4060. Epub 2018 Jan 29. Nat Biotechnol. 2018. PMID: 29431738 Free PMC article.
De novo assembly of haplotype-resolved genomes with trio binning.
Koren S, Rhie A, Walenz BP, Dilthey AT, Bickhart DM, Kingan SB, Hiendleder S, Williams JL, Smith TPL, Phillippy AM. Koren S, et al. Among authors: rhie a. Nat Biotechnol. 2018 Oct 22:10.1038/nbt.4277. doi: 10.1038/nbt.4277. Online ahead of print. Nat Biotechnol. 2018. PMID: 30346939 Free PMC article.
HLA*LA-HLA typing from linearly projected graph alignments.
Dilthey AT, Mentzer AJ, Carapito R, Cutland C, Cereb N, Madhi SA, Rhie A, Koren S, Bahram S, McVean G, Phillippy AM. Dilthey AT, et al. Among authors: rhie a. Bioinformatics. 2019 Nov 1;35(21):4394-4396. doi: 10.1093/bioinformatics/btz235. Bioinformatics. 2019. PMID: 30942877 Free PMC article.
Integrating Hi-C links with assembly graphs for chromosome-scale assembly.
Ghurye J, Rhie A, Walenz BP, Schmitt A, Selvaraj S, Pop M, Phillippy AM, Koren S. Ghurye J, et al. Among authors: rhie a. PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. doi: 10.1371/journal.pcbi.1007273. eCollection 2019 Aug. PLoS Comput Biol. 2019. PMID: 31433799 Free PMC article.
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.
78 results