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Page 1
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: yokoyama tt. F1000Res. 2019 Oct 14;8:1751. doi: 10.12688/f1000research.19630.2. eCollection 2019. F1000Res. 2019. PMID: 34386196 Free PMC article.
MoMI-G: modular multi-scale integrated genome graph browser.
Yokoyama TT, Sakamoto Y, Seki M, Suzuki Y, Kasahara M. Yokoyama TT, et al. BMC Bioinformatics. 2019 Nov 5;20(1):548. doi: 10.1186/s12859-019-3145-2. BMC Bioinformatics. 2019. PMID: 31690272 Free PMC article.
Long-read sequencing for non-small-cell lung cancer genomes.
Sakamoto Y, Xu L, Seki M, Yokoyama TT, Kasahara M, Kashima Y, Ohashi A, Shimada Y, Motoi N, Tsuchihara K, Kobayashi SS, Kohno T, Shiraishi Y, Suzuki A, Suzuki Y. Sakamoto Y, et al. Among authors: yokoyama tt. Genome Res. 2020 Sep;30(9):1243-1257. doi: 10.1101/gr.261941.120. Epub 2020 Sep 4. Genome Res. 2020. PMID: 32887687 Free PMC article.
A chromosome-level genome assembly of a model conifer plant, the Japanese cedar, Cryptomeria japonica D. Don.
Fujino T, Yamaguchi K, Yokoyama TT, Hamanaka T, Harazono Y, Kamada H, Kobayashi W, Ujino-Ihara T, Uchiyama K, Matsumoto A, Izuno A, Tsumura Y, Toyoda A, Shigenobu S, Moriguchi Y, Ueno S, Kasahara M. Fujino T, et al. Among authors: yokoyama tt. BMC Genomics. 2024 Nov 5;25(1):1039. doi: 10.1186/s12864-024-10929-4. BMC Genomics. 2024. PMID: 39501145 Free PMC article.
Efficient indexing and querying of annotations in a pangenome graph.
Novak AM, Chung D, Hickey G, Djebali S, Yokoyama TT, Garrison E, Narzisi G, Paten B, Monlong J. Novak AM, et al. Among authors: yokoyama tt. bioRxiv [Preprint]. 2024 Oct 15:2024.10.12.618009. doi: 10.1101/2024.10.12.618009. bioRxiv. 2024. PMID: 39464141 Free PMC article. Preprint.