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EAGLE: Explicit Alternative Genome Likelihood Evaluator.
Kuo T, Frith MC, Sese J, Horton P. Kuo T, et al. Among authors: sese j. BMC Med Genomics. 2018 Apr 20;11(Suppl 2):28. doi: 10.1186/s12920-018-0342-1. BMC Med Genomics. 2018. PMID: 29697369 Free PMC article.
Homeolog expression quantification methods for allopolyploids.
Kuo TCY, Hatakeyama M, Tameshige T, Shimizu KK, Sese J. Kuo TCY, et al. Among authors: sese j. Brief Bioinform. 2020 Mar 23;21(2):395-407. doi: 10.1093/bib/bby121. Brief Bioinform. 2020. PMID: 30590436 Free PMC article. Review.
Involvement of Rev1 in alkylating agent-induced loss of heterozygosity in Oryzias latipes.
Fujikawa Y, Ishikawa-Fujiwara T, Kuo T, Shinkai N, Shoji T, Kawasaki T, Kamei Y, Sakuraba Y, Sato A, Kinoshita M, Gondo Y, Yuba S, Tsujimura T, Sese J, Todo T. Fujikawa Y, et al. Among authors: sese j. Genes Cells. 2020 Feb;25(2):124-138. doi: 10.1111/gtc.12746. Epub 2020 Feb 5. Genes Cells. 2020. PMID: 31917895 Free PMC article.
Multiple wheat genomes reveal global variation in modern breeding.
Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala D, Klymiuk V, Byrns B, Gundlach H, Bandi V, Siri JN, Nilsen K, Aquino C, Himmelbach A, Copetti D, Ban T, Venturini L, Bevan M, Clavijo B, Koo DH, Ens J, Wiebe K, N'Diaye A, Fritz AK, Gutwin C, Fiebig A, Fosker C, Fu BX, Accinelli GG, Gardner KA, Fradgley N, Gutierrez-Gonzalez J, Halstead-Nussloch G, Hatakeyama M, Koh CS, Deek J, Costamagna AC, Fobert P, Heavens D, Kanamori H, Kawaura K, Kobayashi F, Krasileva K, Kuo T, McKenzie N, Murata K, Nabeka Y, Paape T, Padmarasu S, Percival-Alwyn L, Kagale S, Scholz U, Sese J, Juliana P, Singh R, Shimizu-Inatsugi R, Swarbreck D, Cockram J, Budak H, Tameshige T, Tanaka T, Tsuji H, Wright J, Wu J, Steuernagel B, Small I, Cloutier S, Keeble-Gagnère G, Muehlbauer G, Tibbets J, Nasuda S, Melonek J, Hucl PJ, Sharpe AG, Clark M, Legg E, Bharti A, Langridge P, Hall A, Uauy C, Mascher M, Krattinger SG, Handa H, Shimizu KK, Distelfeld A, Chalmers K, Keller B, Mayer KFX, Poland J, Stein N, McCartney CA, Spannagl M, Wicker T, Pozniak CJ. Walkowiak S, et al. Among authors: sese j. Nature. 2020 Dec;588(7837):277-283. doi: 10.1038/s41586-020-2961-x. Epub 2020 Nov 25. Nature. 2020. PMID: 33239791 Free PMC article.
De Novo Genome Assembly of the Japanese Wheat Cultivar Norin 61 Highlights Functional Variation in Flowering Time and Fusarium-Resistant Genes in East Asian Genotypes.
Shimizu KK, Copetti D, Okada M, Wicker T, Tameshige T, Hatakeyama M, Shimizu-Inatsugi R, Aquino C, Nishimura K, Kobayashi F, Murata K, Kuo T, Delorean E, Poland J, Haberer G, Spannagl M, Mayer KFX, Gutierrez-Gonzalez J, Muehlbauer GJ, Monat C, Himmelbach A, Padmarasu S, Mascher M, Walkowiak S, Nakazaki T, Ban T, Kawaura K, Tsuji H, Pozniak C, Stein N, Sese J, Nasuda S, Handa H. Shimizu KK, et al. Among authors: sese j. Plant Cell Physiol. 2021 Mar 25;62(1):8-27. doi: 10.1093/pcp/pcaa152. Plant Cell Physiol. 2021. PMID: 33244607 Free PMC article.
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.
Grapotte M, Saraswat M, Bessière C, Menichelli C, Ramilowski JA, Severin J, Hayashizaki Y, Itoh M, Tagami M, Murata M, Kojima-Ishiyama M, Noma S, Noguchi S, Kasukawa T, Hasegawa A, Suzuki H, Nishiyori-Sueki H, Frith MC; FANTOM consortium; Chatelain C, Carninci P, de Hoon MJL, Wasserman WW, Bréhélin L, Lecellier CH. Grapotte M, et al. Nat Commun. 2021 Jun 2;12(1):3297. doi: 10.1038/s41467-021-23143-7. Nat Commun. 2021. PMID: 34078885 Free PMC article.
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw.
Milosavljevic S, Kuo T, Decarli S, Mohn L, Sese J, Shimizu KK, Shimizu-Inatsugi R, Robinson MD. Milosavljevic S, et al. Among authors: sese j. BMC Genomics. 2021 Jul 17;22(1):547. doi: 10.1186/s12864-021-07845-2. BMC Genomics. 2021. PMID: 34273949 Free PMC article.
95 results