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CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors.
Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, Natoli G, Buendia MA, Faivre J, Carninci P. Hashimoto K, et al. Genome Res. 2015 Dec;25(12):1812-24. doi: 10.1101/gr.191031.115. Epub 2015 Oct 28. Genome Res. 2015. PMID: 26510915 Free PMC article.
Single-Nucleotide Resolution Mapping of Hepatitis B Virus Promoters in Infected Human Livers and Hepatocellular Carcinoma.
Altinel K, Hashimoto K, Wei Y, Neuveut C, Gupta I, Suzuki AM, Dos Santos A, Moreau P, Xia T, Kojima S, Kato S, Takikawa Y, Hidaka I, Shimizu M, Matsuura T, Tsubota A, Ikeda H, Nagoshi S, Suzuki H, Michel ML, Samuel D, Buendia MA, Faivre J, Carninci P. Altinel K, et al. Among authors: hashimoto k. J Virol. 2016 Nov 14;90(23):10811-10822. doi: 10.1128/JVI.01625-16. Print 2016 Dec 1. J Virol. 2016. PMID: 27681123 Free PMC article.
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance.
Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H; FANTOM Consortium; Hasegawa Y, Forrest AR, Carninci P. Fort A, et al. Among authors: hashimoto k. Nat Genet. 2014 Jun;46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28. Nat Genet. 2014. PMID: 24777452
Functional annotation of human long noncoding RNAs via molecular phenotyping.
Ramilowski JA, Yip CW, Agrawal S, Chang JC, Ciani Y, Kulakovskiy IV, Mendez M, Ooi JLC, Ouyang JF, Parkinson N, Petri A, Roos L, Severin J, Yasuzawa K, Abugessaisa I, Akalin A, Antonov IV, Arner E, Bonetti A, Bono H, Borsari B, Brombacher F, Cameron CJ, Cannistraci CV, Cardenas R, Cardon M, Chang H, Dostie J, Ducoli L, Favorov A, Fort A, Garrido D, Gil N, Gimenez J, Guler R, Handoko L, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto K, Hayatsu N, Heutink P, Hirose T, Imada EL, Itoh M, Kaczkowski B, Kanhere A, Kawabata E, Kawaji H, Kawashima T, Kelly ST, Kojima M, Kondo N, Koseki H, Kouno T, Kratz A, Kurowska-Stolarska M, Kwon ATJ, Leek J, Lennartsson A, Lizio M, López-Redondo F, Luginbühl J, Maeda S, Makeev VJ, Marchionni L, Medvedeva YA, Minoda A, Müller F, Muñoz-Aguirre M, Murata M, Nishiyori H, Nitta KR, Noguchi S, Noro Y, Nurtdinov R, Okazaki Y, Orlando V, Paquette D, Parr CJC, Rackham OJL, Rizzu P, Sánchez Martinez DF, Sandelin A, Sanjana P, Semple CAM, Shibayama Y, Sivaraman DM, Suzuki T, Szumowski SC, Tagami M, Taylor MS, Terao C, Thodberg M, Thongjuea S, Tripathi V, Ulitsky I, Verardo R, Vorontsov IE, Yamamoto C, Young RS, Baillie JK, Forrest ARR, Guigó R, Hoffman … See abstract for full author list ➔ Ramilowski JA, et al. Among authors: hashimoto k. Genome Res. 2020 Jul;30(7):1060-1072. doi: 10.1101/gr.254219.119. Epub 2020 Jul 27. Genome Res. 2020. PMID: 32718982 Free PMC article.
Prevention of hepatocellular carcinoma by targeting MYCN-positive liver cancer stem cells with acyclic retinoid.
Qin XY, Suzuki H, Honda M, Okada H, Kaneko S, Inoue I, Ebisui E, Hashimoto K, Carninci P, Kanki K, Tatsukawa H, Ishibashi N, Masaki T, Matsuura T, Kagechika H, Toriguchi K, Hatano E, Shirakami Y, Shiota G, Shimizu M, Moriwaki H, Kojima S. Qin XY, et al. Among authors: hashimoto k. Proc Natl Acad Sci U S A. 2018 May 8;115(19):4969-4974. doi: 10.1073/pnas.1802279115. Epub 2018 Apr 23. Proc Natl Acad Sci U S A. 2018. PMID: 29686061 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.
7,698 results