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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. Among authors: forrest ar. 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.
Whole genome transcriptome analysis.
Forrest AR, Carninci P. Forrest AR, et al. RNA Biol. 2009 Apr-Jun;6(2):107-12. doi: 10.4161/rna.6.2.7931. RNA Biol. 2009. PMID: 19875928 Review.
Unamplified cap analysis of gene expression on a single-molecule sequencer.
Kanamori-Katayama M, Itoh M, Kawaji H, Lassmann T, Katayama S, Kojima M, Bertin N, Kaiho A, Ninomiya N, Daub CO, Carninci P, Forrest AR, Hayashizaki Y. Kanamori-Katayama M, et al. Among authors: forrest ar. Genome Res. 2011 Jul;21(7):1150-9. doi: 10.1101/gr.115469.110. Epub 2011 May 19. Genome Res. 2011. PMID: 21596820 Free PMC article.
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing.
Kawaji H, Lizio M, Itoh M, Kanamori-Katayama M, Kaiho A, Nishiyori-Sueki H, Shin JW, Kojima-Ishiyama M, Kawano M, Murata M, Ninomiya-Fukuda N, Ishikawa-Kato S, Nagao-Sato S, Noma S, Hayashizaki Y, Forrest AR, Carninci P; FANTOM Consortium. Kawaji H, et al. Among authors: forrest ar. Genome Res. 2014 Apr;24(4):708-17. doi: 10.1101/gr.156232.113. Epub 2014 Mar 27. Genome Res. 2014. PMID: 24676093 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: forrest ar. 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 MM, Hon… See abstract for full author list ➔ Ramilowski JA, et al. 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.
Deep sequencing of short capped RNAs reveals novel families of noncoding RNAs.
de Hoon M, Bonetti A, Plessy C, Ando Y, Hon CC, Ishizu Y, Itoh M, Kato S, Lin D, Maekawa S, Murata M, Nishiyori H, Shin JW, Stolte J, Suzuki AM, Tagami M, Takahashi H, Thongjuea S, Forrest ARR, Hayashizaki Y, Kere J, Carninci P. de Hoon M, et al. Among authors: forrest arr. Genome Res. 2022 Aug 12;32(9):1727-35. doi: 10.1101/gr.276647.122. Online ahead of print. Genome Res. 2022. PMID: 35961773 Free PMC article.
218 results