Research Summary

Research Subjects

• Non-coding RNA
• FANTOM6
• RNA structure
• Bioinformatics

Selected Publications

• 1.De Hoon, M., Shin, J.W., Carninci, P.:
  "Paradigm shifts in genomics through the FANTOM projects"
  Mammalian Genome 26, 391-402 (2015).
• 2.Arner, E.; Daub, C.O.; Vitting-Seerup, K.; Andersson, R.; Lilje, B.; Drabløs, F.; Lennartsson, A.; Rönnerblad, M.; Hrydziuszko, O.; Vitezic, M.; Freeman, T.C.; Alhendi, A.M.; Arner, P.; Axton, R.; Baillie, J.K.; Beckhouse, A.; Bodega, B.; Briggs, J.; Brombacher, F.; Davis, M.; Detmar, M.; Ehrlund, A.; Endoh, M.; Eslami, A.; Fagiolini, M.; Fairbairn, L.; Faulkner, G.J.; Ferrai, C.; Fisher, M.E.; Forrester, L.; Goldowitz, D.; Guler, R.; Ha, T.; Hara, M.; Herlyn, M.; Ikawa, T.; Kai, C.; Kawamoto, H.; Khachigian, L.M.; Klinken, S.P.; Kojima, S.; Koseki, H.; Klein, S.; Mejhert, N.; Miyaguchi, K.; Mizuno, Y.; Morimoto, M.; Morris, K.J.; Mummery, C.; Nakachi, Y.; Ogishima, S.; Okada-Hatakeyama, M.; Okazaki, Y.; Orlando, V.; Ovchinnikov, D.; Passier, R.; Patrikakis, M.; Pombo, A.; Qin, X.Y.; Roy, S.; Sato, H.; Savvi, S.; Saxena, A.; Schwegmann, A.; Sugiyama, D.; Swoboda, R.; Tanaka, H.; Tomoiu, A.; Winteringham, L.N.; Wolvetang, E.; Yanagi-Mizuochi, C.; Yoneda, M.; Zabierowski, S.; Zhang, P.; Abugessaisa, I.; Bertin, N.; Diehl, A.D.; Fukuda, S.; Furuno, M.; Harshbarger, J.; Hasegawa, A.; Hori, F.; Ishikawa-Kato, S.; Ishizu, Y.; Itoh, M.; Kawashima, T.; Kojima, M.; Kondo, N.; Lizio, M.; Meehan, T.F.; Mungall, C.J.; Murata, M.; Nishiyori-Sueki, H.; Sahin, S.; Nagao-Sato, S.; Severin, J.; De Hoon, M.J.L.; Kawai, J.; Kasukawa, T.; Lassmann, T.; Suzuki, H.; Kawaji, H.; Summers, K.M.; Wells, C.; FANTOM Consortium; Hume, D.A.; Forrest, A.R.; Sandelin, A.; Carninci, P.; Hayashizaki, Y.:
  "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells"
  Science 347, 1010-1014 (2015).
• 3.Boele, J., Persson, H., Shin, J.W., Ishizu, Y., Newie, I.S., Søkilde, R., Hawkins, S.M., Coarfa, C., Ikeda, K., Takayama, K.I., Horie-Inoue, K., Ando, Y., Burroughs, A.M., Sasaki, C,, Suzuki, C., Sakai, M., Aoki, S., Ogawa, A., Hasegawa, A., Lizio, M., Kaida, K., Teusink, B., Carninci, P., Suzuki, H., Inoue, S., Gunaratne, P.H., Rovira, C., Hayashizaki, Y., De Hoon, M.J.L.:
  "PAPD5-mediated 3' adenylation and subsequent degradation of miR-21 is disrupted in proliferative disease"
  Proceedings of the National Academy of Sciences USA 111, 11467-11472 (2014).
• 4.Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C.A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C.H., De Hoon, M.J.L., Andersson, R., Sandelin, A., Suzuki, H., Wei, C.L., Koseki, H., The FANTOM Consortium, Hasegawa, Y., Forrest, A.R.R., Carninci, P.:
  "Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance"
  Nature Genetics 46, 558-566 (2014).
• 5.FANTOM Consortium and the RIKEN PMI and CLST (DGT).:
  "A promoter-level mammalian expression atlas"
  Nature 507, 462-470 (2014)
• 6.Francia, S., Michelini, F., Saxena, A., Tang, D., De Hoon, M.J.L., Anelli, V., Mione, M., Carninci, P., d'Adda di Fagagna, F.:
  "Site-specific DICER and DROSHA RNA products control the DNA-damage response"
  Nature 488, 231-235 (2012)
• 7.Burroughs, A.M., Ando, Y., De Hoon, M.J.L., Tomaru, Y., Nishibu, T., Ukekawa, R., Funakoshi, T., Kurokawa, T., Suzuki, H., Hayashizaki, Y., Daub, C.O.:
  "A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness"
  Genome Research 20, 1398-1410 (2010)
• 8.De Hoon, M.J.L., Taft, R.J., Hashimoto, T., Kanamori-Katayama, M., Kawaji, H., Kawano, M., Kishima, M., Lassmann, T., Faulkner, G.J., Mattick, J.S., Daub, C.O., Carninci, P., Kawai, J., Suzuki, H., Hayashizaki, Y.:
  "Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries"
  Genome Research 20, 257-264 (2010)
• 9.Cock, P.J., Antao, T., Chang, J.T., Chapman, B.A., Cox, C.J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., De Hoon, M.J.L.:
  "Biopython: freely available Python tools for computational molecular biology and bioinformatics"
  Bioinformatics 25, 1422-1423 (2009)
• 10.The FANTOM Consortium & Riken Omics Science Center.:
  "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line"
  Nature Genetics 41, 553-562 (2009)

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