Research Summary

Selected Publications

• 1.Hon C.C., Ramilowski, J.A., Harshbarger, J., Bertin, N., Rackham, O.J., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T.M., Severin, J., Lizio, M., Kawaji, H., Kasukawa, T., Itoh, M., Burroughs, A.M., Noma, S., Djebali, S., Alam, T., Medvedeva, Y.A., Testa, A.C., Lipovich, L., Yip, C.W., Abugessaisa, I., Mendez, M., Hasegawa, A., Tang, D., Lassmann, T., Heutink, P., Babina, M., Wells, C.A., Kojima, S., Nakamura, Y., Suzuki, H., Daub, C.O., de Hoon, M.J., Arner, E., Hayashizaki, Y., Carninci, P., Forrest, A.R.:
  "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells."
  Science 347 (6225), 1010-1014. (2015).
• 2.Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D., Mathelier, A., Medvedeva, Y.A., Lennartsson, A., Drabløs, F., Ramilowski, J.A., Rackham, O., Gough, J., Andersson, R., Sandelin, A., Ienasescu, H., Ono, H., Bono, H., Hayashizaki, Y., Carninci, P., Forrest, A.R.:
  "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells."
  Science 347 (6225), 1010-1014. (2015).
• 3.Abugessaisa, I., Shimoji, H., Sahin, S., Kondo, A., Harshbarger, J., Lizio, M., Hayashizaki, Y., Carninci, P.; FANTOM consortium, Forrest, A., Kasukawa, T., Kawaji, H.:
  "FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki"
  Database (Oxford), baw105. (2016).
• 4.Medvedeva, Y.A., Lennartsson, A., Ehsani, R., Kulakovskiy, I.V., Vorontsov, I.E., Panahandeh, P., Khimulya, G., Kasukawa, T.; FANTOM Consortium, Drabløs, F.:
  "EpiFactors: a comprehensive database of human epigenetic factors and complexes"
  Database (Oxford), bav067. (2015).
• 5.Arner, E. et al.:
  "Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells."
  Science 347 (6225), 1010-1014. (2015).
• 6.Marina Lizio, Jayson Harshbarger, Hisashi Shimoji, Jessica Severin, Takeya Kasukawa, Serkan Sahin, Imad Abugessaisa, Shiro Fukuda, Fumi Hori, Sachi Ishikawa-Kato, et al.:
  "Gateways to the FANTOM5 promoter level mammalian expression atlas."
  Genome Biol. 16, 22. (2015).
• 7.FANTOM Consortium and the RIKEN PMI and CLST (DGT).:
  "A promoter-level mammalian expression atlas."
  Nature 507 (7493), 462-470. (2014).
• 8.Kasukawa, T., Masumoto, K., Nikaido, I., Nagano, M., Uno, K.D., Tsujino, K., Hanashima, C., Shigeyoshi, Y., and Ueda, H.R.:
  "Quantitative Expression Profile of Distinct Functional Regions in the Adult Mouse Brain."
  PLoS ONE. 6(8), e23228. (2011).
• 9.Maeda, N., Kasukawa, T., Oyama, R., Gough, J., Frith, M., Engstrom, P.G., Lenhard, B., Aturaliya, R.N., Batalov, S., Beisel, K.W., Bult, C.J., Fletcher, C.F., Forrest, A., Furuno, M., Hill, D., Itoh, M., Kanamori-Katayama, M., Katayama, S., Katoh, M., Kawashima, T., Quackenbush, J., Ravasi, T., Ring, B.Z., Shibata, K., Sugiura. K., Takenaka, Y., Teasdale, R.D., Wells, C.A., Zhu, Y., Kai, C., Kawai, J., Hume, D.A., Carninci, P., and Hayashizaki, Y.:
  "Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs."
  PLoS Genet. 2 (4), e62. (2006).
• 10.The FANTOM Consortium and RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group):
  "The Transcriptional Landscape of the Mammalian Genome."
  Science. 309, 1559-1563, (2005).

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