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RIKEN Center for Integrative Medical Sciences Laboratory for Large-Scale Biomedical Data Technology

Team Leader: Takeya Kasukawa (Ph.D.)

Research Summary

Takeya  Kasukawa(Ph.D.)

Today, life scientist should find and investigate various achievements and findings from journals and published databases each by each, and that they should collect and annotate additional information for their further studies. The mission is to create tools to analyze and compare large datasets and to set up a computational environment that is adequate, which address increasingly larger amount of next generation sequencing data produced inside and outside the division, in order to utilize such knowledge to further applied researches including drug discoveries and medical practices.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Informatics
  • Biology
  • Medicine, Dentistry & Pharmacy


  • Bioinformatics
  • Database
  • Data engineering
  • Genomics/Transcriptomics
  • Statistics

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).

Related Links

Lab Members

Principal investigator

Takeya Kasukawa
Team Leader

Core members

Imad Abugessaisa
Research Scientist
Nobuyuki Takeda
Technical Staff I
Teruaki Kitakura
Technical Staff I
Atsushi Kondo
Technical Staff I
Akira Furukawa
Technical Staff I

Contact Information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan