Centers & Labs

RIKEN Center for Life Science Technologies

Large Scale Data Managing Unit

Unit Leader: Takeya Kasukawa (Ph.D.)
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 Field

Biology & Biochemistry

Related Research Fields

Engineering / Molecular Biology & Genetics / Computer Science

Research Subjects

  • Development of large-scale biological data management
  • Development of large-scale data analysis
  • Development of biological database construction

Selected Publications

  1. Erik Arner et al.:
    “Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.”
    Science. in press 2015.
  2. 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.
  3. FANTOM Consortium and the RIKEN PMI and CLST (DGT).:
    “A promoter-level mammalian expression atlas.”
    Nature 507 (7493) 462-470. 2014.
  4. 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.
  5. Kawaguchi, A., Ikawa, T., Kasukawa, T., Ueda, H. R., Kurimoto, K., Saitou, M., and Matsuzaki, F.
    Single-cell gene profiling defines differential progenitor subclasses in mammalian neurogenesis,
    Development 135 (18) 3113-3124. 2008.
  6. 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.
  7. 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.
  8. RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group) and the FANTOM Consortium.:
    “Antisense Transcription in the Mammalian Transcriptome.”
    Science. 309 1564-1566. 2005.
  9. Kasukawa, T., Katayama, S., Kawaji, H., Suzuki, H., Hume D.A., and Hayashizaki., Y.:
    “Construction of representative transcript and protein sets of human, mouse, and rat as a platform for their transcriptome and proteome analysis.”
    Genomics. 84 913-921. 2004.
  10. Kasukawa, T., Furuno, M., Nikaido, I., Bono, H., Hume, D.A., Bult, C., Hill, D.P., Baldarelli, R., Gough, J., Kanapin, A., Matsuda, H., Schriml, L.M., Hayashizaki, Y., Okazaki, Y., and Quackenbush, J.:
    “Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System.”
    Genome Res. 13 1542-1551. 2003.

Lab Members

Principal Investigator

Takeya Kasukawa
Unit Leader

Core Members

Imad Abugessaisa
Research Scientist
Shuhei Noguchi
Postdoctoral Researcher
Nobuyuki Takeda
Technical Staff 1
Teruaki Kitakura
Technical Staff 1
Atsushi Kondo
Technical Staff 1
Akira Furukawa
Technical Staff 1