Large Scale Data Managing Unit

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.

Research Fields

Engineering / Biology & Biochemistry / 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

Publications

1. *Kasukawa, T., Sugimoto, S., Hida, A., Minami, Y., Mori, M., Honma, S., Honma, K., Mishima, K., Soga, T., and Ueda, H.R.:
   "Human blood metabolite timetable indicates internal body time"
   Proc Natl Acad Sci U S A. 109 (37), 15036-15041 (2012).
2. *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).
3. *Ukai-Tadenuma, M., Kasukawa, T., and Ueda, H.R.:
   "Proof-by-synthesis of the transcriptional logic of mammalian circadian clocks"
   Nat Cell Biol. 10, 1154-1163, (2008).
4. *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).
5. *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).
6. *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).
7. *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).
8. *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).
9. *The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team:
   "Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs"
   Nature 420, 563-573 (2002).