Research Summary

Selected Publications

• 1. Fukushima, A., Takahashi, M., Nagasaki, H., Aono, Y., Kobayashi, M., Kusano, M., Saito, K., Kobayashi, N., and Arita, M.:
  "Development of RIKEN Plant Metabolonome MetaDatabase"
  Plant and Cell Physiology 63(3), 433-440. (2021). doi: 10.1093/pcp/pcab173
• 2. Swedlow, J. R., Kankaanpää, P., Sarkans, U., Goscinski, W., Galloway, G., Malacrida, L., Sullivan, R. P., Härtel, S., Brown, C. M., Wood, C., Keppler, A., Paina, F., Loos, B., Zullino, S., Longo, D. L., Aime, S., and Onami, S.:
  "A Global view of standards for open image data formats and repositories"
  Nature Methods 18, 1440-1446. (2021). doi: 10.1038/s41592-021-01113-7
• 3. Kita, Y., Nishibe, H., Wang, Y., Hashikawa, T., Kikuchi, S. S., U, M., Yoshida, A. C., Yoshida, C., Kawase, T., Ishii, S., Skibbe, H., and Shimogori, T.:
  "Cellular-resolution gene expression profiling in the neonatal marmoset brain reveals dynamic species- and region-specific differences"
  Proceedings of the National Academy of Sciences 118(18), e2020125118. (2021). doi: 10.1073/pnas.2020125118
• 4. Abugessaisa, I., Ramilowski, JA., Lizio, M., Severin, J., Hasegawa, A., Harshbarger, J., Kondo, A., Noguchi, S., Yip, C., Ooi, J., Tagami, M., Hori, F., Agrawal, S., Hon, C., Cardon, M., Ikeda, S., Ono, H., Bono, H., Kato, M., Hashimoto. K., Bonetti. A., Kato, M., Kobayashi, N., Shin, J., de Hoon, M., Hayashizaki, Y., Carninci, P., Kawaji, H., and Kasukawa, T.:
  "FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs"
  Nucleic Acids Research 49, gkaa1054. (2020). doi: 10.1093/nar/gkaa1054
• 5. Tsugawa, H., Ikeda, K., Takahashi, M., Satoh, A., Mori, Y., Uchino, H., Okahashi, N., Yamada, Y., Tada, I., Bonini, P., Higashi, Y., Okazaki, Y., Zhou, Z., Zhu, Z., Koelmel, J., Cajka, T., Fiehn, O., Saito, K., Arita, M., and Arita, M.:
  "A lipidome atlas in MS-DIAL 4"
  Nature Biotechnology 38, 1159–1163 (2020). doi: 10.1038/s41587-020-0531-2
• 6. Tanaka, N., and Masuya, H.:
  "An atlas of evidence-based phenotypic associations across the mouse phenome"
  Scientific Reports 10, 3957 (2020). doi: 10.1038/s41598-020-60891-w
• 7. Morita, M., Shimokawa, K., Nishimura, M., Nakamura, S., Tsujimura, Y., Takemoto, S., Tawara, T., Yokota, H., Wemler, S., Miyamoto, D., Ikeno, H., Sato, A., Furuichi, T., Kobayashi, N., Okumura, Y., Yamaguchi, Y., and Okamura- Oho, Y.:
  "ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks"
  Nucleic Acids Research 47(D1), D859-D866 (2019). doi: 10.1093/nar/gky951
• 8. Kobayashi, N., Kume, S., Lenz, K., and Masuya, H.:
  "RIKEN MetaDatabase: a database platform for health care and life sciences as a microcosm of linked open data cloud"
  International Journal on Semantic Web and Information Systems 14(1), 140-164 (2018). doi: 10.4018/IJSWIS.2018010106
• 9. Shimogori, T., Abe, A., Go, Y., Hashikawa, T., Kishi, N., Kikuchi, S. S., Kita, Y., Niimi, K., Nishibe, H., Okuno, M., Saga, K., Sakurai, M., Sato, M., Serizawa, T., Suzuki, S., Takahashi, E., Tanaka, M., Tatsumoto, S., Toki, M., U, M., Wang, Y., Windak, K. J., Yamagishi, H., Yamashita, K., Yoda, T., Yoshida, A. C., Yoshida, C., Yoshimoto, T., and Okano, H.:
  "Digital gene atlas of neonate common marmoset brain"
  Neuroscience Research 128, 1-13 (2018). doi: 10.1016/j.neures.2017.10.009
• 10. Tohsato, Y., Ho, K. H. L., Kyoda, K., and Onami, S.:
  "SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena"
  Bioinformatics 32(22), 3471-3479 (2016). doi: 10.1093/bioinformatics/btw417

Related Links

• RIKEN Open Life Science Platform

Lab Members

Contact Information

2-2-3 Minatojima-minamimachi, Chuo-ku,
Kobe, Hyogo
650-0047 Japan

Email: sonami [at] riken.jp