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論文リスト

論文

  • Nelson, G., Boehm, U., Bagley, S., Bajcsy, P., Bischof, J., Brown, C. M., Dauphin, A., Dobbie, I. M., Eriksson, J. E., Faklaris, O., Fernandez-Rodriguez, J., Ferrand, A., Gelman, L., Gheisari, A., Hartmann, H., Kukat, C., Laude, A., Mitkovski, M., Munck, S., North, A. J., Rasse, T. M., Resch-Genger, U., Schuetz, L. C., Seitz, A., Strambio-De-Castillia, C., Swedlow, J. R., Alexopoulos, I., Aumayr, K., Avilov, S., Bakker, G., Bammann, R. R., Bassi, A., Beckert, H., Beer, S., Belyaev, Y., Bierwagen, J., Birngruber, K. A., Bosch, M., Breitlow, J., Cameron, L. A., Chalfoun, J., Chambers, J. J., Chen, C., Conde-Sousa, E., Corbett, A. D., Cordelieres, F. P., Del, Nery, E., Dietzel, R., Eismann, F., Fazeli, E., Felscher, A., Fried, H., Gaudreault, N., Goh, W. I., Guilbert, T., Hadleigh, R., Hemmerich, P., Holst, G. A., Itano, M. S., Jaffe, C. B., Jambor, H. K., Jarvis, S. C., Keppler, A., Kirchenbuechler, D., Kirchner, M., Kobayashi, N., Krens, G., Kunis, S., Lacoste, J., Marcello, M., Martins, G. G., Metcalf, D. J., Mitchell, C. A., Moore, J., Mueller, T., Nelson, M. S., Ogg, S., Onami, S., Palmer, A. L., Paul-Gilloteaux, P., Pimentel, J. A., Plantard, L., Podder, S., Rexhepaj, E., Royeck, M., Royon, A., Saari, M. A., Schapman, D., Schoonderwoert, V., Schroth-Diez, B., Schwartz, S., Shaw, M., Spitaler, M., Stoeckl, M. T., Sudar, D., Teillon, J., Terjung, S., Thuenauer, R., Wilms, C. D., Wright, G. D., Nitschke, R. QUAREP-LiMi: a community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. (2021). [arXiv]
  • Masuya, H., Usuda, D., Nakata, H., Yuhara, N., Kurihara, K., Namiki, Y., Iwase, S., Takada, T., Tanaka, N., Suzuki, K., Yamagata, Y., Kobayashi, N., Yoshiki, A., Kushida, T. Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. Laboratory Animal Research 37, 6 (2021). [OpenAccess]
  • 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 (D1), D892-D898 (2020). [OpenAccess]
  • Swedlow, J. R., Kankaanpää, P., Sarkans, U., Goscinski, W., Galloway, G., Sullivan, R. P., Brown, C. M., Wood, C., Keppler, A., Loos, B., Zullino, S., Longo, D. L., Aime, S., Onami, S. A Global view of standards for open image data formats and repositories. (2020). [arXiv]
  • Kyoda, K., Okada, H., Itoga, H., Onami, S. Deep collection of quantitative nuclear division dynamics data in RNAi-treated Caenorhabditis elegans embryos. (2020).  [bioRxiv]
  • Yamagata, Y., Yamada, H. Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. Scientific Reports 10, 14581 (2020). [OpenAccess]
  • Kyoda, K., Ho, K.H.L., Itoga, H., Tohsato, Y., Onami, S. BD5: an open HDF5-based data format to represent quantitative biological dynamics data. PLOS ONE 15, e0237468 (2020). [OpenAccess]
  • 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). [OpenAccess]
  • Tanaka, N., and Masuya, H. An atlas of evidence-based phenotypic associations across the mouse phenome. Scientific Reports 10, 3957 (2020). [OpenAccess]
  • Ozaki, H., Hayashi, T., Umeda, M., Nikaido, I. Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets. BMC Genomics 21, 177 (2020). [OpenAccess]
  • Matsumoto, H., Hayashi, T., Ozaki, H., Tsuyuzaki, K., Umeda, M., Iida, T., Nakamura, M., Okano, H., Nikaido, I. An NMF-based approach to discover overlooked differentially expressed gene regions from single-cell RNA-seq data. NAR Genomics and Bioinformatics 2 (1), lqz020 (2020). [OpenAccess]
  • Tsuyuzaki, K., Sato, H., Sato, K., Nikaido, I. Benchmarking principal component analysis for large-scale single-cell RNA-sequencing. Genome Biology 21, 9 (2020). [OpenAccess]
  • Kadota, M., Nishimura, O., Miura, H., Tanaka, K., Hiratani, I., Kuraku, S. Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?. GigaScience 9 (1), giz158 (2020). [OpenAccess]
  • 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). [OpenAccess]
  • 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). [OpenAccess]
  • Tsuyuzaki K., Nikaido. I. Biological systems as heterogeneous information networks: a mini-review and perspectives. HeteroNAM’18. WSDM2018 (2018). [arXiv]
  • Matsumoto, H., Kiryu, H., Furusawa, C., Ko, MSH., Ko, SBH., Gouda, N., Hayashi, T., Nikaido, I. SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation. Bioinformatics 33 (15), 2314–2321 (2017). [OpenAccess]