publications

Takayama, J., Tajima, T., Onami, S., Nishimura, H. (2021). C. elegans spermatozoa lacking spe-45 are incapable of fusing with the oocyte plasma membrane. MicroPubl. Biol. [PubMed][OpenAccess]

Imakubo, M., Takayama, J., Okada, H., Onami, S. (2021). Statistical image processing quantifies the changes in cytoplasmic texture associated with aging in Caenorhabditis elegans oocytes. BMC Bioinformatics 22, 73. [PubMed][OpenAccess]

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. (2021). QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy. [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. (2021). Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center. Lab Anim Res 37, 6. [PubMed][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. (2020). A Global View of Standards for Open Image Data Formats and Repositories. [arXiv]

Kyoda, K., Okada, H., Itoga, H., Onami, S. (2020). Deep collection of quantitative nuclear division dynamics data in RNAi-treated Caenorhabditis elegans embryos. [bioRxiv]

Yamagata, Y., Yamada, H. (2020). Ontological approach to the knowledge systematization of a toxic process and toxic course representation framework for early drug risk management. Sci. Rep. 10, 14581.  [PubMed][OpenAccess]

Shinkai, S., Onami, S., Nakato, R. (2020). Toward understanding the dynamic state of 3D genome. Comput. Struct. Biotechnol. J. 18, 2259–2269. [PubMed][OpenAccess]

Kyoda, K., Ho, K.H.L., Itoga, H., Tohsato, Y., Onami, S. (2020). BD5: An open HDF5-based data format to represent quantitative biological dynamics data. PLoS One 15, e0237468. [PubMed] [OpenAccess]

Shinkai, S., Sugawara, T., Miura, H., Hiratani, I.Onami, S. (2020). Microrheology for Hi-C Data Reveals the Spectrum of the Dynamic 3D Genome Organization. Biophys. J. 118, 2220–2228. [PubMed] [OpenAccess]

Shinkai, S., Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Taniguchi, Y., Onami, S. (2020). PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genom. Bioinform. 2, lqaa020. [PubMed][OpenAccess]

Imakubo, M., Takayama, J., Onami, S. (2018). Improvement and evaluation of a mathematical model for fertilization calcium wave in Caenorhabditis elegans. IPSJ Transactions on Bioinformatics 11, 24-30. [OpenAccess]

Onoue, Y., Kyoda, K., Kioka, M., Baba, K., Onami, S., Koyamada, K. (2018). Development of an integrated visualization system for phenotype character networks. In Proceedings of 2018 IEEE Pacific Visualization Symposium (PacificVis), pp. 21-25.

Azuma, Y., Onami, S. (2017). Biologically constrained optimization based cell membrane segmentation in C. elegans embryos. BMC Bioinformatics 18, 307. [PubMed][OpenAccess]

Takayama, J., Fujita, M., Onami, S. (2017). In vivo live imaging of calcium waves and other cellular processes during fertilization in Caenorhabditis elegans. Bio Protoc. 7, e2205. doi: 10.21769/BioProtoc.2205. [OpenAccess]

Yang, S., Han, X., Tohsato, Y., Kyoda, K., Onami, S., Nishikawa, I., Chen, Y. (2017). Phenotype analysis method for identification of gene functions involved in asymmetric division of Caenorhabditis elegans. J. Comput. Biol. 24, 436-446. [PubMed]

Han, X., Tohsato, Y., Kyoda, K., Onami, S., Nishikawa, I., and Chen, Y. (2016). Nuclear detection in 4D microscope images of developing embryo using an enhanced probability map of top-ranked intensity-ordered descriptors. IPSJ Trans Comput Vis Appl 8:8. [Open Access]

Tohsato, Y., Ho, K.H.L., Kyoda, K., and Onami, S. (2016). SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. Bioinformatics 32, 3471-3479. [PubMed][Open Access]

Takayama, J. and Onami, S. (2016). The sperm TRP-3 channel mediates the onset of a Ca2+ wave in the fertilized C. elegans oocyte. Cell Rep. 15, 625-637. [PubMed][Open Access]

Han, X., Tohsato, Y., Kyoda, K., Onami, S., Nishikawa, I., and Chen, Y. (2015). Nuclear detection in 4D microscope images using enhanced probability map of top-ranked intensity-ordered descriptors. In Proceedings of the 3rd Asian Conference on Pattern Recognition (ACPR2015), pp. 554-558.

Atupelage, C., Kyoda, K., Onami, S., Nagahashi, H. (2015). Cytoplasmic motion visualization and analysis of C. elegans embryo. In Proceedings of the International Conference on Biology and Biomedical Engineering (BBE2015), pp. 27-32.

Kyoda, K., Tohsato, Y., Ho, K.H.L., and Onami, S. (2015) Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. Bioinformatics 31, 1044-1052. [PubMed][Open Access]

Azuma, Y. and Onami, S. (2014). Automatic cell identification in the unique system of invariant embryogenesis in Caenorhabditis elegans. Biomed Eng Lett 4, 328-337. [Online First]

Azuma, Y. and Onami, S. (2013). Evaluation of the effectiveness of simple nuclei-segmentation methods on Caenorhabditis elegans embryogenesis images. BMC Bioinformatics 14, 295. [PubMed][Open Access]

Shimozawa, T., Yamagata, K., Kondo, T., Hayashi, S., Shitamukai, A., Konno, D., Matsuzaki, F., Takayama, J., Onami, S., Nakayama, H., Kosugi, Y., Watanabe, T.M., Fujita, K., and Mimori-Kiyosue, Y. (2013). Improving spinning disk confocal microscopy by preventing pinhole cross-talk for intravital imaging. Proc. Natl. Acad. Sci. USA 110, 3399-3404. [PubMed]

Kyoda, K., Adachi, E., Masuda, E., Nagai, Y., Suzuki, Y., Oguro, T., Urai, M., Arai, R., Furukawa, M., Shimada, K., Kuramochi, J., Nagai, E., and Onami, S. (2013). WDDD: Worm Developmental Dynamics Database. Nucleic Acids Res. 41, D732-D737. [PubMed][Open Access]

Fujita, M. and Onami, S. (2012). Cell-to-cell heterogeneity in cortical tension specifies curvature of contact surfaces in Caenorhabditis elegans embryos. PLoS One 7, e30224. [PubMed][Open Access]

Fujita, M. and Onami, S. (2011). Estimating intercellular surface tension by laser-induced cell fusion. Phys. Biol. 8, 064001. [PubMed][Preprint]

Kyoda, K., Baba, K., Kitano, H., and Onami, S. (2011). A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks. Source Code Biol. Med. 6, 12. [PubMed][Open Access]

Kimura, A., and Onami, S. (2010). Modeling microtubule-mediated forces and centrosome positioning in Caenorhabditis elegans embryos. Methods Cell Biol. 97, 437-453.

Hamahashi, S., Kitano, H., and Onami, S. (2007). A system for measuring cell division patterns of early Caenorhabditis elegans embryos by using image processing and object tracking. Systems Comput. Jpn. 38(11), 12-24.

Kimura, A., and Onami, S. (2007). Local cortical pulling-force repression switches centrosomal centration and posterior displacement in C. elegans. J. Cell Biol. 179, 1347-1354. [PubMed]

Kyoda, K., and Onami, S. (2007). DBRF-MEGN method: an algorithm for inferring gene regulatory networks from large-scale gene expression profiles. In Introduction to Systems Biology, S. Choi, ed. (Totowa, NJ: Humana Press), pp. 435-448.

Onami, S., and Kitano, H. (2006). Genome-wide prediction of genetic interactions in a metazoan. Bioessays 28, 1087-1090. [PubMed]

Hamahashi, S., and Onami, S. (2005). Objective measurement of spindle orientation in early Caenorhabditis elegans. Genome Inform. 16, 86-93. [PubMed][Open Access]

Hamahashi, S., Onami, S., and Kitano, H. (2005). Detection of nuclei in 4D Nomarski DIC microscope images of early Caenorhabditis elegans embryos using local image entropy and object tracking. BMC Bioinformatics 6, 125. [PubMed][Open Access]

Kimura, A., and Onami, S. (2005). Computer simulations and image-processing reveal length-dependent pulling force as the primary mechanism for C. elegans male pronuclear migration. Dev. Cell 8, 765-775. [PubMed][Cover]

Kyoda, K., Baba, K., Onami, S., and Kitano, H. (2004). DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. Bioinformatics 20, 2662-2675. [PubMed][Open Access]

Onami, S., Hamahashi, S., Nagasaki, M., Miyano, S., and Kitano, H. (2001). Automatic acquisition of cell lineage through 4D microscope and analysis of early C. elegans embryogenesis. In Foundations of Sysmtes Biology, H. Kitano, ed (Cambridge, MA: MIT Press), pp. 39-55.

Onami, S., Kyoda, K. M., Morohashi, M., and Kitano, H. (2001). The DBRF method for inferring a gene network from large-scale steady-state gene expression data. In Foundations of Systems Biology, H. Kitano, ed. (Cambridge, MA: MIT Press), pp. 59-75.

Kyoda, K. M., Morohashi, M., Onami, S., and Kitano, H. (2000). A gene network inference method from continuous-value gene expression data of wild-type and mutants. Genome Inform. 11, 196-204. [PubMed][Open Access]

Nagasaki, M., Onami, S., Miyano, S., and Kitano, H. (1999). Bio-calculus: its concept and molecular interaction. Genome Inform. 10, 133-143. [PubMed]

Yasuda, T., Bannai, H., Onami, S., Miyano, S., and Kitano, H. (1999). Towards automatic construction of cell-lineage of C. elegans from Nomarski DIC microscope images. Genome Inform. 10, 144-154. [PubMed]