Shinkai, S., Onami, S. (2025). 4D Genome Analysis Using PHi-C2. In: Nakato, R. (eds) Computational Methods for 3D Genome Analysis. Methods in Molecular Biology, vol 2856. Humana, New York, NY. pp 271–279. [PubMed]
Kyoda, K., Itoga, H., Yamagata, Y., Fujisawa, E., Wang, F., Miranda-Miranda, M., Yamamoto, H., Nakano, Y., Tohsato, Y., Onami, S.(2024) SSBD: an ecosystem for enhanced sharing and reuse of bioimaging data. Nucleic Acids Res. gkae860. [Open Access] [PubMed]
Shinkai, S., Onami, S., Miyaguchi, T. (2024). Generalized Langevin dynamics for single beads in linear elastic networks. Phys. Rev. E. 110, 044136. [Open Access]
Sugawara, K., Uno, S.N., Kamiya, M., Sakamoto, A., Urano, Y., Funatsu, T., Okabe, K. (2024). Nanoscale dynamics and localization of single endogenous mRNAs in stress granules. Nucleic Acids Res. 52, 8675-8686. [Open Access][PubMed]
Matsumoto, M., Matsushita, K., Hane, M., Wen, C., Kurematsu, C., Ota, H., Nguyen, B.H., Thai, Q.T., Herranz-Perez, V., Sawada, M., Fujimoto, K., Garcia-Verdugo, M.J., Kimura, D.K., Seki, T., Sato, C., Ohno, N., Sawamoto, K. (2024) Neuraminidase inhibition promotes the collective migration of neurons and recovery of brain function. EMBO Mol. Med. 16, 1228 – 1253. [Open Access]
Hiraki-Kajiyama, T., Miyasaka, N., Ando, R., Wakisaka, N., Itoga, H., Onami, S., Yoshihara, Y. (2024). An atlas and database of neuropeptide gene expression in the adult zebrafish forebrain. J. Comp. Neurol. 532, e25619. [Open Access][PubMed]
Yamagata, Y., Kushida, T., Onami, S., Masuya, H. (2024). Homeostasis imbalance process ontology: a study on COVID-19 infectious processes. BMC Med. Inform. Decis. Mak. 23, 301. [Open Access][PubMed]
Yamagata, Y., Fukuyama, T., Onami, S., Masuya, H. (2024). Prototyping an Ontological Framework for Cellular Senescence Mechanisms: A Homeostasis Imbalance Perspective. Sci Data 11, 485. [Open Access][PubMed]
Wen, C. (2024). Deep Learning-Based Cell Tracking in Deforming Organs and Moving Animals. In: Imaging Cell Signaling. Methods Mol. Biol. vol 2800. Wuelfing, C., Murphy, R.F. eds. (New York, NY: Humana Press) pp. 203-215.
Sprague, D.Y., Rusch, K., Dunn, R.L., Borchardt, J., Bubnis, G., Chiu, G., Wen, C., Suzuki, R., Chaudhary, S., Dichter, B., Ly, R., Onami, S., Lu, H., Kimura, K., Yemini, E.I., Kato, S. (2024). Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans. [bioRxiv]
Ichimura, T., Kakizuka, T., Sato, Y., Itano, K., Seiriki, K., Hashimoto, H., Itoga, H., Onami, S., Nagai, T. (2024). Volumetric trans-scale imaging of massive quantity of heterogeneous cell populations in centimeter-wide tissue and embryo. eLife, 13:RP93633. [Open Access]
Bajcsy, P., Bhattiprolu, S., Borner, K., Cimini, B., Collinson. L., Ellenberg, J., Fiolka, R., Giger, M., Goscinski, W., Hartley, M., Hotaling, N., Horwitz, R., Jug, F., Kreshuk, A., Lundberg, E., Mathur, A., Narayan, K., Onami, S., Plant, A.L., Prior, F., Swedlow, J., Taylor, A., Keppler, A. (2024). Enabling Global Image Data Sharing in the Life Sciences. [arXiv]
Bialy, N., Alber, F., Andrews, B., Angelo, M., Beliveau, B., Bintu, L., Boettiger, A., Boehm, U., Brown, C.M., Bukar, M.M., Chambers, J.J., Cimini, B.A., Eliceiri, K., Errington, R., Faklaris, O., Gaudreault, N., Germain, R.N., Goscinski, W., Grunwald, D., Halter, M., Hanein, D., Hickey, J.W., Lacoste, J., Laude, A., Lundberg, E., Ma, J., Malacrida, L., Moore, J., Nelson, G., Neumann, E.K., Nitschke, R., Onami, S., Pimentel, J.A., Plant, A.L., Radtke, A.J., Sabata, B., Schapiro, D., Schöneberg, J., Spraggins, J.M., Sudar, D., Vierdag, W.A.M., Volkmann, N., Wählby, C., Siyuan, W., Yaniv, Z., Strambio-De-Castillia, C. (2024). Harmonizing the Generation and Pre-publication Stewardship of FAIR Image Data. [arXiv][PubMed]
Ohishi, H., Shinkai, S., Owada, H., Fujii, T., Hosoda, K., Onami, S., Yamamoto, T., Ohkawa, Y., Ochiai, H. (2023). Transcription-coupled changes in higher-order genomic structure and transcription hub viscosity prolong enhancer-promoter connectivity. [bioRxiv]
Okamoto, K., Fujita, H., Okada, Y., Shinkai, S., Onami, S., Abe, K., Fujimoto, K., Sasaki, K., Shioi, Go., Watanabe, T. M. (2023). Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance. EMBO J. 42, e112305.[PubMed]
Moore, J., Basurto-Lozada, D., Besson, S., Bogovic, J., Bragantini, J., Brown, E. M., Burel, JM., Casas, Moreno, X., de Medeiros, G., Diel, E. E., Gault, D., Ghosh, S. S., Gold, I., Halchenko, Y. O., Hartley, M., Horsfall, D., Keller, M. S., Kittisopikul, M., Kovacs, G., Küpcü Yoldaş, A., Kyoda, K., le Tournoulx, de la Villegeorges, A., Li, T., Liberali, P., Lindner, D., Linkert, M., Lüthi, J., Maitin-Shepard, J., Manz, T., Marconato, L., McCormick, M., Lange, M., Mohamed, K., Moore, W., Norlin, N., Özdemir, B., Palla, G., Pape, C., Pelkmans, L., Pietzsch, T., Preibisch, S., Prete, M., Rzepka, N., Samee, S., Schaub, N., Sidky, H., Solak, A. C., Stirling, D. R., Striebel, J., Tischer, C., Toloudis, D., Virshup, I., Walczysko, P., Watson, A. M., Wong, F., Yamauchi, K. A., Bayraktar, O., Haniffa, M., Hotaling, N., Onami, S., Royer, L. A., Saalfeld, S., Stegle, O., Theis, F. J., Swedlow, J. R. (2023) .OME-Zarr: a cloud-optimized bioimaging file format with international community support. Histochem. Cell Biol. 160, 223-251.[Open Access][PubMed]
Sugawara, K. (2023). Training deep learning models for cell image segmentation with sparse annotations. [bioRxiv]
Hara, M., Ariyoshi, M., Sano, T., Nozawa, R., Shinkai, S., Onami, S., Jansen, I., Hirota, T., Fukagawa, T. (2023). Centromere/kinetochore is assembled through CENP-C oligomerization. Mol. Cell 83, 2188-2205.e13. [Open Access][Pubmed]
Wen, C., Matsumoto, M., Sawada, M., Sawamoto, K., Kimura, D.K. (2023). Seg2Link: an efficient and versatile solution for semi-automatic cell segmentation in 3D image stacks. Sci. Rep. 13, 7109. [Open Access][Pubmed]
Shioi, G., Watanabe, M., T., Kaneshiro, J., Azuma, Y., Onami, S. (2023). Trans-scale live imaging of an E5.5 mouse embryo using incubator-type dual-axes light-sheet microscopy. [bioRxiv]
Nozaki, T., Shinkai, S., Ide, S., Higashi, K., Tamura, S., Shimazoe, M. A., Nakagawa, M., Suzuki, Y., Okada, Y., Sasai, M., Onami, S., Kurokawa, K., Iida, S., Maeshima, K. (2023). Condensed but liquid-like domain organization of active chromatin regions in living human cells. Sci. Adv. 9, eadf1488. [Open Access][PubMed]
Azuma, Y., Okada, H., Onami, S. (2023). Systematic analysis of cell morphodynamics in C. elegans early embryogenesis. Front. Bioinform. 3,1082531. [Open Access][PubMed]
Ito, E., Ueda, T., Takano, R., Tohsato, Y., Kyoda, K., Onami, S., Nishikawa, I. (2022). Phenotype anomaly detection for biological dynamics data using a deep generative model. Proceedings of the 31st International Conference on Artificial Neural Networks (ICANN 2022). Lecture Notes in Computer Science (LNCS) 13530, 432-444. [Open Access]
Shinkai, S., Itoga, H., Kyoda, K., Onami, S. (2022). PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. Bioinformatics 38, 4984–4986. [PubMed][Open Access]
Iida S., Shinkai, S., Itoh, Y., Tamura, S., Kanemaki, M. T., Onami, S., Maeshima, K. (2022). Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. Sci. Adv. 8, eabn5626. [PubMed][Open Access]
Kubota, Y., Ota, N., Takatsuka, H., Unno, T., Onami, S., Sugimoto, A., Ito, M. (2022). The PAF1 complex cell-autonomously promotes oogenesis in Caenorhabditis elegans. Genes Cells. 27, 409-420. [PubMed][Open Access]
Kaneshiro, J., Shioi, G., Okamoto, K., Onami, S., Watanabe, T. (2021). Improvement in image quality via the pseudo confocal effect in multidirectional digital scanned laser light-sheet microscopy. Opt. Express 29, 24278-24288. [PubMed][Open Access]
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. -J., 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. -L., Conde-Sousa, E., Corbett, A. D., Cordelieres, F. P., Nery, E. D., 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., 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. J. Microsc. 284, 56-73.[PubMed][Open Access]
Imakubo, M., Kyoda, K., Itoga, H., Takayama, J., Onami, S. (2021). Texture-Based Screening to Identify Genes Involved in Reproductive Aging in Caenorhabditis Elegans. Int. J. Biosci. Biochem. Bioinform. 11, 40-49. [Open Access]
Hirata, T., Tohsato, Y., Itoga, H., Shioi, G., Kiyonari, H., Oka, S., Fujimori, T., Onami, S. (2021). NeuroGT: A brain atlas of neurogenic tagging CreER drivers for birthdate-based classification and manipulation of mouse neurons. Cell Rep. Methods 1, 100012. [PubMed][Open Access]
Sarkans, U., Chiu, W., Collinson, L., Darrow, M. C., Ellenberg, J., Grunwald, D., Hériché, J. K., Iudin, A., Martins, G. G., Meehan, T., Narayan, K., Patwardhan, A., Russell, M. R. G., Saibil, H. R., Strambio-De-Castillia, C., Swedlow, J. R., Tischer, C., Uhlmann, V., Verkade, P., Barlow, M., Bayraktar, O., Birney, E., Catavitello. C., Cawthorne, C., Wagner-Conrad, S., Duke, E., Paul-Gilloteaux, P., Gustin, E., Harkiolaki, M., Kankaanpää, P., Lemberger, T., McEntyre, J., Moore, J., Nicholls, A. W., Onami, S., Parkinson, H., Parsons, M., Romanchikova, M., Sofroniew, N., Swoger, J., Utz, N., Voortman, L. M., Wong, F., Zhang, P., Kleywegt, G. J., Brazma, A. (2021). REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology. Nat. Methods 18, 1418-1422. [PubMed][Open Access]
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., Onami, S. (2021). A global view of standards for open image data formats and repositories. Nat. Methods 18, 1440-1446. [PubMed][Open Access]
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][Open Access]
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][Open Access]
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][Open Access]
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][Open Access]
Shinkai, S., Onami, S., Nakato, R. (2020). Toward understanding the dynamic state of 3D genome. Comput. Struct. Biotechnol. J. 18, 2259–2269. [PubMed][Open Access]
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] [Open Access]
Shinkai, S.,
Shinkai, S., Nakagawa, M., Sugawara, T., Togashi, Y., Ochiai, H., Nakato, R., Taniguchi, Y., Onami, S. PHi-C: deciphering Hi-C data into polymer dynamics. NAR Genom. Bioinform. 2, lqaa020. [PubMed][Open Access]
Moore, J., Kobayashi, N., Kunis, S., Onami, S., Swedlow, J. R., the OME Consortium (2019) On bringing bioimaging data into the open (world). Proceedings of 12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4HCLS 2019), 44-53. [Open Access (PDF 693KB)
]
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. [Open Access]
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][Open Access]
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. [Open Access]
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]