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]