New Directions: Biology: See it Again - For the First Time. - Sean Luke; Shugo Hamahashi; Koji Kyoda; Hiroki Ueda (IEEE Intell. Syst., 1998)

A Model of Axis Determination for the Drosophila Wing Disc. - Koji Kyoda; Hiroaki Kitano (ECAL, 1999)

Simulation of Genetic Interaction for Drosophila Leg Formation. - Koji Kyoda; Hiroaki Kitano (Pacific Symposium on Biocomputing, 1999)

DBRF-MEGN method: an algorithm for deducing minimum equivalent gene networks from large-scale gene expression profiles of gene deletion mutants. - Koji Kyoda; Kotaro Baba; Shuichi Onami; Hiroaki Kitano (Bioinform., 2004)

A proof of the DBRF-MEGN method, an algorithm for deducing minimum equivalent gene networks. - Koji Kyoda; Kotaro Baba; Hiroaki Kitano; Shuichi Onami (Source Code Biol. Medicine, 2011)

WDDD: Worm Developmental Dynamics Database. - Koji Kyoda; Eru Adachi; Eriko Masuda; Yoko Nagai; Yoko Suzuki; Taeko Oguro; Mitsuru Urai; Ryoko Arai; Mari Furukawa; Kumiko Shimada; Junko Kuramochi; Eriko Nagai; et al. (Nucleic Acids Res., 2013)

Nuclear detection in 4D microscope images using enhanced probability map of top-ranked intensity-ordered descriptors. - Xian-Hua Han; Yukako Tohsato; Koji Kyoda; Shuichi Onami; Ikuko Nishikawa; Yen-Wei Chen 001 (ACPR, 2015)

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. - Koji Kyoda; Yukako Tohsato; Kenneth H. L. Ho; Shuichi Onami (Bioinform., 2015)

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. - Yukako Tohsato; Kenneth H. L. Ho; Koji Kyoda; Shuichi Onami (Bioinform., 2016)

Nuclear detection in 4D microscope images of a developing embryo using an enhanced probability map of top-ranked intensity-ordered descriptors. - Xian-Hua Han; Yukako Tohsato; Koji Kyoda; Shuichi Onami; Ikuko Nishikawa; Yen-Wei Chen 001 (IPSJ Trans. Comput. Vis. Appl., 2016)

Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of Caenorhabditis elegans. - Sihai Yang; Xian-Hua Han; Yukako Tohsato; Koji Kyoda; Shuichi Onami; Ikuko Nishikawa; Yen-Wei Chen 001 (J. Comput. Biol., 2017)

Development of an Integrated Visualization System for Phenotypic Character Networks. - Yosuke Onoue; Koji Kyoda; Miki Kioka; Kazutaka Baba; Shuichi Onami; Koji Koyamada (PacificVis, 2018)

Phenotype Anomaly Detection for Biological Dynamics Data Using a Deep Generative Model. - Eisuke Ito; Takaya Ueda; Ryo Takano; Yukako Tohsato; Koji Kyoda; Shuichi Onami; Ikuko Nishikawa (ICANN (2), 2022)

PHi-C2: interpreting Hi-C data as the dynamic 3D genome state. - Soya Shinkai; Hiroya Itoga; Koji Kyoda; Shuichi Onami (Bioinform., 2022)

SSBD Ontology: A Two-Tier Approach for Interoperable Bioimaging Metadata. - Yuki Yamagata; Koji Kyoda; Hiroya Itoga; Emi Fujisawa; Shuichi Onami (ISWC (2), 2025)