| 2009 | IJCNN | Inference of genetic networks using linear programming machines: Application of a priori knowledge. | Shuhei Kimura, Yuichi Shiraishi, Mariko Hatakeyama |
| 2007 | IJCNN | Inference of Genetic Networks using a Reduced NGnet Model. | Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Kotaro Yoshida, Koki Matsumura, Mariko Hatakeyama |
| 2006 | IJCNN | Function Approximation Approach to the Inference of Normalized Gaussian Network Models of Genetic Networks. | Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama |
| 2005 | CEC | Inference of genetic networks using neural network models. | Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Koki Matsumura, Mariko Hatakeyama |
| 2005 | ICDE | Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. | Aki Hasegawa, Kazumi Kuriyama-Matsumura, Xiaomei Yu, Mariko Hatakeyama, Akihiko Konagaya |
| 2003 | CEC | Inference of S-system models of genetic networks using a genetic local search. | Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya |