| 2012 | PSB | Functional Annotation of Intrinsically Disordered Domains by Their Amino Acid Content Using IDD Navigator. | Ashwini Patil, Shunsuke Teraguchi, Huy Dinh, Kenta Nakai, Daron M. Standley |
| 2011 | WABI | Seed-Set Construction by Equi-entropy Partitioning for Efficient and Sensitive Short-Read Mapping. | Kouichi Kimura, Asako Koike, Kenta Nakai |
| 2006 | APBC | Protein Subcellular Localisation Prediction with WoLF PSORT. | Paul Horton, Keun-Joon Park, Takeshi Obayashi, Kenta Nakai |
| 2005 | PSB | Bayesian Joint Prediction of Associated Transcription Factors in Bacillus subtilis. | Yuko Makita, Michiel J. L. de Hoon, Naotake Ogasawara, Satoru Miyano, Kenta Nakai |
| 2004 | DIS | Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance. | Shunsuke Inenaga, Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2004 | ISMB | Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data. | Michiel J. L. de Hoon, Yuko Makita, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Kenta Nakai, Satoru Miyano |
| 2004 | RECOMB | Parameter Landscape Analysis for Common Motif Discovery Programs. | Natalia Polouliakh, Michiko Konno, Paul Horton, Kenta Nakai |
| 2004 | WABI | Finding Optimal Pairs of Patterns. | Hideo Bannai, Heikki Hyyr, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano |
| 2003 | PSB | Intrasplicing - Analysis of Long Intron Sequences. | Sascha Ott, Yoshinori Tamada, Hideo Bannai, Kenta Nakai, Satoru Miyano |
| 2001 | FlAIRS | Views: Fundamental Building Blocks in the Process of Knowledge Discovery. | Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano |
| 1997 | ISMB | Better Prediction of Protein Cellular Localization Sites with the it k Nearest Neighbors Classifier. | Paul Horton, Kenta Nakai |
| 1997 | ISMB | Functional Prediction of B. subtilis Genes from Their Regulatory Sequences. | Tetsushi Yada, Yasushi Totoki, Takahiro Ishii, Kenta Nakai |
| 1996 | ISMB | A Probabilistic Classification System for Predicting the Cellular Localization Sites of Proteins. | Paul Horton, Kenta Nakai |