| 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 |
| 2005 | RECOMB | Comparative Systems Biology of the Sporulation Initiation Network in Prokaryotes. | Michiel J. L. de Hoon, Dennis Vitkup |
| 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 | PSB | Predicting the Operon Structure of Bacillus subtilis Using Operon Length, Intergene Distance, and Gene Expression Information. | Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano |
| 2003 | PSB | Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data of Bacillus Subtilis Using Differential Equations. | Michiel J. L. de Hoon, Seiya Imoto, Kazuo Kobayashi, Naotake Ogasawara, Satoru Miyano |
| 2002 | DIS | Inferring Gene Regulatory Networks from Time-Ordered Gene Expression Data Using Differential Equations. | Michiel J. L. de Hoon, Seiya Imoto, Satoru Miyano |