| 2019 | BIBE | DegSampler3: Pairwise Dependency Model in Degradation Motif Site Prediction of Substrate Protein Sequences. | Osamu Maruyama, Fumiko Matsuzaki |
| 2018 | BIBE | DegSampler: Collapsed Gibbs Sampler for Detecting E3 Binding Sites. | Osamu Maruyama, Fumiko Matsuzaki |
| 2005 | ICCS | Reconstructing Phylogenetic Trees of Prokaryote Genomes by Randomly Sampling Oligopeptides. | Osamu Maruyama, Akiko Matsuda, Satoru Kuhara |
| 2004 | PSB | Extensive Search for Discriminative Features of Alternative Splicing. | Hiroki Sakai, Osamu Maruyama |
| 2004 | WABI | Searching for Regulatory Elements of Alternative Splicing Events Using Phylogenetic Footprinting. | Daichi Shigemizu, Osamu Maruyama |
| 2003 | ECCB | Finding optimal degenerate patterns in DNA sequences. | Daisuke Shinozaki, Tatsuya Akutsu, Osamu Maruyama |
| 2002 | DIS | Toward Drawing an Atlas of Hypothesis Classes: Approximating a Hypothesis via Another Hypothesis Model. | Osamu Maruyama, Takayoshi Shoudai, Satoru Miyano |
| 2001 | DIS | VML: A View Modeling Language for Computational Knowledge Discovery. | Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Satoru Miyano |
| 2001 | DIS | Learning Conformation Rules. | Osamu Maruyama, Takayoshi Shoudai, Emiko Furuichi, Satoru Kuhara, Satoru Miyano |
| 2001 | FlAIRS | Views: Fundamental Building Blocks in the Process of Knowledge Discovery. | Hideo Bannai, Yoshinori Tamada, Osamu Maruyama, Kenta Nakai, Satoru Miyano |
| 1999 | DIS | Designing Views in HypothesisCreator: System for Assisting in Discovery. | Osamu Maruyama, Tomoyuki Uchida, Kim Lan Sim, Satoru Miyano |
| 1998 | DIS | Toward Genomic Hypothesis Creator: View Designer for Discovery. | Osamu Maruyama, Tomoyuki Uchida, Takayoshi Shoudai, Satoru Miyano |
| 1998 | SODA | Identification of Gene Regulatory Networks by Strategic Gene Disruptions and Gene Overexpressions. | Tatsuya Akutsu, Satoru Kuhara, Osamu Maruyama, Satoru Miyano |
| 1996 | STACS | Extracting Best Consensus Motifs from Positive and Negative Examples. | Erika Tateishi, Osamu Maruyama, Satoru Miyano |
| 1995 | MFCS | Graph Inference from a Walk for TRees of Bounded Degree 3 is NP-Complete. | Osamu Maruyama, Satoru Miyano |
| 1992 | MFCS | Inferring a Tree from Walks. | Osamu Maruyama, Satoru Miyano |