| 2010 | CiE | Development of a Bacteria Computer: From | Yasubumi Sakakibara |
| 2010 | PSB | Improvement of Structure Conservation Index with Centroid Estimators. | Yohei Okada, Kengo Sato, Yasubumi Sakakibara |
| 2009 | WABI | A Non-parametric Bayesian Approach for Predicting RNA Secondary Structures. | Kengo Sato, Michiaki Hamada, Toutai Mituyama, Kiyoshi Asai, Yasubumi Sakakibara |
| 2008 | DNA | Operon Structure Optimization by Random Self-assembly. | Yusuke Nakagawa, Katsuyuki Yugi, Kenji Tsuge, Mitsuhiro Itaya, Hiroshi Yanagawa, Yasubumi Sakakibara |
| 2006 | APBC | Discriminative Detection of Cis-Acting Regulatory Variation From Location Data. | Yuji Kawada, Yasubumi Sakakibara |
| 2005 | DNA | Intensive | Junna Kuramochi, Yasubumi Sakakibara |
| 2005 | DNA | Development of an | Hirotaka Nakagawa, Kensaku Sakamoto, Yasubumi Sakakibara |
| 2005 | ECCB | RNA secondary structural alignment with conditional random fields. | Kengo Sato, Yasubumi Sakakibara |
| 2003 | DNA | In Vitro Translation-Based Computations. | Yasubumi Sakakibara, Takahiro Hohsaka |
| 2003 | ISMB | Pair hidden Markov models on tree structures. | Yasubumi Sakakibara |
| 2002 | DNA | A DNA-based Computational Model Using a Specific Type of Restriction Enzyme. | Yasubumi Sakakibara, Hiroshi Imai |
| 2001 | CEC | Probabilistic logical inference using quantities of DNA strands. | Yasubumi Sakakibara |
| 2001 | DNA | Population Computation and Majority Inference in Test Tube. | Yasubumi Sakakibara |
| 2000 | DNA | Solving Computational Learning Problems of Boolean Formulae on DNA Computers. | Yasubumi Sakakibara |
| 1999 | ICML | GA-based Learning of Context-Free Grammars using Tabular Representations. | Yasubumi Sakakibara, Mitsuhiro Kondo |
| 1995 | ALT | Grammatical Inference: An Old and New Paradigm. | Yasubumi Sakakibara |
| 1994 | ALT | Learning Languages by Collecting Cases and Tuning Parameters. | Yasubumi Sakakibara, Klaus P. Jantke, Steffen Lange |
| 1994 | CPM | Recent Methods for RNA Modeling Using Stochastic Context-Free Grammars. | Yasubumi Sakakibara, Michael Brown, Richard Hughey, I. Saira Mian, Kimmen Sjlander, Rebecca C. Underwood, David Haussler |
| 1992 | COLT | A Noise Model on Learning Sets of Strings. | Yasubumi Sakakibara, Rani Siromoney |
| 1991 | ALT | ACE: A syntax-directed editor customizable from examples and queries. | Yuji Takada, Yasubumi Sakakibara, Takeshi Ohtani |
| 1990 | ALT | Occam Algorithms for Learning From Noisy Examples. | Yasubumi Sakakibara |
| 1990 | ALT | Exact Learning of Semilinear Sets. | Yuji Takada, Kunihiko Hiraishi, Yasubumi Sakakibara |
| 1988 | COLT | Learning Context-Free Grammars from Structural Data in Polynomial Time. | Yasubumi Sakakibara |