| 2018 | CiE | Computing with Multisets: A Survey on Reaction Automata Theory. | Takashi Yokomori, Fumiya Okubo |
| 2014 | DNA | The Computational Capability of Chemical Reaction Automata. | Fumiya Okubo, Takashi Yokomori |
| 2005 | DNA | Linearizer and Doubler : Two Mappings to Unify Molecular Computing Models Based on DNA Complementarity. | Kaoru Onodera, Takashi Yokomori |
| 2002 | DNA | On the Computational Power of Insertion-Deletion Systems. | Akihiro Takahara, Takashi Yokomori |
| 1999 | DLT | Computation = self-assembly + conformational change: toward new computing paradigms. | Takashi Yokomori |
| 1998 | ALT | Locality, Reversibility, and Beyond: Learning Languages from Positive Data. | Tom Head, Satoshi Kobayashi, Takashi Yokomori |
| 1998 | MCU | On the Universality of Post and Splicing Systems. | Claudio Ferretti, Giancarlo Mauri, Satoshi Kobayashi, Takashi Yokomori |
| 1997 | ALT | Identifiability of Subspaces and Homomorphic Images of Zero-Reversible Languages. | Satoshi Kobayashi, Takashi Yokomori |
| 1997 | ICEC | DNA implementation of simple Horn clause computation. | Satoshi Kobayashi, Takashi Yokomori, G. Sampei, K. Mizobuchi |
| 1997 | ICEC | On the power of circular splicing systems and DNA computability. | Takashi Yokomori, Satoshi Kobayashi, Claudio Ferretti |
| 1995 | ALT | On Approximately Identifying Concept Classes in the Limit. | Satoshi Kobayashi, Takashi Yokomori |
| 1994 | ALT | Learning Concatenations of Locally Testable Languages from Positive Data. | Satoshi Kobayashi, Takashi Yokomori |
| 1994 | ALT | Inductive Inference of Monogenic Pure Context-free Languages. | Noriyuki Tanida, Takashi Yokomori |
| 1993 | COLT | Learning Two-Tape Automata from Queries and Counterexamples. | Takashi Yokomori |
| 1992 | ALT | On Learning Systolic Languages. | Takashi Yokomori |
| 1991 | ALT | Polynomial-time identification of very regular languages in the limit. | Noriyuki Tanida, Takashi Yokomori |
| 1991 | COLT | Polynomial-Time Learning of Very Simple Grammars from Positive Data. | Takashi Yokomori |
| 1987 | IJCAI | Inductive Inference of Context-free Languages - Context-free Expression Method. | Takashi Yokomori |
| 1986 | VLDB | On Analogical Query Processing in Logic Database. | Takashi Yokomori |
| 1985 | IJCAI | A Logic Program Schema and Its Applications. | Takashi Yokomori |