| 2007 | DIS | Time and Space Efficient Discovery of Maximal Geometric Graphs. | Hiroki Arimura, Takeaki Uno, Shinichi Shimozono |
| 2004 | CPM | Approximate Point Set Pattern Matching on Sequences and Planes. | Tomoaki Suga, Shinichi Shimozono |
| 2004 | SPIRE | A Space-Saving Linear-Time Algorithm for Grammar-Based Compression. | Hiroshi Sakamoto, Takuya Kida, Shinichi Shimozono |
| 2001 | DIS | Mining Semi-structured Data by Path Expressions. | Katsuaki Taniguchi, Hiroshi Sakamoto, Hiroki Arimura, Shinichi Shimozono, Setsuo Arikawa |
| 2001 | ISAAC | Fragmentary Pattern Matching: Complexity, Algorithms and Applications for Analyzing Classic Literary Works. | Hideaki Hori, Shinichi Shimozono, Masayuki Takeda, Ayumi Shinohara |
| 2000 | ISAAC | A Simple and Quick Approximation Algorithm for Traveling Salesman Problem in the Plane. | Norihiro Kubo, Shinichi Shimozono, Katsuhiro Muramoto |
| 2000 | RECOMB | On approximation algorithms for local multiple alignment. | Tatsuya Akutsu, Hiroki Arimura, Shinichi Shimozono |
| 1998 | DIS | An Efficient Tool for Discovering Simple Combinatorial Patterns from Large Text Databases. | Hiroki Arimura, Atsushi Wataki, Ryoichi Fujino, Shinichi Shimozono, Setsuo Arikawa |
| 1998 | ISAAC | Maximizing Agreement with a Classification by Bounded or Unbounded Number of Associated Words. | Hiroki Arimura, Shinichi Shimozono |
| 1995 | ISAAC | An Approximation Algorithm for Alphabet Indexing Problem. | Shinichi Shimozono |
| 1995 | ISMB | BONSAI Garden: Parallel Knowledge Discovery System for Amino Acid Sequences. | Takayoshi Shoudai, Michael Lappe, Satoru Miyano, Ayumi Shinohara, Takeo Okazaki, Setsuo Arikawa, Tomoyuki Uchida, Shinichi Shimozono, Takeshi Shinohara, Satoru Kuhara |