| 2021 | WALCOM | Overall and Delay Complexity of the CLIQUES and Bron-Kerbosch Algorithms. | Alessio Conte, Etsuji Tomita |
| 2017 | WALCOM | Efficient Algorithms for Finding Maximum and Maximal Cliques and Their Applications. | Etsuji Tomita |
| 2016 | FAW | A Much Faster Branch-and-Bound Algorithm for Finding a Maximum Clique. | Etsuji Tomita, Kohei Yoshida, Takuro Hatta, Atsuki Nagao, Hiro Ito, Mitsuo Wakatsuki |
| 2016 | PAKDD | A Fast and Complete Enumeration of Pseudo-Cliques for Large Graphs. | Hongjie Zhai, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita |
| 2015 | DIS | Enumerating Maximal Clique Sets with Pseudo-Clique Constraint. | Hongjie Zhai, Makoto Haraguchi, Yoshiaki Okubo, Etsuji Tomita |
| 2013 | SNPD | A Polynomial-Time Algorithm for Checking the Equivalence for Real-Time Deterministic Restricted One-Counter Transducers Which Accept by Final State. | Mitsuo Wakatsuki, Etsuji Tomita, Tetsuro Nishino |
| 2012 | DIS | Structural Change Pattern Mining Based on Constrained Maximal k-Plex Search. | Yoshiaki Okubo, Makoto Haraguchi, Etsuji Tomita |
| 2011 | CISIS | An Improved Clique-Based Method for Computing Edit Distance between Unordered Trees and Its Application to Comparison of Glycan Structures. | Tatsuya Akutsu, Tomoya Mori, Takeyuki Tamura, Daiji Fukagawa, Atsuhiro Takasu, Etsuji Tomita |
| 2010 | WALCOM | A Simple and Faster Branch-and-Bound Algorithm for Finding a Maximum Clique. | Etsuji Tomita, Yoichi Sutani, Takanori Higashi, Shinya Takahashi, Mitsuo Wakatsuki |
| 2007 | PDPTA | A More Efficient Algorithm for Finding a Maximum Clique with an Improved Approximate Coloring. | Etsuji Tomita, Yoichi Sutani, Takanori Higashi |
| 2005 | ALT | Editors' Introduction. | Sanjay Jain, Hans Ulrich Simon, Etsuji Tomita |
| 2005 | APBC | Clique-based algorithms for protein threading with profiles and constraints. | Dukka Bahadur, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto, Tatsuya Akutsu |
| 2004 | ALT | Learning Boolean Functions in AC | Akinobu Miyata, Jun Tarui, Etsuji Tomita |
| 2004 | APBC | Protein Side-chain Packing Problem: A Maximum Edge-weight Clique Algorithmic Approach. | Dukka Bahadur, Tatsuya Akutsu, Etsuji Tomita, Tomokazu Seki |
| 2004 | BIBE | Protein Threading with Profiles and Constraints. | Tatsuya Akutsu, Morihiro Hayashida, Etsuji Tomita, Jun'ichi Suzuki, Katsuhisa Horimoto |
| 2004 | COCOON | The Worst-Case Time Complexity for Generating All Maximal Cliques. | Etsuji Tomita, Akira Tanaka, Haruhisa Takahashi |