| 2022 | ISAAC | On Algorithmic Self-Assembly of Squares by Co-Transcriptional Folding. | Szilrd Zsolt Fazekas, Hwee Kim, Ryuichi Matsuoka, Shinnosuke Seki, Hinano Takeuchi |
| 2019 | UC | DNA Origami Words and Rewriting Systems. | James Garrett, Natasa Jonoska, Hwee Kim, Masahico Saito |
| 2018 | DLT | Site-Directed Deletion. | Da-Jung Cho, Yo-Sub Han, Hwee Kim, Kai Salomaa |
| 2018 | DNA | Construction of Geometric Structure by Oritatami System. | Yo-Sub Han, Hwee Kim |
| 2018 | DNA | Transcript Design Problem of Oritatami Systems. | Yo-Sub Han, Hwee Kim, Shinnosuke Seki |
| 2017 | DNA | Ruleset Optimization on Isomorphic Oritatami Systems. | Yo-Sub Han, Hwee Kim |
| 2017 | UC | Deduplication on Finite Automata and Nested Duplication Systems. | Da-Jung Cho, Yo-Sub Han, Hwee Kim |
| 2016 | DNA | Nondeterministic Seedless Oritatami Systems and Hardness of Testing Their Equivalence. | Yo-Sub Han, Hwee Kim, Makoto Ota, Shinnosuke Seki |
| 2015 | LATA | Frequent Pattern Mining with Non-overlapping Inversions. | Da-Jung Cho, Yo-Sub Han, Hwee Kim |
| 2015 | UC | Duplications and Pseudo-Duplications. | Da-Jung Cho, Yo-Sub Han, Hwee Kim, Alexandros Palioudakis, Kai Salomaa |
| 2014 | FAW | Space-Efficient Approximate String Matching Allowing Inversions in Fast Average Time. | Hwee Kim, Yo-Sub Han |
| 2014 | SPIRE | Online Multiple Palindrome Pattern Matching. | Hwee Kim, Yo-Sub Han |
| 2014 | UC | Pseudo-inversion on Formal Languages. | Da-Jung Cho, Yo-Sub Han, Shin-Dong Kang, Hwee Kim, Sang-Ki Ko, Kai Salomaa |
| 2014 | WALCOM | Alignment with Non-overlapping Inversions on Two Strings. | Da-Jung Cho, Yo-Sub Han, Hwee Kim |