| 2025 | DLT | A Comparative Analysis of Deletion Closure Operations and Their Properties. | Da-Jung Cho, Tikhon Pshenitsyn |
| 2025 | DNA | Programmable Co‑Transcriptional Splicing: Realizing Regular Languages via Hairpin Deletion. | Da-Jung Cho, Szilrd Zsolt Fazekas, Shinnosuke Seki, Max Wiedenhft |
| 2025 | IJCNN | MaCSE: Multi-Agent Ranking Distillation for Contrastive Learning of Sentence Embeddings. | Zekai Zhi, Zhilan Wang, Rize Jin, Kehui Song, Da-Jung Cho, He Wang |
| 2025 | NAACL | Unsupervised Sentence Representation Learning with Syntactically Aligned Negative Samples. | Zhilan Wang, Zekai Zhi, Rize Jin, Kehui Song, He Wang, Da-Jung Cho |
| 2018 | DLT | Site-Directed Deletion. | Da-Jung Cho, Yo-Sub Han, Hwee Kim, Kai Salomaa |
| 2017 | UC | Deduplication on Finite Automata and Nested Duplication Systems. | Da-Jung Cho, Yo-Sub Han, Hwee Kim |
| 2016 | DLT | Outfix-Guided Insertion - (Extended Abstract). | Da-Jung Cho, Yo-Sub Han, Timothy Ng, Kai Salomaa |
| 2016 | SOFSEM | Pseudoknot-Generating Operation. | Da-Jung Cho, Yo-Sub Han, Timothy Ng, Kai Salomaa |
| 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 | 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 |