| 2015 | CPM | Improved Algorithms for the Boxed-Mesh Permutation Pattern Matching Problem. | Sukhyeun Cho, Joong Chae Na, Jeong Seop Sim |
| 2013 | COCOA | Fast Order-Preserving Pattern Matching. | Sukhyeun Cho, Joong Chae Na, Kunsoo Park, Jeong Seop Sim |
| 2013 | IWOCA | Suffix Tree of Alignment: An Efficient Index for Similar Data. | Joong Chae Na, Heejin Park, Maxime Crochemore, Jan Holub, Costas S. Iliopoulos, Laurent Mouchard, Kunsoo Park |
| 2013 | SPIRE | Suffix Array of Alignment: A Practical Index for Similar Data. | Joong Chae Na, Heejin Park, Sunho Lee, Minsung Hong, Thierry Lecroq, Laurent Mouchard, Kunsoo Park |
| 2010 | CPM | Finding Optimal Alignment and Consensus of Circular Strings. | Taehyung Lee, Joong Chae Na, Heejin Park, Kunsoo Park, Jeong Seop Sim |
| 2009 | ISAAC | Improved Algorithms for Finding Consistent Superstrings Based on a New Graph Model. | Jin Wook Kim, Siwon Choi, Joong Chae Na, Jeong Seop Sim |
| 2009 | SPIRE | Consensus Optimizing Both Distance Sum and Radius. | Amihood Amir, Gad M. Landau, Joong Chae Na, Heejin Park, Kunsoo Park, Jeong Seop Sim |
| 2009 | SPIRE | On-Line Construction of Parameterized Suffix Trees. | Taehyung Lee, Joong Chae Na, Kunsoo Park |
| 2007 | ALENEX | Faster Filters for Approximate String Matching. | Juha Krkkinen, Joong Chae Na |
| 2007 | CPM | A Simple Construction of Two-Dimensional Suffix Trees in Linear Time. | Dong Kyue Kim, Joong Chae Na, Jeong Seop Sim, Kunsoo Park |
| 2005 | COCOON | O(n | Joong Chae Na, Raffaele Giancarlo, Kunsoo Park |
| 2005 | CPM | Linear-Time Construction of Compressed Suffix Arrays Using o(n log n)-Bit Working Space for Large Alphabets. | Joong Chae Na |
| 2004 | SPIRE | Simple Implementation of String B-Trees.. | Joong Chae Na, Kunsoo Park |
| 2000 | DCC | Data Compression with Truncated Suffix Trees. | Joong Chae Na, Kunsoo Park |