| 2013 | CIBCB | Classifying protein interaction type with associative patterns. | Huang-Cheng Kuo, Ping-Lin Ong |
| 2011 | BIBE | Classification and Screening of Recognition Protein Complexes with Genetic Programming. | Huang-Cheng Kuo, Jia-Hao Li |
| 2009 | HIS | Finding Time-Delayed Gene Regulation Patterns from Microarray Data. | Huang-Cheng Kuo, Pei-Cheng Tsai, Jen-Peng Huang |
| 2008 | ISDA | Predicting Protein-Protein Recognition Using Feature Vector. | Huang-Cheng Kuo, Ping-Lin Ong, Jiajie Li, Jen-Peng Huang |
| 2006 | PAKDD | Filtering Bio-sequence Based on Sequence Descriptor. | Te-Wen Hsieh, Huang-Cheng Kuo, Jen-Peng Huang |
| 2005 | KES | A Divisive Ordering Algorithm for Mapping Categorical Data to Numeric Data. | Huang-Cheng Kuo |
| 2004 | KES | Distance Preserving Mapping from Categories to Numbers for Indexing. | Huang-Cheng Kuo, Yi-Sen Lin, Jen-Peng Huang |
| 1998 | DEXA | Selecting Actions to Trigger in Active Database Applications. | Huang-Cheng Kuo, Gultekin zsoyoglu |
| 1997 | ICRA | A database server architecture for agile manufacturing. | Sungkil Lee, Huang-Cheng Kuo, Nevzat Hurkan Balkir, Gultekin zsoyoglu |
| 1996 | SSDBM | A Scientific Multimedia Database System for Polymer Science Experiments. | Taekyong Lee, Tolga Bozkaya, Huang-Cheng Kuo, Gultekin zsoyoglu, Z. Meral zsoyoglu |