| 2025 | COCOON | A Sparse Dynamic Programming Algorithm for Solving the Coding Sequence Design Problem. | Long-Shang Cho, Kai-Wei Chang, Chin Lung Lu |
| 2013 | COCOON | An Efficient Algorithm for One-Sided Block Ordering Problem with Block-Interchange Distance. | Kun-Tze Chen, Chi-Long Li, Chung-Han Yang, Chin Lung Lu |
| 2006 | CPM | Efficient Algorithms for Regular Expression Constrained Sequence Alignment. | Yun Sheng Chung, Chin Lung Lu, Chuan Yi Tang |
| 2003 | COCOON | On the Full and Bottleneck Full Steiner Tree Problems. | Yen Hung Chen, Chin Lung Lu, Chuan Yi Tang |
| 2002 | COCOON | The Full Steiner Tree Problem in Phylogeny. | Chin Lung Lu, Chuan Yi Tang, Richard Chia-Tung Lee |
| 2001 | COCOON | A New Measure of Edit Distance between Labeled Trees. | Chin Lung Lu, Zheng-Yao Su, Chuan Yi Tang |
| 2000 | ISAAC | Efficient Minus and Signed Domination in Graphs. | Chin Lung Lu, Sheng-Lung Peng, Chuan Yi Tang |
| 2000 | ISAAC | An Approximate Algorithm for the Weighted Hamiltonian Path Completion Problem on a Tree. | Q. S. Wu, Chin Lung Lu, Richard C. T. Lee |
| 1997 | COCOON | Effincient Domination of Permutation Graphs and Trapezoid Graphs. | Y. Daniel Liang, Chin Lung Lu, Chuan Yi Tang |