| 2012 | CloudCom | Efficient protein structure alignment algorithms under the MapReduce framework. | Che-Lun Hung, Yaw-Ling Lin, Chen-En Hsieh, Guan-Jie Hua |
| 2012 | RECOMB | Synthetic Sequence Design for Signal Location Search. | Yaw-Ling Lin, Charles B. Ward, Steven Skiena |
| 2011 | HPCC | CUDA-FRESCO: Frequency-Based RE-Sequencing Tool Based on CO-clustering Segmentation by GPU. | Chun-Yuan Lin, Chuan Yi Tang, Sheng-Ta Li, Yaw-Ling Lin, Che-Lun Hung |
| 2011 | TrustCom | Efficient GPGPU-Based Parallel Packet Classification. | Che-Lun Hung, Yaw-Ling Lin, Kuan-Ching Li, Hsiao-Hsi Wang, Shih-Wei Guo |
| 2011 | WADS | Constructing Orthogonal de Bruijn Sequences. | Yaw-Ling Lin, Charles B. Ward, Bharat Jain, Steven Skiena |
| 2008 | COCOON | Efficient Algorithms for SNP Haplotype Block Selection Problems. | Yaw-Ling Lin |
| 2005 | AINA | Performance Issues of Grid Computing Based on Different Architecture Cluster Computing Platforms. | Hsun-Chang Chang, Kuan-Ching Li, Yaw-Ling Lin, Chao-Tung Yang, Hsiao-Hsi Wang, Liang-Teh Lee |
| 2004 | BIBE | The Application of Alternative Splicing Graphs in Quantitative Analysis of Alternative Splicing Form from EST Database. | Hsun-Chang Chang, Po-Shun Yu, Tze-Wei Huang, Yaw-Ling Lin, Fang-Rong Hsu |
| 2004 | BIBE | Genome-Wide Alternative Splicing Events Detection through Analysis of Large Scale ESTs. | Fang-Rong Hsu, Hwan-You Chang, Yaw-Ling Lin, Yin-Te Tsai, Hui-Ling Peng, Ying Tsong Chen, Che Feng Chen, Chia Yang Cheng, Chia-Hung Liu, Min Yao Shih |
| 2003 | ISAAC | Efficient Algorithms for Descendent Subtrees Comparison of Phylogenetic Trees with Applications to Co-evolutionary Classifications in Bacterial Genome. | Yaw-Ling Lin, Tsan-sheng Hsu |
| 2002 | COCOON | Minimum Back-Walk-Free Latency Problem. | Yaw-Ling Lin |
| 2002 | MFCS | Efficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis. | Yaw-Ling Lin, Tao Jiang, Kun-Mao Chao |
| 2000 | COCOON | Efficient Algorithms for the Minimum Connected Domination on Trapezoid Graphs. | Yaw-Ling Lin, Fang-Rong Hsu, Yin-Te Tsai |
| 1999 | ISAAC | Parallel Algorithms for Shortest Paths and Related Problems on Trapezoid Graphs. | Fang-Rong Hsu, Yaw-Ling Lin, Yin-Te Tsai |
| 1998 | ISAAC | Fast Algorithms for Independent Domination and Efficient Domination in Trapezoid Graphs. | Yaw-Ling Lin |