| 2018 | IWOCA | Placing Segments on Parallel Arcs. | Yen Kaow Ng, Wenlong Jia, Shuai Cheng Li |
| 2013 | RECOMB | Detecting Protein Conformational Changes in Interactions via Scaling Known Structures. | Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang |
| 2013 | WABI | Towards Reliable Automatic Protein Structure Alignment. | Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Ming Li |
| 2012 | CPM | Finding Longest Common Segments in Protein Structures in Nearly Linear Time. | Yen Kaow Ng, Hirotaka Ono, Ling Ge, Shuai Cheng Li |
| 2012 | RECOMB | LoopWeaver - Loop Modeling by the Weighted Scaling of Verified Proteins. | Daniel Holtby, Shuai Cheng Li, Ming Li |
| 2012 | WABI | How Accurately Can We Model Protein Structures with Dihedral Angles? | Xuefeng Cui, Shuai Cheng Li, Dongbo Bu, Babak Alipanahi Ramandi, Ming Li |
| 2011 | RECOMB | Pedigree Reconstruction Using Identity by Descent. | Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp, Eran Halperin |
| 2009 | ISAAC | On Protein Structure Alignment under Distance Constraint. | Shuai Cheng Li, Yen Kaow Ng |
| 2008 | CPM | Finding Largest Well-Predicted Subset of Protein Structure Models. | Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li |
| 2008 | FAW | A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance. | Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang |
| 2008 | ISMB | Designing succinct structural alphabets. | Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li |
| 2007 | CPM | Finding Compact Structural Motifs. | Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, Jinbo Xu |
| 2006 | WABI | On the Complexity of the Crossing Contact Map Pattern Matching Problem. | Shuai Cheng Li, Ming Li |
| 2005 | DASFAA | Indexing DNA Sequences Using q-Grams. | Xia Cao, Shuai Cheng Li, Anthony K. H. Tung |
| 2004 | COCOON | New Approximation Algorithms for Some Dynamic Storage Allocation Problems. | Shuai Cheng Li, Hon Wai Leong, Steven K. Quek |
| 2004 | SSDBM | String Join Using Precedence Count Matrix. | Xia Cao, Anthony K. H. Tung, Beng Chin Ooi, Kian-Lee Tan, Shuai Cheng Li |