Publications (DBLP Bibliography Server | Google-Scholar )
Journal Papers
  1. Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?
    Xuefeng Cui, Shuai Cheng Li, Babak Alipanahi, Ming Li
    Algorithms for Molecular Biology 8: 5 (2013)

  2. LoopWeaver: Loop Modeling by the Weighted Scaling of Verified Proteins. Journal of Computational Biology
    Daniel Holtby, Shuai Cheng Li, Ming Li
    Journal of Computational Biology 20(3): 212-223 (2013)

  3. Detecting Protein Conformational Changes in Interactions via Scaling Known Structures
    Fei Guo, Shuai Cheng Li, Wenji Ma, Lusheng Wang
    Journal of Computational Biology 20(10): 765-779 (2013)

  4. The Difficulty Of Protein Structure Alignment Under The RMSD
    Shuai Cheng Li
    Algorithms for Molecular Biology 8: 1 (2013)

  5. Protein-protein binding site identification by enumerating the configurations
    Fei Guo, Shuai Cheng Li, Lusheng Wang, Daming Zhu
    BMC Bioinformatics 13: 158 (2012)

  6. Clustering 100, 000 Protein Structure Decoys in Minutes
    Shuai Cheng Li, Dongbo Bu, and Ming Li
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB),9(3): 765-773 (2012).

  7. Hexagon codes accurate information for side chain conformation
    Shuai Cheng Li, Dongbo Bu, and Ming Li
    IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE TCBB), 9(1): 240-248 (2012).

  8. Finding Nearly Optimal GDT Scores
    Shuai Cheng Li, Dongbo Bu, Jinbo Xu and Ming Li
    Journal of Computational Biology (JCB), 2011 May;18(5):693-704

  9. Protein Secondary Structure Prediction Using NMR Chemical Shift Data
    Yuzhong Zhao, Babak Alipanahi, Shuai Cheng Li, and Ming Li
    Journal of Bioinformatics and Computational Biology (JBCB) Vol. 8, No. 5, pages 867-884, 2010.

  10. On Protein Structure Alignment under Distance Constraint
    Shuai Cheng Li and Yen Kaow Ng
    Theoretical Computer Science (TCS): Special Issue for ISAAC 2009. Vol. 412, No. 32, pages 4187-4199, 2011

  11. Calibur: a tool for clustering large numbers of protein decoys
    Shuai Cheng Li and Yen Kaow Ng
    BMC Bioinformatics (BMCBI), Vol. 11, No. 25,

  12. Finding compact structural motifs
    Dongbo Bu, Ming Li, Shuai Cheng Li, Jianbo Qian, Jinbo Xu
    Theoretical Computer Science (TCS) Vol. 410, No. 30-32, pages 2834-2839, 2009

  13. On Two Open Problems in 2-interval Patterns
    Shuai Cheng Li, Ming Li
    Theoretical Computer Science (TCS) Vol. 410, No. 24-25, pages 2410-2423, 2009

  14. Predicting local quality of a sequence-structure alignment
    Xin Gao, Jinbo Xu, Shuai Cheng Li, Ming Li
    Journal of Bioinformatics and Computational Biology (JBCB) Vol. 7, No. 5, pages 789-810, 2009.

  15. Discriminative Learning for Protein Conformation Sampling.
    Feng Zhao, Shuai Cheng Li, Beckett W. Sterner, Jinbo Xu
    PROTEINS: Structure, Function and Bioinformatics, Vol. 73 No. 1, pages 228-240, 2008.

  16. Designing succinct structural alphabets
    Shuai Cheng Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li
    Bioinformatics: Special Issue for ISMB 2008, Vol. 24, No. 13, pages 182-189, 2008

  17. A PTAS for the k-Consensus Structures Problem Under Euclidean Squared Distance
    Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang
    Algorithms, Vol. 1, No. 2, pages 43-51, 2008.

  18. Piers: An Efficient Model for Similarity Search in DNA Sequence Databases
    Xia Cao, Shuai Cheng Li, Beng Chin Ooi, Anthony K. H. Tung
    SIGMOD Record, Vol. 33, No. 2, pages 39-44, 2004.

Conference/Workshop Papers
  1. Pedigree Reconstruction using Identity by Descent
    Bonnie Kirkpatrick, Shuai Cheng Li, Richard M. Karp and Eran Halperin
    Research in Computational Molecular Biology - 15th Annual International Conference (RECOMB 2011). Accepted

  2. Finding Largest Well-Predicted Subset of Protein Structure Models
    Shuai Cheng Li, Dongbo Bu, Jinbo Xu, and Ming Li
    Combinatorial Pattern Matching, 19th Annual Symposium (CPM 2008)

  3. FragQA: predicting local fragment quality of a sequence-structure alignment (Best Paper Award)
    Xin Gao, Dongbo Bu, Shuai Cheng Li, Jinbo Xu, and Ming Li
    The 18th International Conference on Genome Informatics (GIW 2007)

  4. Finding Compact Structural Motifs
    Jianbo Qian, Shuai Cheng Li, Dongbo Bu, Ming Li, and Jinbo Xu
    Combinatorial Pattern Matching, 18th Annual Symposium (CPM 2007)

  5. Faster Algorithms for Finding Missing Patterns
    Shuai Cheng Li
    Theory of Computing 2006, Proceedings of the Twelfth Computing: The Australasian Theory Symposium (CATS 2006)

  6. On the Complexity of the Crossing Contact Map Pattern Matching Problem
    Shuai Cheng Li and Ming Li
    Algorithms in Bioinformatics, 6th International Workshop (WABI 2006)

  7. Indexing DNA Sequences Using q-Grams (Best Paper Award)
    Xia Cao, Shuai Cheng Li, and Anthony K. H. Tung
    Database Systems for Advanced Applications, 10th International Conference (DASFAA 2005)

  8. New Approximation Algorithms for Some Dynamic Storage Allocation Problems
    Shuai Cheng Li, Hon Wai Leong, Steven K. Quek
    Computing and Combinatorics, 10th Annual International Conference (COCOON 2004)

  9. String Join Using Precedence Count Matrix
    Xia Cao, Shuai Cheng Li, Beng Chin Ooi, Anthony K. H. Tung
    The 16th International Conference on Scientific and Statistical Database Management (SSDBM 2004)

System Demonstration Papers
  1. Fragment-HMM: A New Approach To Protein Structure Prediction
    Shuai Cheng Li, Dongbo Bu, Jinbo Xu, Ming Li
    Protein Science, Vol. 17, No. 11, pages 1925-1934, 2008

  Book Chapters
 
  1. Consensus Approaches to Protein Structure Prediction
    Dongbo Bu, Shuai Cheng Li, Xin Gao, Libo Yu, Jinbo Xu and Ming Li
    Machine Learning in Bioinformatics, Edited by Yan-Qing Zhang and Jagath C. Rajapakse, John Wiley & Sons, ISBN 978-0-4701-1662-3, 2007.