In the era of big data, the field of computing is merging with the biological sciences to form a new age for interdisciplinary knowledge discovery. Consequently, computer scientists have invested substantial resources and time into discovering how patterns emerge in nature and in society. Dr. Lee's research addresses challenges arisen from big data based on discovering, compressing, and analyzing patterns in sequential data. Dr. Lee is interested discovering patterns from biological and social data so as to uncover the underlying functions and knowledge.

Selected Publications

Refereed Publications

Journal Papers

  1. En-Shiun Annie Lee, and Andrew K. C. Wong. "Revealing and Validating Protein Class Characteristics from Align Pattern Clusters", IEEE Transactions on Computational Biology and Bioinformatics, 2014 (Submitted).
  2. En-Shiun Annie Lee, Sanderz Fung, Ho-Yin Sze-To, and Andrew K. C. Wong. "Discovering co-occurring patterns and their biological significance in protein families", BMC Bioinformatics, 2014 (Selected for Special Journal edition from BIBM).
  3. Andrew K.C. Wong, and En-Shiun Annie Lee. "Aligning and Clustering Patterns to Reveal the Functionality of Biosequences", IEEE Transactions on Computational Biology and Bioinformatics, 11(3), pp. 1-13, 2014.
  4. En-Shiun Annie Lee, and Andrew KC Wong. "Ranking and compacting binding segments of protein families using aligned pattern clusters." Proteome Science 11.Suppl 1 (2013): S8.
  5. Andrew K.C. Wong, Dennis Zhuang, Gary C.L. Li, and En-Shiun Annie Lee. "Discovery of Delta Closed Patterns and Non-induced Patterns from Sequences", IEEE Transactions on Knowledge and Data Engineering, 24(8), pp. 1408-1421, 2012.
  6. Andrew G. Woolley, En-Shiun Lee, Fuzhong Zhang. "sGAL: a computational method for finding surface exposed sites in proteins suitable for Cys-mediated cross-linking." Bioinformatics. Vol. 22(24), pp. 3101 - 3102, 2006.
    Software: http://www.chem.utoronto.ca/staff/GAW/woolley_3_004.htm

Refereed Conference Papers

  1. En-Shiun Annie Lee, Sanderz Fung, Ho-Yin Sze-To, and Andrew K. C. Wong. "Confirming Biological Significance of Co-occurrence Clusters of Aligned Pattern Clusters", Bioinformatics and Biomedicine (BIBM), 2013 IEEE International Conference on. Submission B436. IEEE, 2013 (accepted)
  2. En-Shiun Annie Lee, and Andrew KC Wong. "Classifying Proteins by Amino Acid Variations of Sequential Patterns." In Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, p. 276. ACM, 2013.
  3. En-Shiun Annie Lee. "Applying Activity Theory of Mobile Learning to Context-Aware Smartphones", Association for the Advancement of Computing in Education, 2012, Montreal, (Accepted as Research Paper, Invited to submit to International Journal on E-Learning).
  4. En-Shiun Annie Lee, and Andrew KC Wong. "Identifying protein binding functionality of protein family sequences by Aligned Pattern clusters." In Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference on, pp. 1-6. IEEE, 2012 (Accepted as Regular Paper, Invited to Submit to Proteome Science ).
  5. En-Shiun Annie Lee, Dennis Zhuang, and Andrew K. C. Wong. "Aligning Discovered Patterns from Protein Family Sequences", The 7th IAPR International Conference on Pattern Recognition in Bioinformatics, pp. 243 - 254, 2012.
  6. Andrew K.C. Wong, Dennis Zhuang, Gary C.L. Li, and En-Shiun Annie Lee. "Discovery of Non-induced Patterns from Sequences", in Pattern Recognition in Bioinformatics, 2010, pp. 149-160.

Other Research Activities

Scholarships

  1. KDD Travel Scholarship, Brodening Participation in Data Mining, August 2013
  2. Student Travel Scholarship, IEEE BIBM, October 2012
  3. Grace Hopper Travel Scholarship, Women in Computer Science Committee, Octobeer 2012
  4. Summer Institute in Taiwaan, NSERC and NSC, July-August 2012
  5. President's Graduate Scholarship for 3 years, 2009-2012
  6. NSERC Post Graduate Scholarship for 3 years, 2009-2012
  7. Graduate Scholarship, University of Waterloo, Winter 2011
  8. Student Travel Scholarship, NIPS WiML, December 2010
  9. Provost's Doctoral Entrance Award for Women, 2009
  10. Ontario Graduate Scholarship, 2007
  11. President's Graduate Scholarship, 2007

Courses Taken

  1. Computer-Mediated Advertising (Audit)
  2. Information Retrieval (Audit)
  3. Infomation, Patterns, Pattern Analysis, Synthesis and Discovery
  4. Computational Techniques in Structural Bioinformatics
  5. Computational Techniques for Genome Analysis
  6. Protein Structure Computation
  7. Statistical Natural Language Processing and Information Retrieval
  8. Succinct & Self-Adjusting Data Structures