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Limsoon's Papers

Good judgment comes from experience and experience comes from bad judgment.

Books

1. Hideo Matsuda, Limsoon Wong, Satoru Miyano, Toshihisa Takagi, editors. Genome Informatics 2001, Universal Academic Press, Tokyo, Japan, December 2001.

2. Louxin Zhang, Limsoon Wong, editors. Selected Topics in Post-Genome Knowledge Discovery, Singapore University Press, Singapore, May 2004. (176 pages)

3. Limsoon Wong, editor. The Practical Bioinformatician, World Scientific, New Jersey, May 2004. (540 pages)

4. Yi-Ping Phoebe Chen, Limsoon Wong, editors. Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, Imperial College Press, London, January 2005. (384 pages)

5. Tao Jiang, Ueng-Cheng Yang, Phoebe Chen, Limsoon Wong, editors. Proceedings of the 4th Asia-Pacific Bioinformatics Conference, Imperial College Press, London, February 2006. (363 pages)

6. Jagath C. Rajapakse, Limsoon Wong, Raj Acharya, editors. Pattern Recognition in Bioinformatics, Springer-Verlag, Berlin, 25 September 2006. (186 pages)

7. See-Kiong Ng, Hiroshi Mamitsuka, Limsoon Wong, editors. Genome Informatics 2007, Imperial College Press, London, December 2007. (199 pages)

8. Martin Vingron, Limsoon Wong, editors. Proceedings of the 12th Annual International Conference on Research in Computational Molecular Biology, Springer-Verlag, Berlin, March 2008. (480 pages)

9. Taesung Park, Stephen Tsui, Luonan Chen, Michael Ng, Limsoon Wong, Xiaohua Hu, editors. Proceedings of 4th IEEE International Conference on Bioinformatics and Biomedicine, IEEE, Hong Kong, December 2010. (704 pages)

10. Val Tannen, Limsoon Wong, Leonid Libkin, Wenfei Fan, Wang-Chiew Tan, Michael Fourman, editors. In Search of Elegance in the Theory and Practice of Computation, Springer, Berlin, October 2013. (569 pages)

11. Sriganesh Srihari, Chern Han Yong, Limsoon Wong. Computational Prediction of Protein Complexes from Protein Interaction Networks, Morgan & Claypool, San Rafael, July 2017. (281 pages)

    

    Book Chapters

12. Susan Davidson, Peter Buneman, Jonathan Crabtree, Val Tannen, Chris Overton, Limsoon Wong. BioKleisli: Integrating Biomedical Data and Analysis Packages. Bioinformatics: Databases and Systems, edited by Stanley Letovsky, chapter 17, pages 201--212. Kluwer Academic, Boston, 1999.

13. Limsoon Wong. Bioinformatics Integration Simplified: The Kleisli Way. Frontiers in Human Genetics: Diseases and Technologies, edited by Poh-San Lai and Eric Yap, chapter 6, pages 79--90. World Scientific, Singapore, 2001.

14. Limsoon Wong. Datamining: Discovering Information from Bio-data. Current Topics in Computational Biology, edited by Tao Jiang, Ying Xu, and Michael Zhang, chapter 13, pages 317--342, MIT Press, Cambridge, MA, 2002.

15. Jing Chen, Su-Yun Chung, Limsoon Wong. The Kleisli Query System as a Backbone for Bioinformatics Data Integration and Analysis. Bioinformatics: Managing ScientificData, edited by Zoe Lacroix and Terence Critchlow, chapter 6, pages 147--187, Morgan Kaufmann, San Francisco, CA, 2003.

16. Susan Davidson, Limsoon Wong. The Kleisli Approach to Data Transformation and Integration. The Functional Approach to Data Management: Modeling, Analyzing, and Integrating Heterogeneous Data, edited by Peter Gray, Larry Kerschberg, Peter King, Alex Poulovassilis, chapter 6, pages 135--165. Springer-Verlag, September 2003.

17. Mohammed Zaki, Limsoon Wong. Data Mining Techniques. Selected Topics in Post-Genome Knowledge Discovery, edited by Limsoon Wong, Louxin Zhang, chapter 4, pages 125--163. National University of Singapore Press, May 2004.

18. Jinyan Li, Huiqing Liu, Anthony Tung, Limsoon Wong. Data Mining Techniques for the Practical Bioinformatician. The Practical Bioinformatician, edited by Limsoon Wong, chapter 3, pages 35--70, World Scientific, May 2004.

19. Jinyan Li, Huiqing Liu, Limsoon Wong, Roland Yap. Techniques for Recognition of Translation Initiation Sites. The Practical Bioinformatician, edited by Limsoon Wong, chapter 4, pages 71--90, World Scientific, May 2004.

20. Jinyan Li, Limsoon Wong. Techniques for Analysis of Gene Expression. The Practical Bioinformatician, edited by Limsoon Wong, chapter 14, pages 319--346, World Scientific, May 2004.

21. Limsoon Wong. Technologies for Biological Data Integration. The Practical Bioinformatician, edited by Limsoon Wong, chapter 17, pages 375--400, World Scientific, May 2004.

22. Kui Lin, Jianhua Liu, Lance Miller, Limsoon Wong. Genome-Wide cDNA Oligo Probe Design and its Applications in Schizosaccharomyces Pombe. The Practical Bioinformatician, edited by Limsoon Wong, chapter 15, pages 347--358, World Scientific, May 2004.

23. Guozhu Dong, Jinyan Li, Limsoon Wong. The Use of Emerging Patterns in the Analysis of Gene Expression Profiles for the Diagnosis and Understanding of Diseases. New Generation of Data Mining Applications, edited by M. Kantardzic and J. Zurada, chapter 14, pages 331--354. John Wiley, April 2005.

24. Huiqing Liu, Limsoon Wong, Ying Xu. Patient Survival Prediction from Gene Expression Data. Knowledge Discovery in Bioinformatics: Techniques, Methods, and Applications, edited by Xiaohua Hu and Yi Pan, chapter 6, pages 89--111, Wiley, July 2007.

25. Hon Nian Chua, Limsoon Wong. Predicting Protein Functions from Protein Interaction Networks. Biological Data Mining in Protein Interaction Networks, edited by See-Kiong Ng and Xiao-Li Li, chapter XII, pages 204--223, Medical Information Science Reference, May 2009.

26. Mengling Feng, Jinyan Li, Guozhu Dong, Limsoon Wong. Maintenance of Frequent Patterns: A Survey. Post-Mining of Association Rules: Techniques for Effective Knowledge Extraction, edited by Yanchang Zhao, Chengqi Zhang, and Longbing Cao, chapter XIV, pages 275--295, IGI Global, May 2009.

27. Guozhu Dong, Jinyan Li, Guimei Liu, Limsoon Wong. Mining Conditional Contrast Patterns. Post-Mining of Association Rules: Techniques for Effective Knowledge Extraction, edited by Yanchang Zhao, Chengqi Zhang, and Longbing Cao, chapter XV, pages 296--311, IGI Global, May 2009.

28. Hon Nian Chua, Guimei Liu, Limsoon Wong. Protein Function Prediction: Using Protein-Protein Interaction Networks. Protein Function Prediction for Omics Era, edited by Daisuke Kihara, chapter 13, pages 243--270, Springer, April 2011.

29. Jinyan Li, Limsoon Wong. Emerging Pattern Based Rules Characterizing Subtypes of Leukemia. Contrast Data Mining: Concepts, Algorithms, and Applications, edited by Guozhu Dong and James Bailey, pages 219--232, CRC, September 2012.

30. Limsoon Wong. The Dichotomous Intensional Expressive Power of the Nested Relational Calculus with Powerset. In Search of Elegance in the Theory and Practice of Computation, edited by Val Tannen, Limsoon Wong, Leonid Libkin, Wenfei Fan, Wang-Chiew Tan, Michael Fourman, pages 542--556, Springer, October 2013.

31. Stefano Perna, Arif Canakoglu, Pietro Pinoli, Stefano Ceri, Limsoon Wong. Implementing a Transcription Factor Interaction Prediction System Using the GenoMetric Query Language. Data Mining for Systems Biology: Methods and Protocols, edited by Hiroshi Mamitsuka, Chapter 6, pages 63--81, Springer, July 2018.

32. Limsoon Wong. An intensional expressiveness gap of comprehension syntax. The Provenance of Elegance in Computation - Essays dedicated to Val Tannen, OASIcs, vol. 119, article no. 11: pp. 11.1--11.14, May 2024.

    

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    Journal Papers

33. Limsoon Wong, Beng Chong Ooi. Treating Failure as Value ACM SIGPLAN Notices, 25(1):29-32, January 1990.

34. Limsoon Wong, Beng Chong Ooi. Treating Failure as State. ACM SIGPLAN Notices, 25(8):24-27, August 1990.

35. Peter Buneman, Leonid Libkin, Dan Suciu, Val Tannen, Limsoon Wong. Comprehension Syntax. ACM SIGMOD Record, 23(1):87-96, March 1994. (Reviewed invited paper)

36. Leonid Libkin, Limsoon Wong. Conservativity of Nested Relational Calculi with Internal Generic Functions. Information Processing Letters, 49(6):273-280, March 1994.

37. Limsoon Wong. Polymorphic Queries Across Sets, Bags, and Lists. ACM SIGPLAN Notices, 30(4):39-44, April 1995.

38. Peter Buneman, Shamim Naqvi, Val Tannen, Limsoon Wong. Principles of Programming with Complex Objects and Collection Types. Theoretical Computer Science, 149(1):3--48, September 1995. PDF (Reviewed invited paper)

39. Limsoon Wong. An Introduction to Remy's Fast Polymorphic Record Projection. ACM SIGMOD Record, 24(3):34--39, September 1995. PDF

40. Leonid Libkin, Limsoon Wong. On Representation and Querying Incomplete Information in Databases with Multisets. Information Processing Letters, 56:209--214, November 1995.

41. Leonid Libkin, Limsoon Wong. Semantic Representations and Query Languages for Or-sets. Journal of Computer and System Sciences, 52(1):125--142, February 1996.

42. Limsoon Wong. Normal Forms and Conservative Extension Properties for Query Languages over Collection Types. Journal of Computer and System Sciences, 52(3):495--505, June 1996. PDF (Reviewed invited paper)

43. Stephane Grumbach, Leonid Libkin, Tova Milo, Limsoon Wong. Query Languages for Bags: Expressive Power and Complexity. ACM SIGACT News, 27(2):30--37, June 1996. (Guest database column)

44. Guozhu Dong, Limsoon Wong. Some Relationships between the FOIES and Sigma-1-1 Arity Hierarchies , Bulletin of the EATCS, 61:72--79, February 1997.

45. Susan Davidson, Chris Overton, Val Tannen, Limsoon Wong. BioKleisli: A Digital Library for Biomedical Researchers , International Journal of Digital Libraries, 1(1):36--53, April 1997.

46. Leonid Libkin, Limsoon Wong. Query Languages for Bags and Aggregate Functions. Journal of Computer and System Sciences, 55(2):241--272, October 1997. (Reviewed invited paper.)

47. WangChiew Tan, Ke Wang, Limsoon Wong. A Graphical Interface to Genome Multidatabases, Journal of Database Management, 9(1):24--32, Winter 1998.

48. Michael Benedikt, Guozhu Dong, Leonid Libkin, Limsoon Wong. Relational Expressive Power of Constraint Query Languages, Journal of the ACM, 45(1):1--34, January 1998.

49. Su-Yun Chung, Limsoon Wong. Kleisli, a new tool for data integration in biology. Trends in Biotechnology, 17(9):351--355, September 1999. Paper

50. Guozhu Dong, Leonid Libkin, Jianwen Su, Limsoon Wong. Maintaining Transitive Closure of Graphs in SQL. International Journal of Information Technology, 5(1):46--78, October 1999. (Reviewed invited paper.)

51. Elisa Bertino, Barbara Catania, Limsoon Wong. Finitely Representable Nested Relations. Information Processing Letters, 70(4):165--173, 1999.

52. Jiren Wang, Limsoon Wong. An Example in Kleisli: Codon Usage Extraction Made Easy. Science Asia, 25:23--29, 1999. (Reviewed invited paper.)

53. Limsoon Wong. The Functional Guts of the Kleisli Query System. ACM SIGPLAN Notices, 35(9):1--10, 2000.

54. Guozhu Dong, Leonid Libkin, Limsoon Wong. Local Properties of Query Languages. Theoretical Computer Science, 239:277--308, 2000. (Reviewed invited paper.)

55. Limsoon Wong. Kleisli, a Functional Query System Journal of Functional Programming, 10(1):19--56, January 2000. PDF (Reviewed invited paper.)

56. Christian Schoenbach, Judice Koh, Xin Sheng, Limsoon Wong, Vladimir Brusic. FIMM, a database of functional molecular immunology. Nucleic Acids Research, 28(1), 222--224, January 2000.

57. Lauri Hella, Leonid Libkin, Juha Nurmonen, Limsoon Wong. Logics with Aggregate Operators, Journal of the ACM, 48(4):880--907, 2001.

58. Christian Schoenbach, Judice Koh, Daren Flower, Limsoon Wong, Vladimir Brusic. FIMM, a Database of Functional Molecular Immunology---Update 2001. Nucleic Acids Research, 30:226--229, January 2002.

59. Jinyan Li, Limsoon Wong. Identifying good diagnostic genes or genes groups from gene expression data by using the concept of emerging patterns. Bioinformatics. 18:725--734, 2002. Corrigendum. Bioinformatics, 18:1407--1408, 2002.

60. Leonid Libkin, Limsoon Wong. Lower Bounds for Invariant Queries in Logics with Counting. Theoretical Computer Science, 288(1):153--180, 2002. (Reviewed invited paper.)

61. Limsoon Wong. Gaps in Text-based Knowledge Discovery for Biology. Drug Discovery Today. 7(17):897--898, 2002. (Reviewed invited comments.)

62. Eng-Juh Yeoh, Mary E. Ross, Sheila A. Shurtleff, W. Kent William, Divyen Patel, Rami Mahfouz, Fred G. Behm, Susana C. Raimondi, Mary V. Reilling, Anami Patel, Cheng Cheng, Dario Campana, Dawn Wilkins, Xiaodong Zhou, Jinyan Li, Huiqing Liu, Chin-Hon Pui, William E. Evans, Clayton Naeve, Limsoon Wong, James R. Downing. Classification, subtype discovery, and prediction of outcome in pediatric acute lymphoblastic leukemia by gene expression profiling. Cancer Cell, 1:133--143, March 2002. Video

63. Lynette Hirschman, Jong C. Park, Junichi Tsujii, Limsoon Wong, Cathy H. Wu. Accomplishments and Challenges in Literature Data Mining for Biology. Bioinformatics, 18:1553--1561, December 2002.

64. Limsoon Wong. Technologies for Integrating Biological Data. Briefings in Bioinformatics, 3(4):389--404, 2002. (Reviewed invited paper)

65. Lance D. Miller, Phillip M. Long, Limsoon Wong, Sayan Mukherjee, Lisa M. McShane, Edison T. Liu. Optimal gene expression analysis by microarrays. Cancer Cell, 2:353--361, November 2002. (Reviewed invited paper)

66. Jinyan Li, Huiqing Liu, James R. Downing, Allen Eng-Juh Yeoh, Limsoon Wong. Simple Rules Underlying Gene Expression Profiles of More than Six Subtypes of Acute Lymphoblastic Leukemia (ALL) Patients. Bioinformatics. 19:71--78, 2003.

67. Guozhu Dong, Leonid Libkin, Limsoon Wong. Incremental Recomputation in Local Languages. Information and Computation, 181:88--98, 2003.

68. Huiqing Liu, Limsoon Wong. Data Mining Tools for Biological Sequences. Journal of Bioinformatics & Computational Biology, 1(1):139--168, April 2003. (Reviewed invited paper.)

69. Jinyan Li, Huiqing Liu, See-Kiong Ng, Limsoon Wong. Discovery of Significant Rules for Classifying Cancer Diagnosis Data. Bioinformatics, 19(suppl. 2):ii93--ii102, September 2003.

70. Jinyan Li, Guozhu Dong, Kotagiri Ramamohanarao, Limsoon Wong. DeEPs: A New Instance-based Discovery and Classification System. Machine Learning, 54(2):99--124, 2004.

71. See-Kiong Ng, Limsoon Wong. Accomplishments and Challenges in Bioinformatics. IEEE IT Professional Magazine, 6(1):44-50, January/February 2004. (Reviewed invited paper.)

72. Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong. Using Amino Acid Patterns to Accurately Predict Translation Initiation Sites. In silico Biology, 4(3):255--269, 2004. Draft. Server

73. Shao-Wu Meng, Zhuo Zhang, Limsoon Wong. A +1 programmed ribosomal frameshifting in a human C2H2 zinc finger gene discovered by computational analysis. Biotechnology, 4(4):316--324, 2005.

74. Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong. DNAFSMiner: A Web-Based Software Toolbox to Recognize Two Types of Functional Sites in DNA Sequences. Bioinformatics, 21:671--673, March 2005. Server

75. Xu Peng, R. Krishna Murthy Karuturi, Lance D. Miller, Kui Lin, Yonghui Jia, Pinar Konda, Long Wang, Limsoon Wong, Edison T. Liu, Mohan K. Balasubramanian, Jianhua Liu. Identification of Cell Cycle-regulated Genes in Fission Yeast. Molecular Biology of the Cell, 16(3):1026--1042, March 2005.

76. Huiqing Liu, Jinyan Li, Limsoon Wong. Use of Extreme Patient Samples for Outcome Prediction from Gene Expression Data. Bioinformatics, 21(16):3377--3384, 2005.

77. Jinyan Li, Limsoon Wong. Structural Geography of the Space of Emerging Patterns. Intelligent Data Analysis, 9(6):567--588, 2005.

78. Haiquan Li, Jinyan Li, Limsoon Wong. Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteom-Wide Scale. Bioinformatics, 22(8):989--996, 2006.

79. Rajesh Chowdhary, Limsoon Wong, Vladimir Bajic. Finding Functional Promoter Motifs By Computational Methods: A Word of Caution. International Journal of Bioinformatics Research and Applications, 2(3):282--288, 2006.

80. Rajesh Chowdhary, Sin Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, and Vladimir B Bajic. Dragon Promoter Mapper (DPM): A Bayesian Framework for Modeling Promoter Structures. Bioinformatics, 22:2310--2312, September 2006.

81. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Bioinformatics, 22:1623--1630, July 2006. Corrigendum. Bioinformatics, 24:452, February 2008. FSWeight V1.0 Software

82. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Using Indirect Protein Interactions for the Prediction of Gene Ontology Functions. BMC Bioinformatics, 8(Suppl 4):S8, May 2007. FSWeight V2.1 Software

83. Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Enabling More Sophisticated Gene Expression Analysis for Understanding Diseases and Optimizing Treatments. ACM SIGKDD Explorations, 9(1):3--14, June 2007. (Invited reviewed paper.)

84. Jinyan Li, Guimei Liu, Haiquan Li, Limsoon Wong. Maximal Biclique Subgraphs and Closed Pattern Pairs of the Adjacency Matrix: A 1-to-1 Correspondence and Mining Algorithms. IEEE Transactions on Knowledge and Data Engineering, 19(2):1625--1637, December 2007. LCM-MBC Software

85. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. An Efficient Strategy for Extensive Integration of Diverse Biological Data for Protein Function Prediction. Bioinformatics, 23(24):3364--3373, December 2007 FSWeight V2.1 Software

86. Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong. Using Indirect Protein-Protein Interactions for Protein Complex Prediction. Journal of Bioinformatics and Computational Biology, 6(3):435--466, June 2008. (Reviewed invited paper.) PCP V1.0 Software

87. Liang Huai Yang, Mong-Li Lee, Wynne Hsu, Decai Huang, Limsoon Wong. Efficient mining of frequent XML query patterns with repeating-siblings. Information & Software Technology, 50(5):375-389, April 2008.

88. Guimei Liu, Jinyan Li, Limsoon Wong. A New Concise Representation of Frequent Itemsets Using Generators and a Positive Border. Knowledge and Information Systems, 17(1):35--56, October 2008. GrGrowth-PBd Software

89. Hon Nian Chua, Limsoon Wong. Increasing the Reliability of Protein Interactomes. Drug Discovery Today, 13(15/16):652--658, August 2008. (Reviewed invited paper.)

90. Wen-Son Hsieh, Ross Soo, Bee-Keow Peh, Thomas Loh, Difeng Dong, Donny Soh, Limsoon Wong, Simon Green, Judy Chiao, Chun-Ying Cui, Yoke-Fong Lai, Soo-Chin Lee, Benjamin Mow, Richie Soong, Manuel Salto-Tellez, Boon-Cher Goh. Pharmacodynamic Effects of Seliciclib, an Orally Administered Cell Cycle Modulator, in Undifferentiated Nasopharyngeal Cancer. Clinical Cancer Research, 15(4):1435--1442, February 2009.

91. Hon Nian Chua, Willy Hugo, Guimei Liu, Xiaoli Li, Limsoon Wong, See-Kiong Ng. A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein-Protein Subnetwork Prediction Challenge. Annals of New York Academy of Sciences, 1158:224-233, March 2009. (Reviewed invited paper.)

92. David Lo, Siau-Cheng Khoo, Limsoon Wong. Non-Redundant Sequential Rules---Theory and Algorithm. Information Systems, 34(4-5):438-453, June-July 2009.

93. Yubo Wang, Gaoxi Xiao, Jie Hu, Tee Hiang Cheng, Limsoon Wong. Imperfect Targeted Immunization in Scale-Free Networks. Physica A: Statistical Mechanics and its Applications, 388(12):2535--2546, June 2009.

94. Guimei Liu, Limsoon Wong, Hon Nian Chua. Complex Discovery from Weighted PPI Networks. Bioinformatics, 25(15):1891--1897, August 2009. CMC V1.0

95. Frank Eisenhaber, Chee-Keong Kwoh, See-Kiong Ng, Wing-Kin Sung, Limsoon Wong. Brief Overview of Bioinformatics Activities in Singapore. PLoS Computational Biology, 5(9):e1000508, September 2009. (Reviewed invited paper.)

96. Chuan Hock Koh, Sharene Lin, Gregory Jedd, Limsoon Wong. Sirius PSB: A Generic System for Analysis of Biological Sequences. Journal of Bioinformatics and Computational Biology, 7(6):973--990, December 2009. Sirius PSB V2.33, Sirius PSB Server

97. Guimei Liu, Kelvin Sim, Jinyan Li, Limsoon Wong. Efficient Mining of Distance-Based Subspace Clusters. Statistical Analysis and Data Mining, 2(5):427--444, December 2009. nClusters V1.1

98. Limsoon Wong, Guimei Liu. Protein Interactome Analysis for Countering Pathogen Drug Resistance. Journal of Computer Science and Technology, 25(1):124--130, January 2010.(Reviewed invited paper.)

99. Guimei Liu, Yue Wang, Limsoon Wong. FastTagger: An Efficient Algorithm for Genome-wide Tag SNP Selection Using Multi-marker Linkage Disequilibrium. BMC Bioinformatics, 11:66, February 2010. FastTagger V1.0

100. Rajesh Chowdhary, Vladimir B. Bajic, Difeng Dong, Limsoon Wong, Jun S. Liu. Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology, 4(Suppl 1):S4, May 2010.

101. Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano. DA 1.0: Parameter Estimation of Biological Pathways Using Data Assimilation Approach. Bioinformatics, 26(14):1794--1796, July 2010. DA V1.0

102. Jie Zhou, Gaoxi Xiao, Limsoon Wong, Xiuju Fu, Stefan Ma, Tee Hiang Cheng. Generation of arbitrary two-point-correlated directed networks with given modularity. Physics Letters A, 374(31-32):3129--3135, July 2010.

103. Mengling Feng, Guozhu Dong, Jinyan Li, Yap-Peng Tan, Limsoon Wong. Pattern Space Maintenance for Data Updates. Computational Intelligence, 26(3):282--317, August 2010. (Reviewed invited paper.)

104. Harold Soh, Sonja Lim, Tianyou Zhang, Xiuju Fu, Gary Kee Khoon Lee, Terence Gih Guang Hung, Limsoon Wong, Pan Di, Silvester Prakasam. Weighted Complex Network Analysis of Travel Routes on the Singapore Public Transportation System. Physica A: Statistical Mechanics and its Applications, 389(24):5852--5863, December 2010.

105. Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Consistency, Comprehensiveness, and Compatibility of Pathway Databases. BMC Bioinformatics, 11:449, September 2010. PathwayAPI Server

106. Mahnaz Habibi, Changiz Eslahchi, Limsoon Wong. Protein Complex Prediction based on k-Connected Subgraphs in Protein Interaction Network. BMC Systems Biology, 4:129, September 2010.

107. Li Lin, Limsoon Wong, Tze-Yun Leong, Poh San Lai. Efficient Mining of Haplotype Patterns for Linkage Disequilibrium Mapping. Journal of Bioinformatics and Computational Biology, 8(Suppl. 1):127--146, December 2010.

108. Thomas Thamboo, Richie Soong, Limsoon Wong, Baidah Ahmad, Yaw-Chyn Lim, Ming Teh. Determination of a molecular signature of acute T-cell-mediated renal allograft rejection using quantitative real-time RT-PCR of 45 genes on a low density array. Pathology, 43(1):72--75, January 2011.

109. David Lo, Jinyan Li, Limsoon Wong, Siau-Cheng Khoo. Mining Iterative Generators and Representative Rules for Software Specification Discovery. IEEE Transactions on Knowledge and Data Engineering, 23(2):282--296, February 2011.

110. Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano. MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models. Bioinformatics, 27(5):734-735, March 2011. MIRACH V1.0

111. Wen Lee Tan, Bhaskar Bhattacharya, Marie Chiew Hsia Loh, Indirikumar Balasubramanian, Mohamed Akram, Difeng Dong, Limsoon Wong, Bhavin Thakkar, Manuel Salto-Tellez, Ross Soo, Iduna Fichtner, Barry Iacopetta, Richie Soong. Low cytosine triphosphate synthase 2 expression renders resistance to 5-fluorouracil in colorectal cancer. Cancer Biology & Therapy, 11(6):599--608, March 2011.

112. Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. eCEO: An efficient Cloud Epistasis cOmputing model in genome-wide association study. Bioinformatics, 27(8):1045--1051, April 2011. eCEO V1.0

113. Tianyou Zhang, Xiuju Fu, Chee Keong Kwoh, Gaoxi Xiao, Limsoon Wong, Stefan Ma, Harold Soh, Gary Kee Khoon Lee, Terence Hung, Michael Lees. Temporal Factors in School Closure Policy for Mitigating the Spread of Influenza. Journal of Public Health Policy, 32(2):180--197, May 2011.

114. Wilson Wen Bin Goh, Yie Hou Lee, Ramdzan Zubaidah, Jingjing Jin, Difeng Dong, Qingsong Lin, Maxey Chung, Limsoon Wong. A Network-based pipeline for analyzing MS data---An application towards liver cancer. Journal of Proteome Research, 10(5):2261--2272, May 2011.

115. Zhenhua Li, Limsoon Wong, Jinyan Li. DBAC: A simple prediction method for protein binding hot spots based on burial levels and deeply buried atomic contacts. BMC Systems Biology, 5(Suppl 1):S5, June 2011.

116. Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. CAMBer: An appproach to support comparative analysis of multiple bacterial strains. BMC Genomics, 12(Suppl. 2):S6, July 2011. CAMBer Software

117. Qian Liu, Steven C. H. Hoi, Chinh T. T. Su, Zhenhua Li, Chee-Keong Kwoh, Limsoon Wong, Jinyan Li. Structural analysis of the hot spots in the binding between H1N1 HA and the 2D1 antibody: Do mutations of H1N1 from 1918 to 2009 affect much on this binding? Bioinformatics, 27(18):2529--2536, September 2011.

118. Yubo Wang, Goaxi Xiao, Limsoon Wong, Xiuju Fu, Stefan Ma, Tee Hiang Cheng. Effects of Fear Factors in Disease Propagation. Journal of Physics A: Mathematical and Theoretical, 44(35):355101, September 2011.

119. Guimei Liu, Chern Han Yong, Hon Nian Chua, Limsoon Wong. Decomposing PPI Networks for Complex Discovery. Proteome Science, 9(Suppl. 1):S15, October 2011.

120. Guimei Liu, Haojun Zhang, Limsoon Wong. Controlling False Positives in Association Rule Mining. Proceedings of the VLDB Endowment, 5(2):145--156, October 2011.

121. Hufeng Zhou, Limsoon Wong. Comparative Analysis and Assessment of M. Tuberculosis H37Rv Protein-Protein Interaction Datasets. BMC Genomics, 12(Suppl 3):S20, November 2011.

122. Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Finding Consistent Disease Subnetworks Across Microarray Datasets. BMC Bioinformatics, 12(Suppl. 13):S15, November 2011.

123. Yue Wang, Guimei Liu, Mengling Feng, Limsoon Wong. An Empirical Comparison of Several Recent Epistatic Interaction Detection Methods. Bioinformatics, 27(21):2936--2943, November 2011. Corrigendum. Bioinformatics, 28(1):147--148, January 2012.

124. Liang Zhao, Limsoon Wong, Jinyan Li. Antibody-specific B-cell epitope prediction in line with the principle of context-awareness. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(6):1483--1494, November 2011.

125. Limsoon Wong. Using Biological Networks in Protein Function Prediction and Gene Expression Analysis. Internet Mathematics, 7(4):274--298, December 2011.

126. Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. CAMBerVis: Visualization software to support comparative analysis of multiple bacterial strains. Bioinformatics, 27(23):3313--3314, December 2011. CAMBerVis Software

127. Wilson Wen Bin Goh, Hirotaka Oikawa, Judy Sng, Marek Sergot, Limsoon Wong. The role of miRNAs in complex formation and control. Bioinformatics, 28(4):453--456, February 2012.

128. Wilson Wen Bin Goh, Yie Hou Lee, Maxey Chung, Limsoon Wong. How advancement in biological network analysis methods empowers proteomics. Proteomics, 12(4-5):550--563, February 2012.

129. Wilson Wen Bin Goh, Yie Hou Lee, Zubaidah Ramdzan, Marek Sergot, Maxey Chung, Limsoon Wong. Proteomics Signature Profiling (PSP): A novel contextualization approach for cancer proteomics. Journal of Proteome Research, 11(3):1571--1581, March 2012.

130. Tianyou Zhang, Xiuju Fu, Stefan Ma, Gaoxi Xiao, Limsoon Wong, Chee Keong Kwoh, Michael Lees, Gary Lee, Terence Hung. Evaluating Temporal Factors in Combined Interventions of Workforce Shift and School Closure for Mitigating the Spread of Influenza. PLoS ONE, 7(3):e32203, March 2012.

131. J. Zhou, G. Xiao, S. A. Cheong, X. Fu, L. Wong, S. Ma, T. H. Cheng. Epidemic Reemergence in Adaptive Complex Networks. Physical Review E, 85(3):036107, March 2012.

132. Zhenhua Li, Ying He, Limsoon Wong, Jinyan Li. Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. BMC Bioinformatics, 13:51, March 2012.

133. Peng Chen, Limsoon Wong, Jinyan Li. Detection of outlier residues for improving interface prediction in protein hetero-complexes. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(4):1155--1165, July 2012.

134. Zhenhua Li, Ying He, Longbing Cao, Limsoon Wong, Jinyan Li. Conservation of water molecules in protein binding interfaces. International Journal of Bioinformatics Research and Applications, 8(3/4):228--244, August 2012.

135. Wilson Wen Bin Goh, Yie Hou Lee, Zubaidah M. Ramdzan, Maxey Chung, Limsoon Wong, Marek Sergot. A network-based maximum link approach towards MS identifies potentially important roles for undetected ARRB1/2 and ACTB in liver cancer progression. International Journal of Bioinformatics Research and Applications, 8(3/4):155--170, August 2012.

136. Rajesh Chowdhary, Sin Lam Tan, Giulio Pavesi, Jingjing Jin, Difeng Dong, Sameer K. Mathur, Arthur Burkart, Vipin Narang, Ingrid Glurich, Benjamin A. Raby, Scott T Weiss, Limsoon Wong, Jun S. Liu, Vladimir B. Bajic. A database for annotated promoters of genes associated with common respiratory and related diseases. American Journal of Respiratory Cell and Molecular Biology, 47(1):112-119, July 2012.

137. Min Wu, Xiaoli Li, Chee-Keong Kwoh, See-Kiong Ng, Limsoon Wong. Discovery of Protein Complexes with Core-Attachment Structures from TAP Data. Journal of Computational Biology, 19(9):1027--1042, September 2012.

138. Julian Lai, Chuan Hock Koh, Monika Tjota, Laurent Pieuchot, Vignesh Raman, Karthik Balakrishna Chandrababu, Daiwen Yang, Limsoon Wong, Gregory Jedd. Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity. Proceedings of the National Academy of Sciences of the United States of America, 109(39):15781-15786, September 2012.

139. Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li. B-cell epitope prediction through a graph model. BMC Bioinformatics, 13(Suppl 17):S20, December 2012.

140. Chuan Hock Koh, Sucheendra K. Palaniappan, P. S. Thiagarajan, Limsoon Wong. Improved statistical model checking methods for pathways analysis. BMC Bioinformatics, 13(Suppl 17):S15, December 2012.

141. Michal Wozniak, Jerzy Tiuryn, Limsoon Wong. An approach to identifying drug resistance associated mutations in bacterial strains. BMC Genomics, 13(Suppl 7):S23, December 2012.

142. Kevin Lim, Limsoon Wong. CMPF: Class-switching Minimized Pathfinding in Metabolic Networks. BMC Bioinformatics, 13(Suppl 17):S17, December 2012.

143. Qian Liu, Limsoon Wong, Jinyan Li. Z-score biological significance of binding hot spots of protein interfaces by using crystal packing as the reference state. Biochim Biophys Acta---Proteins and Proteomics, 1824(12):1457--1467, December 2012.

144. Hufeng Zhou, Jingjing Jin, Haojun Zhang, Bo Yi, Michal Wozniak, Limsoon Wong. IntPath---an integrated pathway gene relationship database for model organisms and important pathogens. BMC Systems Biology, 6(Suppl 2):S2, December 2012.

145. Chuan Hock Koh, Limsoon Wong. Embracing noise to improve cross-batch prediction accuracy. BMC Systems Biology, 6(Suppl 2):S3, December 2012.

146. Chern Han Yong, Guimei Liu, Hon Nian Chua, Limsoon Wong. Supervised maximum-likelihood weighting of composite protein networks for complex prediction. BMC Systems Biology, 6(Suppl 2):S13, December 2012. SWC Software

147. Liang Zhao, Steven C. H. Hoi, Limsoon Wong, Tobias Hamp, Jinyan Li. Structural and functional analysis of multi-interface domains. PLoS ONE, 7(12):e50821, December 2012.

148. Wilson Wen Bin Goh, Mengyuan Fan, Hong Sang Low, Marek Sergot, Limsoon Wong. Enhancing the utility of Proteomics Signature Profiling (PSP) with Pathway Derived Subnets (PDSs), performance analysis and specialised ontologies. BMC Genomics, 14:35, February 2013.

149. Hufeng Zhou, Jingjing Jin, Limsoon Wong. Progress in computational studies of host-pathogen interactions. Journal of Bioinformatics and Computational Biology, 11(2):1230001, April 2013.

150. Golnaz Taheri, Mahnaz Habibi, Limsoon Wong, Changiz Eslahchi. Disruption of protein complexes. Journal of Bioinformatics and Computational Biology, 11(3):1341008, June 2013.

151. Guimei Liu, Andre Suchitra, Limsoon Wong. A performance study of three disk-based structures for indexing and querying frequent itemsets. Proceedings of the VLDB Endowment, 6(7):505--516, May 2013.

152. Jingjing Jin, Jun Liu, Huan Wang, Limsoon Wong, Nam-Hai Chua. PLncDB: Plant Long noncoding RNA Database. Bioinformatics, 29(8):1068--1071, April 2013.

153. Wilson Wen Bin Goh, Marek J. Sergot, Judy Sng, Limsoon Wong. Comparative network-based recovery analysis and proteomic profiling of neurological changes in valporic acid-treated mice. Journal of Proteome Research, 12(5):2116--2127, April 2013.

154. Yie Hou Lee, Wilson Wen Bin Goh, Choon Keow Ng, Manfred Raida, Limsoon Wong, Qingsong Lin, Urs A. Boelsterli, Maxey Chung. Integrative toxicoproteomics implicates impaired mitochondrial glutathione import as off-target effect of troglitazone. Journal of Proteome Research, 12(6):2933--2945, May 2013.

155. Peng Chen, Jinyan Li, Limsoon Wong, Hiroyuki Kuwahara, Jianhua Huang, Xin Gao. Accurate prediction of hot spot residues through physicochemical characteristics of amino acid sequences. Proteins: Structure, Function, and Bioinformatics, 81(8):1351--1362, August 2013.

156. Yue Wang, Wilson Wen Bin Goh, Limsoon Wong, Giovanni Montana. Random forests on Hadoop for genome-wide studies of multivariate neuroimaging phenotypes. BMC Bioinformatics, 14(Suppl 16):S6, October 2013.

157. Zhenhua Li, Ying He, Qian Liu, Liang Zhao, Limsoon Wong, Chee Keong Kwoh, Hung Nguyen, Jinyan Li. Structural analysis on mutation residues and interfacial water molecules for human TIM disease understanding. BMC Bioinformatics, 14(Suppl 16):S11, October 2013.

158. Daniel Portal, Hufeng Zhou, Bo Zhao, Peter V. Kharchenko, Elizabeth Lowry, Limsoon Wong, John Quackenbush, Dustin Holloway, Sizun Jiang, Yong Lu, Elliott Kieff. Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proceedings of the National Academy of Sciences of the United States of America, 110(46):18537--18542, November 2013.

159. Wilson Wen Bin Goh, Limsoon Wong. Networks in proteomic analysis of cancer. Current Opinion in Biotechnology, 24(6):1122--1128, December 2013.

160. Wilson Wen Bin Goh, Limsoon Wong, Judy Chia Ghee Sng. Contemporary network proteomics and its requirements. Biology, 3(1):22--38, December 2013.

161. Hufeng Zhou, Javad Rezaie, Willy Hugo, Shangzhi Gao, Jingjing Jin, Mengyuan Fan, Chern-Han Yong, Michal Wozniak, Limsoon Wong. Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. BMC Systems Biology, 7(Suppl 6):S6, December 2013. BITBUCKET

162. Kevin Lim, Limsoon Wong. Finding consistent disease subnetworks using PFSNet. Bioinformatics, 30(2):189--196, January 2014. PFSNet v1.0, PFSNet v2.0

163. Liang Zhao, Steven C. H. Hoi, Zhenhua Li, Limsoon Wong, Hung Nguyen, Jinyan Li. Coupling graphs, efficient algorithms and B-cell epitope prediction. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(1):7--16, January - February 2014.

164. Qian Liu, Steven C. H. Hoi, Chee Keong Kwoh, Limsoon Wong, Jinyan Li. Integrating water exclusion theory into beta contacts to predict binding free energy changes and binding hot spots. BMC Bioinformatics, 15:57, February 2014.

165. Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. eCAMBer: Efficient support for large-scale comparative analysis of multiple bacterial strains. BMC Bioinformatics, 15:65, March 2014. eCAMBer software

166. Wilson Wen Bin Goh, Limsoon Wong. Computational proteomics: Designing a comprehensive analytical strategy. Drug Discovery Today, 19(3):266-274, March 2014.

167. Hufeng Zhou, Shangzhi Gao, Nam Ninh Nguyen, Mengyuan Fan, Jingjing Jin, Bing Liu, Liang Zhao, Geng Xiong, Min Tan, Shijun Li, Limsoon Wong. Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. Biology Direct, 9:5, April 2014.

168. Mengyuan Fan, Hong Sang Low, Hufeng Zhou, Markus R. Wenk, Limsoon Wong. LipidGO: Database for lipid-related GO terms and applications. Bioinformatics, 30(7):1043--1044, April 2014. LipidGO Server, LipidGO .Zip Archive

169. J. M. Saju, Sz. Nemeth, Reka Szucs, Rashmi Sukumaran, Z. Lim, L. Wong, L. Orban, M. Bercsenyi. PCR-based identification of Adriatic specimen of three scorpionfish species (Scorpaenidae, Teleostei). Acta Biologica Hungarica, 65(2):132--143, June 2014.

170. Guimei Liu, Haojun Zhang, Limsoon Wong. A flexible approach to finding representative pattern sets. IEEE Transactions on Knowledge and Data Engineering, 26(7):1562-1574, July 2014.

171. Alireza Vazifedoost, Maseud Rahgozar, Behzad Moshiri, Mehdi Sadeghi, Hon Nian Chua, See Kiong Ng, Limsoon Wong. Using data fusion for scoring reliability of protein-protein interactions. Journal of Bioinformatics and Computational Biology, 12(4):1450014, August 2014.

172. Mengyuan Fan, Hong Sang Low, Markus Wenk, Limsoon Wong. A semi-automated methodology for finding lipid-related GO terms. Database, 2014:bau089, September 2014. LipidGO .Zip Archive

173. Jingjing Jin, Deepa Panicker, Qian Wang, Mi Jung Kim, Jun Liu, Jun-Lin Yin, Limsoon Wong, In-Cheol Jang, Nam-Hai Chua, Rajani Sarojam. Next generation sequencing unravels the biosynthetic ability of spearmint (Mentha spicata) peltate glandular trichomes through comparative transcriptomics. BMC Plant Biology, 14:292, November 2014.

174. Renhua Song, Qian Liu, Gyorgy Hutvagner, Hung Nguyen, Kotagiri Ramamohanarao, Limsoon Wong, Jinyan Li. Rule discovery and distance separation to detect reliable miRNA biomarkers for the diagnosis of lung squamous cell carcinoma. BMC Genomics, 15(Suppl 9):S16, December 2014.

175. Chern Han Yong, Osamu Maruyama, Limsoon Wong. Discovery of small protein complexes from PPI networks with size-specific supervised weighting. BMC Systems Biology, 8(Suppl 5):S3, December 2014.

176. Michal Wozniak, Jerzy Tiuryn, Limsoon Wong. GWAMAR: Genome-wide assessment of mutations associated with drug resistance in bacteria. BMC Genomics, 15(Suppl 10):S10, December 2014.

177. Allen Eng Juh Yeoh, Zhenhua Li, Difeng Dong, Yi Lu, Jan Trka, Shirley Kow Yin Kham, Ah Moy Tan, Hany Ariffin, Limsoon Wong. Effective response metric (ERM-D8) using time-series gene expression profiling at diagnosis and day 8 of remission-induction therapy is a novel early prognostic marker to predict relapse in childhood acute lymphoblastic leukamia (ALL)---a Malaysia-Singapore ALL study. Blood, 124(21):2393, December 2014.

178. Golnaz Taheri, Marzieh Ayati, Limsoon Wong, Changiz Eslahchi. Two scenarios for overcoming drug resistance by co-targeting . International Journal of Bioinformatics Research and Applications, 11(1):72--89, February 2015.

179. May Lee, Jun Hong Xia, Zhongwei Zou, Jian Ye, Rahmadsyah, Yuzer Alfiko, Jingjing Jin, Jessica Virginia Lieando, Maria Indah Purnamasari, Chin Huat Lim, Antonius Suwanto, Limsoon Wong, Nam-Hai Chua, Gen Hua Yue. A consensus linkage map of oil palm and a major QTL for stem height. Scientific Reports, 5:8232, February 2015.

180. Zhenhua Li, Ying He, Limsoon Wong, Jinyan Li. Burial level change defines a high energetic relevance for protein binding interfaces. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(2):410--421, March 2015.

181. Chern Han Yong, Limsoon Wong. From the static interactome to dynamic protein complexes: Three challenges. Journal of Bioinformatics and Computational Biology, 13(2):1571001, April 2015.

182. Guimei Liu, Haojun Zhang, Mengling Feng, Limsoon Wong, See-Kiong Ng. Supporting exploratory hypothesis testing and analysis. ACM Transactions on Knowledge Discovery from Data, 9(4):Article 31, April 2015.

183. Dimitrios Kleftogiannis, Limsoon Wong, John A. C. Archer, Panos Kalnis. Hi-Jack: A novel computational framework for pathway-based inference of host-pathogen interactions. Bioinformatics, 31(14):2332-2339, July 2015.

184. Jingjing Jin, Mi Jung Kim, Savitha Dhandapani, Jessica Gambino Tjhang, Jun-Lin Yin, Limsoon Wong, Rajani Sarojam, Nam-Hai Chua, In-Cheol Jang. The floral transcriptome of ylang ylang (Cananga odorata var. fruticosa) uncovers biosynthetic pathways for volatile organic compounds and a multifunctional and novel sesquiterpene synthase. Journal of Experimental Botany, 66(13):3959--3975, July 2015.

185. Kevin Lim, Zhenhua Li, Kwok Pui Choi, Limsoon Wong. A quantum leap in the reproducibility, precision, and sensitivity of gene expression profile analysis even when sample size is extremely small. Journal of Bioinformatics and Computational Biology, 13(4):1550018, August 2015.

186. Chern Han Yong, Limsoon Wong. Prediction of problematic complexes from PPI networks: Sparse, embedded, and small complexes. Biology Direct, 10:40, August 2015. IntegratedComplexPrediction Software

187. Sriganesh Srihari, Chern Han Yong, Ashwini Patil, Limsoon Wong. Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes. FEBS Letters, 589(19):2590--2602, September 2015.

188. Sriganesh Srihari, Jitin Singla, Limsoon Wong, Mark Ragan. Inferring synthetic lethal interactions from mutual exclusivity of genetic events in cancer. Biology Direct, 10:57, October 2015.

189. Hirotaka Oikawa, Wilson Wen Bin Goh, Vania Lim, Limsoon Wong, Judy Sng. Valporic acid mediates BDNF through miR-124 by down-regulating a novel protein target, GNAI1. Neurochemistry International, 91:62--71, December 2015.

190. Mi Jung Kim, Jingjing Jin, Junshi Zheng, Limsoon Wong, Nam Hai Chua, In-Cheol Jang. Comparative transcriptomics unravel biochemical specialization of leaf tissues of Stevia for diterpenoid production. Plant Physiology, 169(4):2462--2480, December 2015.

191. Wilson Wen Bin Goh, Tiannan Guo, Ruedi Aebersold, Limsoon Wong. Quantitative proteomics signature profiling based on network contextualization. Biology Direct, 10:71, December 2015.

192. Wilson Wen Bin Goh, Limsoon Wong. Design principles for clinical network-based proteomics. Drug Discovery Today, 21(7):1130--1138, July 2016.

193. Wilson Wen Bin Goh, Limsoon Wong. Advancing clinical proteomics via analysis based on biological complexes: A tale of five paradigms. Journal of Proteome Research, 15(9):3167--3179, July 2016.

194. Wilson Wen Bin Goh, Limsoon Wong. Spectra-first feature analysis in clinical proteomics---a case study in renal cancer. Journal of Bioinformatics and Computational Biology, 14(5):1644004, October 2016.

195. Wilson Wen Bin Goh, Limsoon Wong. Evaluating feature-selection stability in next-generation proteomics. Journal of Bioinformatics and Computational Biology, 14(5):1650029, October 2016.

196. Wilson Wen Bin Goh, Limsoon Wong. Integrating networks and proteomics: Moving forward. Trends in Biotechnology, 34(12):951--959, December 2016.

197. Jingjing Jin, May Lee, Bin Bai, Yanwei Sun, Jing Qu, Rahmadsyah, Yuzer Alfiko, Chin Huat Lim, Antonius Suwanto, Maria Sugiharti, Limsoon Wong, Jian Ye, Nam-Hai Chua, Gen Hua Yue. Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm. DNA Research, 23(6):527--533, December 2016.

198. Abha Belorkar, Limsoon Wong. GFS: Fuzzy preprocessing for effective gene expression analysis. BMC Bioinformatics, 17(Suppl 17):540, December 2016.

199. Wilson Wen Bin Goh, Limsoon Wong. Protein complex-based analysis is resistant to the obfuscating consequences of batch effects---a case study in clinical proteomis. BMC Genomics, 18(Suppl 2):142, March 2017.

200. Jingjing Jin, Yanwei Sun, Jing Qu, Rahmadsyah, Chin-Huat Lim, Yuzer Alfiko, Nur Estya Bte Rahman, Antonius Suwanto, Genhua Yue, Limsoon Wong, Nam Hai Chua, Jian Ye. Transcriptome and functional analysis reveals hybrid vigor for oil biosynthesis in oil palm. Scientific Reports, 7:439, March 2017.

201. Wilson Wen Bin Goh, Limsoon Wong. Class-paired Fuzzy SubNETs: A paired variant of the rank-based network analysis family for feature selection based on protein complexes. Proteomics, 17(10):1700093, May 2017.

202. Wilson Wen Bin Goh, Wei Wang, Limsoon Wong. Why batch effects matter in omics data, and how to avoid them. Trends in Biotechnology, 35(6):498--507, June 2017.

203. Wilson Wen Bin Goh, Limsoon Wong. NetProt: Complex-based feature selection. Journal of Proteome Research, 16(8):3102--3112, June 2017.

204. Wei Zhong Toh, Kwok Pui Choi, Limsoon Wong. Redhyte: A self-diagnosing, self-correcting, and helpful hypothesis analysis platform. Journal of Information and Telecommunication, 1(3):241--258, July 2017.

205. Daniel Boon Loong Teh, Ankshita Prasad, Wenxuan Jiang, Mohd Zacky Ariffin, Sanjay Khanna, Abha Belorkar, Limsoon Wong, Xiaogang Liu, Angelo H. All. Transcriptome analysis reveals neuroprotective aspects of human reactive astrocytes induced by interleekin 1beta. Scientific Reports, 7(1):13988, October 2017.

206. Yuansheng Liu, Hui Peng, Limsoon Wong, Jinyan Li. High-speed and high-ratio referential genome compression. Bioinformatics, 33(21):3364-3372, November 2017.

207. Wilson Wen Bin Goh, Judy Chia-Ghee Sng, Jie Yin Yee, Yuen Mei See, Tih-Shih Lee, Limsoon Wong, Jimmy Lee. Can peripheral blood-derived gene expression characterize individuals at ultra-high risk for psychosis? Computational Psychiatry, 1:168--183, December 2017.

208. Liang Zhao, Qingfeng Chen, Wencui Li, Peng Jiang, Limsoon Wong, Jinyan Li. MapReduce for accurate error correction of next-generation sequencing data. Bioinformatics, 33(23):3844--3851, December 2017.

209. Soheil Jahangiri-Tazehkand, Limsoon Wong, Changiz Eslahchi. OrthoGNC: A software for accurate identification of orthologs based on gene neighborhood conservation. Genomics, Proteomics, & Bioinformatics, 15(6):361--379, December 2017. orthoGNC v2.0

210. Longjian Zhou, Limsoon Wong, Wilson Wen Bin Goh. Understanding missing proteins: A functional perspective. Drug Discovery Today, 23(3):644--651, March 2018. Brief intro in Science Trends

211. Abha Belorkar, Rajanikanth Vadigepalli, Limsoon Wong. SPSNet: Subpopulation-sensitive network-based analysis of heterogeneous gene expression data. BMC Systems Biology, 12(Suppl 2):28, March 2018. SPSNet v1.0

212. Wilson Wen Bin Goh, Limsoon Wong. Dealing with confounders in -omics analysis. Trends in Biotechnology, 36(5):488--498, May 2018.

213. Limsoon Wong. Big data and a bewildered lay analyst. Statistics and Probability Letters, 136:73--77, May 2018.

214. Allen E.-J. Yeoh, Zhenhua Li, Difeng Dong, Yi Lu, Nan Jiang, Jan Trka, An Moy Tan, Hai Peng Lin, Thuan Chong Quah, Hany Ariffin, Limsoon Wong. Effective Response Metric: A novel tool to predict relapse in childhood acute lymphoblastic leukaemia using time-series gene expression profiling. British Journal of Haematology, 181(5):653--663, June 2018.

215. Iana Pyrogova, Limsoon Wong. Protein complex prediction by date-hub removal. Computational Biology and Chemistry, 74:407--419, June 2018. PPT

216. Qian Liu, Shameek Ghosh, Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao. Discovering pan-correlation patterns from time course data sets by efficient mining algorithms. Computing, 100(4):421--437, April 2018.

217. Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong. TICA: Transcription interaction and coregulation analyser. Genomics, Proteomics, & Bioinformatics, 16(5):342--353, October 2018.

218. Wilson Wen Bin Goh, Limsoon Wong. Why breast cancer signatures are no better than random signatures explained. Drug Discovery Today, 23(11):1818--1823, November 2018.

219. Wilson Wen Bin Goh, Limsoon Wong. Turning straw into gold: Building robustness into gene signature inference. Drug Discovery Today, 24(1):31--36, January 2019.

220. Wilson Wen Bin Goh, Limsoon Wong. Advanced bioinformatics methods for practical applications in proteomics. Briefings in Bioinformatics, 20(1):347--355, January 2019.

221. Peng Jiang, Jie Luo, Yiqi Wang, Pingji Deng, Bertil Schmidt, Xiangjun Tang, Ningjiang Chen, Limsoon Wong, Liang Zhao. kmcEx: Memory-frugal and retrieval-erfficient encoding of counted k-mers. Bioinformatics, 35(23):4871--4878, December 2019.

222. Wilson Wen Bin Goh, Yaxing Zhao, Andrew Chi-Hau Sue, Tiannan Guo, Limsoon Wong. Proteomic investigation of intra-tumor heterogeneity using network-based contextualization---a case study on prostate cancer. Journal of Proteomics, 206:103446, August 2019.

223. Daniel Boon Loong Teh, Ankshita Prasad, Wenxuan Jiang, Nianchen Zhang, Yang Wu, Hyunsoo Yang, Sanyang Han, Zhigao Yi, Yanzhuang Yeo, Toru Ishizuka, Limsoon Wong, Nitish Thakor, Hiromu Yawo, Xiaogang Liu, Angelo ALL. Driving neurogenesis in neural stem cells with high sensitivity optogenetics. NeuroMolecular Medicine, 22:139--149, March 2020.

224. Wilson Wen Bin Goh, Limsoon Wong. The birth of bio-data science: Trends, expectations, and applications. Genomics, Proteomics, & Bioinformatics, 18(1):5--15, February 2020.

225. Sung Yang Ho, Limsoon Wong, Wilson Wen Bin Goh. Avoid oversimplifications in machine learning: Going beyond the class-prediction accuracy. Patterns, 1(2):100025, May 2020.

226. Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong. NAUTICA: Classifying transcription factor interactions by positional and protein-protein interaction information. Biology Direct, 15:13, September 2020.

227. Yaxing Zhao, Limsoon Wong, Wilson Wen Bin Goh. How to do quantile normalization correctly for gene expression data analysis. Scientific Reports, 10:15534, September 2020.

228. Sung Yang Ho, Kimberly Phua, Limsoon Wong, Wilson Wen Bin Goh. Extensions of the external validation for checking learned model interpretability and generalizability. Patterns, 1(8):100129, November 2020.

229. Yuansheng Liu, Limsoon Wong, Jinyan Li. Allowing mutations in maximal matches boosts genome compression performance. Bioinformatics, 36(18):4675--4681, September 2020.

230. Sung Yang Ho, Sophia Tan, Chun Chau Sze, Limsoon Wong, Wilson Wen Bin Goh. What can Venn diagrams teach us about doing data science better? International Journal of Data Science and Analytics, 11(1):1--10, January 2021.

231. Luyu Xie, Limsoon Wong. PDR: A new genome assembly evaluation metric based on genetics concerns. Bioinformatics, 37(3):289--295, February 2021.

232. Runbin Tang, Zuguo Yu, Yuanlin Ma, Yi-Ping Phoebe Chen, Limsoon Wong, Jinyan Li. Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning. Bioinformatics, 37(6):750--758, March 2021.

233. Pietro Pinoli, Sriganesh Srihari, Limsoon Wong, Stefano Ceri. Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response. BMC Bioinformatics, 22:250, May 2021.

234. Chern Han Yong, Shawn Hoon, Sanjay De Mel, Stacy Xu, Jonathan Adam Scolnick, Xiaojing Huo, Michael Lovci, Wee Joo Chng, Limsoon Wong. MapBatch: Conservative batch normalization for single cell RNA-sequencing data enables discovery of rare cell populations in a multiple myeloma cohort. Blood, 138(Suppl. 1):2954-2954, November 2021.

235. Weijia Kong, Bertrand Jernhan Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong, Wilson Wen Bin Goh. PROTREC: A probability-based approach for recovering missing proteins based on biological networks. Journal of Proteomics, 250:104392, January 2022.

236. Zelu Huang, Weijia Kong, Bertrand Jernhan Wong, Huanhuan Gao, Tiannan Guo, Xianming Liu, Xiaoxian Du, Limsoon Wong, Wilson Wen Bin Goh. Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF. Data in Brief, 41:107919, April 2022.

237. Li Rong Wang, Limsoon Wong, Wison Wen Bin Goh. How Doppelganger effects in biomedical data confound machine learning. Drug Discovery Today, 27(3):678--685, March 2022.

238. Mohammad Neamul Kabir, Limsoon Wong. EnsembleFam: Towards more accurate protein family prediction in the twilight zone. BMC Bioinformatics, 23:90, March 2022.

239. Wilson Wen Bin Goh, Chern Han Yong, Limsoon Wong. Are batch effects still relevant in the age of big data? Trends in Biotechnology, 40(9):1029--1040, September 2022.

240. Stefano Perna, Val Tannen, Limsoon Wong. Iterating on multiple collections in synchrony. Journal of Functional Programming, 32:e9, July 2022.

241. Bertrand Jernhan Wong, Weijia Kong, Limsoon Wong, Wilson Wen Bin Goh. Resolving missing protein problems using functional class scoring. Scientific Reports, 12(1):11358, July 2022.

242. Tian Lan, Gyorgy Hutvagner, Xuan Zhang, Tao Liu, Limsoon Wong, Jinyan Li. Density-based detection of cell transition states to construct disparate and bifurcating trajectories. Nucleic Acids Research, 50(21):e122, November 2022.

243. Wei Xin Chan, Limsoon Wong. Accounting for treatment during the development or validation of prediction models. Journal of Bioinformatics and Computational Biology, 20(6):2271001, December 2022.

244. Wilson Wen Bin Goh, Reuben Jyong Kiat Foo, Limsoon Wong. What can scatterplots teach us about doing data science better?. International Journal of Data Science and Analytics, 17:111--125, 2024. DOI: https://doi.org/10.1007/s41060-022-00362-9

245. Wilson Wen Bin Goh, Weijia Kong, Limsoon Wong. Evaluating network-based missing protein prediction using p-values, Bayes factors, and probabilities. Journal of Bioinformatics and Computational Biology, 21(1):2350005, March 2023.

246. Wei Xin Chan, Limsoon Wong. Obstacles to effective model deployment in healthcare. Journal of Bioinformatics and Computational Biology, 21(2):2371001, April 2023.

247. Hui Peng, Limsoon Wong, Wilson Wen Bin Goh. ProInfer: An interpretable protein inference tool leveraging on biological networks. PLoS Computational Biology, 19(3):e1010961, March 2023.

248. Wilson Wen Bin Goh, Harvard Wai Hann Hui, Limsoon Wong. How missing value imputation is confounded with batch effects and what you can do about it. Drug Discovery Today, 28(9):103661, September 2023.

249. Weijia Kong, Bertrand Jern Han Wong, Harvard Wai Hann Hui, Kai Peng Lim, Yulan Wang, Limsoon Wong, Wilson Wen Bin Goh. ProJect: A powerful mixed-model missing value imputation method. Briefings in Bioinformatics, 24(4):bbad233, July 2023.

250. Wenhao Jin, Kristopher Brannan, Katannya Kapeli, Samuel Park, Hui Qing Tan, Maya Gosztyla, Mayuresh Mujumdar, Joshua Ahdout, Bryce Henroid, Katherine Rothamel, Joy Xiang, Limsoon Wong, Gene Yeo. HydRA: Deep-learning models for predicting RNA-binding capacity from protein interaction association context and protein sequence. Molecular Cell, 83(14):2595-2611, July 2023.

251. Lakshmi Alagappan, Jia En Chu, Joanna Huixin Chua, Jia Wen Ding, Ronghui Xiao, Zhe Yu, Kun Pan, Untzizu Elejalde, Kevin Junliang Lim, Limsoon Wong. Class-specific correction and classification of NIR spectra of edible oils. Chemometrics and Intelligent Laboratory Systems, 241:104977, September 2023.

252. Yizhi Dong, Hui Xing Lau, Noor Hidayatul Aini Suaini, Michelle Zhi Ling Kee, Delicia Shu Qin Ooi, Lynette Pei Chi Shek, Bee Wah Lee, Keith M. Godfrey, Elizabeth Huiwen Tham, Marcus Eng Hock Ong, Nan Liu, Limsoon Wong, Kok Hian Tan, Jerry Kok Yen Chan, Fabian Kok Peng Yap, Yap Seng Chong, Johan Gunnar Eriksson, Mengling Feng, Evelyn Xiu Ling Loo. A machine-learning exploration of the exposome from preconception in early childhood atopic eczema, rhinitis and wheeze development. Environmental Research, 250:118523, February 2024.

253. Chowdhury Rafeed Rahman, Limsoon Wong. How much can ChatGPT really help computational biologists in programming? Journal of Bioinformatics and Computational Biology, 22(2):2471001 April 2024.

254. Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong. A comparative analysis of ENCODE and Cistrome in the context of TF binding signal. BMC Genomics, 25(Suppl 3):817, August 2024.

255. Wilson Wen Bin Goh, Mohammad Neamul Kabir, Sehwan Yoo, Limsoon Wong. Ten quick tips for ensuring machine learning model validity. PLoS Computational Biology, 20(9):e1012402, September 2024.

256. Xizi Luo, Andre Huikai Lin, Song Yi Amadeus Chi, Limsoon Wong, Chowdhury Rafeed Rahman. Benchmarking recent computational tools for DNA-binding protein identification. Briefings in Bioinformatics, accepted.

257. Fuchu He, Ruedi Aebersold, Mark S. Baker, et al. π-HuB: The proteomic navigator of the human body. Nature, accepted.

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     Conference Papers

258. Limsoon Wong. Inference Rules in Object Oriented Programming Systems. Proceedings of 1st International Conference on Deductive and Object Oriented Databases, Kyoto, Japan, 493-509, December 1989.

259. Anne Ngu, Limsoon Wong, Surjatini Widjojo. On Canonical and Noncanonical Classifications. Proceedings of 2nd International Conference on Deductive and Object Oriented Databases, Munich, Germany, 371-390, December 1991.

260. Val Breazu-Tannen, Peter Buneman, Limsoon Wong. Naturally Embedded Query languages. Proceedings of 4th International Conference on Database Theory, Berlin, Germany, 140-154, October 1992. (Full paper invited to Theoretical Computer Science.)

261. Anne Ngu, Lingling Yan, Limsoon Wong. Heterogeneous Query Optimization using Maximal Subqueries. Proceedings of 3rd International Symposium on Database Systems for Advanced Applications, Taejon, Korea, 413-420, April 1993.

262. Anne Ngu, Limsoon Wong. PINOL: A Persistent Inferential Object Oriented Language for Databases. Proceedings of 3rd International Symposium on Database Systems for Advanced Applications, Taejon, Korea, 57-64, April 1993.

263. Limsoon Wong. Normal Forms and Conservative Properties of Query Languages over Collection Types. Proceedings of 12th ACM Symposium on Principles of Database Systems, Washington, D. C., 26-36, May 1993. (Full paper invited to Journal of Computer and System Sciences.)

264. Leonid Libkin, Limsoon Wong. Semantic Representations and Query Languages for Or-sets. Proceedings of 12th ACM Symposium on Principles of Database Systems, Washington, D. C., 37-48, May 1993.

265. Leonid Libkin, Limsoon Wong. Aggregate Functions, Conservative Extension, and Linear Orders. Proceedings of 4th International Workshop on Database Programming Languages, Manhattan, New York, 282-294, August 1993.

266. Leonid Libkin, Limsoon Wong. Some Properties of Query Languages for Bags. Proceedings of 4th International Workshop on Database Programming Languages, Manhattan, New York, 97-114, August 1993.

267. Leonid Libkin, Limsoon Wong. New Techniques for Studying Set Languages, Bag Languages, and Aggregate Functions. Proceedings of 13th ACM Symposium on Principles of Database Systems, Minneapolis, Minnesota, 155-166, May 1994. (Full paper invited to Journal of Computer and System Sciences.)

268. Dan Suciu, Limsoon Wong. On Two Forms of Structural Recursion. Proceedings of 5th International Conference on Database Theory, Prague, Czech Republic, 111-124, January 1995.

269. Peter Buneman, Susan Davidson, Kyle Hart, Chris Overton, Limsoon Wong. A Data Transformation System for Biological Data Sources. Proceedings of 21st International Conference on Very Large Data Bases, Zurich, Switzerland, 158-169, September 1995.

270. Guozhu Dong, Leonid Libkin, Limsoon Wong. On Impossibility of Decremental Recomputation of Recursive Queries in Relational Calculus and SQL. Springer Electronic Workshop in Computing: Proceedings of 5th International Workshop on Database Programming Languages, Gubbio, Italy, 8, September 1995.

271. Michael Benedikt, Guozhu Dong, Leonid Libkin, Limsoon Wong. Relational Expressive Power of Constraint Query Languages. Proceedings of 15th ACM Symposium on Principles of Database Systems, Montreal, Canada, 5--16, June 1996.

272. Leonid Libkin, Rona Machlin, Limsoon Wong. A Query Language for Multidimensional Arrays: Design, Implementation, and Optimization Techniques. Proceedings of ACM SIGMOD International Conference on Management of Data, Montreal, Canada, 228-239, June 1996.

273. Wang Chiew Tan, Ke Wang, Limsoon Wong. QUICK: Graphical User Interface to Multiple Databases. Proceedings of 7th International Workshop on Database and Expert Systems Applications, Zurich, Switzerland, 404-409, September 1996.

274. Guozhu Dong, Leonid Libkin, Limsoon Wong. Local Properties of Query Languages. Proceedings of 6th International Conference on Database Theory, Delphi, Greece, 140-154, January 1997. (Full paper invited to Theoretical Computer Science.)

275. Leonid Libkin, Limsoon Wong. On the Power of Aggregation in Relational Query Languages, LNCS 1369: Proceedings of 6th International Workshop on Database Programming Languages, Estes Park, Colorado, August 1997, 260--280.

276. Leonid Libkin, Limsoon Wong. Incremental Recomputation of Recursive Queries with Nested Sets and Aggregate Functions, LNCS 1369: Proceedings of 6th International Workshop on Database Programming Languages, Estes Park, Colorado, August 1997, 222--238.

277. P. R. Kolatkar, M. K. Sakharkar, C. R. Tse, B. K. Kiong, L. Wong, T. W. Tan, S. Subbiah. Development of Software Tools at Bioinformatics Centre (BIC) at the National University of Singapore (NUS). Proceedings of Pacific Symposium on Biocomputing'98, Maui, Hawaii, 735--746, January 1998. (Invited paper.)

278. O. P. Wu, K. T. Seow, L. Wong, S. Y. Chung, S. Subbiah. From Sequence to Structure to Literature: The Protocol Approach to Bioinformation. Proceedings of Pacific Symposium on Biocomputing'98, Maui, Hawaii, 747--758, January 1998. (Invited paper.)

279. P.R. Kolatkar, M.K. Sakharkar, T.C. Roderic, B.K. Kiong, L. Wong, T.W. Tan, S. Subbiah. Integration of Bioinformatics tools at the National University of Singapore. Proceedings of 9th World Congress on Medical Informatics, Seoul, Korea, 356--360, 1998.

280. Leonid Libkin, Limsoon Wong. Unary Quantifiers, Transitive Closure, and Relations of Large Degrees , Proceedings of 15th Symposium on Theoretical Aspects of Computer Science, Paris, France, 183-193, February 1998.

281. Jing Chen, Limsoon Wong, Louxin Zhang. A Protein Patent Query System Powered By Kleisli. Proceedings of ACM SIGMOD International Conference on Management of Data, Seattle, Washington, 593--595, June 1998.

282. Jing Chen, Nam-Hai Chua, Daphna Strauss, Limsoon Wong. Extracting Kozak Consensus Sequence Using Kleisli, Proceedings of 1st International Conference on Bioinformatics of Genome Regulation and Structure, Novosibirsk, Russia, August 1998, 218--223.

283. Thangavelu Kandasamy, HweeHwa Pang, Allison Ting, Jiren Wang, Limsoon Wong. Two Tools for Solving Bioinformatics Problems, Proceedings of 1998 IEEE Knowledge and Data Engineering Exchange Workshop, Taiwan, November 1998, 79--86.

284. Kui Lin, Anthony E. Ting, Jiren Wang, Limsoon Wong. Hunting TPR Domains Using Kleisli, Proceedings of 9th Workshop on Genome Informatics, Tokyo, Japan, December 1998, 173--182.

285. Jing Chen, Daphna Strauss, Limsoon Wong. Using Kleisli to bring out features in BLASTP results, Proceedings of 9th Workshop on Genome Informatics, Tokyo, Japan, December 1998, 102--111.

286. Lauri Hella, Leonid Libkin, Juha Nurmonen, Limsoon Wong. Logics with Aggregate Operators, Proceedings of 14th IEEE Symposium on Logic in Computer Science, Trento, Italy, July 1999, 35--44.

287. Leonid Libkin, Limsoon Wong. On the Power of Incremental Evaluation in SQL-like Languages Proceedings of 7th International Workshop on Database Programming Languages, Kinloch Rannach, Scotland, September 1999, 17--30.

288. Guozhu Dong, Xiuzhen Zhang, Jinyan Li, Limsoon Wong. CAEP: Classification by Aggregating Emerging Patterns, Proceedings of 2nd International Conference on Discovery Science, Tokyo, Japan, December 1999, 30--42.

289. Tatsuhiko Tsunoda, Limsoon Wong. Natural Language Processing for Biology, Proceedings of Pacific Symposium on Biocomputing 2000, Hawaii, January 2000, 491--492.

290. Limsoon Wong. The Functional Guts of the Kleisli Query System. Proceedings of 5th ACM SIGPLAN International Conference on Functional Programming, Montreal, Canada, September 2000, 1--10. Talk. (Keynote paper.)

291. Limsoon Wong. Kleisli, its Exchange Format, Supporting Tools, and an Application in Protein Interaction Extraction, Proceedings of IEEE International Symposium on Bio-Informatics and Biomedical Engineering, Washington DC, November 2000, 21--28. Talk

292. Limsoon Wong. Bioinformatics Takes Charge. Proceedings of 10th International Conference on Biomedical Engineering, Singapore, December 2000, 45--46. (Invited paper.) Talk.

293. Limsoon Wong. Visualization and Manipulation of Pedigree Diagrams. Proceedings of 11th Workshop on Genome Informatics, Tokyo, Japan, December 2000, pages 63--72. Talk.

294. Limsoon Wong. A Protein Interaction Extraction System, Proceedings of Pacific Symposium on Biocomputing 2001, Hawaii, January 2001, pages 520--530. Talk.

295. Jun-ichi Tsujii, Limsoon Wong. Natural Language Processing and Information Extraction in Biology, Proceedings of Pacific Symposium on Biocomputing 2001, Hawaii, January 2001, pages 372--373.

296. Jinyan Li, Limsoon Wong. Emerging Patterns and Gene Expression Data. Proceedings of 12th Workshop on Genome Informatics, Tokyo, Japan, December 2001, pages 3--13.

297. Lynette Hirschman, Jong C. Park, Junichi Tsujii, Cathy Wu, Limsoon Wong. Literature Data Mining for Biology Proceedings of Pacific Symposium on Biocomputing 2002, Hawaii, January 2002, pages 323--325. PDF

298. Beng Chin Ooi, Hwee Hwa Pang, Hao Wang, Limsoon Wong, Cui Yu. Fast Filter-and-Refine Algorithms for Subsequence Selection. Proceedings of International Data Engineering and Applications Symposium, pages 243--254, Edmonton, Canada, July 2002.

299. Jinyan Li, Limsoon Wong. Geography of Differences Between Two Classes of Data. Proceedings 6th European Conference on Principles of Data Mining and Knowledge Discovery, pages 325--337, Helsinki, Finland, August 2002.

300. Jinyan Li, Limsoon Wong. Solving the Fragmentation Problem of Decision Trees by Discoverying Boundary Emerging Patterns. Proceedings of IEEE International Conference on Data Mining, pages 653--656, Maebashi City, Japan, December 2002.

301. Jinyan Li, Huiqing Liu, Limsoon Wong. A comparative study on feature selection and classification methods using a large set of gene expression profiles. Proceedings of 13th International Conference on Genome Informatics, pages 51--60, Tokyo, Japan, December 2002.

302. Fanfan Zeng, Roland Yap, Limsoon Wong. Using Feature Generation and Feature Selection for Accurate Prediction of Translation Initiation Sites. Proceedings of 13th International Conference on Genome Informatics, pages 192--200, Tokyo, Japan, December 2002. talk

303. Vladimir Bajic, Vladimir Brusic, Jinyan Li, See-Kiong Ng, Limsoon Wong. From Informatics to Bioinformatics. Proceedings of 1st Asia Pacific Bioinformatics Conference, pages 3--14, Adelaide, Australia, February 2003. (Keynote paper.) talk

304. Jinyan Li, See-Kiong Ng, Limsoon Wong. Bioinformatics Adventures in Database Research. Proceedings of 9th International Conference on Database Theory, pages 31--46, Siena, Italy, January 2003. (Keynote paper.)

305. Jinyan Li, Limsoon Wong. Using Rules to Analyse Bio-medical Data: A Comparison between C4.5 and PCL. Proceedings of 4th International Conference on Web-Age Information Management, pages 254--265, Chengdu, PRC, August 2003.

306. Jinyan Li, Huiqing Liu, Limsoon Wong. Mean-entropy discretized features are effective for classifying high-dimensional biomedical data. Proceedings of 3rd ACM SIGKDD Workshop on Data Mining in Bioinformatics, pages 17--24, Washington, DC, August 2003.

307. Huiqing Liu, Hao Han, Jinyan Li, Limsoon Wong. An in silico method for prediction of polyadenylation signals in human sequences. Proceedings of 14th International Conference on Genome Informatics , pages 84--93, Yokohama, December 2003. Server

308. Jinyan Li, Huiqing Liu, Limsoon Wong. Use of Built-in Features in the Interpretation of High-dimensional Cancer Diagnosis Data. Proceedings of 2nd Asia Pacific Bioinformatics Conference, pages 67--74, Dunedin, New Zealand, January 18-22, 2004.

309. Huiqing Liu, Jinyan Li, Limsoon Wong. Selection of Patient Samples and Genes for Outcome Prediction. IEEE Bioinformatics Proceedings (CSB2004), pages 382--392, Stanford, CA, August 2004.

310. Guozhu Dong, Chunyu Jiang, Jian Pei, Jinyan Li, Limsoon Wong. Mining Succint Systems of Minimal Generators of Formal Concepts. Proceedings of 10th International Conference on Database Systems for Advanced Applications, pages 175--187, Beijing, China, April 2005. Draft

311. Li Lin, Limsoon Wong, Tzeyun Leong, Pohsan Lai. LinkageTracker: A Discriminative Pattern Tracking Approach to Linkage Disequilibrium Mapping. Proceedings of 10th International Conference on Database Systems for Advanced Applications, pages 30--42, Beijing, China, April 2005. Draft

312. Haiquan Li, Jinyan Li, Limsoon Wong, Mengling Feng, Yap-Peng Tan. Relative Risk and Odds Ratio: A Data Mining Perspective. Proceedings of 24th ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems, pages 368--377, Baltimore, Maryland, June 2005. GcGrowth Software

313. Jinyan Li, Haiquan Li, Donny Soh, Limsoon Wong. A Correspondence Between Maximal Complete Bipartite Subgraphs and Closed Patterns. Proceedings of 9th European Conference on Principles and Practice of Knowledge Discovery in Databases, pages 146--156, Porto, Portugal, October 2005. FP-MBC Software

314. Liang Huai Yang, Wynne Hsu, Mong Li Lee, Limsoon Wong. SVM-based Identification of microRNA Precursors, Proceedings of 4th Asia-Pacific Bioinformatics Conference, pages 267--276, Taipei, Taiwan, February 2006.

315. Guimei Liu, Jinyan Li, Limsoon Wong, Wynne Hsu. Positive Borders or Negative Borders: How to Make Generator-Based Lossless Representation Concise, Proceedings of SIAM Conference on Data Mining, pages 469--473, Bethesda, Maryland, April 2006. GrGrowth-PBd Software

316. Jinyan Li, Haiquan Li, Limsoon Wong, Jian Pei, Guozhu Dong. Minimum Description Length Principle: Generators are Preferable to Closed Patterns. Proceedings of 21st National Conference on Artificial Intelligence, pages 409--415, Boston, Mass, July 2006.

317. Yun Zheng, Wynne Hsu, Mong Li Lee, Limsoon Wong. Exploring Essential Attributes for Detecting MicroRNA Precursors from Background Sequences. Proceedings of 2006 VLDB Workshop on Data Mining in Bioinformatics, pages 131--145, Seoul, Korea, September 2006.

318. Jin Chen, Hon Nian Chua, Wynne Hsu, Mong-Li Lee, See-Kiong Ng, Rintaro Saito, Wing-Kin Sung, Limsoon Wong. Increasing Confidence of Protein-Protein Interactomes. Proceedings of 17th International Conference on Genome Informatics, pages 284--297, Yokohama, Japan, 18-20 December 2006. (invited keynote paper) FSWeight V2.1 Software

319. Swee-Seong Wong, Wing-Kin Sung, Limsoon Wong. CPS-tree: A Compact Partitioned Suffix Tree for Disk-Based Indexing on Large Genome Sequences, Proceedings of 23rd IEEE International Conference on Data Engineering, pages 1350--1354, Istanbul, Turkey, April 2007. CPS Software

320. Guimei Liu, Jinyan Li, Kelvin Sin, Limsoon Wong. Distance-Based Subspace Clustering with Flexible Dimension Partitioning, Proceedings of 23rd IEEE International Conference on Data Engineering, pages 1250--1254, Istanbul, Turkey, April 2007.

321. Mengling Feng, Guozhu Dong, Jinyan Li, Yap-Peng Tan, Limsoon Wong. Evolution and Maintenance of Frequent Pattern Space when Transactions are Removed. Proceedings of 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), pages 489--497, Nanjing, China, May 2007. Talk. TRUM Software

322. Limsoon Wong. Manifestation and Exploitation of Invariants in Bioinformatics, Proceedings of 2nd International Conference on Algebraic Biology (AB2007), pages 365--377, Castle of Hagenberg, Austria, 2-4 July 2007. talk

323. Jinyan Li, Guimei Liu, Limsoon Wong. Mining Statistically Important Equivalence Classes and Delta-Discriminative Emerging Patterns. Proceedings of 13th International Conference on Knowledge Discovery and Data Mining, pages 430--439, San Jose, California, 12-15 August 2007. DPM Software

324. Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong. Using Indirect Protein-Protein Interactions for Protein Complex Prediction. Proceedings of 6th Annual International Conference on Computational Systems Bioinformatics (CSB), pages 97--110, San Diego, California, August 2007. PCP V1.0 Software

325. Li Lin, Limsoon Wong, Tzeyun Leong, Pohsan Lai. ECTracker---An Efficient Algorithm for Haplotype Analysis and Classification, Proceedings of 12th Triennial Medinfo 2007 Congress, pages 1270--1274, Brisbane, Australia, 21-24 August 2007.

326. Chuan Hock Koh, Limsoon Wong. Recognition of Polyadenylation Sites from Arabidopsis Genomic Sequences. Proceedings of 18th International Conference on Genome Informatics (GIW), pages 73--82, Singapore, 3-5 December 2007. Datasets and Source Codes

327. Jinyan Li, Kelvin Sim, Guimei Liu, Limsoon Wong. Maximal Quasi-Bicliques with Balanced Noise Tolerance: Concepts and Co-Clustering Applications. Proceedings of SIAM Conference on Data Mining, pages 72--83, Atlanta, Georgia, 24-26 April 2008.

328. Guimei Liu, Limsoon Wong. Effective Pruning Techniques for Mining Quasi-Cliques. Proceedings of European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML/PKDD), part II, pages 33--49, Antwerp, Belgium, 15-19 September 2008. Quick Software

329. Mengling Feng, Jinyan Li, Limsoon Wong, Yap-Peng Tan. Negative Generator Border for Effective Pattern Maintenance. Proceedings of 4th International Conference on Advanced Data Mining and Applications, pages 217--228, Chengdu, China, 8-10 October 2008. (Best Paper Runner-Up at ADMA2008)

330. Guimei Liu, Jinyan Li, Limsoon Wong. Assessing and Predicting Protein Interactions Using Both Local and Global Network Topological Metrics. Proceedings of 19th International Conference on Genome Informatics (GIW), pages 138--149, Gold Coast, Australia, 3 December 2008. PPT

331. Yubo Wang, Jie Hu, Gaoxi Xiao, Limsoon Wong, Stefan Ma, Tee Hiang Cheng. A Preliminary Study on the Effects of Fear Factors in Disease Propagation. Proceedings of 1st International Conference on Complex Sciences: Theory and Applications (Complex'2009), pages 1387-1397, Shanghai, China, 23-25 February 2009.

332. Xiuju Fu, Sonja Lim, Lipo Wang, Gary Lee, Stefan Ma, Limsoon Wong, Gaoxi Xiao. Key Node Selection for Containing Infectious Disease Spread Using Particle Swarm Optimization. Proceedings of IEEE Swarm Intelligence Symposium 2009, pages 109--113, Nashville, USA, 29 March-2 April 2009.

333. Difeng Dong, Chun-Ying Cui, Benjamin Mow, Limsoon Wong. Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma. Proceedings of 1st International Conference on Bioinformatics and Computational Biology (BICOB2009), pages 199--210, New Orleans, USA, 8-10 April 2009.

334. Tianyou Zhang, Soon Hong Soh, Xiuju Fu, Kee Khoon Lee, Limsoon Wong, Stefan Ma, Gaoxi Xiao, Chee Keong Kwoh. HPCgen---A Fast Generator of Contact Networks of Large Urban Cities for Epidemiological Studies. Proceedings of International Conference on Computational Intelligence, Computer Modeling and Simulation, pages 198--203, Brno, Czech Republic, 7-9 September 2009.

335. Thanh-Son Ngo, Mengling Feng, Guimei Liu, Limsoon Wong. Efficiently finding the best parameter for the emerging pattern-based classifier PCL. Proceedings of 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Part I, pages 121--133, Hyderabad, India, June 2010.

336. Guimei Liu, Chern Han Yong, Hon Nian Chua, Limsoon Wong. Decomposing PPI Networks for Complex Discovery. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 280--283, Hong Kong, December 2010.

337. Marzieh Ayati, Golnaz Taheri, Shahriar Arab, Limsoon Wong, Changiz Eslahchi. Overcoming Drug Resistance by Co-Targeting. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 198--201, Hong Kong, December 2010.

338. Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. CAMBer: An Approach to Support Comparative Analysis of Multiple Bacterial Strains. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 121--126, Hong Kong, December 2010. CAMBer Software

339. Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. CEO: A Cloud Epistasis cOmputing model in GWAS. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 85--90, Hong Kong, December 2010.

340. Guimei Liu, Mengling Feng, Yue Wang, Limsoon Wong, See-Kiong Ng, Tzia Liang Mah, Edmund Jon Deoon Lee. Towards Exploratory Hypothesis Testing and Analysis. Proceedings of 27th IEEE International Conference on Data Engineering, pages 745--756, Hannover, Germany, April 2011.

341. Guimei Liu, Haojun Zhang, Limsoon Wong. Finding minimum representative pattern sets. Proceedings of 18th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), pages 51--59, Beijing, China, August 2012.

342. Guimei Liu, Andre Suchitra, Haojun Zhang, Mengling Feng, See-Kiong Ng, Limsoon Wong. AssocExplorer: An association rule visualization system for exploratory data analysis. Proceedings of 18th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD), pages 1536--1539, Beijing, China, August 2012.

343. Limsoon Wong. A dichotomy in the intensional expressive power of nested relational calculi augmented with aggregate functions and a powerset operator. Proceedings of 32nd ACM Symposium on Principles of Database Systems, pages 285--295, New York, 22-27 June 2013.

344. Osamu Maruyama, Limsoon Wong. Regularizing predicted complexes by mutually exclusive protein-protein interactions. Proceedings of IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, pages 1068--1075, Paris, 25-28 August 2015.

345. Wei Zhong Toh, Kwok Pui Choi, Limsoon Wong. Redhyte: Towards a self-diagnosing, self-correcting, and helpful analytic platform. Proceedings of 8th Asian Conference on Intelligent Information and Database Systems (ACIIDS), Part II, pages 3--12, Da Nang, Vietnam, 14-16 March 2016. Demo, Github

346. Qian Liu, Jinyan Li, Limsoon Wong, Kotagiri Ramamohanarao. Efficient mining of pan-correlation patterns from time course data. Proceedings of 12th International Conference on Advanced Data Mining and Applications (ADMA), pages 234--249, Gold Coast, Australia, 12-15 December 2016.

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     Patents

347. Guozhu Dong, Xiuzhen Zhang, Jinyan Li, Limsoon Wong. Classification by Aggregating Emerging Patterns. KRDL Invention Disclosure (CAEP) 20/99, 2 June 1999. Singapore patent application 9903916-6, 14 August 1999. US patent application 09/492753, 27 January 2000. US patent 6,507,843, 14 January 2003.

348. Allison Lim, Jiren Wang, Limsoon Wong. A Method and Apparatus for Searching a Database Containing Biological Information. KRDL Invention Disclosure (Protein Designer) 34/99, 26 July 1999. PCT/SG00/00100, 7 July 2000.

349. See-Kiong Ng, Limsoon Wong. The Protein Interaction Extraction System. KRDL Invention Disclosure (PIES) 36/99, 4 August 1999. US Patent Application 09/6901738, 18 October 2000. EPO Patent Application 01979208.4-2201-SG0100217, 23 May 2003.

350. Chong-See Kwok, Limsoon Wong. A method for eliminating redundant email messages. KRDL Invention Disclosure (UsefulMail) 16/00, 28 April 2000. PCT/SG00/00178, 17 October 2000. EPO Patent Application 00973340.3-2211-SG0000178, 21 May 2003. European Patent No. 1327192, 20 April 2005. Singapore Patent No. 95931 [WO 00/33981], 31 May 2005.

351. Jing Chen, Su-Yun Chung, Limsoon Wong. System and Method for Providing a Searchable Database of Biological Sequence, Function, and Patent Information. KRDL Invention Disclosure (CISP) 17/00, 28 April 2000. US Patent Application 09/721,467, 22 November 2000.

352. Su-Yun Chung, Limsoon Wong. System and Method for Assigning Function by Genome Profiling. KRDL Invention Disclosure (AFGP) 18/00, 28 April 2000. US Patent Application 09/715,843, 17 November 2000.

353. Hwee-Hwa Pang, Mun-Kew Leong, Limsoon Wong. A Method of Connecting a Plurality of Remote Sites to a Server., KRDL Invention Disclosure 12/2001, March 2001. PCT Application PCT/SG01/00244, 3 December 2001. Published WO 03/048963 A1, June 2003. Singapore patent application 200403166-2, 3 December 2001. US patent application 10/497,237, 2 Jun 2004. US patent publication US 2005/0044168 A1, 24 February 2005. Singapore patent no. 104695 [WO 03/48963], 30 June 2006.

354. James R. Downing, Eng-Juh Yeoh, Dawn E. Wilkins, and Limsoon Wong. Classification and Prognosis Prediction of Acute Lymphoblastic Leukemia by Gene Expression Profiling, US Priority Application 60/367,144, 22 March 2002. PCT/US03/????, 19 March 2003.

355. Jinyan Li, Haiquan Li, Limsoon Wong. System and Method for Identifying Sets of Attributes in a Database, System and Method for Constructing a Tree Structure for a Database and Computer Program Elements, I²R Invention Disclosure P2004054. PCT/SG2005/000386, 10 November 2005. WIPO patent publication WO/2007/055655, 18 May 2007.

356. Difeng Dong, Limsoon Wong, Allen Yeoh. Genetic status shifting model using effective response matrix (ERM) is highly predictive of disease outcome in childhood B-lineage ALL, particularly haematological relapse. NUS IRO Ref: 12118N-US/PRV. US Provisional Patent Application 61/730,603, 28 November 2012.

357. Chern Han Yong, Limsoon Wong, Stacy Xu, Xiaojing Huo. Batch normalization using a neural network system. US Provisional Patent Application 63/275,272, 3 November 2021.

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     Keynotes, Talks, Posters, and Other Publications

358. Kyle Hart, Limsoon Wong, Chris Overton, Peter Buneman. Using a Query Language to Integrate Biological Data. Abstracts of 1st Meeting on the Interconnection of Molecular Biology Databases, Stanford, August 1994.

359. Peter Buneman, Kyle Hart, Limsoon Wong. Answering some ``Unanswerable'' Biological Queries. Poster presented at ACM Workshop on Information Retrieval and Genomics, Bethesda, May 1994.

360. Kyle Hart, Limsoon Wong, Chris Overton, Peter Buneman. Querying Heterogeneous Biological Data Sources. Talk given at Meeting on Genome Mapping and Sequencing, Coldspring Harbor, New York, May 1994.

361. Kyle Hart, Limsoon Wong. Pruning Nested Data Values Using Branch Expressions with Wildcards. Abstracts of 2nd Meeting on the Interconnection of Molecular Biology Databases, Cambridge, England, July 1995.

362. Jonathan Crabtree, Limsoon Wong, Peter Buneman, Susan Davidson, Chris Overton. On-Demand Integration of Biological Data. Abstracts of DOE Human Genome Program Contractor-Grantee Workshop V, Santa Fe, New Mexico, January 1996.

363. Li Jie Wong, Limsoon Wong, Chiam Prong Lam. Stereogram Image Extraction by Computer, Proceedings of Science Research Congress, Singapore, 1996, 360--366.

364. Limsoon Wong. Functional Programming and Database Query Languages. Invited position paper at Workshop on Functional Approach to Databases, London, July 1997.

365. Prasanna Kolatkar, Limsoon Wong. Some Bioinformatics and Structural Biology Applications That Can Benefit From A Global High-Speed Network. Invited talk at APAN-SINGAREN Applications Workshop, Singapore, October 1997.

366. Limsoon Wong. BioKleisli, SeqIndex, and Other Bioinformatics Projects in BioInformatics Centre and Institute of Systems Science. Invited talk at Technology Partnership Symposium for the Life Science and Chemicals Industry, Singapore, October 1997.

367. Limsoon Wong. Solving Tough Integration Problems in Biology. Invited poster at IMCB 10th Anniversary Symposium, Singapore, November 1997.

368. Limsoon Wong. Adventures of a Logician-Engineer. Public Lecture by Winner of 1997 Singapore National Academy of Science Young Scientist Award, Singapore, April 1998.

369. Limsoon Wong. Some MEDLINE Queries Powered By Kleisli, ACCESS 25:8--9, June 1998.

370. Limsoon Wong. Industry Perspective and Software Development: Hunting for Domains in Style. Invited talk at Consultative Roundtable Workshop on the Implementation of National Bioinformatics and Biotechnology Network (NABBINet), Bangi, Malaysia, August 1998.

371. Limsoon Wong. Extracting Features from BLASTP Results. Invited talk at BioMedInfo Singapore'98, Singapore, September 1998.

372. Limsoon Wong. Bioinformatics Integration Simplified: The Kleisli Way. Invited talk at International Symposium on Human Genetics and Gene Therapy, Singapore, February 1999.

373. Limsoon Wong. Molecular Circuits. Talk at IRCS/DIMACS Workshop on Logic and Cognitive Science: Linking Finite Model Theory, Descriptive complexity, and the Study of Cognition, Philadelphia, April 1999.

374. Limsoon Wong. Invariants in SQL. Talk at Alfred Renyi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, June 1999.

375. Limsoon Wong. An Introduction to Kent Ridge Digital Labs and Singapore. Talk at Alfred Renyi Institute of Mathematics, Hungarian Academy of Sciences, Budapest, June 1999.

376. Limsoon Wong. Introduction to Integrating Data Sources. Guest lecture for a bioinformatics course at Institute of Molecular and Cell Biology, Singapore, April 2000. (PS version)

377. Limsoon Wong The Functional Guts of Kleisli. Invited keynote at 5th ACM SIGPLAN International Conference on Functional Programming, Montreal, Canada, September 2000.

378. Limsoon Wong. Discovering Information from Biological Data. Invited talk at International Symposium on Bioinformatics, Pohang, Korea, November 2000. Organized by Biological Research Information Center & by Korea Bioinformatics Society.

379. Limsoon Wong The Functional Guts of Kleisli. Invited talk at KAIST Advanced Information Technology Research Center, Taejon, Korea, November 2000.

380. Limsoon Wong. Invariants in SQL. Invited talk at KAIST Advanced Information Technology Research Center, Taejon, Korea, November 2000.

381. Limsoon Wong. From Data Integration to Drug Discovery. Invited talk at National University of Singapore School of Computing, April 2001.

382. Limsoon Wong. The Marriage of Computer Science and Molecular Biology. Invited talk at ICAAS-NLB Public Lecture Series on Life Sciences, April 2001.

383. Limsoon Wong. Datamining: Turning Biological Data Into Gold. Invited talk at 5th NUH-NUS Faculty of Medicine Annual Scientific Meeting, June 2001.

384. Limsoon Wong. From Informatics to Bioinformatics. Invited talk at Taipei International Master Forum on Biotechnology, Tri-Service General Hospital, Neihu, Taipei, Taiwan, August 2001. Short version.

385. Limsoon Wong. From Informatics to Bioinformatics. Invited talk at Bioinformatics: Information Revolution in Biology and Medicine, ICICI Knowledge Park, Hyderabad, October 2001.

386. Limsoon Wong. Role of Bioinformatics in the Genomic Era. Invited talk at ICICI Knowledge Park Foundation Day Round Table Meeting on Building the Knowledge Bridge, ICICI Knowledge Park, Hyderabad, October 2001.

387. A. Yeoh, K. Williams, D. Patel, S. Shurtleff, E.Behm, S. Raimondi, M. Relling, C. Cheng, D. Wilkins, L. Wong, W. Evans, C.-H. Pui, C. Naeve, J.R. Downing. Expression Profiling of Pediatric Acute Lymphoblastic Leukemia (ALL) Blasts at Diagnosis Accurately Predicts Both the Risk of Relapse and of Developing Therapy-Induced Acute Myeloid Leukemia (AML). Blood, 98(11):1816 Part 1, November 2001. Plenary talk at American Society of Hematology 43rd Annual Meeting, Orlando, Florida, December 2001.

388. YM Lee, DD Suteja, D. Wai, L. Wong, E. Chan, SG Lim. The Natural History of HBe AG Positive and anti-HBe Positive Chronic Hepatitis B Patients---A Long Term Study. Hepatology, 34(4):1745 Part 2 Supplement S, October 2001.

389. Limsoon Wong. Some Questions on Assessing the Quality of Gene Expression Class Prediction Results. Invited talk at the Post-Genome Knowledge Discovery Program, Workshop on Sequence and Gene Expression Analysis, Institute for Mathematical Sciences, Singapore, January 2002.

390. Jinyan Li, Limsoon Wong. Identifying Good Diagnostic Gene Groups from Gene Expression Profiles Using the Gene Expression Profiles Using the Concept of Emerging Patterns. Invited talk at Singapore MicroArray Meeting 2002, National Cancer Centre, Singapore, January 2002.

391. Priti Talwar, Iti Das, Appaiah M.M., Udayapriya Loganathan, See-Kiong Ng, Limsoon Wong, and Satish Nair. Challenges in Developing a Post-genome Knowledge Database. Meetings Abstract: Int. Society for Human Genomics' 27th Annual Meeting, Trivandrum, India, Abstract Number P21, page 71, February 2002.

392. Limsoon Wong. Databases and information Discovery. Invited talk at Post-Genome Knowledge Discovery Program Master Class on Language of DNA, Institute for Mathematical Sciences, Singapore, February 2002.

393. Jinyan Li, Huiqing Liu, Limsoon Wong. Emerging Patterns: A New Approach to Analysing Gene Expression Data. Talk and poster at HUGO 7th International Human Genome Meeting, Shanghai, April 2002.

394. Limsoon Wong. Practical Knowledge Management for Drug Discovery. Invited talk at Biotechnology in Asia 2002, Singapore, April 2002.

395. Limsoon Wong. Biotech-infotech Convergence.. Invited talk at BioITWorld, Singapore, May 2002. PPT slides.

396. Limsoon Wong. From Informatics to Bioinformatics. Invited Panel at 3rd International Conference on Web-Age Information Management, Beijing, August 2002.

397. Limsoon Wong. From Informatics to Bioinformatics. Invited Panel at AusBiotech 2002, Melbourne, Australia, August 2002.

398. Limsoon Wong. The Practical Aspects of Artificial Intelligence. Invited lecture at Singapore-MIT Alliance Computer Science Program, September 2002.

399. Limsoon Wong. From Informatics to Bioinformatics. Invited talk at the Knowledge Group Bioinformatics Conference, Kuala Lumpur, September 2002.

400. Limsoon Wong. Enabling Creativity: Imagination to Reality. Invited talk at Forum on Creativity in the Arts, Science, & Technology, organized by the Tan Kah Kee Foundation, National Arts Council, and Singapore National Academy of Science, November 2002.

401. Limsoon Wong. Imagination to Reality. I²R Postgrad Student Recruitment Talk, Kuala Lumpur, December 2002.

402. Limsoon Wong. Bioinformatics in Singapore. Asia Pacific Biotech News, 7(3):88--92, 3 Feb 2003.

403. Limsoon Wong. Identifying Good Diagnostic Gene Groups from Gene Expression Profiles Using the Concept of Emerging Patterns. Invited talk at University of Queensland, Brisbane, 10 February 2003.

404. Limsoon Wong. Guts of Dragon Promoter Finder. Invited talk at Institute for Molecular Bioscience, Brisbane, 11 February 2003.

405. Limsoon Wong. Using Feature Generation and Feature Selection for Accurate Prediction of Translation Initiation Sites. Invited talk at Queensland University of Technology, Brisbane, 12 February 2003.

406. Limsoon Wong. Using Feature Generation and Feature Selection for Accurate Prediction of Translation Initiation Sites. Invited talk at 1st KAIST-Singapore Joint Workshop on Bioinformatics & Natual Language Processing, KAIST, Daejon, South Korea. 24 February 2003.

407. Limsoon Wong. Some Sample Problems and Solutions in Post-Genome Knowledge Discovery. Invited talk at COE Technology Week Focus Seminar on Recent Advances in Bioinformatics and Computational Biology, NTU. 8 March 2003.

408. Limsoon Wong. Introduction to the Knowledge Discovery Department of I²R. Joint Singapore-Canada Workshop on the Interface of Biology with Information Technology, I²R, 17--18 March 2003.

409. Limsoon Wong. Imagination to Reality. I²R Postgrad Student Recruitment Talk, NTU, 3 April 2003.

410. Limsoon Wong. I²R's Dare-to-dream Collaborations Imagination to Reality Powers Up Symposium, I²R, 1 April 2003.

411. Limsoon Wong. Data Mining of Gene Expression Profiles for the Diagnosis and Understanding of Diseases. Keynote address at 7th International Database Engineering and Application Symposium, Hong Kong, July 2003.

412. Limsoon Wong. Gene Expression Profile for the Diagnosis and Understanding of Diseases. Invited talk at DuNmAn Life-Sciences & Technology Day, Dunman Secondary School, Tampines, 2 August 2003.

413. Limsoon Wong. Accurate Recognition of Translation Initiation Sites. Invited talk at 10th Congress of the Federation of Asian and Oceanic Biochemists and Molecular Biologists, Bangalore, India, December 2003.

414. Limsoon Wong. Diagnosis of Childhood Acute Lymphoblastic Leukaemia and Optimization of Risk-Benefit Ratio of Therapy. Invited talk at 1st Annual Symposium of Association of Asian Societies for Bioinformatics, Yokohama, Japan, December 2003. ppt.

415. Limsoon Wong. From Informatics to Bioinformatics: The Knowledge Discovery Perspective. Invited lecture at Singapore-MIT Alliance Computer Science Program, 28 October 2003.

416. Limsoon Wong. Diagnosis of Childhood Acute Lymphoblastic Leukaemia and Optimization of Risk-Benefit Ratio of Therapy. Invited talk at NTU School of Computer Engineering, 24 November 2003. ppt.

417. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Lilly Systems Biology Symposium, BioPolis, Singapore, 4 February 2004.

418. Limsoon Wong. Imagination to Reality: Life as a Researcher. Invited talk at Hwa Chong Junior College Annual Student Research Symposium , Hwa Chong Junior College, 3 April 2004.

419. Limsoon Wong. Exciting Media. Invited talk at World Scientific, 6 April 2004.

420. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at National Yang Ming University, Taipei, Taiwan, 26 May 2004.

421. Limsoon Wong. Convexity of Itemset Spaces. Invited talk at Academia Sinica, Taipei, Taiwan, 28 May 2004.

422. Limsoon Wong. Diagnosis of Childhood Acute Lymphoblastic Leukaemia and Optimization of Risk-Benefit Ratio of Therapy. Invited talk at National Cheng Kung University, Tainan, Taiwan, 21 May 2004.

423. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Genome Institute of Singapore, 4 June 2004.

424. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at 3rd International Conference on Bioinformatics, Auckland, New Zealand, 4-8 September 2004.

425. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at 5th HUGO Pacific Meeting and 6th Asia-Pacific Meeting on Human Genetics, BioPolis, Singapore, 17-20 November 2004.

426. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Tsing Hua University, Beijing, 25 November 2004.

427. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Edinburgh University, Edinburgh, 1 October 2004.

428. Limsoon Wong. Diagnosis of Childhood Acute Lymphoblastic Leukaemia and Optimization of Risk-Benefit Ratio of Therapy. Invited talk at Edinburgh University, Edinburgh, 1 October 2004.

429. Limsoon Wong. Knowledge Discovery in Biomedicine. Invited talk at National Healthcare Group Annual Scientific Congress, Raffles Convention Centre, Singapore, October 2004.

430. Limsoon Wong. Research & Discovery: Technologies Today for Solving Problems Tomorrow . Talk at Pre-Horizon Seminar, Infocomm Horizon 2004, I²R, Singapore, 1 November 2004.

431. C. Y. Cui, B. C. Goh, J. H. Chiao, S. R. Green, S. Pervaiz, R. Soong, L. Wong, R. Soo, B. Mow. In vitro activity of cyclin-dependent kinase inhibitor seliciclib (CYC202 or R-roscovitine) in nasopharyngeal carcinoma (NPC) cell lines. Clinical Cancer Research, 11(24):9109S-9109S Part 2 Suppl. S, December 2005.

432. Limsoon Wong. Selection of Patient Samples and Genes for Disease Prognosis. Invited talk at "Informatics Inspired Biology" Symposium, BioPolis, Singapore, 16 January 2005.

433. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited keynote at 3rd Korea-Singapore Joint Workshop on Bioinformatics and Natural Language Processing, Muju Resort, 20-22 February 2005.

434. Limsoon Wong. Building gene networks by information extraction, cleansing, and integration. Invited plenary lecture at 3rd International Symposium on e-Biology Initiative: Towards New Frontiers of Biology, Takeda Hall, University of Tokyo, Tokyo, Japan, 11 March 2005.

435. Limsoon Wong. Some interesting issues in constructing gene/protein networks, Invited round-table presentation at 3rd International Symposium on e-Biology Initiative: Towards New Frontiers of Biology, National Institute of Informatics, Tokyo, Japan, 10 March 2005.

436. Limsoon Wong. Exciting Bioinformatics Adventures. Invited talk at NTU 2nd year Bioengineering students, 24 March 2005.

437. Limsoon Wong. Convexity in Itemset Spaces. CS Seminar at NUS School of Computing, 11 April 2005.

438. Haiquan Li, Jinyan Li, Limsoon Wong. Binding Motif Pairs from Interacting Protein Groups. Invited talk at Workshop on Data Analysis and Data Mining in Proteomics, Institute for Mathematical Sciences, NUS, Singapore, 12 May 2005.

439. Limsoon Wong. Building Gene Networks by Information Extraction, Cleansing, & Integration. Invited talk at Tamkang University, Taiwan, 31 May 2005.

440. Limsoon Wong. Discovering Binding Motif Pairs from Interacting Protein Groups. Invited talk at Tamkang University, Taiwan, 31 May 2005.

441. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Tamkang University, Taiwan, 1 June 2005.

442. Limsoon Wong. Assessing Reliability of Protein-Protein Interaction Experiments. Invited talk at Changchun International Bioinformatics Workshop, Changchun, Jilin, China, 5-7 July 2005.

443. Hon-Nian Chua, Wing-Kin Sung, Limsoon Wong. Protein Function Prediction from Protein Interactions. Invited talk at Singapore-Bangalore Biomedical Symposium, Biopolis, Singapore, 8-9 September 2005.

444. Limsoon Wong. Exciting Bioinformatics Adventures. NUS Dept of Pathology Seminar , Dental Auditorium, Faculty of Dentistry, NUH, 17 October 2005.

445. Limsoon Wong. Some Data Mining Challenges Learned From Bioinformatics & Actions Taken. Invited talk at 1st Bertinoro Workshop on Data Mining, University of Bologna Residential Center, Bertinoro, Italy, 24-27 October 2005.

446. Limsoon Wong. Protein Function Prediction From Protein Interactions. Invited talk at 1st International Symposium on Languages in Biology and Medicine, KAIST, Daejon, Korea, 24-26 November 2005.

447. Limsoon Wong. Protein Function Prediction From Protein Interactions. Invited talk at "Figuring Out Life: NUS-Karolinska Joint Symposium on Application of Mathematics in Biomedicine", Institute for Mathematical Sciences, Singapore, 28-29 November 2005.

448. Limsoon Wong. Exciting Bioinformatics Adventures. Invited keynote at 12th International Conference on Biomedical Engineering, Suntec Singapore International Convention and Exhibition Centre, Singapore, 7-10 December 2005.

449. Yi Lu, Huiqing Liu, Ying Xu, Pei Lin Koh, Ariffin Hany, Limsoon Wong, Allen Yeoh. Gene expression profiling of paired pre- and post-prednisolone (PRED) BM samples from childhood ALL identifies robust signatures for PRED response and eventual outcome. Blood, 108(11):70A-70A 222 Part 1, November 2006.

450. Limsoon Wong. Protein Function Prediction From Protein Interactions. Invited talk at University of Hong Kong , Hong Kong, 6 March 2006.

451. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions Invited keynote at BioDM2006, Singapore, 9 April 2006. Proc. PAKDD 2006 Workshop on Data Mining for Biomedical Applications (BioDM2006), Singapore, 9 April 2006, page 1. ppt

452. Limsoon Wong. The Bright and Dark Side of Data Mining Research. Invited panel discussion at PAKDD 2006, Hilton Hotel, Singapore, 11 April 2006.

453. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Invited talk at 2nd Sino-Singapore Workshop on Computation and Systems Biology, Shanghai Jiao Tong University, Shanghai, 22-24 May 2006.

454. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Invited talk at Academia Sinica, Taipei, Taiwan, 1 June 2006.

455. Limsoon Wong. Building Gene Networks by Information Extraction, Cleansing, & Integration. Invited talk at National Taiwan University, Taipei, Taiwan, 1 June 2006.

456. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Invited talk at Bioinformatics Minisymposium---from Sequences, Structures, to Systems, National Chiao Tung University, Hsinchu, Taiwan, 2 June 2006.

457. Limsoon Wong. Building Gene Networks by Information Extraction, Cleansing, & Integration. Invited talk at Bioinformatics Minisymposium---from Sequences, Structures, to Systems, National Chiao Tung University, Hsinchu, Taiwan, 2 June 2006.

458. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Invited talk at Yang Ming National University, Taiwan, 5 June 2006.

459. Limsoon Wong. Building Gene Networks by Information Extraction, Cleansing, & Integration. Invited talk at Yang Ming National University, Taiwan, 6 June 2006.

460. Limsoon Wong. Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteome-Wide Scale. Invited talk at Yang Ming National University, Taiwan, 7 June 2006.

461. Limsoon Wong. An Introduction to Knowledge Discovery Applications in Biomedical Sciences. Invited talk at Taipei Medical University, Taiwan, 8 June 2006.

462. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Invited talk at Taipei Medical University, Taiwan, 8 June 2006.

463. Limsoon Wong. Guilt by Association of Common Interaction Partners. Invited talk at IMS Workshop on BioAlgorithmics, Institute for Mathematical Sciences, Singapore, 12-14 July 2006.

464. Limsoon Wong. Exciting Media. Invited talk at ICAAS-UIAAS Innovation Symposium, NLB @ Victoria Street, Singapore, 26 August 2006.

465. Limsoon Wong. Increasing Confidence of Protein-Protein Interactomes. Invited talk at Hong Kong Baptist University, Kowloon Tong, Hong Kong, 4 September 2006.

466. Limsoon Wong. Adventures of a Logician-Engineer: A Journey Through Logic, Engineering, Medicine, Biology, and Statistics. Invited talk at 8th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing (SYNASC 2006), Timisoara, Romania, 26-29 September 2006.

467. Limsoon Wong. Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteome-Wide Scale. Invited talk at Renyi Institute of Mathematics, Budapest, Hungary, 2 October 2006.

468. Limsoon Wong. Guilt by Association of Common Interaction Partners. Talk at Xi'an Jiaotong University, Xi'an, China, 23 October 2006.

469. Limsoon Wong. Adventures of a Logician-Engineer: A Journey Through Logic, Engineering, Medicine, Biology, and Statistics. Talk at Northwestern Polytechnical University, Xi'an, China, 23 October 2006.

470. Limsoon Wong. Increasing Confidence of Protein-Protein Inteactomes. Talk at Southeast University, Nanjing, China, 25 October 2006.

471. Limsoon Wong. Guts of Dragon Promoter Finder and Mapper. Invited talk at 5th East Asian Biophysics Symposium & 44th Annual Meeting of the Biophysical Society of Japan, Okinawa, Japan, 14 November 2006.

472. Limsoon Wong. Exciting the Reluctant Bioinformatician. Invited talk at International Symposium on Bioinformatics Education and Research, Yokohama, Japan, 17 December 2006.

473. Limsoon Wong. Increasing Confidence of Protein-Protein Inteactomes. Keynote talk at 17th International Conference on Genome Informatics, Yokohama, Japan, 18-20 December 2006.

474. Limsoon Wong. Protein Function Inference Enhanced by Text Mining. Invited talk at Forum on Advanced NLP and Text Mining, Tokyo, Japan, 11-13 March 2007.

475. Limsoon Wong. Protein Function Inference Enhanced by Text Mining. Invited talk at Molecular Connections Pvt Ltd, Bangalore, India, 5 June 2007.

476. Limsoon Wong. The Bright and Dark Sides of Bioinformatics. Invited talk at Grid Asia 2007, Biopolis, Singapore, 7 June 2007.

477. Limsoon Wong. Guilt by Association. Invited talk at University of Edinburgh, Edinburgh, Scotland, 16 October 2007.

478. Limsoon Wong. Guilt by Association. Invited talk at Duke-NUS Graduate Medical School, Singapore, 20 November 2007.

479. Limsoon Wong. Constructing More Reliable Protein-Protein Interaction Maps. Invited keynote at Bioinformatica Indica '08: International Symposium on Computational Biology & Bioinformatics, University of Kerala, 17-19 January 2008. PPT

480. Limsoon Wong. Two Applications of Text Mining in Bioinformatics: Enhancing Protein Function Prediction and Enhancing Drug Pathway Inference. Invited talk at 7th Korea-Singapore Workshop on Bioinformatics & NLP, Seoul, Korea, 15 February 2008.

481. Limsoon Wong. Guilt by Association. Invited keynote at 1st Japan-Taiwan Young Researchers Conference on Computational and Systems Biology, Hsinchu, Taiwan, 9-11 March 2008.

482. Limsoon Wong. Manifestation and Exploitation of Invariants in Bioinformatics. Invited keynote at 3rd International Computer Science Symposium in Russia (CSR 2008), Moscow, Russia, 7-12 June 2008.

483. Limsoon Wong. Guilt by Association as a Search Principle. Invited keynote at 31st Annual International ACM SIGIR Conference, Singapore, 20-24 July 2008.

484. Difeng Dong, Guimei Liu, Limsoon Wong. Drug Pathway Decipherer and Some Exciting Results in Protein Complex Prediction. Invited talk at Symposium on Biomolecular Mechanism Discovery with Computational Biology, Biopolis, Singapore, 14 August 2008.

485. Limsoon Wong. Increasing Confidence of Protein-Protein Interactomes. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Institute for Studies in Theoretical Physics and Mathematics, Tehran, Iran, 17-18 November 2008.

486. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Institute for Studies in Theoretical Physics and Mathematics, Tehran, Iran, 17-18 November 2008.

487. Limsoon Wong. Guilt by Association of Common Interaction Partners. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Institute for Studies in Theoretical Physics and Mathematics, Tehran, Iran, 17-18 November 2008.

488. Limsoon Wong. Adventures of a Logician-Engineer: A Journey through Logic, Engineering, Medicine, Biology, Invited talk at University of Tehran Institute of Biochemistry and Biophysics, Tehran, Iran, 17 November 2008.

489. Limsoon Wong. Adventures of a Logician-Engineer: A Journey through Logic, Engineering, Medicine, Biology, Invited talk at Shahid Behesti University, Tehran, Iran, 19 November 2008.

490. Limsoon Wong. "Guilt by Association" as a Search Principle. Invited keynote at BioSearch08: HCSNet Next-Generation Search Workshop on Search in Biomedical Information, Queensland University of Technology, Brisbane, Australia, 30 November 2008.

491. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited talk at Joint 5th Structural Biology & Functional Genomics and 1st Biological Physics International Conference, University of Cultural Centre, NUS, Singapore, 9-11 December 2008.

492. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited Keynote at 8th Korea-Singapore Joint Workshop on Bioinformatics and NLP, KAIST, Daejeon, Korea, 15 December 2008.

493. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited keynote at IEEE International Workshop on Data Mining and Artificial Intelligence (DMAI 2008) , Khulna, Bangladesh, 25-27 December 2008.

494. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited talk at ASI Symposium on Bioinformatics and Data Mining, Hong Kong Baptist University, 26-27 February 2009.

495. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited talk at International Conference on Open Source for Computer Aided Drug Discuvery (OSCADD 2009), IMTECH, Chandigarh, India, 22-26 March 2009.

496. Limsoon Wong. A Gentle Introduction to Bioinformatics: The Invariant Perspective. Invited talk at Hwa Chong Institution, 13 April 2009.

497. Limsoon Wong. Topology of PPI Networks: Applications and Questions. Talk at Barbados Workshop on Biological and Computational Analysis of Protein-Protein Interaction Networks, Bellairs Research Institute, Barbados, 19-25 April 2009.

498. Limsoon Wong. Tag SNP Selection and Disease Gene Location Inference. Invited talk at Hong Kong University, Hong Kong, 12 May 2009.

499. Limsoon Wong. Challenges in Understanding Pathways, Predicting Complexes, & Inferring Protein Function. Invited keynote at First International Workshop on Neuroinformatics, Bioinformatics, and Cognitive Science., South China University of Technology, Guangzhou, China, 4-6 June 2009.

500. Limsoon Wong. A Few Simple Ideas for Efficient Tag SNP Selection. Invited talk at Peking University, Beijing, China, 22 July 2009.

501. Limsoon Wong. Topology of PPI Networks: Applications and Questions. Invited talk at Shanghai Center for Bioinformation Technology, Shanghai, China, 24 July 2009.

502. Limsoon Wong. My Headaches in Gene Expression Analysis. Invited talk at Department of Pediatrics, NUH, Singapore, 14 October 2009.

503. Chern Han Yong, Limsoon Wong. Reliable Augmentation of Protein Interaction Data with Interologs for Protein Function Prediction. Poster at 20th International Conference on Genome Informatics, Yokohama, Japan, 14-16 December 2009.

504. Yue Wang, Guimei Liu, Limsoon Wong. A Study of Different Rule Selection Strategies for Rule-Based SNP Imputation. Poster at 20th International Conference on Genome Informatics, Yokohama, Japan, 14-16 December 2009.

505. Limsoon Wong. Topology of PPI Networks: Applications and Questions. Invited talk at University of Warsaw, Warsaw, Poland, 13 January 2010.

506. Limsoon Wong. Consistency and Comprehensiveness of Pathway Databases. Invited talk at 9th Korea-Singapore Workshop on Bioinformatics and NLP, KAIST, Daejeon, Korea, 23 February 2010.

507. Limsoon Wong. Finding Consistent Disease Subnetworks. Invited talk at HKUST, Hong Kong, 26 March 2010.

508. Limsoon Wong. Two Computational Biology Challenges: A Call to Arm on Countering Pathogen Drug Resistance and Computational Lipid Biology. Invited talk at ACM-HK Bioinformatics Symposium, HKUST, Hong Kong, 27 March 2010.

509. Limsoon Wong. Recent Progress in Protein Complex Prediction from PPI Networks. Invited talk at Chinese University of Hong Kong, Hong Kong, 29 March 2010.

510. Limsoon Wong. What do gambling, magic, human evolution, leukemia treatment, database design (and a few other things) have in common?. Opening talk at Klang Valley Independent High School Computing Camp 2010, Kuala Lumpur, Malaysia, 5 June 2010.

511. Limsoon Wong. Theory, Practice, and an Application of Frequent Pattern Space Maintenance. Invited talk at 6th International Conference on Information Technology for Education and Research (IT@EDU2010), Ho Chi Minh City, Vietnam, 18 August 2010.

512. Limsoon Wong. The impact of microRNAs on the organization of protein interactions and formation of protein complexes. Invited talk at CSHA Conference on Computational Biology, Suzhou, China, 29 September 2010.

513. Limsoon Wong. What do human evolution, leukemia treatment, database design (and a few other things) have in common? Opening talk at SOC Computing Camp for JC Students, NUS, 22 November 2010.

514. Limsoon Wong. What do human evolution, leukemia treatment, database design (and a few other things) have in common? Opening talk at SOC Computing Camp for International High School Students, NUS, 8 December 2010.

515. Limsoon Wong. Some inventions that made it big. Invited talk at Launch of Innovation Programme, Singapore Polytechnic, 11 February 2011.

516. Limsoon Wong. Two Computational Biology Challenges: A Call to Arm on Countering Pathogen Drug Resistance and Computational Lipid Biology. Invited talk at Soochow University, Suzhou, China, 24 February 2011.

517. Limsoon Wong. Enabling Reproducible Gene Expression Analysis. International Outstanding Scientist Series, Key Laboratory of Systems Biology, SIBS, CAS, Shanghai, China, 26 February 2011.

518. Limsoon Wong. Singapore Bioinformatics in the Early Days. Invited talk at BII SAB Dinner, Singapore Botanic Gardens, 17 March 2011.

519. Limsoon Wong. Enabling Reproducible Gene Expression Analysis Using Biological Pathways. Invited talk at 2nd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 6 April 2011.

520. Limsoon Wong. Impact on MicroRNAs on Organization of Protein Interactions and Formation of Protein Complexes. Invited talk at 2nd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 6 April 2011.

521. Limsoon Wong. Enabling Reproducible Gene Expression Analysis. Invited talk at 5th Moscow Conference on Computational Molecular Biology (MCCMB), Moscow State University, Moscow, Russia, 24 July 2011.

522. Limsoon Wong. Delivering Reproducible Gene Expression Analysis. Invited lecture for Microarray Workshop on Gene Expression Analysis for Aspiring Clinician Researchers, Clinical Research Centre, NUS, 23 September 2011.

523. Limsoon Wong. Epistasis Testing on the Cloud. Invited talk at 22nd FAOBMB Conference, Biopolis, Singapore, 5 October 2011.

524. Limsoon Wong. Impact of microRNAs on Organization of Protein Interactions and Formation of Protein Complexes. Invited talk at BIRC Student Symposium on Bioinformatics 2011, LT9, Nanyang Technological University, Singapore, 29 October 2011.

525. Limsoon Wong. A Novel Principle for Childhood ALL Relapse Prediction. Invited talk at 10th Korea-Singapore Workshop on Bioinformatics and NLP (KSW), Daegeon, South Korea, 12 December 2011.

526. Limsoon Wong. A Novel Principle for Childhood ALL Relapse Prediction. Invited talk at UTS AAAI Bioinformatics Workshop 2012, University of Technology Sydney, NSW, Australia, 12 January 2012.

527. Limsoon Wong. A Novel Contextualization Approach to Proteomic Profile Analysis. Invited talk at Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Hotel Grand Park City Hall, Singapore, 28 February 2012.

528. Limsoon Wong. Invariants: The Golden Thread of (Computer) Science. Keynote talk at 24th Science Research Congress, UTown Plaza Auditorium, NUS, 21 April 2012.

529. Limsoon Wong. Logic in Computational Biology. Invited talk at Joint Workshop of IMS and IMI on Mathematics for Industry: Biological and Climatic Prospects, Institute for Mathematical Sciences, National University of Singapore, 3 September 2012.

530. Limsoon Wong. Living with Noise. Invited talk at SinFra 2012, UPMC, Paris, 15 October 2012.

531. Limsoon Wong. A Novel Contextualization Approach to Proteomic Profile Analysis. Invited plenary talk at 2nd Biomarker Discovery Conference (BDC2012), Shoal Bay, Australia, 6 December 2012.

532. Limsoon Wong. A Novel Principle for Childhood ALL Relapse Prediction. Invited talk at Inaugural Post-BDC2012 Personalized Medicine Workshop, Hunter Medical Research Institute, University of Newcastle, Australia, 7 December 2012.

533. Limsoon Wong. Computational Biology Explained. Research talk for SOC/CAA Mingling Session, SR1 @ COM1, NUS, 23 January 2013.

534. Limsoon Wong. A Novel Principle for Childhood ALL Relapse Prediction. Invited talk at University of Tehran, Tehran, Iran, 25 February 2013.

535. Limsoon Wong. Improving Proteomic Profile Analysis by Contextualization. Invited talk at 3rd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 25 February 2013.

536. Limsoon Wong. Supervised Maximum Likelihood Weighting of Composite Protein Networks for Protein Complex Prediction. Invited talk at 3rd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 25 February 2013.

537. Limsoon Wong. Exploratory Hypothesis Testing and Analysis. Invited talk at 3rd IPM-NUS Workshop on Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 26 February 2013.

538. Limsoon Wong. A Novel Principle for Childhood ALL Relapse Prediction. Talk at NUS-POLITEHNICA Workshop, University Politechnica Bucharest, Bucharest, Romania, 28 February 2013.

539. Limsoon Wong. The use of context in gene expression and proteomic profile analysis. Invited talk at NUS-ENS Workshop on Novel Genome-Wide Approaches to Decipher Transcriptional and Epigenetic Regulation in Mammalian Cells, Paris, France, 30-31 May 2013.

540. Limsoon Wong. Protein complex prediction from PPIN. Invited talk at SNU Bioinformatics Workshop and Biofestival 2013, Seoul National University, Seoul, Korea, 23 May 2013.

541. Limsoon Wong. Mining testable hypothesis from big data. Invited panel at SNU Bioinformatics Workshop and Biofestival 2013, Seoul National University, Seoul, Korea, 24 May 2013.

542. Limsoon Wong. More data is not better. Talk at 3rd South Asia Workshop on Research Frontiers in Computing, National University of Singapore, 28 May 2013.

543. Limsoon Wong. Protein complex prediction from PPIN. Invited talk at Rockefeller University, New York, USA, 25 June 2013.

544. Limsoon Wong. Enabling more reproducible gene expression analysis. Invited talk at 13th Annual International Workshop on Bioinformatics and Systems Biology (IBSB2013), Kyoto, Japan, 1 August 2013.

545. Limsoon Wong. The use of context in gene expression analysis. Invited talk at the 2013 Symposium on Complex Biodynamics & Networks, Institute for Advanced Biosciences - Keio University, Tsuruoka, Japan, 12 November 2013.

546. Limsoon Wong. How logic empowers statistics in the analysis of extremely high-dimensional data with extremely small sample sizes. Invited talk ar 4th Singapore Conference on Statistical Science, National University of Singapore, 7 February 2014.

547. Limsoon Wong. Computational thinking in genome and proteome analysis. Invited talk at International Conference on Next Generation Genomic View on Plants, Animals, and Microbes, National University of Singapore, 5 March 2014.

548. Peter Buneman, Val Tannen, Limsoon Wong. A retrospective on naturally embedded query languages. Test of Time Award talk at 17th International Conference on Database Theory, Athens, Greece, 25 March 2014.

549. Limsoon Wong. Finding consistent disease subnetworks in data with extremely small sample size. Invited talk at Qatar Biomedical Research Institute, Doha, Qatar, 30 March 2014.

550. Limsoon Wong. Big data in bioinformatics: Is more better?. Invited talk at KAUST CBRC Inauguration Symposium, Thuwal, Saudi Arabia, 8 June 2014.

551. Limsoon Wong. Analysis of gene expression data of extremely small sample size. Invited talk at University of Waraw, Warsaw, Poland, 9 August 2014.

552. Limsoon Wong. Analysis of gene expression data of extremely small sample size. Invited talk at Guangxi University, Nanning, China, 22 September 2014.

553. Limsoon Wong. Some issues that are often overlooked in big data analytics. Invited talk at ACM International Conference on Information and Knowledge Management (CIKM), Shanghai, China, 4 November 2014.

554. Limsoon Wong. Exciting promises and potential pitfalls of big data in biology and medicine. Invited keynote at Shenzhen Institute of Advanced Technology CAS Research Centre for e-Health Opening Ceremony-cum-Workshop, Shenzhen, China, 29 November 2014.

555. Limsoon Wong. A quantum leap in the reproducibility, precision, and sensitivity of gene-expression-profile analysis even when sample size is extremely small. Invited keynote at the 25th International Conference on Genome Informatics (GIW/ISCB-Asia), Tokyo, Japan, 15-17 December 2014.

556. Limsoon Wong. Some often-overlooked issues in analytics. Invited talk at Iran University of Science and Technology, Tehran, Iran, 8 March 2015.

557. Limsoon Wong. A quantum leap in the reproducibility, precision, and sensitivity of gene-expression-profile analysis even when sample size is extremely small. Invited talk at the 4th IPM-NUS Workshop on Computational Biology, Tehran, Iran, 10 March 2015.

558. Limsoon Wong. Progress on three challenges in predicting dynamic protein complexes from a static protetin interactome. Invited talk at University of Tehran, Tehran, Iran, 11 March 2015.

559. Limsoon Wong. A novel principle for childhood ALL relapse prediction. Invited talk at Tianjin University, Tianjin, China, 9 April 2015.

560. Limsoon Wong. A novel principle for childhood ALL relapse prediction. Invited talk at 9th Asian Biophysics Association Symposium (ABA2015), Shangyu, China, 9-12 May 2015.

561. Limsoon Wong. Advancing clinical proteomics using protein complexes as a contextualization framework. Invited talk at Networks in Biological Sciences: The Protein Network Workshop, Institute for Mathematical Sciences, Singapore, 8 June 2015.

562. Limsoon Wong. Some issues that are often overlooked in big-data analytics. Keynote talk at 7th International Conference on Knowledge and Systems Engineering (KSE2015), Ho Chi Minh City, Vietnam, 8-10 October 2015.

563. Limsoon Wong. Network-based analysis of proteomics profiles. Keynote talk at KAUST Research Conference on Computational and Experimental Interfaces of Big Data and Biotechnology, Thuwal, Saudi Arabia, 25-27 January 2016.

564. Limsoon Wong. Enabling more sophisticated proteomic profile analysis. Invited talk at the St. Petersburg International Symposium on Systems Biology and Bioinformatics (SBBI'2016), St. Petersburg, 30 June - 2 July 2016.

565. Limsoon Wong. Enabling more sophisticated analysis of proteomics profiles. Invited talk at the Workshop on Gene Dynamics and Chromosomes, IAS, City University of Hong Kong, 11-15 August 2016.

566. Limsoon Wong. Some issues that are often overlooked in big data analytics. Talk at Seoul National University, Seoul, Korea, 19 September 2016.

567. Limsoon Wong. Some issues that are often overlooked in big data analytics. Talk at KAIST, Daejeon, Korea, 21 September 2016.

568. Limsoon Wong. Improving coverage and consistency of MS-based proteomics. Invited talk at 12th Korea-Singapore Joint Workshop on Bioinformatics and Natural Language Processing, KAIST, Daejeon, Korea, 22-23 September 2016.

569. Limsoon Wong. Some issues that are often overlooked in big data analytics. Invited talk at University of Malaya Symposium on Data Science, Kuala Lumpur, Malaysia, 25 October 2016.

570. Limsoon Wong. Improving coverage and consistency of MS-based proteomics. Invited keynote at 16th IEEE International Conference on Bioinformatics and Bioengineering, Taichung, Taiwan, 31 October - 2 November 2016.

571. Limsoon Wong. Accurate correction of next-generation sequencing data. Invited talk at c-BIG Symposium, Biopolis, Singapore, 10 November 2016.

572. Limsoon Wong. A logician-engineer's adventures in data science and analytics. Invited keynote at International Conference on Intelligent Computing, Instrumentation & Control Technologies, Vimal Jyothi Engineering College, Kannur, Kerala, India, 6 - 7 July 2017.

573. Limsoon Wong. Robust gene expression and proteomics profile analysis in the presence of undeclared heterogeneity. Invited talk at IPM Workshop on Systems Biology, Institute for Research in Fundamental Sciences, Tehran, Iran, 2 - 3 August 2017.

574. Limsoon Wong. Anna Karenina and the careless null hypothesis in omics data analysis. Invited talk at IPM- Workshop on Systems Biology, Institute for Research in Fundamental Sciences, Tehran, Iran, 2 - 3 August 2017.

575. Limsoon Wong. Advancing clinical proteomics via analysis based on biological complexes. Keynote at 16th International Conference on Bioinformatics (InCoB), Shenzhen, China, 20 - 22 September 2017.

576. Limsoon Wong. Some simple tactics for deriving a deeper analysis of data. Keynote at 4th International Conference on Computational Science and Technology, Kuala Lumpur, Malaysia, 29 - 30 November 2017.

577. Limsoon Wong. A simple model of childhood acute lymphoblastic leukemia treatment response. Keynote at 3rd Iranian Conference on Systems Biology, Tehran, Iran, 27 - 28 February 2018.

578. Limsoon Wong. Big data and a bewildered lay analyst. Talk at BUET-NUS Computer Science Workshop, Dhaka, Bangladesh, 2 March 2018.

579. Limsoon Wong. Logic in computational biology. Keynote at 12th International Conference and Workshop on Algorithms and Computation (WALCOM), Dhaka, Bangladesh, 3 - 5 March 2018.

580. Limsoon Wong. Advancing clinical proteomics via analysis based on biological complexes. Invited talk at A*STAR BioTrans, Level 4, Proteos, BioPolis, 23 March 2018.

581. Limsoon Wong. Robust gene expression and proteomics profile analysis in the presence of undeclared heterogeneity. Invited talk at Duke-NUS Medical School, 7 March 2018.

582. Limsoon Wong. From bewilderment to enlightenment: Logic in cancer research. Plenary talk at 5th NCIS Annual Research Meeting (NCAM2018), National University Hospital, Singapore, 3 August 2018.

583. Limsoon Wong. Dealing with confounders in omics data analysis. Plenary talk at 14th International Conference on Intelligent Computing, Wuhan, China, 15-18 August 2018.

584. Wilson Wen Bin Goh and Limsoon Wong. Understanding missing proteins: Why should you care? Science Trends, 22 August 2018. Invited article. Available at http://doi.org/10.31988/SciTrends.28556

585. Limsoon Wong. From bewilderment to enlightenment: Logic in cancer research. Keynote address at International Multi-Conference on Engineering and Technology Innovation (IMETI 2018), Taoyuan, Taiwan, 2-6 November 2018.

586. Limsoon Wong. A law of genetic linkage interdicts unlawful assemblies. Keynote address at Workshop on Intelligent Computing and Bioinformatics (ICBio 2018), Xiangtan University, China, 1-2 December 2018.

587. Limsoon Wong. Dealing with confounders in omics data analysis. Invited talk at 9th International Conference on Computational Systems Biology and Bioinformatics (CSBio 2018), Bangkok, Thailand, December 2018.

588. Limsoon Wong. Some thoughts on designing a genomic query language. Invited talk at GeCo Workshop on Challenges in Data-Driven Genomic Computing, Villa del Grumello, Como, Italy, 6-8 March 2019.

589. Limsoon Wong. From bewilderment to enlightenment in cancer research... hopefully. Invited talk at GeCo Workshop on Challenges in Data-Driven Genomic Computing, Villa del Grumello, Como, Italy, 6-8 March 2019.

590. Limsoon Wong. Robustness of protein complex-based analysis of proteomics data. Invited talk at 1st Westlake Symnposium for Proteomic Big Data, Westlake University, Hangzhou, China, 30 June 2019.

591. Limsoon Wong. Some opinion and advice on machine learning in population-based genomic medicine. Invited talk at NUS-Cambridge Joint Research Symposium n Population-based Genomic Medicine, National University of Singapore, 24-25 October 2019.

592. Limsoon Wong. Law of genetic linkage interdicts unlawful assembly. Invited talk at University of Technology Sydney, 6 December 2019.

593. Limsoon Wong. Law of genetic linkage interdicts unlawful assembly. Invited keynote at 5th IASBS Symposium in Biological Sciences, Institute for Advanced Studies in Basic Sciences, Zanjan, Iran, 16 January 2020.

594. Limsoon Wong. Genome assembly quality assessment integrating contiguity, completeness, and correctness. Invited talk at IMS Program on Computational Approaches to the Analysis of Biomolecular Sequences, Structures and their Functions and Applications to Biotechnology and Clinical Data Studies, Institute for Mathematical Sciences, Singapore, 23-27 March 2020.

595. Limsoon Wong. From bewilderment to enlightenment in cancer research. Invited keynote at 3rd International Conference on Big Data Technologies, Qingdao, China, 18-20 September 2020.

596. Limsoon Wong. Some opinion and advice on machine learning in population-based genomic medicine. Invited keynote at 13th International Conference on Frontiers of Information Technology, Applications and Tools (FITAT2020) and 16th International Conference on Intelligent Information Hiding and Multimedia Signal Processing (IIH-MSP2020), Ho Chi Minh City, Vietnam, 5-7 November 2020.

597. Limsoon Wong. From bewilderment to enlightenment in cancer research. Invited talk at KnowDis Machine Learning Day, School of AI, IIT Delhi, India, 5 December 2020.

598. Limsoon Wong. Conservative batch-effect correction for single-cell RNA-seq data enables discovery of rare cell populations. Invited keynote at 1st International and 10th National Iranian Conference on Bioinformatics (ICB10), Kish Island, Iran, 22-24 February 2022.

599. Limsoon Wong. Iterating on multiple collections in synchrony. JFP talk at 27th ACM SIGPLAN International Conference on Functional Programming (ICFP2022), Ljubljana, Slovenia, 11-16 September 2022.

600. Limsoon Wong. Some bad practices in data analysis and machine learning. Invited keynote at 9th IEEE International Conference on Data Science and Advanced Analytics (DSAA2022), Shenzhen, China, 13-16 October 2022.

601. Limsoon Wong. How to throw away unwanted differences and how to make use of them: Two stories pertaining to analytics for food science. Invited keynote at A*STAR BII-Dassault Systemes Symposium on AI for Food Sustainability & Health, Biopolis, Singapore, 25 October 2022.

602. Limsoon Wong. Recognizing and avoiding misleading data analysis. Talk at 3rd International Research Workshop in Computer Science and Information Systems, University of Indonesia, Surabaya, Indonesia, 4-6 November 2022.

603. Limsoon Wong. Single-cell RNA-seq dataset integration without loss of unique rare cell populations. Invited talk at the Westlake Proteomics Series Roundtble, Westlake University, Hangzhou, China, 18 January 2023 (via Zoom).

604. Limsoon Wong. Illuminating the twilight zone of protein function prediction and deep learning model assessment. Invited talk at Joint 11th AOHUPO and 7th AOAPO Congress Post-Congress Workshop, NUS, 11 May 2023.

605. Limsoon Wong. Single-cell RNA-seq dataset integration without loss of unique rare cell populations. Invite talk at 5th China-ASEAN Forum on Health Cooperation, Nanning, Guangxi, China, 26 - 27 May 2023.

606. Limsoon Wong. Single-cell RNA-seq dataset integration without loss of unique rare cell populations. Invited talk at Shenzhen Institute of Advanced Technology, Shenzhen, China, 6 May 2024.

607. Limsoon Wong. Single-cell RNA-seq dataset integration without loss of unique rare cell populations. Invited talk at Central South University, Changsha, China, 8 May 2024.

608. Limsoon Wong. From comprehension syntax to efficient non-equijoins: A journey with Val Tannen. Invited talk at ValFest @ UPenn, University of Pennsylvania, Philadelphia, USA, 24-25 May 2024.

609. Limsoon Wong. The hidden truths of principal component analysis. Distinguished lecture at Hong Kong Baptist University, 18 October 2024.

610. Limsoon Wong. Illuminating the twilight zone of protein function prediction. Invited keynote at 13th International Conference on Bioinformatics and Biomedical Science (ICBBS 2024), Prince of Wales Hospital, Hong Kong, 18-20 October 2024.

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     Lecture Slides and Notes for Formal Courses and Tutorials Taught

611. Please click here for courses, tutorials, and master classes taught by Limsoon.

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     Manuscripts

612. Xiuzhen Zhang, Guozhu Dong, Limsoon Wong. Using CAEP to Predict Translation Initiation Sites from Genomic DNA Sequences. August 1999.

613. Joxan Jaffar, Limsoon Wong, Roland Yap. Open Constraint Programming. December 1999.

614. Joxan Jaffar, Limsoon Wong, Roland Yap. A Calculus for Reactive Databases. January 2000.

615. Susan Davidson, Hartmut Liefke, Limsoon Wong. Creating and Maintaining Curated View Databases. June 2000.

616. Jing Chen, Limsoon Wong. Turning Relation DBMS into Nested Relational DBMS. March 2001.

617. Vladimir B. Bajic, Suisheng Tang, Allen Chong, Seng Hong Seah, Limsoon Wong, Dhinoth Kumar Bangarusamy, Vinsensius Berlian Vega, Anders Strom, Jan-Ake Gustafsson, Edison T. Liu, Chin-Yo Lin. Modeling and predictions of estrogen response elements reveal potential roles for Alu repeats in motif propagation and transcriptional regulation. September 2002.

618. Xue Qin Chen, Xianming Du, Kui Lin, Limsoon Wong, Jianhua Lin, Mohan K. Balasubramanian, David Balasundaram. Functional analysis of 39 deletion mutants related to nuclear-cytoplasmic transport in Schizosaccharmomyces pombe. November 2002.