Publications
A partial list of papers published by faculty members of the lab and their students.
To include a paper, please contact Limsoon Wong (wongls@comp.nus.edu.sg)

2008

• Books

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

• Book chapters

  1. Wing-Kin Sung. Constructing a Galled Phylogenetic Network. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.

  2. Wing-Kin Sung. Indexed Approximate String Matching. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.

  3. Wing-Kin Sung. Maximum Agreement Supertree. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.

• Journal Papers

  1. Zeyar Aung, Soon Heng Tan, See Kiong Ng, Kian Lee Tan. PPiClust: Efficient Clustering of 3-D Protein-Protein Interaction Interfaces. Journal of Bioinformatics and Computational Biology, 6(3):415--433, June 2008.

  2. X. Chen, H. Xu, P. Yuan, F. Fang, M. Huss, V. B. Vega, E. Wong, Y. L. Orlov, W. Zhang, J. Jiang, Y. H. Loh, H. C. Yeo, Z. X. Yeo, V. Narang, K. R. Govindarajan, B. Leong, A. Shahab, Y. Ruan, G. Bourque, W. K. Sung, N. D. Clarke, C. L. Wei, H. H. Ng. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133(6):1106--1117, June 2008.

  3. 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.

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

  5. H. H. Do, K. P. Choi, F. P. Preparata, W. K. Sung, L. Zhang. Spectrum-based de novo repeat detection in genomic sequences. Journal of Computational Biology, 15(5):469-487, June 2008.

  6. T. W. Lam, W. K. Sung, S. L. Tam, C. K. Wong, and S. M. Yiu. Compressed indexing and local alignment of DNA. Bioinformatics, 24:791-797, March 2008.

  7. Tak-Wah Lam, Wing-Kin Sung, Swee-Seong Wong. Improved Approximate String Matching Using Compressed Suffix Data Structures. Algorithmica, 51(3):298-314, July 2008.

  8. W. H. Lee, W. K. Sung. RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints. Journal of Computational Biology, 15(7):881-898, September 2008.

  9. W. H. Lee, C. W. Wong, W. Y. Leong, L. D. Miller, W. K. Sung. LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens. BMC Bioinformatics, 9:368, September 2008.

  10. C. Y. Lim, W. L. Tam, J. Zhang, H. S. Ang, H. Jia, L. Lipovich, H. H. Ng, C. L. Wei, W. K. Sung, P. Robson, H. Yang, B. Lim. Sall4 Regulates Distinct Transcription Circuitries in Different Blastocyst-Derived Stem Cell Lineages. Cell Stem Cell, accepted.

  11. Guimei Liu, Jinyan Li, Limsoon Wong. A New Concise Representation of Frequent Itemsets Using Generators and a Positive Border. Knowledge and Information Systems, to appear.

  12. A. Nigham, L. Tucker-Kellogg, I. Mihalek, C. Verma, D. Hsu. pFlexAna: Detecting conformational changes in remotely related proteins. Nucleic Acids Reseach, 36(Web Server issue):W246-W251, July 2008.

  13. A. Nigham and D. Hsu. Protein conformational flexibility analysis with noisy data. Journal of Computational Biology, 15(7):813--828, September 2008.

  14. Kang Ning, Nan Ye, Hon Wai Leong. On preprocessing and anti-symmetry in de novo peptide sequencing: Improving efficiency and accuracy. Journal of Bioinformatics and Computational Biology, 6(3):467--492, June 2008.

  15. E. Wijaya, S. M. Yiu, N. T. Son, R. Kanagasabai, W. K. Sung. MotifVoter: A novel ensemble method for fine-grained integration of generic motif finders. Bioinformatics, 24(20):2288-2295, October 2008.

  16. H. Xu, C. L. Wei, F. Lin, W. K. Sung. An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics, 24(20):2344-2349, October 2008.

  17. Jeffrey Xu Yu, Zhiheng Li, Guimei Liu. A data mining proxy approach for efficient frequent itemset mining. VLDB Journal, 17(4):947--970, July 2008.

• Conference Papers

  1. Judice Koh, Mong Li Lee, Wynne Hsu, Wee Tiong Ang. Correlation-based Attribute Outlier Detection in XML. Proceedings of 24th International Conference on Data Engineering (ICDE), pages 1522-1524, Cancun, Mexico, April 2008.

  2. V. T. Hoang, W. K. Sung. Fixed Parameter Polynomial Time Algorithms for Maximum Agreement and Compatible Supertrees. Proceedings of 25th Annual Symposium on Theoretical Aspects of Computer Science (STACS), pages 361-372, Bordeaux, France, 21-23 February 2008.

  3. Qiangfeng Peter Lau, Wynne Hsu, Judice Koh, Mong Li Lee. DeepDetect: An Extensible System for Detecting Attribute Outliers & Duplicates in XML. Proceedings of DASFAA2008 Workshop on Data Quality in Collaborative Information Systems, pages ??--??, New Delhi, India, March 2008.

  4. 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.

  5. 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.

  6. Sriganesh Srihari, Hoong Kee Ng, Kang Ning, Hon Wai Leong. Detecting Hubs and Quasi Cliques in Scale-free Networks. Proceedings of International Conference on Pattern Recognition (ICPR), pages ??--??, Tampa, Florida, USA, 8-11 December 2008.

  7. Vinsensius B. Vega, Yijun Ruan, Wing-Kin Sung. A Streamlined and Generalized Analysis of Chromatin ImmunoPrecipitation Paired-End diTag Data. Proceedings of 8th International Conference on Computational Science, Part III, pages 130--139, June 2008, Krakow, Poland.

  8. Nan Wang, Srinivasan Parthasarathy, Kian-Lee Tan, Anthony K. H. Tung. CSV: Visualizing and Mining Cohesive Subgraphs. Proceedings of ACM SIGMOD'International Conference on Management of Data, pages 445--458, Vancouver, Canada, 9-12 June 2008.

  9. Melvin Zhang, Hon Wai Leong. Gene Team Tree: A Compact Tree Representation of All Gene Teams. Proceedings of RECOMB Workshop on Comparative Genomics (RCG), pages ??--??, Paris, France, 13-15 Oct 2008.

• Invited Keynotes, Talks, & Tutorials

  1. 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

  2. Hon Wai Leong. Gene Team Tree: Visualizing all Gene Teams. Invited talk at CAS-MPG Partner Institute for Computational Biology, Shanghai, China, 17 May 2008.

  3. Hon Wai Leong. Gene Team Tree: Visualizing all Gene Teams. Invited talk at Shanghai Center for BioInformation Technology, Shanghai, China, 21 May 2008.

  4. Hon Wai Leong. The Shortest Common Supersequence Problem: Algorithms and Application in Synthesis of MicroArrays. Invited talk at Shanghai University, Mathematics Department, Shanghai, China, 22 May 2008.

  5. Hon Wai Leong. Gene Team Tree: Visualizing all Gene Teams. Invited round-table talk at Center for Genomics BioInformatics (CGB), Indiana University, Bloomington, IN, USA, 16 July 2008.

  6. Hon Wai Leong. Peptide Sequencing in Multi-Charged MS/MS Spectra. Invited talk at Dept of Pathology, Univ of Michigan, Ann Arbor, MI, USA, 14 July 2008.

  7. Hon Wai Leong. Gene Team Tree: Visualizing all Gene Teams. Invited talk at School of Computer Science, Univ of Waterloo, Waterloo, Ontario, Canada, 11 July 2008.

  8. Guimei Liu. An Iterative Approach to Weighting and Expanding Protein Interaction Networks and its Impact on Complex Discovery. Invited talk at IMS Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks, Institute for Mathematical Sciences, NUS, Singapore, 20-25 November 2008.

  9. Wing-Kin Sung. Genome-wide identification of differential histone modification sites from ChIP-seq data using HMM. Invited talk at IMS Workshop on Computational Systems Biology Approaches to Analysis of Genome Complexity and Regulatory Gene Networks, Institute for Mathematical Sciences, NUS, Singapore, 20-25 November 2008.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

  15. Limsoon Wong. Guilt by Association: A Tutorial on Data Mining Techniques for Protein Function Inference. Invited tutorial at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Shahid Behesti University, Tehran, 17-18 November 2008.

  16. Limsoon Wong. Increasing Confidence of Protein-Protein Interactomes. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Shahid Beheshti University, Tehran, Iran, 17-18 November 2008.

  17. Limsoon Wong. Identifying Protein Complexes from Protein Interactome Maps. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Shahid Beheshti University, Tehran, Iran, 17-18 November 2008.

  18. Limsoon Wong. Guilt by Association of Common Interaction Partners. Invited talk at IPM-NUS Workshop on Analysis and Application of Protein Interaction Networks, Shahid Beheshti University, Tehran, Iran, 17-18 November 2008.

  19. 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.

  20. 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.

  21. 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.

  22. 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.

2007

• Books

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

• Book chapters

  1. 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.

• Journal Papers

  1. Zeyar Aung, Kian Lee Tan. Rapid Retrieval of Protein Structures from Databases. Drug Discovery Today, 12(17/18):732--739, September 2007.

  2. Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, and Jean-Claude Latombe. Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Value. Journal of Computational Biology, 14(5):578--593, June 2007.

  3. Kuo Ping Chiu, Pramila Ariyaratne, Han Xu, Adrian Tan, Patric Ng, Edison Liu, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung. Pathway aberations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer, 7:109, 2007.

  4. Ket Fah Chong, Hon Wai Leong. A Merge-Decoupling Dead End Elimination Algorithm for Protein Side-Chain Conformation. International Journal on Data Mining and Bioinformatics, 1(4):372-388, July 2007.

  5. 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.

  6. 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.

  7. ENCODE Project Consortium (Wing-Kin Sung). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature, 447(7146):799-816, April 2007.

  8. Xu Han, Wing-Kin Sung, Lin Feng. Identifying Differentially Expressed Genes in Time-Course Microarray Experiment without Replicate. Journal of Bioinformatics and Computational Biology, 5(2A):281-296, April 2007.

  9. Wing-Kai Hon, Tak-Wah Lam, Kunihiko Sadakane, Wing-Kin Sung. A Space and Time Efficient Algorithm for Constructing Compressed Suffix Arrays. Algorithmica, 48(1):23-36, June 2007.

  10. Liping Ji, Kian-Lee Tan, Anthony K. H. Tung. Compressed Hierarchical Mining of Frequent Closed Patterns from Dense Data Sets. IEEE Transactions on Knowledge and Data Engineering, 19(9):1175-1187, September 2007.

  11. 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.

  12. Yi Li, Wing-Kin Sung, Jian Jun Liu. Association Mapping via Regularized Regression Analysis of Single-Nucleotide Polymorphism Haplotypes in Variable-Sized Sliding Windows. American Journal of Human Genetics, 80(4):705-715, April 2007.

  13. Ching-Ang Lim, Fai Yao, Joyce Wong, Joshy George, Han Xu, Kuo Ping Chui, Wing-Kin Sung, Leonard Lipovich, Vinsensius Vega, Joanne Chen, Atif Shahab, Xiao Dong Zhao, Martin Hibberd, Chia-Lin Wei, Bing Lim, Huck-Hui Ng, Yijun Ruan, Keh-Chuang Chin. Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kB upon TLR4 activation, Molecular Cell, 27(4):622-635, 2007.

  14. Guimei Liu, Jinyan Li, Limsoon Wong. A New Concise Representation of Frequent Itemsets Using Generators and a Positive Border. Knowledge and Information Systems, to appear.

  15. Kwang Loong Stanley Ng, Santosh K. Mishra. De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures. Bioinformatics, 23:1321-1330, June 2007.

  16. Cam Thach Nguyen, Nguyen Bao Nguyen, Wing-Kin Sung, Louxin Zhang. Reconstructing Recombination Network from Sequence Data: The Small Parsimony Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(3):394-402, July-Sept 2007.

  17. Nguyen Bao Nguyen, C. Thach Nguyen, Wing-Kin Sung. Fast Algorithms for Computing the Tripartition-Based Distance between Phylogenetic Networks. Journal of Combinatorial Optimization, 13(3):223--242, April 2007.

  18. Yijun Ruan, Hong Sain Ooi, Siew Woh Choo, Kuo Ping Chiu, Xiao Dong Zhao, K. G. Srinivasan, Fei Yao, Chiou Yu Choo, Jun Liu, Pramila Nuwantha, Wilson Bin, Vladimir Kuznetsov, Atif Shahab, Wing-Kin Sung, Guillaume Bourque, Nallasivam Palanisamy, Chia-Lin Wei. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Research, 17(6):828-838, 2007.

  19. 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):3-13, June 2007. (reviewed invited paper)

  20. Edward Wijaya, Rajaraman Kanagasabai, Siu-Ming Yiu, Wing-Kin Sung. Detection of Generic Spaced Motifs Using Submotif Pattern Mining. Bioinformatics, 23(12):1476-1485, June 2007.

  21. Christopher Wong, Charlie Lee, Wan Yee Leong, Shirlena Soh, Cissy Kartasasmita, Eric Simoes, Martin Hibberd, Wing-Kin Sung, Lance Miller. Optimization and clinical validation of a pathogen detection microarray. Genome Biology, 8(5):R93, 2007.

  22. Xiao Dong Zhao, Xu Han, Joon Lin Chew, Jun Liu, Kuo Ping Chiu, Andre Choo, Yuriy L. Orlov, Wing-Kin Sung, Atif Shahab, Vladimir A. Kuznetsov, Guillaume Bourque, Steve Oh, Yijun Ruan, Huck-Hui Ng, and Chia-Lin Wei. Whole genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell, 1:286--298, September 2007.

• Conference Papers

  1. Zeyar Aung, Soon Heng Tan, See-Kiong Ng, and Kian-Lee Tan. Uncovering the structural basis of protein interactions with efficient clustering of 3-D interaction interfaces. Proceedings of 6th International Conference on Computational Systems Bioinformatics Conference (CSB), pages 287--298, San Diego, California, August 2007.

  2. Jin Chen, Wynne Hsu, Mong Li Lee, See-Kiong Ng. Labeling network motifs in protein interactomes for protein function prediction. Proceedings of 23rd International Conference on Data Engineering (ICDE), pages 546--555, Istanbul, Turkey, April 2007.

  3. Francis Chin, Henry Leung, Wing-Kin Sung, Siu-Ming Yiu. The point placement problem on a line---improved bounds for pairwise distance queries. Proceedings of 7th Workshop on Algorithms in Bioinformatics (WABI), pages ???--???, Philadelphia, USA, September 2007.

  4. Hon Nian Chua, Kang Ning, Wing-Kin Sung, Hon Wai Leong, Limsoon Wong. A Novel algorithm for Protein Complex Prediction based on PPI Networks. Proceedings of 6th Annual International Conference on Computational Systems Bioinformatics (CSB), pages 97--110, San Diego, California, August 2007.

  5. Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Ultra-succinct Representation of Ordered Trees. Proceedings of ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 575-584, New Orleans, Luisiana, January 2007.

  6. Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Compressed dynamic tries with applications to LZ-compression in sublinear time and space. Proceedings of International Conference on Foundations of software Technology and Theoretical Computer Science 2007, pages 424--435, New Delhi, India, December 2007.

  7. 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, December 2007.

  8. Geoffrey Koh, Lisa Tucker-Kellogg, David Hsu, and P.S. Thiagarajan. Globally consistent pathway parameter estimates through belief propagation. Proceedings of 7th Workshop on Algorithms in Bioinformatics (WABI), pages 420--430, Philadelphia, September 2007.

  9. Judice Koh, Mong Li Lee, Wynne Hsu, Kai Tak Lam. Correlation-based Detection of Attribute Outliers. Proceedings of 12th International Conference on Database Systems for Advanced Applications (DASFAA), pages 164-175, Thailand, April 2007.

  10. Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Chi-Kwong Wong, Siu-Ming Yiu. An Experimental Study of Compressed Indexing and Local Alignments of DNA. Proceedings of 1st International Conference on Combinatorial Optimization and Applications (COCOA), pages 242--254, August 2007.

  11. Tak Wah Lam, Wing-Kin Sung, S.-L. Lam, Siu-Ming Yiu. Space efficient indexes for string matching with don't cares. Proceedings of 18th International Symposium on Algorithm and Computation, pages 846--857, Sendai, Japan, December 2007.

  12. Wah-Heng Lee, Wing-Kin Sung. RB-Finder: An Improved Distance-based Sliding Window Method to Detect Recombination Breakpoints. Proceedings of 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 518-532, San Francisco, CA, April 2007.

  13. Henry C.M. Leung, M.H. Siu, S.M. Yiu, Francis Y.L. Chin, Wing-Kin Sung. Finding Linear Motif Pair from Protein Interaction Networks: A Probabilistic Approach. Proceedings of 6th Annual International Conference on Computational Systems Bioinformatics (CSB), pages 111--120, San Diego, California, August 2007.

  14. Jinyan Li, Guimei Liu, Limsoon Wong. Mining Statistically Important Equivalence Classes. Proceedings of 13th International Conference on Knowledge Discovery and Data Mining (KDD), pages 430--439, San Jose, California, 12-15 August 2007.

  15. 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.

  16. 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 (ICDE), pages 1250--1254, Istanbul, Turkey, April 2007.

  17. Hoong Kee Ng, Kang Ning, Hon Wai Leong. A New Approach for Similarity Queries of Biological Sequences in Databases. Proceedings of 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), pages 728--736, Nanjing, China, May 2007.

  18. Anshul Nigham, David Hsu. Protein Conformational Flexibility Analysis with Noisy Data. Proceedings of 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 396--411, San Francisco, CA, April 2007.

  19. Kang Ning, Ket Fah Chong, Hon Wai Leong. De Novo Sequencing for Mass Spectra based on Multi-Charge Strong Tags. Proceedings of 5th Asia-Pacific Bioinformatics Conference (APBC), pages 287--296, Hong Kong, January 2007.

  20. Kang Ning, Hon Wai Leong. Algorithm for Peptide Sequencing by Tandem Mass Spectrometry Based on Better Preprocess and Anti-symmetric Computational Model. Proceedings of 6th Annual International Conference on Computational Systems Bioinformatics (CSB), pages 19--30, San Diego, California, August 2007.

  21. Kang Ning, Hoon Kee Ng, Hon Wai Leong. An Accurate and Efficient Algorithm for Peptide and PTM Identification by Tandem Mass Spectrometry. Proceedings of 18th International Conference on Genome Informatics (GIW), pages 119--130, Singapore, 3-5 December 2007.

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

  23. 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.

  24. Nan Ye, Hon Wai Leong. Determining Charge State for Low Resolution Tandem Mass Spectra based on Complementary Peak Pairs. Proceedings of 2nd PAKDD Workshop on Data Mining for Biomedical Applications (BioDM), pages ???-???, Nanjing, China, May 2007.

• Invited Keynotes, Talks, & Tutorials

  1. Hon Wai Leong. Algorithms for Peptide Sequencing from Tandem Mass Spectrometry. Invited talk at NUS Office of Life Sciences Conference 2007, NUS, Singapore, 6 February 2007.

  2. Hon Wai Leong. Peptide Sequencing from Tandem Mass Spectrometry. Invited talk at IMS Workshop on Computational Methods in Biomolecular Structures and Interaction Networks, Institute for Mathematical Sciences, Singapore, 30 July - 3 August 2007.

  3. Hon Wai Leong. Modelling and characterization of multi-charge mass spectra. Invited talk at DAAD Summer School on Methods from Mathematics and Computer Science for Pattern Recognition in Biology , Shanghai, China, 30 September - 13 October 13, 2007.

  4. Anthony Tung. Advice for a Successful Career in Asia. Invited panel presentation at ACM SIGMOD2007 New Researcher Symposium, Beijing, China, 12 June 2007.

  5. Limsoon Wong. Guilt by Association: A Tutorial on Protein Function Inference. Tutorial at 5th Asia-Pacific Bioinformatics Conference (APBC2007), Hong Kong, 15-17 January 2007.

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

  7. Limsoon Wong. An Introduction to Knowledge Discovery Applications and Challenges in Life Sciences. Advanced Seminar at IEEE 23rd International Conference on Data Engineering (ICDE2007), Istanbul, Turkey, 16-20 April 2007.

  8. Limsoon Wong. Guilt by Association: A Tutorial on Data Mining Techniques for Protein Function Inference. Tutorial at 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2007), Nanjing, China, 22-25 May 2007.

  9. Limsoon Wong. Manifestation and Exploitation of Invariants in Bioinformatics. Invited tutorial at 2nd International Conference on Algebraic Biology (AB2007), Castle of Hagenberg, Austria, 2-4 July 2007.

  10. Limsoon Wong. Increasing Confidence of Protein-Protein Interactomes. Invited tutorial at Computational Methods in Biomolecular Structures and Interaction Networks Program, Institute for Mathematical Sciences, Singapore, 13 July 2007.

2006

• Books

  1. 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)

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

• Journal papers

  1. Zeyar Aung, Kian-Lee Tan. MatAlign: Precise Protein Structure Comparison by Matrix Alignment. Journal of Bioinformatics and Computational Biology, 4(6):1197--1216, December 2006.

  2. Jin Chen, Wynne Hsu, Mong Li Lee, See-Kiong Ng. Increasing Confidence of Protein Interactomes Using Network Topological Metrics. Bioinformatics, 22:1998--2004, 2006.

  3. Kuo Ping Chiu, Chee-Hong Wong, Qiongyu Chen, Pramila Ariyaratne, Hong Sain Ooi, Chia-Lin Wei, Wing-Kin Sung, Yijun Ruan. PET-Tool: A Software Suite for Comprehensive Processing and Managing of Paired-End diTag (PET) Sequence Data. BMC Bioinformatics, 7:390, 2006.

  4. Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel Pevzner. Modeling and Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. Journal of Bioinformatics and Computational Biology, 4(6):1329--1352, December 2006.

  5. 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(18):2310--2312, 2006.

  6. 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.

  7. 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, 2006.

  8. Ying-Jun He, Trinh N. D. Huynh, Jesper Jansson, Wing-Kin Sung. Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. Journal of Bioinformatics and Computational Biology, 4(1):59-74, 2006.

  9. Trinh N. D. Huynh, Wing-Kai Hon, Tak Wah Lam, Wing-Kin Sung. Approximate string matching using compressed suffix arrays. Theor. Comput. Sci., 352(1-3):240-249, 2006.

  10. Jesper Jansson, See-Kiong Ng, Wing-Kin Sung, Hugo Willy. A Faster and More Space-Efficient Algorithm for Inferring Arc-Annotations of RNA Sequences through Alignment. Algorithmica, 46(2):223-245, 2006.

  11. Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. SIAM Journal of Computing, 35(5):1098--1121, 2006.

  12. Jesper Jansson, Ngo Trung Hieu, Wing-Kin Sung. Local Gapped Subforest Alignment and Its Application in Finding RNA Structural Motifs . Journal of Computational Biology, 13(3):702-718, April 2006.

  13. Jesper Jansson, Wing-Kin Sung. Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets. Theoretical Computing Science, 363(1):60--68, 2006.

  14. Kang Ning and Hon Wai Leong. Towards a Better Solution to the Shortest Common Supersequence Problem: The Deposition and Reduction Algorithm. BMC Bioinformatics, 7(Suppl 4):S12, 2006.

  15. Geoffrey Koh, Huey Fern Carol Teong, Marie-Veronique Clement, David Hsu, P. S. Thiagarajan. A Decompositional Approach to Parameter Estimation in Pathway Modeling: A Case Study of the Akt and MAPK Pathways and their Crosstalk. Bioinformatics, 22:e271--e280, 2006.

  16. 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.

  17. Tie-Fei Liu, Wing-Kin Sung, Ankush Mittal. Model gene network by semi-fixed Bayesian network. Expert Syst. Appl., 30(1):42--49, 2006.

  18. Tie-Fei Liu, Wing-Kin Sung, Ankush Mittal. Learning Gene Network Using Time-delayed Bayesian Network. International Journal on Artificial Intelligence Tools, 15(3):353--370, 2006.

  19. Yuin-Han Loh, Qiang Wu, Joon-Lin Chew, Vinsensius Vega, Weiwei Zhang, Xi Chen, Guillaume Bourque, Joshy George, Bernard Leong, Jun Liu, Kee-Yew Wong, Wing-Kin Sung, Charlie W. H. Lee, Xiao-Dong Zhao, Kuo-Ping Chiu, Leonard Lipovich, Vladimir A Kuznetsov, Paul Robson, Lawrence W. Stanton, Chia-Lin Wei, Yijun Ruan, Bing Lim, Huck-Hui Ng. The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nature Genetics, 38(4):431-440, 2006.

  20. Patrick Ng, Jack Tan, Hong Sain Ooi, Yen Ling Lee, Kuo Ping Chiu, Melissa Fullwood, Kandhadayar Srinivasan, Clotilde Perbost, Lei Du, Wing-Kin Sung, Chia-Lin Wei, Yijun Ruan. Multiplex Sequencing of Paired-End Ditags (MS-PET): A Strategy for the Ultra-High-Throughput Analysis of Transcriptomes and Genomes. Nucleic Acids Research, 34(12):e84, 2006.

  21. Kang Ning, Hon Wai Leong. Towards a better solution to the shortest common supersequence problem: The deposition and reduction algorithm. BMC Bioinformatics, 7(Suppl 4):S12, December 2006.

  22. Bin Song, Jeong-Hyeon Choi, Guangyu Chen, Jacek Szymanski, Guo-Qiang Zhang, Anthony K. H. Tung, Jaewoo Kang, Sun Kim, and Jiong Yang. ARCS: An Aggregated Related Column Scoring Scheme for Aligned Sequences. Bioinformatics, 22(19):2326-2332, 2006.

  23. Soon-Heng Tan, Willy Hugo, Wing-Kin Sung, See-Kiong Ng. A Correlated Motif Approach for Finding Short Linear Motifs from Protein Interaction Networks. BMC Bioinformatics, 7:502, 2006.

  24. Chia-Lin Wei, Qiang Wu, Vinsensius B. Vega, Kuo Ping Chiu, Patrick Ng, Tao Zhang, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, JianJun Liu, Xiao Dong Zhao, Joon-Lin Chew, Yen Ling Lee, Vladimir A. Kuznetsov, Wing-Kin Sung, Lance D. Miller, Bing Lim, Edison T. Liu, Qiang Yu, Huck-Hui Ng and Yijun Ruan. A Global Map of p53 Transcription-Factor Binding Sites in the Human Genome. Cell, 124(1):207-219, 2006.

  25. Karen I. Zeller, XiaoDong Zhao, Charlie W. H. Lee, Kuo Ping Chiu, Fei Yao, Jason T. Yustein, Hong Sain Ooi, Yuriy L. Orlov, Atif Shahab, How Choong Yong, YuTao Fu, Zhiping Weng, Vladimir A. Kuznetsov, Wing-Kin Sung, Yijun Ruan, Chi V. Dang, and Chia-Lin Wei. Global mapping of c-Myc binding sites and target gene networks in human B cells. PNAS, 103:17834-17839, 2006.

• Conference papers

  1. Manindra Agrawal, Frank Stephan, P. S. Thiagarajan, Shaofa Yang. Behavioural Approximations for Restricted Linear Differential Hybrid Automata. Proceedings of 9th International Workshop on Hybrid Systems: Computation and Control, pages 4--18, March 2006.

  2. Zong He Cai and Hon Wai Leong. Improving Performance of DNA Sequencing-by-Hybridization with Gapped-Probes via Domain Knowledge. Proceedings of BioTechnology and Bioinformatics Symposium (BIOT-2006), pages 74--82, October 2006, Provo, Utah, USA.

  3. Ho-Leung Chan, Tak-Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong. Compressed Indexes for Approximate String Matching. Proc. 16th Annual European Symposium on Algorithms (ESA 2006), pages 208--219, September 2006.

  4. Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong. A Linear Size Index for Approximate Pattern Matching. Proc. 17th Annual Symposium on Combinatorial Pattern Matching (CPM 2006), pages 49--59, July 2006.

  5. Jin Chen, Wynne Hsu, Mong Li Lee, See-Kiong Ng. NeMoFinder: Dissecting Genome-Wide Protein-Protein Interactions with Repeated and Unique Network Motifs. Proc. 12th ACM SIGKDD Interactional Conference on Knowledge Discovery and Data Mining (KDD), pages 106--115, Philadelphia, PA, August 2006.

  6. 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 Inteactomes. Proceedings of 17th International Conference on Genome Informatics (GIW), pages 284--297, Yokohama, Japan, 18-20 December 2006. (invited keynote paper)

  7. Tsung-Han Chiang, Mehmet Serkan Apaydin, Douglas L. Brutlag, David Hsu, and Jean-Claude Latombe. Predicting Experimental Quantities in Protein Folding Kinetics using Stochastic Roadmap Simulation. Proceedings of 10th Annual International Conference on Research in Computational Molecular Bioloy (RECOMB), pages 410--424, Venice, Italy, April 2006.

  8. Ket Fah Chong, Kang Ning, Hon Wai Leong, Pavel A. Pevzner. Characterization of Multi-Charge Mass Spectra for Peptide Sequencing. Proceedings of 4th Asia-Pacific Bioinformatics Conference (APBC), pages 109--119, Taipei, Taiwan, February 2006.

  9. Ket Fah Chong, Hon Wai Leong. An Extension of Dead End Elimination for Protein Side-Chain Conformation Using Merge-Decoupling. 21st ACM Symposium on Applied Computing (SAC), pages 195--199, Dijon, France, April 2006.

  10. Ankit Goel, Sun Meng, Abhik Roychoudhury, P. S. Thiagarajan. Interacting process classes. Proceedings of 28th International Conference on Software Engineering, pages 302-311, May 2006.

  11. Liping Ji, Kian Lee Tan, Anthony K. H. Tung. Mining Frequent Closed Cubes in 3D Datasets. Proceedings of 32nd International Conference on Very Data Bases, pages 811-822, September 2006.

  12. Liping Ji, Kenneth Mock, Kian-Lee Tan. Quick Hierarchical Biclustering on Microarray Gene Expression Data. Proceedings of 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE-2006), pages 110--117, October 2006, Washington DC.

  13. Wen Jin, Anthony K. H. Tung, Jiawei Han, Wei Wang. Ranking Outliers Using Symmetric Neighborhood Relationship. Proceedings of 10th Pacific-Asia Conference on Advances in Knowledge Discovery and Data Mining, pages 577-593, April 2006.

  14. 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.

  15. 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.

  16. Tie-Fei Liu, Wing-Kin Sung. Learning Gene Network Using Conditional Dependence. Proceedings of 18th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2006), pages 800--804, Washington, D.C., November 2006.

  17. Karuturi R. Krishna Murthy, Silvia Wong, Wing-Kin Sung, Lance D. Miller. Differential Friendly Neighbors Algorithm for Differential Relationships Based Gene Selection and Classification Using Microarray Data. Proceedings of 2006 International Conference on Data Mining (DMIN 2006), pages 175-181, Las Vegas, Nevada, June 2006.

  18. Vipin Narang, Wing-Kin Sung, Ankush Mittal. LocalMotif---An In Silico Tool for Detecting Localized Motifs in Regulatory Sequences. Proceedings 18th IEEE International Conference on Tools with Artificial Intelligence (ICTAI 2006), pages 791--799, Washington D.C., November 2006.

  19. Vipin Narang, Wing-Kin Sung, Ankush Mittal. Computational Annotation of Transcription Factor Binding Sites in D. Melanogaster Developmental Genes. Proceedings of 17th International Conference on Genome Informatics (GIW 2006), pages 14--24, Yokohama, Japan, December 2006.

  20. Kang Ning, Ket Fah Chong, Hon Wai Leong. A Database Search Algorithm for Identification of Peptide with Multiple Charges Using Tandem Mass Spectrometry. LNBI 3916: Proceedings of PAKDD 2006 Workshop on Data Mining for Biomedical Applications (BioDM 2006), pages 2--13, Singapore, April 2006.

  21. Kang Ning, Hon Nian Chua. Automated Identification of Protein Classification and Detection of Annotation Errors in Protein Databases Using Statistical Approaches. LNBI 3886: Proceedings of PAKDD 2006 Workshop on Knowledge Discovery in Life Science Literature (KDLL2006), pages 123--138, Singapore, April 2006.

  22. Kang Ning, Ket Fah Chong, Hon Wai Leong. Towards a Better Solution to the Shortest Common Supersequence Problem. International Multi-Symposiums on Computer and Computational Sciences (IMSCCS), pages 84--90, Hangzhou, China, June 2006.

  23. Kang Ning, Hoong Kee Ng, and Hon Wai Leong. Finding Patterns in Biological Sequences by Longest Commom Subsequences and Shortest Common Supersequences. Proceedings of 6th IEEE Symposium on Bioinformatics and Bioengineering (BIBE-2006), pages 53--60, October 2006, Washington DC.

  24. Kang Ning, Hon Wai Leong. The Distribution and Restoration of Hybridization Problems in Affymetrix GeneChip Data by Parametric Scanning. Proceedings of 17th International Conference on Genome Informatics (GIW 2006), pages 89--99, Yokohama, Japan, December 2006.

  25. Kang Ning, Hoong Kee Ng, Hon Wai Leong. PepSOM: An Algorithm for Peptide Identification by Tandem Mass Spectrometry Based on SOM. Proceedings of 17th International Conference on Genome Informatics (GIW 2006), pages 194--205, Yokohama, Japan, December 2006.

  26. Xin Xu, Ying Lu, Anthony K. H. Tung, Wei Wang. Mining Shifting-and-Scaling Co-Regulation Patterns on Gene Expression Profiles. Proceedings of 22nd International Conference on Data Engineering, pages 89, April 2006.

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

  28. Yun Zheng, Wynne Hsu, Mong Li Lee, Limsoon Wong. Exploring Essential Attributes for Detecting MicroRNA Precursors from Background Sequences. LNBI 4316: Proceedings of 2006 VLDB Workshop on Data Mining in Bioinformatics, pages 131-145, September 2006.

  29. Yun Zheng, Chee Kwoh. Informative MicroRNA Expression Patterns for Cancer Classification. LNBI 3916: Proceedings of PAKDD 2006 Workshop on Data Mining for Biomedical Applications (BioDM 2006), pages 143-154, Singapore, April 2006.

• Invited Keynotes, Talks, & Tutorials

  1. 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.

  2. Hon Nian Chua. A Graph-Based Approach to Inferring Protein Function from Heterogeneous Data Sources. Invited talk at IMS Workshop on BioAlgorithmics, Institute for Mathematical Sciences, Singapore, 12-14 July 2006.

  3. 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.

  4. 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.

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

  6. Wing-Kin Sung. Phylogenetic Network Construction and Comparison. Invited talk at 3rd Association of Asian Societies for Bioinformatics Symposum (AASBi 2006), National Taiwan University, 12 February 2006.

  7. Wing-Kin Sung. Annotating the Genome Using Paired-End diTag. Invited talk at Symposium on Bioinformatics in Taiwan (BIT2006), National Chung-Hsing University, Taichung, Taiwan, 12-15 September 2006.

  8. Wing-Kin Sung. Gene and Transcription Factor Binding Sites Finding Methods. Invited tutorial at Symposium on Bioinformatics in Taiwan (BIT2006), National Chung-Hsing University, Taichung, Taiwan, 12-15 September 2006.

  9. P.S. Thiagarajan. A Parameter Estimation Technique for Pathway Models. Invited talk at Strand Life Sciences, Bangalore, India, 19 December 2006.

  10. Hugo Willy. On Simultaneous Knowledge Extraction from Protein-Protein Interaction Data. Invited talk at IMS Workshop on BioAlgorithmics, Institute for Mathematical Sciences, Singapore, 12-14 July 2006.

  11. 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.

  12. Limsoon Wong. Knowledge Discovery Techniques for Bioinformatics. Invited master class at Yang Ming National University, Taipei, Taiwan, 6-7 June 2006.

  13. 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.

  14. Limsoon Wong. An Introduction to Knowledge Discovery Applications and Challenges in Life Sciences. Invited tutorial at EEI PhD Winter School in Data Mining & Bioinformatics, ARC Research Network in Enterprise Information Infrastructure, Lorne, Victorial, Australia, 13-17 August 2006.

  15. 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.

  16. 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.

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

  18. 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.

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

  20. 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.

  21. 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.

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

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

  24. Melvin Zhang. Rearrangements in Genomes with Unequal Content. Invited talk at IMS Workshop on BioAlgorithmics, Institute for Mathematical Sciences, Singapore, 12-14 July 2006.

2005

• Books

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

• Book chapters

  1. 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, 2005.

• Journal papers

  1. Z. Aung and K.L. Tan. Automatic 3D Protein Structure Classification Without Structural Alignment. Journal of Computational Biology, 12(9):1221-1241, 2005.

  2. H. L. Chan, T. W. Lam, W. K. Sung, Prudence W. H. Wong, S. M. Yiu, and X. Fan. The Mutated Subsequence Problem and Locating Conserved Genes. Bioinformatics, 21(10):2271-2278, 2005

  3. J. Chen, W. Hsu, M.L. Lee, and S.-K. Ng. Discovering Reliable Protein Interactions from High-Throughput Experimental Data Using Network Topology. Artificial Intelligence in Medicine, 35:37-47, 2005.

  4. Arunkumar Chinnasamy, W. K. Sung, and A. Mittal. Protein structure and fold prediction using tree-augmented naive Bayesian classifier. Journal of Bioinformatics and Computational Biology, 3(4):803-820, 2005.

  5. C.H. Chionh, Z. Huang, K.L. Tan, Z. Yao. Towards Scaleable Protein Structure Comparison and Database Search. International Journal on Artificial Intelligence Tools, 14(5):827-848, 2005.

  6. C. Choy, J. Jansson, K. Sadakane, and W. K. Sung. Computing the Maximum Agreement of Phylogenetic Networks. Theoretical Computer Science, 335(1): 93-107, 2005.

  7. Jesper Jansson, Joseph H. K. Ng, Kunihiko Sadakane, Wing-Kin Sung. Rooted Maximum Agreement Supertrees. Algorithmica, 43(4):293--307, 2005.

  8. Liping Ji, Kian-Lee Tan. Identifying time-lagged gene clusters using gene expression data. Bioinformatics, 21(4):509-516, 2005.

  9. Kang Ning, Kwok Pui Choi, Hon Wai Leong, Louxin Zhang. A Post Processing Method for Optimizing Synthesis Strategy for Oligonucleotide Microarrays. Nucleic Acids Research, 33:e144, 2005.

  10. W. Leong, F. P. Preparata, W. K. Sung, and H. Willy. Adaptive control of hybridization noise in DNA Sequencing-by-Hybridization. Journal of Bioinformatics and Computational Biology, 3(1):79-98, 2005.

  11. 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, 2005.

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

  13. Tie-Fei Liu, Wing-Kin Sung, Yi Li, Jian-Jun Liu, Ankush Mittal, Pei-lin Mao. Effective Algorithms for Tag SNP Selection. Journal of Bioinformatics and Computational Biology, 3(5):1089--1106, 2005.

  14. 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.

  15. V. Narang, W. K. Sung, and A. Mittal. Computational Modeling of Oligonucleotide Positional Densities for Human Promoter Prediction. Artificial Intelligence in Medicine, 35:107-119, 2005.

  16. Partick Ng, Chia-Lin Wei, Wing-Kin Sung, Kuo Ping Chiu, Leonard Lipovich, Chin Chin Ang, Sanjay Gupta, Atif Shahab, Azmi Ridwan, Chee Hong Wong, Edison T. Liu, Yijun Ruan. Gene Identification Signature (GIS) Analysis for Transcriptome Characterization and Genome Annotation. Nature Methods, 2:105-111, 2005.

  17. K. Ning, K.P. Choi, H.W. Leong and L. Zhang. A post processing method for optimizing synthesis strategy for oligonucleotide microarray. Nucleic Acids Research, 33:e144, 2005.

  18. 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, 2005.

  19. Lisa Skipper, Yi Li, Carine Bonnard, Ratnagopal Pavanni, Yuan Yih, Eva Chua, Wing-Kin Sung, Louis Tan, Meng-Cheong Wong, Eng-King Tan, Jianjun Liu. Comprehensive Evaluation of Common Genetic Variation within LRRK2 Reveals Evidence for Association with Sporadic Parkinson's Disease. Human Molecular Genetics, 14(23):3549--3556, 2005.

  20. J. Wang, W. K. Sung, A. Krishnan, and K. B. Li. Protein subcellular localization prediction for Gramnegative bacteria using amino acid subalphabets and a combination of multiple support vector machines. BMC Bioinformatics, 6:174, 2005.

  21. Ji Zhang, Wynne Hsu, Mong-Li Lee. Clustering in Dynamic Spatial Databases. J. Intell. Inf. Syst., 24(1):5-27, 2005.

• Conference papers

  1. Chee Yong Chan, Pin-Kwang Eng, Kian-Lee Tan. Stratified Computation of Skylines with Partially-Ordered Domains. Proceedings of ACM SIGMOD International Conference on Management of Data, pages 203-214, Baltimore, MD, June 2005.

  2. Xia Cao, Beng Chin Ooi, HweeHwa Pang, Kian-Lee Tan, Anthony K. H. Tung. DSIM: A Distance-Based Indexing Method for Genomic Sequences. Proceedings of 5th IEEE Symposium on Bioinformatics and Bioengineering, pages 97-104, Minneapolis, Minnesota, October 2005.

  3. Xia Cao, Shuai Cheng Li, Anthony K. H. Tung. Indexing DNA Sequences Using q-Grams. Proceedinhgs of 10th International Conference on Database Systems for Advanced Applications, pages 4-16, Beijing, China, April 2005.

  4. Gao Cong, Kian-Lee Tan, Anthony K. H. Tung, Xin Xu. Mining Top-k Covering Rule Groups for Gene Expression Data. Proceedings of ACM SIGMOD International Conference on Management of Data, pages 670-681, Baltimore, MD, June 2005.

  5. Hon Nian Chua and Wing-Kin Sung. A better gap penalty for pairwise SVM. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, Singapore, pages 11-20, January 2005.

  6. Bin Cui, Heng Tao Shen, Jialie Shen, Kian-Lee Tan. Exploring Bit-Difference for Approximate KNN Search in High-dimensional Databases. Proceedings of 16th Australasian Database Conference, pages 165-174, Newcastle, Australia, February 2005.

  7. Stefan Dobrev, Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Finding Short Right-Hand-on-the-Wall Walks in Graphs. Proc. 12th International Colloquium on Structural Information and Communication Complexity (SIROCCO 2005), pages 127--139, 2005.

  8. Y.-J. He, T.N.D. Huynh, J. Jansson, W.-K. Sung. Inferring phylogenetic relationships avoiding forbidden rooted triplets. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, Singapore, pages 339-348, January 2005.

  9. Trinh N. D. Huynh, J. Jansson, N. B. Nguyen, and W. K. Sung. Constructing a Smallest Refining Galled Phylogenetic Network. Proceedings of 9th Annual International Conference on Research in Computational Molecular Biology, pages 265-280, Cambridge, MA, May 2005.

  10. Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung. Algorithms for combining rooted triplets into a galled phylogenetic network. Proc. 16th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA 2005), pages 349--358, 2005.

  11. Liang Jin, Nick Koudas, Chen Li, Anthony K. H. Tung. Indexing Mixed Types for Approximate Retrieval. Proceedings of 31st International Conference on Very Large Data Bases, pages 793-804, Trondheim, Norway, August 2005.

  12. Judice L.Y. Koh, Mong Li Lee, Vladimir Brusic. A Classification of Biological Data Artifacts. Proceedings of ICDT Workshop on Database Issues in Biological Databases (DBiBD), Edinburgh, Scotland, UK, January 2005.

  13. Tak Wah Lam, Wing-Kin Sung, Swee-Seong Wong. Improved Approximate String Matching Using Compressed Suffix Data Structures. Proc. 16th International Symposium on Algorithms and Computation (ISAAC 2005), pages 339--348, 2005.

  14. 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.

  15. 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.

  16. Yi Li, Wing-Kin Sung, Lance D. Miller. Multimodality as a Criterion for Feature Selection in Unsupervised Analysis of Gene Expression Data. Proc. 5th IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2005), pages 276--280, 2005.

  17. 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.

  18. Yingren Liu, Karuturi R. Krishna Murthy, Wing-Kin Sung. ConstrainedMotif: A Periodicity Constraint Based Algorithm to Predict Cell-Cycle Associated Promoter Motifs Using Time-Course Gene Expression Data. Proc. 5th IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2005), pages 250--257, 2005.

  19. Nguyen Bao Nguyen, C. Thach Nguyen, Wing-Kin Sung. Fast Algorithms for Computing the Tripartition-Based Distance between Phylogenetic Networks. Proc. 16th International Symposium on Algorithms and Computation (ISAAC 2005), pages 402--411, 2005.

  20. Junmei Wang, Wynne Hsu, Mong-Li Lee. A framework for mining topological patterns in spatio-temporal databases. Proceedings of 14th ACM Conference on Information and Knowledge Management, pages 429-436, Bremen, Germany, November 2005.

  21. Chenyi Xia, Wynne Hsu, Mong-Li Lee. ERkNN: efficient reverse k-nearest neighbors retrieval with local kNN-distance estimation. Proceedings of 14th ACM Conference on Information and Knowledge Management, pages 533-540, Bremen, Germany, November 2005.

  22. Rui Yang, Panos Kalnis, Anthony K. H. Tung. Similarity Evaluation on Tree-structured Data. Proceedings of ACM SIGMOD International Conference on Management of Data, pages 754-765, Baltimore, MD, June 2005.

  23. Siu-Ming Yiu, P. Y. Chan, Tak Wah Lam, Wing-Kin Sung, Hing-Fung Ting, Prudence W. H. Wong. Allowing mismatches in anchors for wholw genome alignment: Generation and effectiveness. Proc. 3rd Asia-Pacific Bioinformatics Conference, pages 1--10, 2005.

• Invited Keynotes, Talks, & Tutorials

  1. 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.

  2. 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.

  3. Jinyan Li, Limsoon Wong. Bioinformatics and Machine Learning. Tutorial talk at 20th National Conference on Artificial Intelligence (AAAI-05), Pittsburgh, 9-13 July 2005.

  4. Ken Sung, Limsoon Wong. Bioinformatics in Practice. Invited tutorial at 8th International Conference on Discovery Science, Marina Mandarin Hotel, Singapore, 8 October 2005.

  5. Wing-Kin Sung. DTSeq: Decison Tree Based De Novo Peptide Sequencing. Invited talk at Workshop on Data Analysis and Data Mining in Proteomics, Institute for Mathematical Sciences, NUS, Singapore, 12 May 2005.

  6. 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.

  7. 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.

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

  9. 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.

  10. 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.

Selected Older Papers

• Z. Aung, K.L. Tan. Rapid 3D Protein Structure Database Searching using Information Retrieval Techniques. Bioinformatics, 20(7):1045-1052, 2004.

• L. Ji, K.L. Tan. Mining Gene Expression Data for Positive and Negative Co-regulated Gene Clusters. Bioinformatics, 20(16):2711-2718, 2004.

• Limsoon Wong, editor. The Practical Bioinformatician, World Scientific, New Jersey, May 2004.

• M.S. Apaydin, D.L. Bruglag, C. Guestrin, D. Hsu, J.C. Latombe, and C. Varma. Stochastic roadmap simulation: An efficient representation and algorithm for analyzing molecular motion. Journal of Computational Biology, 10(3-4):247--281, 2003.

• Wing-Kai Hon, Kunihiko Sadakane, Wing-Kin Sung. Breaking a Time-and-Space Barrier in Constructing Full-Text Indices. Proc. 44th Annual IEEE Symposium on Foundations of Computer Science (FOCS 2003), Cambridge, MA, October 2003, pp 251--260.

• Huiqing Liu, Limsoon Wong. Data Mining Tools for Biological Sequences. Journal of Bioinformatics and Computational Biology, 1(1):139--168, April 2003.

• H. Wang, B.C. Ooi, K.L. Tan, T.H. Ong, L. Zhou. BLAST++: BLASTing Queries in Batches. Bioinformatics, 19:2323-2324, 2003.

• D. Brutlag, M.S. Apaydin, C. Guestrin, D. Hsu, C. Varma, A. Singh, and J.-C. Latombe. Using robotics to fold proteins and dock ligands. Bioinformatics, 18:S74--S83, 2002.

• T.H. Ong, K.L. Tan and H. Wang. Indexing Genomic Databases for Fast Homology Searching. Proceedings of 13th International Conference on Database and Expert Systems Applications, September 2002, Aix-en-Provence, France, pp. 871-880.

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

• 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. (Coverpage feature article.)

• 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.