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

2008

• Books

  1. Kun Mao Chao, Louxin Zhang. Sequence Comparison: Theory and Method, Springer, Berlin, November 2008. (232 pages).
  2. Martin Vingron, Limsoon Wong. Proceedings of 12th Annual International Conference on Research in Computational Molecular Biology, Springer, Berlin, March 2008. (480 pages).

• Journal papers

  1. J. O. Ahn, H. W. Lee, R. Saha, M. S. Park, J.-K. Jung, D.-Y. Lee. Exploring the effects of carbon sources on the metabolic capacity for shikimic acid production in Escherichia coli using in silico metabolic predictions. J. Microbiol. Biotechnol., to appear.
  2. 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.
  3. Christelle En Lin Chua, Bor Luen Tang. Syntaxin 16 is enriched in neuronal dendrites and may have a role in neurite outgrowth. Molecular Membrane Biology, 25(1):35-45, January 2008.
  4. Christelle En Lin Chua, Bor Luen Tang. SIRT2, tubulin deacetylation, and oligodendroglia differentiation. Cell Motility and the Cytoskeleton, 65(3):179-182, March 2008.
  5. 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.
  6. Hon Nian Chua, Limsoon Wong. Increasing the Reliability of Protein Interactomes. Drug Discovery Today, 13(15/16):652--658, August 2008.
  7. Q. Hou, Y. H. Wu, H. Grabsch, Y. Zhu, S. H. Leong, K. Ganesan, D. Cross, L. K. Tan, J. Tao, V. Gopalakrishnan, B. L. Tang, O. L. Kon, P. Tan. Integrative genomic identify Rab23 as an invasion mediator gene in diffuse gastric cancer. Cancer Res., 68(12):4623--4630, June 2008.
  8. A. M. Khan, O. Miotto, E. J. Nascimento, K. N. Srinivasan, A. T. Heiny, G. L. Zhang, J. Salmon, E. Marques, T. W. Tan, V. Brusic. Conservation and Variability of Dengue Virus Proteins: Implications for Vaccine Design. PLoS Neglected Tropical Diseases, to appear.
  9. 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.
  10. 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.
  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. C. B. Low, Y. C. Liou, B. L. Tang. Neural differentiation and potential use of stem cells from the human umbilical cord for CNS transplantation therapy. J. Neurosci. Res., 86(8):1670--1679, June 2008.
  13. O. Miotto, A. T. Heiny, T. W. Tan, J. T. August, V. Brusic. Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. BMC Bioinformatics, 9(Suppl 1):S18, February 2008.
  14. O. Miotto, T. W. Tan, V. Brusic. Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses. BMC Bioinformatics, 9(Suppl 1):S7, February 2008.
  15. E. L. Ng, B. L. Tang. Rab GTPases and their roles in brain neurons and glia. Brain Res. Rev., 58(1):236--246, June 2008.
  16. 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.
  17. D. S.-W. Ow, D.-Y. Lee, M. G.-S. Yap, S. K.-W. Oh. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol. Prog., to appear.
  18. Emmanuel C. Picaa, Paramasivam Kathirvela, Zacharias A.D. Pramonoa, Poh-San Laic, Woon-Chee Yee. Characterization of a novel S13F desmin mutation associated with desmin myopathy and heart block in a Chinese family. Neuromuscular Disorders, to appear.
  19. S. Ranganathan, M. Gribskov, T. W. Tan. Bioinformatics research in the Asia Pacific: A 2007 update. BMC Bioinformatics, 9(Suppl 1):S1, February 2008.
  20. Unitsa Sangket, Amornrat Phongdara, Wilaiwan Chotigeat, Darran Nathan, Woo-Yeon Kim, Jong Bhak, Chumpol Ngamphiw, Sissades Tongsima, Asif M. Khan, Honghuang Lin, Tin Wee Tan. Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries. Bioinformatics, 24:299-301, January 2008.
  21. B. L. Tang. Leptin as a neuroprotective agent. Biochem. Biophys. Res. Commun., 368(2):181-185, April 2008.
  22. B. L. Tang. Emerging aspects of neuronal membrane traffic in dendritic growth. Biochim. Biophys. Acta, 1783(2):169-176, February 2008.
  23. B. L. Tang, C. E. Chua. SIRT1 and neuronal diseases. Mol. Aspects Med., 29(3):187--200, June 2008.
  24. F. Y. Teng, B. L. Tang. Nogo-A and Nogo-66 receptor in amyotrophic lateral sclerosis. J. Cell. Mol. Med., to appear.
  25. F. Y. Teng, B. L. Tang. Cell autonomous function of Nogo and reticulons - the emerging story at the endoplasmic reticulum. J. Cell. Physiol., 216(2):303--308, August 2008.
  26. Joo Chuan Tong, Martti Tapani Tammi. Methods and protocols for the assessment of protein allergenicity and cross-reactivity. Frontiers in Bioscience, 13:4882--4888, May 2008.
  27. Joo Chuan Tong, Martti T. Tammi. Prediction of protein allergenicity using local description of amino acid sequence. Frontiers in Bioscience, 13:6072--6078, May 2008.
  28. L. Yang, J. M. Clinton, M. L. Blackburn, Q. Zhang, A. Zielinska-Kwiatkowska, B. L. Tang, H. A. Chansky HA. Rab23 regulates differentiation of ATDC5 chondroprogenitor cells. J. Biol. Chem., 283:10649-10657, April 2008.
  29. 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.
  30. F. N. K. Yusufi, W. Park, M. M. Lee, D.-Y. Lee. An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioproc. Biosys. Eng., to appear.
  31. G. L. Zhang, A. M. Khan, K. N. Srinivasan, A. T. Heiny, K. X. Lee, C. K. Kwoh, J. T. August, V. Brusic. Hotspot Hunter: A computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics, 9(Suppl 1):S19, February 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 ??--??, 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. 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.
  7. 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.
  8. Jialiang Yang, Louxin Zhang. Run Probability of High-Order Seed Patterns and its Applications to Finding Good Transition Seeds. Proceedings of 6th Asia-Pacific Bioinformatics Conference, pages 123--132, Kyoto, Japan, 14--17 January 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. H. Ariffin, S. P. Chen, C. S. Kwok, T. C. Quah, H. P. Lin, A. E.-J. Yeoh. Ethnic differences in the frequency of subtypes of childhood acute lymphoblastic leukemia: Results of the Malaysia-Singapore Leukemia Study Group. J Pediatr Hematol Oncol., 29(1):27-31, January 2007.
  2. Erik Arner, Ellen Kindlund, Daniel Nilsson, Fatima Farzana, Marcella Ferella, Martti T. Tammi, Bjorn Andersson. Database of Trypanosoma cruzi repeated genes: 20 000 additional gene variants. BMC Genomics, 8(1):391, October 2007.
  3. Zeyar Aung, Kian Lee Tan. Rapid Retrieval of Protein Structures from Databases. Drug Discovery Today, 12(17/18):732--739, September 2007.
  4. Kuo Ping Chiu, Pramila Ariyaratne, Han Xu, Adrian Tan, Patric Ng, Edison Liu, Yijun Ruan, Chia-Lin Wei, Wing-Kin Sung. Pathway aberrations of murine melanoma cells observed in Paired-End diTag transcriptomes. BMC Cancer, 7:109, June 2007.
  5. H. S. Choi, T. Y. Kim, D.-Y. Lee and S. Y. Lee. Incorporating metabolic flux ratios into constraint-based flux analysis by using artificial metabolites and converging ratio determinants. J. Biotechnol., 129(4):696-705, May 2007.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. Xu Han, Wing-Kin Sung, Lin Feng. PEM: A General Statistical Approach for Identifying Differentially Expressed Genes in Time-course cDNA Microarray Experiment without Replicate. Journal of Bioinformatics and Computational Biology, 5(2A):281-296, April 2007.
  11. A. T. Heiny, O. Miotto, K. N. Srinivasan, A. M. Khan, G. L. Zhang, V. Brusic, T. W. Tan, J. T. August. Evolutionarily conserved protein sequences of influenza a viruses, avian and human, as vaccine targets. PLoS ONE, 2(11):e1190, November 2007.
  12. 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.
  13. 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.
  14. Pan-Jun Kim, Dong-Yup Lee, Tae Yong Kim, Kwang Ho Lee, Hawoong Jeong, Sang Yup Lee, Sunwon Park. Metabolite essentiality elucidates robustness of Escherichia coli metabolism. PNAS, 104(34):13638-13642, August 2007.
  15. Ellen Kindlund, Martti T. Tammi, Bjorn Andersson. Genome-Scale Rapid Alignment Tool, G-RAT. Computer Methods and Programs in Biomedicine, 86(1):87-92, April 2007.
  16. Y. Kong. Generalized correlation functions and their applications in selection of optimal multiple spaced seeds for homology search. J. Comp. Biol., 14:238-254, March 2007.
  17. Yong Kong. Asymptotics of monomer-dimer model on rectangular semi-infinite lattices. Phys. Rev. E, 75:051123, May 2007.
  18. 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.
  19. 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.
  20. 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, August 2007.
  21. H. Lin and P. J. Antsaklis. Switching stabilizability for continuous-time uncertain switched linear systems. IEEE Trans on Auto. Control, 52(4):633-646, April 2007.
  22. Y. Lu, S. K.-Y. Kham, T.C. Foo, A. Hany, T. C. Quah, A. E.-J. Yeoh. Genotyping of eight polymorphic genes encoding drug-metabolizing enzymes and transporters using a customized oligonucleotide array. Anal Biochem, 360(1):105-113, January 2007.
  23. 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.
  24. Ee Ling Ng, Ya Wang, Bor Luen Tang. Rab22B’s role in trans-Golgi network membrane dynamics. Biochemical and Biophysical Research Communications, 361(3):751-757, September 2007.
  25. Nguyen Bao Nguyen, Cam Thach 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.
  26. 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.
  27. 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, June 2007.
  28. S. Selvarasu, D.-Y. Lee and I. A. Karimi. Identifying synergistically switching pathways for multi-product strain improvement using multiobjective flux balance analysis. Computer-Aided Chemical Engineering, 24, 1007-1012, 2007.
  29. J. Shen, Y. Tai, J. Zhou, C. Stephen Wong, P. Cheang, W. Fred Wong, Z. Xie, M. Khan, J. Han, C. Chen. Synergistic antileukemia effect of genistein and chemotherapy in mouse xenograft model and potential mechanism through MAPK signaling. Experimental Hematology, 35(1):75-83, January 2007.
  30. 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.
  31. Jinsong Tan, Kok Seng Chua, Louxin Zhang. Algorithmic and complexity issues of three clustering methods in microarray data analysis. Algorithmica, 48(2):203-219, June 2007.
  32. Jinsong Tan, Louxin Zhang. The consecutive ones submatrix problem for sparse matrices. Algorithmica, 48(3):287-299, July 2007.
  33. R. M. Tan, T. C. Quah, L. Aung, S. Liang, R. C. Kirk, A. E.-J. Yeoh. Improved outcome in childhood acute myeloid leukemia in Singapore with the MRC AML 10 protocol. Pediatr Blood Cancer, 48(3):262-267, March 2007.
  34. B. L. Tang, Y. C. Liou. Novel modulators of amyloid beta precursor processing. J. Neurochem., 100:314-323, January 2007.
  35. B. L. Tang, C. B. Low. Genetic manipulation of neural stem cells for transplantation into the injured spinal cord. Cell Mol. Neurobiol., 27(1):75-85, February 2007.
  36. Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan. In silico grouping of peptide/HLA class I complexes using structural interaction characteristics. Bioinformatics, 23(1):177-183, January 2007.
  37. Joo Chuan Tong, Zong Hong Zhang, J. Thomas August, Vladimir Brusic, Tin Wee Tan, Shoba Ranganathan. In silico characterization of immunogenic epitopes presented by HLA-Cw*0401. Immunome Research, 3:7, August 2007.
  38. Joo Chuan Tong, Tin Wee Tan, Shoba Ranganathan. Methods and protocols for prediction of immunogenic epitopes. Briefings in Bioinformatics, 8(2):96-108, March 2007
  39. Lawrence J.K. Wee, Tin Wee Tan, and Shoba Ranganathan. CASVM: Web server for SVM-based prediction of caspase substrates cleavage sites. Bioinformatics, 23(23):3241--4243, December 2007.
  40. 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.
  41. 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, May 2007.
  42. L. P. Yang, M. Q. Wang, W. Wu and L. Zhang. Transcriptome Analysis of Cold Syndrome Using Microarray. American Journal of Chinese Medicine, 35:609-620, August 2007.
  43. Louxin Zhang. Superiority of spaced seeds for homology search. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 4(3):496-505, July-September 2007.
  44. Zong Hong Zhang, Judice L. Y. Koh, Guang Lan Zhang, Khar Heng Choo, Martti T. Tammi, and Joo Chuan Tong. AllerTool: A web server for predicting allergenicity and allergic cross-reactivity in proteins. Bioinformatics, 23(4):504--506, February 2007.
  45. 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. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. C. T. Nguyen, J. Shen, M. M. Hou, Li Sheng, Webb Miller, L. X. Zhang. Approximating the Spanning Star Forest Problem and its Applications to Genomic Sequence Alignment. Proceedings of SIAM-ACM Symposium on Discrete Algorithms (SODA), pages 645-654, New Orleans, Louisiana, January 2007.
  18. 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.
  19. 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.
  20. Kang Ning, Hoong 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.
  21. 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.
  22. 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 (ICDE), pages 1350--1354, Istanbul, Turkey, April 2007.
  23. 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.

  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, 2006. (363 pages)
  2. Jagath C. Rajapakse, Limsoon Wong, Raj Acharya, editors. Pattern Recognition in Bioinformatics, Springer-Verlag, Berlin, 2006. (186 pages)

• Journal papers

  1. E. Arner, M. T. Tammi, A. N. Tran, E. Kindlund, B. Andersson. DNPTrapper: An assembly editing tool for finishing and analysis of complex repeat regions. BMC Bioinformatics, 7:155, March 2006.
  2. S. Aulia, B. L. Tang. Cdh1-APC/C, cyclin B-Cdc2, and Alzheimer's disease pathology. Biochem. Biophys. Res. Commun., 339(1):1--6, 2006.
  3. 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.
  4. Guillaume Bourque, Louxin Zhang. Models and Methods in Comparative Genomics. Advances in Computers, 68:60-105, 2006.
  5. Jin Chen, Wynne Hsu, Mong Li Lee, and See-Kiong Ng. Increasing confidence of protein interactomes using network topological metrics. Bioinformatics, 22:1998-2004, August 2006.
  6. Y. Chen, S. Aulia, B. L. Tang BL. Myelin-associated glycoprotein (MAG)-mediated signaling in CNS pathophysiology. Mol. Neurobiol., 34:81-92, 2006.
  7. Y. Chen, S. Aulia, L. Li, B. L. Tang. AMIGO and friends: An emerging family of brain-enriched, neuronal growth modulating, type I transmembrane proteins with leucine-rich repeats (LRR) and cell adhesion molecule motifs. Brain Res. Brain Res. Rev., 51(2):265--274, August 2006.
  8. Y. Chen, B. L. Tang. The amyloid precursor protein and postnatal neurogenesis/neuroregenerstion. Biochem. Biophys. Res. Commun., 341(1):1--5, 2006.
  9. Y. Chen, F. Y. H. Teng, B. L. Tang. Coaxing bone marrow stromal mesenchymal stem cells towards neuronal differentiation: progress and uncertainties. Cell. Mol. Life Sci., 63:1649-1657, July 2006.
  10. 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, August 2006.
  11. 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.
  12. 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.
  13. 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.
  14. C. E. Chua, and B. L. Tang. Alpha-synuclein and Parkinson's disease---the first roadblock. J. Cell. Mol. Med., 10:837-846, 2006.
  15. 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.
  16. A. Guo, T. Wang, E. L. Ng, S. Aulia, K. H. Chong, F. Y. Teng, Y. Wang, B. L. Tang. Open brain gene product Rab23: Expression pattern in the adult mouse brain and functional characterization. J. Neurosci. Res., 83(6):1118--1127, 2006.
  17. 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, February 2006.
  18. 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, March 2006.
  19. 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, September 2006.
  20. Jesper Jansson, Nguyen Bao Nguyen, Wing-Kin Sung. Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. SIAM J. Comput., 35(5):1098-1121, 2006.
  21. 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.
  22. 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, October 2006.
  23. 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.
  24. A. M. Khan, A. T. Heiny, K. X. Lee, K. N. Srinivasan, T. W. Tan, J. T. August, V. Brusic. Large-scale analysis of antigenic diversity of T-cell epitopes in dengue virus. BMC Bioinformatics , 7(Suppl 5):S4, December 2006.
  25. Y. Kong. Distribution of Runs and Longest Runs: A New Generating Function Approach. J. Amer. Statist. Assoc. (JASA), 101:1253-1263, September 2006.
  26. Y. Kong. Monomer-dimer model in two-dimensional rectangular lattices with fixed dimer density. Phys. Rev. E, 74(061102):1-15, December 2006.
  27. Y. Kong. Logarithmic corrections in the free energy of monomer-dimer model on plane lattices with free boundaries. Phys. Rev. E, 74(011102):1-8, July 2006.
  28. Y. Kong. Packing Dimers on (2p+1) x (2q+1) Lattices. Phys. Rev. E, 73(016106):1-11, January 2006.
  29. P. S. Lai, P. Y. Cheah, P. Kadam, C. L. Chua, D. K. Lie, H. H. Li, K. W. Eu, F. Seow-Choen, A. S. Lee. Overexpression of RB1 transcript is significantly correlated with 13q14 allelic imbalance in colorectal carcinomas. Int. J. Cancer, 119(5):1061--1066, September 2006.
  30. D. Y. Lee, C. Yun, A. Cho, B. K. Hou, S. Park, S. Y. Lee. WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks. Bioinformatics, 22(9):1150-1151, May 2006.
  31. D. Y. Lee, R. Zimmer, S. Y. Lee, S. Park. Colored Petri net modeling and simulation of signal transduction pathways. Metab Eng., 8(2):112-122, 2006.
  32. Haiquan Li, Jinyan Li, Limsoon Wong. Discovering Motif Pairs at Interaction Sites from Protein Sequences on a Proteome-Wide Scale. Bioinformatics, 22(8):989--996, April 2006.
  33. Tie-Fei Liu, Wing-Kin Sung, Ankush Mittal. Model gene network by semi-fixed Bayesian network. Expert Syst. Appl., 30(1):42--49, January 2006.
  34. 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, June 2006.
  35. 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.
  36. J. Ma, L. X. Zhang, B. Suh, B. J. Raney, W. J. Kent, M. Blanchette, D. Haussler and W. Miller. Reconstructing Contiguous Regions of An Ancestral Genome. Genome Research, 16:1557-1565, December 2006.
  37. 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, July 2006.
  38. K. Ning, H. W. Leong. Towards a better solution to the shortest common supersequence problem: the deposition and reduction algorithm . BMC Bioinformatics, 7(Suppl 4):S12, December 2006.
  39. Z.A.D. Pramono, P.S. Lai, C. L. Tan, S. Takeda, W.C. Yee. Characterization and identification of a novel human dysferlin transcript, dysferlin v_1. Hum Genetics, 120(3):410-419, 2006.
  40. S. Ranganathan, M. Tammi, M. Gribskov, T. W. Tan. Establishing bioinformatics research in the Asia Pacific. BMC Bioinformatics, 7(Suppl 5):S1, December 2006.
  41. 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, October 2006.
  42. S. H. Tan, W. Hugo, W. K. Sung, S. K. Ng. A correlated motif approach for finding short linear motifs from protein interaction networks . BMC Bioinformatics, 7:502, November 2006.
  43. B. L. Tang. Molecular genetic determinants of human brain size. Biochem Biophys Res Commun, 345(3):911--916, 2006.
  44. B. L. Tang. SIRT1, neuronal cell survival and the insulin/IGF-1 aging paradox. Neurobiol Aging, 27(3):501--505, 2006.
  45. T. F. Tang, L. Hou, B. Tu, W. Y. Hwang, A. E.-J. Yeoh, J. Ng, C. K. Hurley. Identification of nine new HLA class I alleles in volunteers from the Singapore stem cell donor registries. Tissue Antigens, 68(6):518-520, December 2006.
  46. S. K. H. Tay, H. H. Khng, P. S. Low, P. S. Lai. Diagnostic strategy for the detection of dystrophin gene mutations in Asian patients and carriers using immortalized cell lines. J. Child Neurol., 21(2):150--155, February 2006.
  47. S. K. H. Tay, H. H. Khng, P. S. Low, P. S. Lai. A Novel Approach to Detecting Pathogenic Mutations in Asian Patients with Duchenne and Becker Muscular Dystrophy by Protein Truncation Analysis Using a Transformed Lymphocyte Cell Lines. J Child Neurol, 21(2):150-155, 2006.
  48. R. Thadani, M. T. Tammi. MicroTar: predicting microRNA targets from RNA duplexes . BMC Bioinformatics, 7(Suppl 5):S20, December 2006.
  49. J. C. Tong, L. Kong, T. W. Tan, S. Ranganathan. MPID-T: Database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Applied Bioinformatics, 5(2):111--114, 2006.
  50. J. C. Tong, G. L. Zhang, T. W. Tan, J. T. August, V. Brusic, S. Ranganathan. Prediction of HLA-DQ3.2beta ligands: Evidence of multiple registers in class II binding peptides. Bioinformatics, 22(10):1232--1238, May 2006.
  51. J. C. Tong, T. W. Tan, A. A. Sinha, S. Ranganathan. Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6- associated Pemphigus vulgaris. BMC Bioinformatics, 7(Suppl 5):S7, December 2006.
  52. F. Y. Teng, B. L. Tang. Axonal regeneration in adult CNS neurons---signaling molecules and pathways. J. Neurochem., 96(6):1501--1508, 2006.
  53. Y. Wang, and B. L. Tang. SNAREs in the brain: Beyond synaptic vesicle exocytosis. Mol. Membr. Biol., 23:377-384, 2006.

  54. Y. Wang, L. Y. Foo, K. Guo, B. Q. Gan, Q. Zeng, W. Hong, B. L. Tang. Syntaxin9 is enriched in skin hair follicle epithelium and interacts with the epidermal growth factor receptor. Traffic, 7(2):216--226, February 2006.
  55. Y. Wang, E. L. Ng, B. L. Tang. Rab23: What exactly does it traffic? Traffic, 7(6):746--750, June 2006.
  56. L.J.K. Wee, T.W. Tan, S. Ranganathan. SVM-based prediction of caspase substrate cleavage sites . BMC Bioinformatics, 7(Suppl 5):S14, December 2006.
  57. 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.
  58. 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, November 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.
  7. 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, pages 109-119, Taipei, Taiwan, February 2006.
  8. Ket Fah Chong, Hon Wai Leong. An Extension of Dead End Elimination for Protein Side-Chain Conformation Using Merge-Decoupling. Proc. 21st ACM Symposium on Applied Computing (SAC), pages 195--199, Dijon, France, April 2006.
  9. Aaron E. Darling, Todd J. Treangen, Louxin Zhang, Carla Kuiken, Xavier Messeguer, Nicole T. Perna. Procrastination Leads to Efficient Filtration for Local Multiple Alignment. Proceedings of 6th International Workshop on Algorithms in Bioinformatics (WABI), pages 126-137, Zurich, Switzerland, Septmber 2006.
  10. Minmei Hou, Piotr Berman, Louxin Zhang, Webb Miller. Controlling Size When Aligning Multiple Genomic Sequences with Duplications. pages 138-149, Zurich, Switzerland, Septmber 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. Ming Li, Bin Ma, Louxin Zhang. Superiority and complexity of the spaced seeds. Proceedings of 17th ACM-SIAM Symposium on Discrete Algorithms, pages 444-453, 2006.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Kang Ning, Ket Fah Chong, Hon Wai Leong. A Database Search Algorithm for Identification of Peptides with Multiple Charges Using Tandem Mass Spectrometry. Proceedings of PAKDD2006 Workshop on Data Mining for Biomedical Applications, pages 2--13, April 2006.
  22. Kang Ning, Hon Nian Chua. Automated Identification of Protein Classification and Detection of Annotation Errors in Protein Databases Using Statistical Approaches. Proceedings of PAKDD2006 Workshop on Knowledge Discovery in Life Science Literature, pages 123--138, Singapore, April 2006.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. Yun Zheng, Chee Keong Kwoh. Informative MicroRNA Expression Patterns for Cancer Classification. Proceedings of PAKDD2006 Workshop on Data Mining for Biomedical Applications, pages 143-154, April 2006.

  2005

• Books

  1. V.B. Bajic, T.W. Tan, editors. Information Processing and Living Systems, Imperial College Press, 2005. (800 pages)
  2. Yi-Ping Phoebe Chen, Limsoon Wong, editors. Proceedings of the 3rd Asia-Pacific Bioinformatics Conference, Imperial College Press, London, 2005. (384 pages)
  3. M.-Y. Leung, T. Speed and L. Zhang, editors. Statistical Methods in Microarray Data Analysis, World Scientific, 2005.

• 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.
  2. T.W. Tan, K.H. Choo, J.C. Tong, M.T. Tammi, V.B. Bajic. Biological Databases and Web Services: Metrics for Quality. Information Processing and Living Systems, edited by V.B. Bajic and T.W. Tan, chapter 16, pages 771--777. Imperial College Press, 2005.

• Journal papers

  1. T. Allander, M.T. Tammi, M. Eriksson, A. Bjerkner, A. Tiveljung-Lindell, B. Andersson. Cloning of a human parvovirus by molecular screening of respiratory tract samples. PNAS USA, 102(36):12891-12896, 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. Choo KH, Tan TW, Ranganathan S. SPdb: A signal peptide database. BMC Bioinformatics, 6:249, 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. Bin Cui, Beng Chin Ooi, Jianwen Su, Kian-Lee Tan. Indexing High-Dimensional Data for Efficient In-Memory Similarity Search. IEEE Trans. Knowl. Data Eng., 17(3):339-353, 2005.
  8. N.M. El-Sayed, P.J. Myler, D.C. Bartolomeu, D. Nilsson, G. Aggarwal, et al. The Genome Sequence of Trpanosoma cruzi, Etiologic Agent of Chagas Disease. Science, 309(5733):409-415, 2005.
  9. H. V. Jagadish, Beng Chin Ooi, Kian-Lee Tan, Cui Yu, Rui Zhang. iDistance: An adaptive B+-tree based indexing method for nearest neighbor search. ACM Trans. Database Syst., 30(2):364-397, 2005.
  10. Jesper Jansson, Joseph H. K. Ng, Kunihiko Sadakane, Wing-Kin Sung. Rooted Maximum Agreement Supertrees. Algorithmica, 43(4):293--307, 2005.
  11. Liping Ji, Kian-Lee Tan. Identifying time-lagged gene clusters using gene expression data. Bioinformatics, 21(4):509-516, 2005.
  12. 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.
  13. Y. Kong, J. H. Han. MicroRNA: Biological and Computational Perspective. Genomics, Proteomics, and Bioinformatics, 3:62-72, 2005.
  14. Y. Kong. Extension of Goulden-Jackson cluster method on pattern occurrences in random sequences and comparison with Regnier-Szpankowski method. J. Difference Equ. Appl., 11:1265-1271, 2005.
  15. W. Leong, F. P. Preparata, W. K. Sung, and H. Willy. On the control of hybridization noise in DNA Sequencing-by-Hybridization. Journal of Bioinformatics and Computational Biology, 3(1):79-98, 2005.
  16. Ming-Ying Leung, Kwok Pui Choi, Aihua Xia, Louis H.Y. Chen. Nonrandom Clusters of Palindromes in Herpesvirus Genomes . Journal of Computational Biology, 12(3):331-354, April 2005.
  17. Guoliang Li, Tze-Yun Leong, Louxin Zhang. Translation Initiation Sites Prediction with Mixture Gaussian Models. IEEE Transactions on Knowledge and Data Engineering, 17(8):1152-1160, 2005.
  18. Jinyan Li, Limsoon Wong. Structural Geography of the Space of Emerging Patterns. Intelligent Data Analysis, 9(6):567--588, 2005.
  19. L. Li, B.L. Tang. Environmental enrichment and neurodegenerative diseases. Biochem. Biophys. Res. Commun., 334:293--297, 2005.
  20. Q. Li, B.T.K. Lee and L. Zhang. Genome-scale analysis of positional clustering of mouse testis-specific genes, BMC genomics, 6:7, 2005.
  21. 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.
  22. Huiqing Liu, Jinyan Li, Limsoon Wong. Use of Extreme Patient Samples for Outcome Prediction from Gene Expression Data. Bioinformatics, 21(16):3377--3384, 2005.
  23. 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.
  24. 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.
  25. 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.
  26. C. Thach Nguyen, Y. C. Tay, Louxin Zhang. Divide-and-conquer approach for the exemplar breakpoint distance, Bioinformatics, 21(10):2171-2176, 2005.
  27. 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.
  28. 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.
  29. Franco P. Preparata, Louxin Zhang, Kwok Pui Choi. Quick, Practical Selection of Effective Seeds for Homology Search. Journal of Computational Biologyw, 12(9):1137-1152, November 2005.
  30. 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.
  31. B.L. Tang. Alzheimer's disease: Channeling APP to non-amyloidogenic processing. Biochem. Biophys. Res. Commun., 331:375--378, 2005.
  32. B.L. Tang, Y. Wang, Y.S. Ong, and W. Hong. COPII and exit from the endoplasmic reticulum. Biochim. Biophys. Acta, 1744:293--303, 2005.
  33. F.Y.H. Teng, and B.L. Tang. Why do Nogo/Nogo-66 receptor gene knockouts not result in superior regeneration compared to treatment with neutralizing agents? J. Neurochem., 94:865--874, 2005.
  34. F.Y.H. Teng, B.L. Tang. APC/C functions in postmitotic neurons: The Liprin-a connections. Cell. Mol. Life Sci., 62:1571--1578, 2005.
  35. F.Y.H. Teng, B.L. Tang. No go for brain tumors? J. Mol. Neurosci., 25:1--6, 2005.
  36. F.Y.H. Teng, B.L. Tang. Widespread g-secretase activity in the cell, but do we need it at the mitochondria? Biochem. Biophys. Res. Commun., 328:1--5, 2005.
  37. F.Y.H. Teng, B.L. Tang. Nogo signaling and non-physical injury induced neuronal pathology. J. Neurosci. Res., 79:273--278, 2005.
  38. 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.
  39. Y. Wang, G. Tai, L. Johannes, W. Hong, and B.L. Tang. Trans-Golgi network syntaxin 10 functions distinctly from syntaxins 6 and 16. Mol. Membr. Biol., 22:313--325, 2005.
  40. D. Zhang, L. K. Tai, L. L. Wong, L. L. Chiu, S. K. Sethi, E. S. Koay. Proteomic study reveals that proteins involved in metabolic and detoxification pathways are highly expressed in HER-2/neu-positive breast cancer. Mol. Cell Proteomics, 4(11):1686--1696, 2005.
  41. D. H. Zhang, L. L. Wong, L. K. Tai, E. S. Koay, R. E. Hewitt. Overexpression of CC3/TIP30 is associated with HER-2/neu status in breast cancer. J. Cancer Res. Clin. Oncol., 131(9):603--608, 2005.
  42. Ji Zhang, Wynne Hsu, Mong-Li Lee. Clustering in Dynamic Spatial Databases. J. Intell. Inf. Syst., 24(1):5-27, 2005.
  43. Yongluan Zhou, Beng Chin Ooi, Kian-Lee Tan, Wee Hyong Tok. An adaptable distributed query processing architecture. Data Knowl. Eng., 53(3):283-309, 2005.

• Conference papers

  1. 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.
  2. 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.
  3. 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.
  4. Yee Seng Chan, Hwee Tou Ng. Scaling Up Word Sense Disambiguation via Parallel Texts. Proceedings of 20th National Conference on Artificial Intelligence, pages 1037-1042, Pittsburgh, PA, July 2005.
  5. Yee Seng Chan, Hwee Tou Ng. Word Sense Disambiguation with Distribution Estimation. Proceedings of 19th International Joint Conference on Artificial Intelligence, pages 1010-1015, Edinburgh, Scotland, August 2005.
  6. Rajesh Chowdhary, R. Ayesha Ali, Vladimir B. Bajic. Modeling 5' regions of histone genes using Bayesian networks. Proceedings of 3rd Asia-Pacific Bioinformatics Conference, Singapore, pages 283-288, January 2005.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. Zheng Ping Jiang, Jia Li, Hwee Tou Ng. Semantic Argument Classification Exploiting Argument Interdependence. Proceedings of 19th International Joint Conference on Artificial Intelligence, pages 1067-1072, Edinburgh, Scotland, August 2005.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. X.-L. Li, S.-H. Tan, S.-K. Ng. Exploring Cross-Function Domain Interaction Map. Proceedings of 2005 International Joint Conference of InCoB, AASBi and KSBI (BIOINFO 2005), Busan, Korea, September 22-24, 2005, pages 431-436.
  19. X-L. Li, S.-H. Tan, S.-K. Ng. Protein Interaction Prediction Using Inferred Domain Interactions and Biologically-Significant Negative Dataset. Proceedings of International Conference on Computational Science and Its Applications, April 2005, pages 318-326.
  20. 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.
  21. Hwee Tou Ng, Yu Zhou, Robert Dale, Mary Gardiner. A Machine Learning Approach to Identification and Resolution of One-Anaphora. Proceedings of 19th International Joint Conference on Artificial Intelligence, pages 1105-1110, Edinburgh, Scotland, August 2005.
  22. HweeHwa Pang, Arpit Jain, Krithi Ramamritham, Kian-Lee Tan. Verifying Completeness of Relational Query Results in Data Publishing. Proceedings of ACM SIGMOD International Conference on Management of Data, pages 407-418, Baltimore, MD, June 2005.
  23. Thanh Phong Pham, Hwee Tou Ng, Wee Sun Lee. Word Sense Disambiguation with Semi-Supervised Learning. Proceedings of 20th National Conference on Artificial Intelligence, pages 1093-1098, Pittsburgh, PA, July 2005.
  24. J. Tan, K.S. Chua and L. Zhang. Algorithmic and Complexity Issues of Three Clustering Methods in Microarray Data Analysis, Proceedings of 11th International Computing and Combinatorics Conference, pages 74-83, Kunming, China, 2005.
  25. 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.
  26. 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.
  27. 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.