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)

2011

• Journals

  1. S. Aggarwal, I. A. Karimi, D. Y. Lee. Flux-based analysis of sulfur metabolism in desulfurizing strains of Rhodococcus erythropolis. FEMS Microbiol Lett, accepted.
  2. Pramila Nuwantha Ariyaratne, Wing-Kin Sung. PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics, 27(2): 167-174, January 2011.
  3. Ruichu Cai, Anthony Tung, Zhenjie Zhang, Zhifeng Hao. What is Unequal among the Equals? Ranking Equivalent Rules from Gene Expression Data. IEEE Transactions on Knowledge and Data Engineering, accepted.
  4. J. Y. Chan, D. G. Ugrasena, D. W. Lum, Y. Lu, A. E. J. Yeoh. Xenobiotic and folate pathway gene polymorphisms and risk of childhood acute lymphoblastic leukaemia in Javanese children. Hematol Oncol, accepted.
  5. Chen Li, Masao Nagasaki, Chuan Hock Koh, Satoru Miyano. Online model checking approach based parameter estimation to a neuronal fate decision simulation model in C. elegans with HFPNe. Molecular Biosystems, accepted.
  6. J. Cheng, O. S. Yim, P. S. Low, S. K. Tay, E. P. Yap, P. S. Lai. Detection of hemi/homozygotes through heteroduplex formation in high-resolution melting analysis. Anal Biochem, accepted.
  7. W. P. Chong, F. N. Yusufi, D. Y. Lee, S. G. Reddy, N. S. Wong, C. K. Heng, M. G. Yap, Y. S. Ho. Metabolomics-based identification of apoptosis-inducing metabolites in recombinant fed-batch CHO culture media. J Biotechnol, accepted.
  8. S. Guillemot, J. Jansson, W. K. Sung. Computing a Smallest Multi-labeled Phylogenetic Tree from Rooted Triplets. IEEE/ACM Trans Comput Biol Bioinform, accepted.
  9. N. Jiang, G. S. Koh, J. Y. S. Lim, S. K. Y. Kham, H. Ariffin, F. T. Chew, A. E. J. Yeoh. BIM is a prognostic biomarker for early prednisolone response in pediatric acute lymphoblastic leukemia. Exp Hematol, accepted.
  10. Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Chen Li, Limsoon Wong, Satoru Miyano. MIRACH: Efficient Model Checker for Quantitative Biological Pathway Models. Bioinformatics, 27(5):734--735, March 2011.
  11. Guimei Liu, Chern Han Yong, Hon Nian Chua, Limsoon Wong. Decomposing PPI Networks for Complex Discovery. Proteome Science, 9(Suppl. 1):???--???, accepted.
  12. Bin Ma, Louxin Zhang. Efficient Estimation of the Accuracy of the Maximum Likelihood Method for Ancestral State Reconstruction. J Combin Optimization, accepted.
  13. Kang Ning and Hon Wai Leong. The Distribution and Deposition Algorithms for Multiple Sequences Sets Problem. Journal of Combinatorial Optimization, accepted.
  14. Kang Ning, Hoong Kee Ng, Hon Wai Leong. Analysis of the Relationships among Longest Common Subsequences, Shortest Common Supersequences and Patterns and its application on Pattern Discovery in Biological Sequences. International Journal on Data Mining and BioInformatics, accepted.
  15. Wen Lee Tan, Bhaskar Bhattacharya, Marie Chiew Hsia Loh, Indirikumar Balasubramanian, Mohamed Akram, Difeng Dong, Limsoon Wong, Bhavin Thakkar, Manuel Salto-Tellez, Ross Soo, Iduna Fichtner, Barry Iacopetta, Richie Soong. Low cytosine triphosphate synthase 2 expression renders resistance to 5-fluorouracil in colorectal cancer. Cancer Biology & Therapy, 11(6):599--608, March 2011.
  16. Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. eCEO: An efficient Cloud Epistasis cOmputing model in genome-wide association study. Bioinformatics, 27(8):1045--1051, April 2011.
  17. H. Widiastuti, J. Y. Kim, S. Selvarasu, I. A. Karimi, H. Kim, J. S. Seo, D. Y. Lee. Genome-scale modeling and in silico analysis of ethanologenic bacteria Zymomonas mobilis. Biotechnol Bioeng, accepted.
  18. Min Wu, Xiaoli Li, Chee-Keong Kwoh, See-Kiong Ng, Limsoon Wong. Discovery of Protein Complexes with Core-Attachment Structures from TAP Data. Journal of Computational Biology, accepted.
  19. Tianyou Zhang, Xiuju Fu, Chee Keong Kwoh, Gaoxi Xiao, Limsoon Wong, Stefan Ma, Harold Soh, Gary Kee Khoon Lee, Terence Hung, Michael Lees. Temporal Factors in School Closure Policy for Mitigating the Spread of Influenza. Journal of Public Health Policy, 32(2):180--197, May 2011.
  20. Liang Zhao, Limsoon Wong, Jinyan Li. Antibody-specific B-cell epitope prediction in line with the principle of context-awareness. IEEE/ACM Transactions on Computational Biology and Bioinformatics, accepted.

• Conference Papers

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

  2010

• Books

  1. Wing-Kin Sung. Algorithms in Bioinformatics: A Practical Introduction. CRC Press, London, January 2010.

• Journals

  1. Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong. Compressed Indexes for Approximate String Matching. Algorithmica, 58(2):263--281, October 2010.
  2. Y. Chen, B. Q. Gan, B. L. Tang. Syntaxin 16: Unraveling cellular physiology through a ubiquitous SNARE molecule. J Cell Physiol, 225(2):326--332, November 2010.
  3. Carol Cheung, Wynne Hsu, Mong Li Lee, Jie Jin Wang, Paul Mitchell, Qiangfeng Peter Lau, Haslina Hamzah, Maisie Ho and Tien Yin Wong. A New Method to Measure Peripheral Retinal Vascular Caliber over an Extended Area. Microcirculation, 17(7):495--503, October 2010.
  4. Juxin Chin, Geoffrey Koh, Dong-Yup Lee. How necessary is a fast testkit for mitigation of pandemic flu?. Journal of the Royal Society Interface, 7(48):1033--1047, July 2010.
  5. W. P. Chong, S. G. Reddy, F. N. Yusufi, D. Y. Lee, N. S. Wong, C. K. Heng, M. G. Yap, Y. S. Ho. Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth: Overexpression of malate dehydrogenase II. J Biotechnol, 147(2):116--121, May 2010.
  6. Rajesh Chowdhary, Vladimir B. Bajic, Difeng Dong, Limsoon Wong, Jun S. Liu. Genome-wide analysis of regions similar to promoters of histone genes. BMC Systems Biology, 4(Suppl 1):S4, May 2010.
  7. C. E. Chua, Y. S. Lim, B. L. Tang. Rab35--a vesicular traffic-regulating small GTPase with actin modulating roles. FEBS Lett, 584(1):1-6, January 2010.
  8. B. K. S. Chung, S. Selvarasu, C. Andrea, J. Ryu, H. Lee, J. Ahn, H. Lee, D. Y. Lee. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement. Microbial Cell Factories, 9:50, July 2010.
  9. Victoria Cosatto, Gerald Liew, Elena Rochtchina, Alain Wainwright, Yong Ping Zhang, Wynne Hsu, Mong Li Lee, Peter Lau, Haslina Hamzah, Paul Mitchell, Tien Yin Wong, Jie Jin Wang. Retinal Vascular Fractal Dimension Measurement and its Influence from Imaging Variation: Results of Two Segmentation Methods. Current Eye Research, 35(9):850--856, September 2010.
  10. Daniel Dahlmeier, Hwee Tou Ng. Domain adaptation for semantic role labeling in the biomedical domain. Bioinformatics, 26(8):1098--1104, April 2010.
  11. Mengling Feng, Guozhu Dong, Jinyan Li, Yap-Peng Tan, Limsoon Wong. Pattern Space Maintenance for Data Updates. Computational Intelligence, 26(3):282--317, August 2010.
  12. B. Q. Gan, B. L. Tang. Sirt1’s beneficial roles in neurodegenerative diseases - a chaperonin containing TCP-1 (CCT) connection? Aging Cell, 9(5):924--929, October 2010.
  13. J. Gruber, S. K. Poovathingal, S. Schaffer, L. F. Ng, R. Gunawan, B. Halliwell. Caenorhabditis elegans life span studies: The challenge of maintaining synchronous cohorts. Rejuvenation Res, 13(2-3):347--349, April 2010.
  14. Mahnaz Habibi, Changiz Eslahchi, Limsoon Wong. Protein Complex Prediction based on k-Connected Subgraphs in Protein Interaction Network. BMC Systems Biology, 4:129, September 2010.
  15. C. H. Hor, B. L. Tang. Sonic hedgehog as a chemoattractant for adult NPCs. Cell Adh Migr, 4(1):1-3, January 2010.
  16. Chuan Hock Koh, Masao Nagasaki, Ayumu Saito, Limsoon Wong, Satoru Miyano. DA 1.0: Parameter Estimation of Biological Pathways Using Data Assimilation Approach. Bioinformatics, 26(14):1794--1796, July 2010.
  17. Fook Choon Lee, Gade Pandu Rangaiah, Dong-Yup Lee. Modeling and optimization of a multi-product biosynthesis factory for multiple objectives. Metabolic Engineering, 12(3):251--267, May 2010.
  18. Wah Heng Lee, Chee Wee Koh, Yang Sun Chan, Pauline Poh Kim Aw, Kuan Hon Loh, Bing Ling Han, Pei Ling Thien, Geraldine Yi Wen Nai, Martin Hibberd, Christopher Wong, Wing-Kin Sung. Large Scale Evolutionary Surveillance of the 2009 H1N1 Influenza A Virus Using Resequencing Arrays. Nucleic Acids Research, 38(9):e111, May 2010.
  19. V. J. Lee, J. Yap, A. R. Cook, M. I. Chen, J. Tay, B. H. Tan, J. P. Loh, S. W. Chew, W. H. Koh, R. Lin, L. Cui, W. H. Lee, W. K. Sung, C. W. Wong, M. L. Hibberd, W. L. Kang, B. Seet, P. A. Tambyah. Oseltamivir ring prophylaxis for containment of Influenza A (H1N1-2009) outbreaks. New England Journal of Medicine, 362(23):2166--2174, June 2010.
  20. S. M. Leong, B. X. Tan, B. Bte Ahmad, T. Yan, L. Y. Chee, S. T. Ang, K. G. Tay, L. P. Koh, A. E. J. Yeoh, E. S. Koay, Y. K. Mok, T. M. Lim. Mutant nucleophosmin deregulates cell death and myeloid differentiation through excessive caspase-6 and -8 inhibition. Blood, 116(17):3286--3296, October, 2010.
  21. Guoliang Li, Melissa J. Fullwood, Fabianus Hendriyan Mulawadi, Stoyan Velkov, Han Xu, Vinsensius B. Vega, Pramila Nuwantha Ariyaratne, Yusoff Bin Mohamed, Hong-Sain Ooi, Chandana Tennakoon, Chia-Lin Wei, Yijun Ruan and Wing-Kin Sung. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biology, 11(2):R22, February 2010.
  22. Guoliang Li, Jian Ma, Louxin Zhang. Greedy Selection of Species for Ancestral State Reconstruction on Phylogenies: Elimination Is Better than Insertion. PLoS One, 5(2):e8985, February 2010.
  23. Haitao Li, Paul Mitchell, Gerald Liew, Elena Rochtchina, Annette Kifley, Tien Yin Wong, Wynne Hsu, Mong Li Lee, Yong Ping Zhang, Jie Jin Wang. Lens Opacity and Refractive Influences on the Measurement of Retinal Vascular Fractal Dimension. Acta Ophthalmologica, 88(6):e234--e240, September 2010.
  24. Li Lin, Limsoon Wong, Tze-Yun Leong, Poh San Lai. Efficient Mining of Haplotype Patterns for Linkage Disequilibrium Mapping. Journal of Bioinformatics and Computational Biology, 8(Suppl. 1):127--146, December 2010.
  25. Guimei Liu, Yue Wang, Limsoon Wong. FastTagger: An Efficient Algorithm for Genome-wide Tag SNP Selection Using Multi-marker Linkage Disequilibrium. BMC Bioinformatics, 11:66, February 2010.
  26. J. Meng, W. Xia, J. Tang, B. L. Tang, F. Liang. Dephosphorylation-dependent inhibitory activity of juxtanodin on filamentous actin disassembly. J Biol Chem, 285(37):28838--28849, September 2010.
  27. T. Nandi, C. Ong, A. P. Singh, J. Boddey, T. Atkins, M. Sarkar-Tyson, A. E. Essex-Lopresti, H. H. Chua, T. Pearson, J. F. Kreisberg, C. Nilsson, P. Ariyaratne, C. Ronning, L. Losada, Y. Ruan, W. K. Sung, D. Woods, R. W. Titball, I. Beacham, I. Peak, P. Keim, W. C. Nierman, P. Tan. A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence. PLoS Pathog, 6(4):41000845, April 2010.
  28. V. Narang, A. Mittal, W. K. Sung. Localized Motif Discovery in Gene Regulatory Sequences. Bioinformatics, 26(9):1152--1159, May 2010.
  29. Hoong Kee Ng, Kang Ning, Hon Wai Leong. Two-phase Filtering Strategy for Efficient Peptide Identification from Mass Spectrometry. Journal of Proteomics & Bioinformatics, 3:121--129, April 2010.
  30. Kang Ning, Hoong Kee Ng, Sriganesh Srihari, Hon Wai Leong, Alexey Nesvizhskii. Examination of the Relationship between Essential Genes in PPI Network and Hub Proteins in Reverse Nearest Neighbor Topology. BMC Bioinformatics, 11:505, October 2010.
  31. Y. S. Ong, B. L. Tang, L. S. Loo, W. Hong. p125A exists as part of the mammalian Sec13/Sec31 COPII subcomplex to facilitate ER-Golgi transport. J Cell Biol, 190(3):331--345, August 2010.
  32. S. K. Poovathingal, R. Gunawan. Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics, 11:414, August 2010.
  33. W. J. Qin, O. S. Yim, P. S. Lai, L. Y. Yung. Dimeric gold nanoparticle assembly for detection and discrimination of single nucleotide mutation in Duchenne muscular dystrophy. Biosens Bioelectron, 25(9):2021--2025, May 2010.
  34. Muhammad Sasongko, Jie Jin Wang, Kim Donaghue, Ning Cheung, Paul Benitez-Aguirre, Alicia Jenkins, Wynne Hsu, Mong Li Lee, Tien Yin Wong. Alterations in Retinal Microvascular Geometry in Young Type 1 Diabetes. Diabetes Care, 33(6):1331--1336, June 2010.
  35. S. Selvarasu, I. A. Karimi, G. H. Ghim, D. Y. Lee. Genome-scale modeling and in silico analysis of mouse cell metabolic network. Molecular Biosystems, 6(1):152--161, January 2010.
  36. S. Selvarasu, D. Y. Kim, I. A. Karimi, D. Y. Lee. Combined data preprocessing and multivariate statistical analysis characterizes fed-batch culture of mouse hybridoma cells for rational medium design. J Biotechnol, 150(1):94--100, October 2010.
  37. Donglai Sheng, Dianbo Qu, Ken Hon Hung Kwok, Seok Shin Ng, Adrian Yin Ming Lim, Charlie Wah Heng Lee, Wing Kin Sung, Eng King Tan, Lufkin Thomas, Suresh Jesuthasan, Mathavan Sinnakaruppan, Jianjun Liu. Deletion of the WD40 domain of LRRK2 in zebrafish causes Parkinsonism-like loss of neurons and locomotive defect. PLoS Genetics, 6(4):e1000914, April 2010.
  38. BM Sim, N Chantratita, WF Ooi, T Nandi, R Tewhey, V Wuthiekanun, J Thaipadungpanit, S Tumapa, P Ariyaratne, WK Sung, XH Sem, HH Chua, K Ramnarayanan, CH Lin, Y Liu, EJ Feil, MB Glass, G Tan, SJ Peacock, P Tan. Genomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates. Genome Biology, 11(8):R89, August 2010.
  39. Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Consistency, Comprehensiveness, and Compatibility of Pathway Databases. BMC Bioinformatics, 11:449, September 2010.
  40. Giltae Song, Louxin Zhang, Tomas Vinar, Webb Miller. CAGE: Combinatorial Analysis of Gene-cluster Evolution. Journal of Computational Biology, 17(9):1227--1242, 2010.
  41. Sriganesh Srihari, Kang Ning and Hon Wai Leong. MCL-CAw: A refinement of MCL for detecting yeast complexes from weighted PPI networks by incorporating core-attachment structure. BMC Bioinformatics, 11:504, October 2010.
  42. S. Srinath, R. Gunawan. Parameter identifiability of power-law biochemical system models. J Biotechnol, 149(3):132--140, September 2010.
  43. Z. Y. Tam, Y. H. Cai, R. Gunawan. Elucidating cytochrome C release from mitochondria: Insights from an in silico three-dimensional model. Biophysical Journal, 99(10):3155--3163, November 2010.
  44. T. W. Tan, J. C. Tong, A. M. Khan, M. de Silva, K. S. Lim, S. Ranganathan. Advancing standards for bioinformatics activities: Persistence, reproducibility, disambiguation and Minimum Information About a Bioinformatics investigation (MIABi). BMC Genomics, 11(Suppl. 4):S27, December 2010.
  45. B. L. Tang. Is Rab25 a tumor promoter or suppressor--context dependency on RCP status? Tumour Biol, 31(4):359--361, August 2010.
  46. B. L. Tang. Sirt1 and cell migration. Cell Adh Migr, 4(2):163--165, April 2010.
  47. B. L. Tang, C. E. Chua. Is systemic activation of Sirt1 beneficial for ageing-associated metabolic disorders? Biochem Biophys Res Commun, 391(1):6-10, January 2010.
  48. F. Y. Teng, B. L. Tang. NF-kappaB signaling in neurite growth and neuronal survival. Rev Neurosci, 21(4):299-313, 2010.
  49. Alan Wainwright, Gerald Liew, George Burlutsky, Elena Rochtchina, Yong Ping Zhang, Wynne Hsu, Mong Li Lee, Tien Yin Wong, Paul Mitchell, Jie Jin Wang. Effect of Image Quality, Color and Format on the Measurement of Retinal Vascular Fractal Dimension. Investigative Ophthalmology and Visual Science, 51(11):5525--5529, November 2010.
  50. Y. Wang, Y. Lu, S. T. Toh, W. K. Sung, P. Tan, P. Chow, A. Y. Chung, L. L. Jooi, C. G. Lee. Lethal-7 is down-regulated by the hepatitis B virus x protein and targets signal transducer and activator of transcription 3. J Hepatol, 53(1):57--66, July 2010.
  51. Hugo Willy, Fushan Song, Zeyar Aung, See-Kiong Ng, Wing-Kin Sung. SLiM on DIet: Finding Short Linear Motifs on Domain Interaction Interfaces in PDB Bioinformatics, 26(8):1036--1042, April 2010.
  52. Limsoon Wong, Guimei Liu. Protein Interactome Analysis for Countering Pathogen Drug Resistance. Journal of Computer Science and Technology, 25(1):124--130, January 2010.
  53. T. K. Wong, T. W. Lam, W. K. Sung, S. M. Yiu. Adjacent nucleotide dependence in ncRNA and order-1 SCFG for ncRNA identification. PLoS One, 5(9):e12848, September 2010.
  54. H. Xu, L. Handoko, X. Wei, C. Ye, J. Sheng, C. L. Wei, F. Lin, W. K. Sung. A Signal-Noise Model for Significance Analysis of ChIP-seq with Negative Control. Bioinformatics, 26(9):1199--1204, May 2010.
  55. A. E. J. Yeoh, Y. Lu, J. Y. Chan, Y. H. Chan, H. Ariffin, S. K. Kham, T. C. Quah. Genetic susceptibility to childhood acute lymphoblastic leukemia shows protection in Malay boys: Results from the Malaysia-Singapore ALL Study Group. Leuk Res, 34(3):276--283, March 2010.
  56. Louxin Zhang, Jian Shen, Jialiang Yang, Guoliang Li. Analyzing the Fitch Method for Reconstructing Ancestral States on Ultrametric Phylogenetic Trees. Bulletin of Mathematical Biology, 72(7):1760--1782. October 2010.
  57. Melvin Zhang, Hon Wai Leong. Bidirectional Best Hit r-Window Gene Clusters. BMC Bioinformatics, 11(Suppl 1):S63, January 2010.
  58. Jie Zhou, Gaoxi Xiao, Limsoon Wong, Xiuju Fu, Stefan Ma, Tee Hiang Cheng. Generation of arbitrary two-point-correlated directed networks with given modularity. Physics Letters A, 374(31-32):3129--3135, July 2010.

• Conference papers

  1. Marzieh Ayati, Golnaz Taheri, Shahriar Arab, Limsoon Wong, Changiz Eslahchi. Overcoming Drug Resistance by Co-Targeting. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 198--201, Hong Kong, December 2010.
  2. Songbo Huang, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Siu-Ming Yiu. Indexing Similar DNA Sequences. Proceedings of 6th International Conference on Algorithmic Aspects in Information and Management (AAIM), pages 180--190, Weihai, China, July 2010.
  3. Jesper Jansson, Wing-Kin Sung. Constructing the R* Consensus Tree of Two Trees in Subcubic Time. Proceedings of 18th Annual European Symposium on Algorithms (ESA), part I, pages 573-584, Liverpool, UK, September 2010.
  4. Guimei Liu, Chern Han Yong, Hon Nian Chua, Limsoon Wong. Decomposing PPI Networks for Complex Discovery. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 280--283, Hong Kong, December 2010.
  5. Thanh-Son Ngo, Mengling Feng, Guimei Liu, Limsoon Wong. Efficiently finding the best parameter for the emerging pattern-based classifier PCL. Proceedings of 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Part I, pages 121--133, Hyderabad, India, June 2010.
  6. Chang Sheng, Wynne Hsu, Mong Li Lee, Joo Chuan Tong, See-Kiong Ng. Mining Mutation Chains in Biological Sequences. Proceedings of 26th IEEE International Conference on Data Engineering (ICDE), pages 473--484, Long Beach, California, March 2010.
  7. Sriganesh Srihari, Shruti Chandrashekar, Srinivasan Parthasarathy. A Framework for SQL-Based Mining of Large Graphs on Relational Databases. Proceedings of 14th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), Part II, pages 160--167, Hyderabad, India, June 2010.
  8. D. M. Tay, K. R. Govindarajan, A. M. Khan, T. Y. Ong, H. M. Samad, W. W. Soh, M. Tong, F. Zhang, T. W. Tan. T3SEdb: Data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. BMC Bioinformatics, 11(Suppl. 7):S4, October 2010.
  9. Zhengkui Wang, Yue Wang, Kian-Lee Tan, Limsoon Wong, Divyakant Agrawal. CEO: A Cloud Epistasis cOmputing model in GWAS. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 85--90, Hong Kong, December 2010.
  10. Michal Wozniak, Limsoon Wong, Jerzy Tiuryn. CAMBer: An Approach to Support Comparative Analysis of Multiple Bacterial Strains. Proceedings of 4th IEEE International Conference on Bioinformatics & Biomedicine, pages 121--126, Hong Kong, December 2010.

  2009

• Book chapters

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

• Journals

  1. L. Aung, Y. H. Chan, E. J. Yeoh, P. L. Tan, T. C. Quah. Retinoblastoma: A recent experience at the National University Hospital, Singapore Ann Acad Med Singapore, 38(8):693--698, August 2009.
  2. Ning Cheung, Kim Donaghue, Gerald Liew, Sophie Rogers, Jie Jin Wang, Shueh-Wen Lim, Alicia Jenkins, Wynne Hsu, Mong Li Lee, Tien Yin Wong. Quantitative Assessment of Early Diabetic Retinopathy Using Fractal Analysis. Diabetes Care, 32:106--110, January 2009.
  3. W.J. Chia, B.L. Tang. Emerging roles for Rab family GTPases in human cancer. Biochim Biophys Acta, 1795(2):110--116, April 2009.
  4. W. P. Chong, L. T. Goh, S. G. Reddy, F. N. Yusufi, D. Y. Lee, N. S. Wong, C. K. Heng, M. G. Yap, Y. S. Ho. Metabolomics profiling of extracellular metabolites in recombinant Chinese Hamster Ovary fed-batch culture. Rapid Communications in Mass Spectrometry, 23(23):3763--3771, December 2009.
  5. K. H. Choo, T. W. Tan, S. Ranganathan. A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics, 10(Suppl. 15):S2, December 2009.
  6. Hon Nian Chua, Willy Hugo, Guimei Liu, Xiaoli Li, Limsoon Wong, See-Kiong Ng. A Probabilistic Graph-Theoretic Approach to Integrate Multiple Predictions for the Protein-Protein Subnetwork Prediction Challenge. Annals of New York Academy of Sciences, 1158:224-233, March 2009.
  7. B. K. Chung, D. Y. Lee. Flux-sum analysis: A metabolite-centric approach for understanding the metabolic network. BMC Systems Biology, 3:117, December 2009.
  8. F. De Santa, V. Narang, Z. H. Yap, B. K. Tusi, T. Burgold, L. Austenaa, G. Bucci, M. Caganova, S. Notarbartolo, S. Casola, G. Testa, W. K. Sung, C. L. Wei, G. Natoli. Jmjd3 contributes to the control of gene expression in LPS-activated macrophages. EMBO Journal, 28(21):3341--3352, November 2009.
  9. Frank Eisenhaber, Chee-Keong Kwoh, See-Kiong Ng, Wing-Kin Sung, Limsoon Wong. Brief Overview of Bioinformatics Activities in Singapore. PLoS Computational Biology, 5(9):e1000508, September 2009.
  10. M. J. Fullwood, M. H. Liu, Y. F. Pan, J. Liu, H. Xu, Y. B. Mohamed, Y. L. Orlov, S. Velkov, A. Ho, P. H. Mei, E. G. Chew, P. Y. Huang, W. J. Welboren, Y. Han, H. S. Ooi, P. N. Ariyaratne, V. B. Vega, Y. Luo, P. Y. Tan, P. Y. Choy, K. D. Wansa, B. Zhao, K. S. Lim, S. C. Leow, J. S. Yow, R. Joseph, H. Li, K. V. Desai, J. S. Thomsen, Y. K. Lee, R. K. Karuturi, T. Herve, G. Bourque, H. G. Stunnenberg, X. Ruan, V. Cacheux-Rataboul, W. K. Sung, E. T. Liu, C. L. Wei, E. Cheung, Y. Ruan. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature, 462(7269):58--64, November 2009.
  11. Sylvain Guillemot, Jesper Jansson, Wing-Kin Sung. Computing a Smallest Multi-labeled Phylogenetic Tree from Rooted Triplets. Proceedings of 20th International Symposium on Algorithms and Computation (ISAAC), pages 1205--1214, Honolulu, Hawaii, December 2009.
  12. R. Hewitt, P.H. Watson, R. Dhir, R. Aamodt, G. Thomas, D. Mercola, W.E. Grizzle, M.M. Morente. Timing of consent for the research use of surgically removed tissue: Is postoperative consenting acceptable? Cancer, 115(1):4--9, January 2009.
  13. Wen-Son Hsieh, Ross Soo, Bee-Keow Peh, Thomas Loh, Difeng Dong, Donny Soh, Limsoon Wong, Simon Green, Judy Chiao, Chun-Ying Cui, Yoke-Fong Lai, Soo-Chin Lee, Benjamin Mow, Richie Soong, Manuel Salto-Tellez, Boon-Cher Goh. Pharmacodynamic Effects of Seliciclib, an Orally Administered Cell Cycle Modulator, in Undifferentiated Nasopharyngeal Cancer. Clinical Cancer Research, 15(4):1435--1442, February 2009.
  14. Wing-Kai Hon, Kunihiko Sadakane, Wing-Kin Sung. Breaking a Time-and-Space Barrier in Constructing Full-Text Indices. SIAM J. Comput., 38(6):2162--2178, February 2009.
  15. J. Jia, J. Cui, X. Liu, J. Han, S. Yang, Y. Wei, Y. Chen. Genome-scale search of tumor-specific antigens by collective analysis of mutations, expressions and T-cell recognition. Mol Immunol, 46(8-9):1824--1829, May 2009.
  16. S. K. Kham, C. K. Soh, D. C. Aw, A. E. J. Yeoh. TPMT*26 (208F-->L), a novel mutation detected in a Chinese. Br J Clin Pharmacol, 68(1):120--123, July 2009.
  17. S. Kharkwal, I. A. Karimi, M. W. Chang, D. Y. Lee. Strain improvement and process development for biobutanol production. Recent Patents on Biotechnol, 3(3):202--210, 2009.
  18. Chuan Hock Koh, Sharene Lin, Gregory Jedd, Limsoon Wong. Sirius PSB: A Generic System for Analysis of Biological Sequences. Journal of Bioinformatics and Computational Biology, 7(6):973--990, December 2009.
  19. Q.Y. Koo, A.M. Khan, K.O. Jung, S. Ramdas, O. Miotto, T.W. Tan, V. Brusic, J. Salmon, J.T. August. Conservation and variability of West Nile virus proteins. PLoS ONE, 4(4):e5352, April 2009.
  20. D. Y. Lee, R. Saha, F. N. Yusufi, W. Park, I. A. Karimi. Web-based applications for building, managing and analysing kinetic models of biological systems. Brief Bioinform, 10(1):65-74, January 2009.
  21. W.H. Lee, V. Narang, H. Xu, F. Lin, K.C. Chin, W.K. Sung. DREAM2 Challenge: Integrated Multi-Array Supervised Learning Algorithm for BCL6 Transcriptional Targets Prediction. Annals of New York Academy of Sciences, 1158:196-204, March 2009.
  22. H. C. M. Leung, M. H. Siu, S. M. Yiu, F. Y. L. Chin, W. K. Sung. Clustering-Based Approach for Predicting Motif Pairs from Protein Interaction Data. Journal of Bioinformatics and Computational Biology, 7(4):701--716, August 2009.
  23. S. J. Lim, A. M. Khan, M. De Silva, K. S. Lim, Y. Hu, C. H. Tan, T. W. Tan. The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: A case study in the National University of Singapore. BMC Bioinformatics, 10(Suppl. 15):S12, December 2009.
  24. Guimei Liu, Limsoon Wong, Hon Nian Chua. Complex Discovery from Weighted PPI Networks. Bioinformatics, 25(15):1891--1897, August 2009.
  25. Guimei Liu, Kelvin Sim, Jinyan Li, Limsoon Wong. Efficient Mining of Distance-Based Subspace Clusters. Statistical Analysis and Data Mining, 2(5):427--444, December 2009.
  26. K.Y. Loke, L.K. Poh, W.W. Lee, P.S. Lai. A case of X-linked adrenal hypoplasia congenita, central precocious puberty and absence of the DAX-1 gene: implications for pubertal regulation. Horm Res, 71(5):298--304, May 2009.
  27. H. C. Muh, J. C. Tong, M. T. Tammi. AllerHunter: A SVM-pairwise system for assessment of allergenicity and allergic cross-reactivity in proteins. PLoS One, 4(6):e5861, June 2009.
  28. E. L. Ng, J. J. Ng, F. Liang, B. L. Tang. Rab22B is expressed in the CNS astroglia lineage and plays a role in epidermal growth factor receptor trafficking in A431 cells. J Cell Physiol, 221(3):716--728, December 2009.
  29. Y.K. Ng, W. Wu, L.X. Zhang. Positive correlation between gene coexpression and positional clustering in the zebrafish genome. BMC Genomics, 10:42, January 2009.
  30. Y.G. Oh, D.Y. Lee, S.Y. Lee, S. Park. Multiobjective flux balancing using the NISE method for metabolic network analysis. Biotechnol. Prog., 25(4):999--1008, July 2009.
  31. 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., 25(1):61-67, January 2009.
  32. T. M. Perumal, Y. Wu, R. Gunawan. Dynamical analysis of cellular networks based on the Green's function matrix. J Theor Biol, 261(2):248--259, November 2009.
  33. S. K. Poovathingal, J. Gruber, B. Halliwell, R. Gunawan. Stochastic drift in mitochondrial DNA point mutations: A novel perspective ex silico. PLoS Comput Biol, 5(11):e1000572, November 2009.
  34. K. Priya, S.R. Jada, B.L. Quah, T.C. Quah, P.S. Lai. High incidence of allelic loss at 16q12.2 region spanning RBL2/p130 gene in retinoblastoma. Cancer Biol Ther, 8(8):714--717, April 2009.
  35. Z.A. Pramono, C.L. Tan, I.A. Seah, J.S. See, S.Y. Kam, P.S. Lai, W.C. Yee. Identification and characterisation of human dysferlin transcript variants: Implications for dysferlin mutational screening and isoforms. Hum Genet, 125(4):413--420, May 2009.
  36. S. Ranganathan, F. Eisenhaber, J. C. Tong, T. W. Tan. Extending Asia Pacific bioinformatics into new realms in the "-omics" era. BMC Genomics, 10(Suppl. 3):S1, December 2009.
  37. S. Selvarasu, V. V. Wong, I. A. Karimi, D. Y. Lee. Elucidation of metabolism in hybridoma cells grown in fed-batch culture by genome-scale modeling. Biotechnol Bioeng, 102(5):1494--1504, April 2009.
  38. S. Selvarasu, D. S. Ow, S. Y. Lee, M. M. Lee, S. K. Oh, I. A. Karimi, D. Y. Lee. Characterizing Escherichia coli DH5alpha growth and metabolism in a complex medium using genome-scale flux analysis. Biotechnol Bioeng, 102(3):923--934, February 2009.
  39. Wing-Kin Sung, Yiwei Lu, Charlie W.H. Lee, Dongwei Zhang, Mostafa Ronaghi, Caroline G.L. Lee. Deregulated direct targets of the hepatitis B viral (HBV) protein, HBx, identified through chromatin immunoprecipitation and expression microarray profiling. Journal of Biological Chemistry, 284(33):21941--21954, August 2009.
  40. T. W. Tan, S. J. Lim, A. M. Khan, S. Ranganathan. A proposed minimum skill set for university graduates to meet the informatics needs and challenges of the "-omics" era. BMC Genomics, 10(Suppl. 3):S36, December 2009.
  41. B. L. Tang. SIRT1's complex roles in neuroprotection. Cell Mol Neurobiol, 29(8):1093--1103, December 2009.
  42. B.L. Tang, E.L. Ng. Rabs and cancer cell motility. Cell Motil Cytoskeleton, 66(7):365-370, July 2009.
  43. B.L. Tang. Neuronal protein trafficking associated with Alzheimer disease: From APP and BACE1 to glutamate receptors. Cell Adh Migr, 3(1):118--128, January 2009.
  44. B. L. Tang. REST regulation of neural development: From outside-in?. Cell Adh Migr, 3(2):1--2, April 2009.
  45. F.Y. Teng, C.H. Hor, B.L. Tang. Emerging cues mediating astroglia lineage restriction of progenitor cells in the injured/diseased adult CNS. Differentiation, 77(2):121--127, February 2009.
  46. J.C. Tong, S.J. Lim, H.C. Muh, F.T. Chew, M.T. Tammi. Allergen Atlas: A comprehensive knowledge center and analysis resource for allergen information. Bioinformatics, 25(7):979--980, April 2009.
  47. V.B. Vega, E. Cheung, N. Palanisamy, W.K. Sung. Inherent Signals in Sequencing-Based Chromatin-Immunoprecipitation Control Libraries. PLoS ONE, 4(4):e5241, April 2009.
  48. Yubo Wang, Gaoxi Xiao, Jie Hu, Tee Hiang Cheng, Limsoon Wong. Imperfect Targeted Immunization in Scale-Free Networks. Physica A: Statistical Mechanics and its Applications, 388(12):2535--2546, June 2009.
  49. L. J. Wee, J. C. Tong, T. W. Tan, S. Ranganathan. A multi-factor model for caspase degradome prediction. BMC Genomics, 10(Suppl. 3):S6, December 2009.
  50. C. Xie, M.T. Tammi. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics, 10:80, March 2009.
  51. M. Xu, M. Zhu, L. X. Zhang. Positive correlation between gene coexpression and positional clustering in the zebrafish genome. BMC Genomics, 10:42, January 2009.
  52. Y. Yang, K. S. Lee, C. Xiang, H. Lin. Biological mechanisms revealed by a mathematical model for p53-Mdm2 core regulation. IEE Transactions on Systems Biology, 3(4):229--238, 2009.
  53. F.N. Yusufi, W. Park, M.M. Lee, D.Y. Lee. An alpha-numeric code for representing N-linked glycan structures in secreted glycoproteins. Bioprocess Biosyst Eng, 32(1):97--107, January 2009.
  54. Melvin Zhang, Hon Wai Leong. Gene Team Tree: A Hierarchical Representation of Gene Teams of All Gap Lengths. Journal of Computational Biology, 16(10):1383--1398, October 2009.
  55. F. Zhu, L. Han, C. Zheng, B. Xie, M. Tammi, S. Yang, Y. Wei, Y. Chen. What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical and systems profiles of successful targets. J Pharmacol Exp Ther, 330(1):304-315, July 2009.

• Conference papers

  1. Jin Chen, Liping Ji, Wynne Hsu, Kian-Lee Tan, Seung Y. Rhee. Exploiting Domain Knowledge to Improve Biological Significance of Biclusters with Key Missing Genes. Proceedings of 25th International Conference on Data Engineering (ICDE 2009), pages 1219--1222, Shanghai, China, March 2009.
  2. Difeng Dong, Chun-Ying Cui, Benjamin Mow, Limsoon Wong. Deciphering Drug Action and Escape Pathways: An Example on Nasopharyngeal Carcinoma. Proceedings of 1st International Conference on Bioinformatics and Computational Biology (BICOB2009), pages 199--210, New Orleans, USA, 8-10 April 2009.
  3. Xiuju Fu, Sonja Lim, Lipo Wang, Gary Lee, Stefan Ma, Limsoon Wong, Gaoxi Xiao. Key Node Selection for Containing Infectious Disease Spread Using Particle Swarm Optimization. Proceedings of IEEE Swarm Intelligence Symposium 2009, pages 109--113, Nashville, USA, 29 March-2 April 2009.
  4. Sriganesh Srihari, Kang Ning, Hon Wai Leong. Refining Markov Clustering for Protein Complex Prediction by Incorporating Core-Attachment Structure. Proceedings of 20th International Conference on Genome Informatics (GIW), pages 159--168, Yokohama, Japan, December 2009.
  5. Yubo Wang, Jie Hu, Gaoxi Xiao, Limsoon Wong, Stefan Ma, Tee Hiang Cheng. A Preliminary Study on the Effects of Fear Factors in Disease Propagation. Proceedings of 1st International Conference on Complex Sciences: Theory and Applications (Complex'2009), pages 1387-1397, Shanghai, China, 23-25 February 2009.
  6. Thomas K.F. Wong, S.M. Yiu, T.W. Lam, Wing-Kin Sung. The 2-Interval Pattern Matching Problems and its Application to ncRNA Scanning. Proceedings of 1st International Conference on Bioinformatics and Computational Biology (BICOB2009), pages 79--89, New Orleans, USA, 8-10 April 2009.
  7. Xin Xu, Ying Lu, Kian-Lee Tan, Anthony K. H. Tung. Finding Time-Lagged 3D Clusters. Proceedings of 25th International Conference on Data Engineering (ICDE 2009), pages 445--456, Shanghai, China, March 2009.

  2008

• Books

  1. Kun Mao Chao, Louxin Zhang. Sequence Comparison: Theory and Method, Springer, Berlin, November 2008. (232 pages).
  2. Hon Wai Leong, Wing-Kin Sung, Eleazar Eskin. Proceedings of 3rd Annual RECOMB Workshop on Regulatory Genomics, Imperial College Press, London, December 2008 (130 pages).
  3. Martin Vingron, Limsoon Wong. Proceedings of 12th Annual International Conference on Research in Computational Molecular Biology, Springer, Berlin, March 2008. (480 pages).

• Book chapters

  1. Bhaskar DasGupta, Xin He, Tao Jiang, Ming Li, John Tromp, Louxin Zhang. Nearest Neighbor Interchange and Related Distances. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.
  2. Wing-Kin Sung. Constructing a Galled Phylogenetic Network. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.
  3. Wing-Kin Sung. Indexed Approximate String Matching. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.
  4. Wing-Kin Sung. Maximum Agreement Supertree. Encyclopedia of Algorithms, edited by Ming-Yang Kao, chapter ?, pages ???--???, Springer, October 2008.

• 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., 18(11):1773-1784, November 2008.
  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. Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Prudence W. H. Wong, S. M. Yiu. Non-overlapping Common Substrings Allowing Mutations. Mathematics in Computer Science, 1(4):543--555, June 2008.
  4. 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.
  5. 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.
  6. Christelle En Lin Chua, Bor Luen Tang. SIRT2, tubulin deacetylation, and oligodendroglia differentiation. Cell Motility and the Cytoskeleton, 65(3):179-182, March 2008.
  7. 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.
  8. Hon Nian Chua, Limsoon Wong. Increasing the Reliability of Protein Interactomes. Drug Discovery Today, 13(15/16):652--658, August 2008.
  9. 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.
  10. 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.
  11. X. Hou, W.W. Hu, L. Shen, L.Y. Lee, Z. Tao, J.H. Han, H. Yu. Global identification of DELLA target genes during Arabidopsis flower development. Plant Physiol, 147(3):1126--1142, July 2008.
  12. K. Ibrahim, S. S. Daud, Y. L. Seah, A. E. Yeoh, H. Ariffin. Rapid detection of prognostically important childhood acute lymphoblastic leukemia chimeric transcripts using multiplex SYBR green real-time reverse transcription PCR. Ann Clin Lab Sci, 38(4):338-343, Autumn 2008.
  13. P. Kathirvel, W.P. Yu, B. Venkatesh, C.C. Lim, P.S. Lai, W.C. Yee. Fugu rubripes and human survival motor neuron genes: Structural and functional similarities in comparative genome studies. Gene, 424(1-2):108--114, November 2008.
  14. 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, 2(8):e272, August 2008.
  15. S. K. Kham, C. K. Soh, T. C. Liu, Y. H. Chan, H. Ariffin, P. L. Tan, A. E. Yeoh. Thiopurine S-methyltransferase activity in three major Asian populations: a population-based study in Singapore. Eur J Clin Pharmacol, 64(4):373-379, April 2008.
  16. A. Kohlmann, T.J. Kipps, L.Z. Rassenti, J.R. Downing, S.A. Shurtleff, K.I. Mills, A.F. Gilkes, W.K. Hofmann, G. Basso, M.C. Dellorto, R. Foa, S. Chiaretti, J. De Vos, S. Rauhut, P.R. Papenhausen, J.M. Hernandez, E. Lumbreras, A.E.-J. Yeoh, E.S. Koay, R. Li, W.M. Liu, P.M. Williams, L. Wieczorek, T. Haferlach. An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: The Microarray Innovations in Leukemia study prephase. Br J Haematol, 142(5):802--807, September 2008.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. G. L. Li, M. Steel, L. X. Zhang. More Taxa Are Not Necessarily Better for the Reconstruction of Ancestral Character States. Systematic Biol, 57(4):647-653, August 2008.
  22. 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, 3(5):543--554, November 2008.
  23. S.J. Lim, J.C. Tong, F.T. Chew, M.T. Tammi. The value of position-specific scoring matrices for assessment of protein allegenicity. BMC Bioinformatics, 9(Suppl 12):S21, December 2008.
  24. Gerald Liew, Jie Jin Wang, Ning Cheung, Yong Ping Zhang, Wynne Hsu, Mong Li Lee, Paul Mitchell, Gabriella Tikellis, Bronwen Taylor, Tien Yin Wong. The Retinal Vasculature as a Fractal: Methodology, Reliability and Relationship to Blood Pressure. Ophthalmology, 11(5):1951--1956, November 2008.
  25. C. Liu, H. Chen, H.L. Er, H.M. Soo, P.P. Kumar, J.H. Han, Y.C. Liou, H. Yu. Direct interaction of AGL24 and SOC1 integrates flowering signals in Arabidopsis. Development, 135(8):1481--1491, April 2008.
  26. Guimei Liu, Jinyan Li, Limsoon Wong. A New Concise Representation of Frequent Itemsets Using Generators and a Positive Border. Knowledge and Information Systems, 17(1):35--56, October 2008.
  27. 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.
  28. Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler. DUPCAR: Reconstructing contiguous ancestral regions with duplications. Journal of Computational Biology, 15(8):1007-1027, October 2008
  29. 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.
  30. 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.
  31. 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.
  32. 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. SIAM J Comput, 38(3):946-962, 2008.
  33. 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.
  34. 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.
  35. S. Ranganathan, M. Gribskov, T. W. Tan. Bioinformatics research in the Asia Pacific: A 2007 update. BMC Bioinformatics, 9(Suppl 1):S1, February 2008.
  36. S. Ranganathan, W.L. Hsu, U.C. Yang, T.W. Tan. Emerging strengths in Asia Pacific bioinformatics. BMC Bioinformatics, 9(Suppl 12):S1, December 2008.
  37. 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.
  38. B. L. Tang. Leptin as a neuroprotective agent. Biochem. Biophys. Res. Commun., 368(2):181-185, April 2008.
  39. B. L. Tang. Emerging aspects of neuronal membrane traffic in dendritic growth. Biochim. Biophys. Acta, 1783(2):169-176, February 2008.
  40. B. L. Tang, C. E. Chua. SIRT1 and neuronal diseases. Mol. Aspects Med., 29(3):187--200, June 2008.
  41. B. L. Tang, R. Kumar. Biomarkers of mild cognitive impairment and Alzheimer's disease. Ann Acad Med Singapore, 37(5):406-410, May 2008.
  42. S.K. Tay, S. Dimauro, A.Y. Pang, P.S. Lai, H.K. Yap. Myotoxicity of lipid-lowering agents in a teenager with MELAS mutation. Pediatr Neurol, 39(6):426--428, December 2008.
  43. F. Y. Teng, B. L. Tang. Nogo-A and Nogo-66 receptor in amyotrophic lateral sclerosis. J. Cell. Mol. Med., 12(4):1199-1204, August 2008.
  44. 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.
  45. 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.
  46. 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.
  47. K.B. Wee, Z. A. Pramono, J. L. Wang, K. F. MacDorman, P. S. Lai, W. C. Yee. Dynamics of co-transcriptional pre-mRNA folding influences the induction of dystrophin exon skipping by antisense oligonucleotides. PLoS One, 3(3):e1844, March 2008.
  48. 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.
  49. 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.
  50. M. Xu, M. Zhu, L. Zhang. A stable iterative method for refining discriminative gene clusters . BMC Genomics, 9(Suppl 2):S18, September 2008.
  51. J. L. Yang, L. X. Zhang. Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds. Journal of Computational Biology, 15(10):1295-1313, 2008.
  52. 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.
  53. 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.
  54. 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.
  55. Yongping Zhang, Wynne Hsu, Mong Li Lee. Detection of retina blood vessels based on nonlinear projections. Journal of Signal Processing Systems, 55(1-3):103--112, June 2008.
  56. J. Zhou, J. Khng, V. J. Jasinghe, C. Bi, C. H. Neo, M. Pan, L. F. Poon, Z. Xie, H. Yu, A. E. Yeoh, Y. Lu, K. B. Glaser, D. H. Albert, S. K. Davidsen, C. S. Chen. In vivo activity of ABT-869, a multi-target kinase inhibitor, against acute myeloid leukemia with wild-type FLT3 receptor. Leuk Res, 32(7):1091-1100, 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. Viet Tung Hoang, Wing-Kin 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. Shuai Cheng Li, Yen Kaow Ng, Louxin Zhang. A PTAS for the k-Consensus Structures Problem under Euclidean Squared Distance. 2nd Annual International Workshop on Frontiers in Algorithmics (FAW), pages 35-44, Changsa, China, 19-21 June 2008.
  6. 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.
  7. Guimei Liu, Jinyan Li, Limsoon Wong. Assessing and Predicting Protein Interactions Using Both Local and Global Network Topological Metrics. Proceedings of 19th International Conference on Genome Informatics (GIW), pages 138--149, Gold Coast, Australia, 1-3 December 2008.
  8. 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 1--4, Tampa, Florida, USA, 8-11 December 2008.
  9. 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.
  10. 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.
  11. 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.
  12. 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 100--112, Paris, France, 13-15 Oct 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.