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

2023

• Journal Papers

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

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

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

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

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

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

  2022

  • Journal Papers

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

    2. Wilson Wen Bin Goh, Reuben Jyong Kiat Foo, Limsoon Wong. What can scatterplots teach us about doing data science better?. International Journal of Data Science and Analytics, accepted.

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

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

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

    6. Tian Lan, Gyorgy Hutvagner, Xuan Zhang, Tao Liu, Limsoon Wong, Jinyan Li. Density-based detection of cell transition states to construct disparate and bifurcating trajectories. Nucleic Acids Research, accepted.

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

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

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

    10. Qiangwei Zhou, Pengpeng Guan, Zhixian Zhu, Sheng Cheng, Cong Zhou, Huanhuan Wang, Qian Xu, Wing-Kin Sung, Guoliang Li. ASMdb: A comprehensive database for allele-specific DNA methylation in diverse organisms. Nucleic Acids Research, 50(D1):D60-D71, January 2022.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Structural variation calling and its application in understanding large indels in 1047 Arabidopsis. Invited keynote at 1st International and 10th National Iranian Conference on Bioinformatics (ICB10), Kish Island, Iran, 22-24 February 2022.

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

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

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

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

  2021

  • Journal Papers

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

    2. Lingling Hu, Xin Chen, Nitin Narwade, Michelle Gek Liang Lim, Zikai Chen, Chandana Tennakoon, Peiyong Guan, Un In Chan, Zuxianglan Zhao, Mokan Deng, Xiaoling Xu, Wing-Kin Sung, Edwin Cheung. Single-cell analysis reveals androgen receptor regulates the ER-to-Golgi trafficking pathway with CREB3L2 to drive prostate cancer progression. Oncogene, 40(47):6479-6493, November 2021.

    3. Jiawen Huang, Mahekta R. Gujar, Qiannan Deng, Sook Y. Chia, Song Li, Patrick Tan, Wing-Kin Sung, Hongyan Wang. Histone lysine methyltransferase Pr-set7/SETD8 promotes neural stem cell reactivation. EMBO Report, 22(4):e50994, April 2021.

    4. Jesper Jansson, Konstantinos Mampentzidis, Ramesh Rajaby, Wing-Kin Sung. Computing the Rooted Triplet Distance Between Phylogenetic Networks. Algorithmica, 83(6):1786--1828, 2021.

    5. Fan Jiang, Yaoxin Jiang, Wenxuan Wang, Changyi Xiao, Ruiyi Lin, Tanghui Xie, Wing-Kin Sung, Shijun Li, Ivan Jakovlic, Jianhai Chen, Xiaoyong Du. A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. BMC Genomics, 22(1):581, July 2021.

    6. Fan Jiang, Ruiyi Lin, Changyi Xiao, Tanghui Xie, Yaoxin Jiang, Jianhai Chen, Pan Ni, Wing-Kin Sung, Jianlin Han, Xiaoyong Du, Shijun Li. Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations. Genetic Selection Evolution, 53(1):35, April 2021.

    7. Dong-Xu Liu, Ramesh Rajaby, Lu-Lu Wei, Lei Zhang, Zhi-Quan Yang, Qing-Yong Yang, Wing-Kin Sung. Calling large indels in 1047 Arabidopsis with IndelEnsembler. Nucleic Acids Research, 49(19):10879-10894, November 2021.

    8. Sanjay De Mel, Jonathan Adam Scolnik, Chern Han Yong, Xiaojing Huo, Stacy Xu, Cinnie Yentia Soekojo, Fangfang Song, Melissa Ooi, Wee Joo Chng. Single cell multi-omics profiling of multiple myeloma with t(4;14) finds an immune microenvironment gene signature that correlates with clinical outcomes. Blood, 138(Suppl. 1):2653, November 2021.

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

    10. Ramesh Rajaby, Wing-Kin Sung. SurVIndel: improving CNV calling from high-throughput sequencing data through statistical testing. Bioinformatics, 37(11):1497--1505, July 2021.

    11. Ramesh Rajabi, Yi Zhou, Yifan Meng, Xi Zeng, Guoliang Li, Peng Wu, Wing-Kin Sung. SurVirus: A repeat-aware virus integration caller. Nucleic Acids Research, 49(6):e33, April 2021.

    12. M. Sohel Rahman, Kunihiko Sadakane, Wing-Kin Sung. Guest editors' foreword. J. Graph Algorithms Appl., 25(2):603-604, 2021.

    13. Anik Sarker, Wing-Kin Sung, M. Sohel Rahman. A linear time algorithm for the r-gathering problem on the line. Theoretical Computer SCience, 866:96--106, 2021.

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

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

    16. Na Yao, Fuchuan Ni, Ziyan Wang, Jun Luo, Wing-Kin Sung, Chaoxi Luo, Guoliang Li. L2MXception: An improved Xception network for classification of peach diseases. Plant Methods, 17(1):36, April 2021.

    17. Liang Xie, Minghao Liu, Lun Zhao, Kai Cao, Peng Wang, Wenhao Xu, Wing-Kin Sung, Xingwang Li, Guoliang Li. RiceENCODE: A comprehensive epigenomic database as a rice Encyclopedia of DNA Elements. Mol Plant, 14(10):1604-1606, October 2021.

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

    19. Xi Zeng, Linghao Zhao, Chenhang Shen, Yi Zhou, Guoliang Li, Wing-Kin Sung. HIVID2: An accurate tool to detect virus integrations in the host genome. Bioinformatics, 37(13):1821--1827, July 2021.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Revisit the problem of virus integration calling using next generation sequencing. Invited talk at 11th International Conference on Bioscience, Biochemistry and Bioinformaics (ICBBB2021), Tokyo, Japan, 9-12 January 2021.

  2020

  • Books

    1. M. Sohel Rahman, Kunihiko Sadakane, Wing-Kin Sung. Proceedings of 14th International Conference on Algorithms and Computation (WALCOM2020), Springer, March 2020.

  • Journal Papers

    1. Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Wing-Kin Sung, Steven Watts. Efficient identification of k-closed strings. Int. J. Found. Comput. Sci., 31(5):595--610, 2020.

    2. Mai Alzamel, Panagiotis Charalampopoulos, Costas S. Iliopoulos, Solon P. Pissis, Jakub Radoszewski, Wing-Kin Sung. Faster algorithms for 1-mappability of a sequence. Theoretical Computer Science, 812:2-12, April 2020.

    3. Canhui Cao, Ping Hong, Xingyu Huang, Da Lin, Gang Cao, Liming Wang, Bei Feng, Ping Wu, Hui Shen, Qian Xu, Ci Ren, Yifan Meng, Wenhua Zhi, Ruidi Yu, Juncheng Wei, Wencheng Ding, Xun Tian, Qinghua Zhang, Wei Li, Qinglei Gao, Gang Chen, Kezhen Li, Wing-Kin Sung, Zheng Hu, Hui Wang, Guoliang Li, Peng Wu. HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer. Journal of Genetics and Genomics, 47(8):437--450, August 2020.

    4. Jason Yongsheng Chan, Jing Quan Lim, Joe Yeong, Vinod Ravi, Peiyong Guan, Arnoud Boot, Timothy Kwang Yong Tay, Sathiyamoorthy Selvarajan, Nur Diyana Md Nasir, Jie Hua Loh, Choon Kiat Ong, Dachuan Huang, Jing Tan, Zhimei Li, Cedric Chuan-Young Ng, Thuan Tong Tan, Mikio Masuzawa, Ken Wing-Kin Sung, Mohamad Farid, Richard Hong Hui Quek, Ngian Chye Tan, Melissa Ching Ching Teo, Steven George Rozen, Patrick Tan, Andrew Futreal, Bin Tean Teh, Khee Chee Soo. Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma. J Clin Invest, 130(11):5833-5846, Novemver 2020.

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

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

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

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

    9. Weihua Ma, Xianxin Zhao, Chuanlin Yin, Fan Jiang, Xiaoyong Du, Taiyu Chen, Qinghua Zhang, Lin Qiu, Hongxing Xu, J. Joe Hull, Guoliang Li, Wing-Kin Sung, Fei Li, Yongjun Lin. A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis. Molecular Ecology Resources, 20(1):268--282, January 2020.

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

    11. Ramesh Rajaby, Wing-Kin Sung. SurVIndel: Improving CNV calling from high-throughput sequencing data through statistical testing. Bioinformatics, accepted.

    12. Runbin Tang, Zuguo Yu, Yuanlin Ma, Yi-Ping Phoebe Chen, Limsoon Wong, Jinyan Li. Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning. Bioinformatics, accepted.

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

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

    15. Qiangwei Zhou, Ze Wang, Jing Li, Wing-Kin Sung, Guoliang Li. MethHaplo: Combining allele-specific DNA methylation and SNPs for haplotype region identification. BMC Bioinformatics, 21(1):451, October 2020.

  • Conference Papers

    1. Mustafa Umit Oner, Hwee Kuan Lee, Wing-Kin Sung. Weakly Supervised Clustering by Exploiting Unique Class Count. 8th International Conference on Learning Representations (ICLR2020), Addis Ababa, Ethiopia, April 2020.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Improving CNV calling from high-throughput sequencing data through statistical testing. Invited talk at 10th International Conference on Bioscience, Biochemistry, and Bioinformatics (ICBBB2020), Kyoto, Japan, 19-22 January 2020.

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

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

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

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

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

  2019

  • Journal Papers

    1. Mai Alzamel, Costas S. Iliopoulos, W. F. Smyth, Wing-Kin Sung. Off-line and on-line algorithms for closed string factorization. Theoretical Computer Science, 792:12--19, November 2019.

    2. S. Fanucchi, E. T. Fok, E. Dalla, Y. Shibayama, K. Börner, E. Y. Chang, S. Stoychev, M. Imakaev, D. Grimm, K. C. Wang, G. Li, W. K. Sung, M. M. Mhlanga. Immune genes are primed for robust transcription by proximal long noncoding RNAs located in nuclear compartments. Nature Genetics, 51(1):138--150, January 2019.

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

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

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

    6. Fanchang Hao, Melvin Zhang, Hon Wai Leong. A 2-approximation algorithm for sorting signed permutations by reversals, transpositions, transreversals, and block-interchanges, IEEE/ACM Transaction on Computational Biology and Bioinformatics, 16(5):1702--1711, September 2019.

    7. Jesper Jansson, Ramesh Rajaby, and Wing-Kin Sung. An efficient algorithm for the rooted triplet distance between galled trees. Journal of Computational Biology, 26(9):893--907, September 2019.

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

    9. Yu Jin, Wai Yeow Lee, Soo Ting Toh, Chandana Tennakoon, Han Chong Toh, Pierce Kah-Hoe Chow, Alexander Y.-F. Chung, Samuel S. Chong, London L.-P.-J. Ooi, Wing-Kin Sung, Caroline G.-L. Lee. Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma. Journal of Translational Medicine, 17(1):273, August 2019.

    10. Z. Zhang, K. R. Chng, S. Lingadahalli, Z. Chen, M. H. Liu, H. H. Do, S. Cai, N. Rinaldi, H. M. Poh, G. Li, Y. Y. Sung, C. L. Heng, L. J. Core, S. K. Tan, X. Ruan, J. T. Lis, M. Kellis, Y. Ruan, W. K. Sung, E. Cheung. An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells. Genome Research, 29(2):223--235, February 2019.

    11. Yingjie Zhang, Chwee Tat Koe, Ye Sing Tan, Joses Ho, Patrick Tan, Fengwei Yu, Wing-Kin Sung, Hongyan Wang. The integrator complex prevents dedifferentiation of intermediate neural progenitors back into neural stem cells. Cell Reports, 27(4):987--996, April 2019.

    12. Lun Zhao, Shuangqi Wang, Zhilin Cao, Weizhi Ouyang, Qing Zhang, Liang Xie, Ruiqin Zheng, Minrong Guo, Meng Ma, Zhe Hu, Wing-Kin Sung, Qifa Zhang, Guoliang Li, Xingwang Li. Chromatin loops associated with active genes and heterochromatin shape rice genome architecture for transcriptional regulation. Nature Communications, 10(1):3640, August 2019.

    13. Qiangwei Zhou, Jing Quan Lim, Wing Kin Sung, Guoliang Li. An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. BMC Bioinformatics, 20(1):47, January 2019.

  • Conference Papers

    1. Jesper Jansson, Konstantinos Mampentzidis, Ramesh Rajaby, Wing-Kin Sung. Computing the Rooted Triplet Distance Between Phylogenetic Networks. Proceedings of 30th International Workshop on Combinatorial Algorithms (IWOCA2019), pages 290--303, Pisa, Italy, July 2019.

    2. Anik Sarker, Wing-Kin Sung, M. Sohel Rahman. A linear time algorithm for the r-gathering problem on the line. Proceedings of 13th International Conference on Algorithms and Computation (WALCOM2019), pages 56-66, Guwahati, India, February 2019.

    3. Wing-Kin Sung. Greedy consensus tree and maximum greedy consensus tree problems. Proceedings of 13th International Conference on Algorithms and Computation (WALCOM2019), pages 305-316, Guwahati, India, February 2019.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Finding structural variations in repeat regions using high-throughput sequencing data. Invited talk at Workshop on Bioinformatics and Data Analysis, Xian Jiaotong University, June 2019.

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

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

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

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

  2018

  • Books

    1. Costas S. Iliopoulos, Hon Wai Leong, Wing-Kin Sung. Proceedings of 29th International Workshop on Combinatorial Algorithms (IWOCA 2018). Springer, July 2018.

    2. M. Sohel Rahman, Wing-Kin Sung, Ryuhei Uehara. Proceedings of 12th International Conference on Algorithms and Computation (WALCOM 2018). Springer, March 2018.

  • Book chapters

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

  • Journal Papers

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

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

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

    4. Jesper Jansson, Ramesh Rajaby, Chuanqi Shen, Wing-Kin Sung. Algorithms for the majority rule (+) consensus tree and the frequency difference consensus tree. IEEE/ACM Transactions on Compututational Biology and Bioinformatics, 15(1):15--26, January 2018.

    5. J. Jansson, A. Lingas, R. Rajaby, W. K. Sung. Determining the consistency of resolved triplets and fan triplets. Journal of Computational Biology, 25(7):740--754, July 2018.

    6. Bing-Xin Lu, Hon Wai Leong. GI-Cluster: Detecting genomic islands via consensus clustering on multiple features. Journal of Bioinformatics and Computational Biology, 16(3):1840010, June 2018.
    7. Stefano Perna, Pietro Pinoli, Stefano Ceri, Limsoon Wong. TICA: Transcriptional interaction and coregulation analyzer. Genomics, Proteomics & Bioinformatics, 16(5):342--353, October 2018.

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

    9. R. Rajaby, W. K. Sung. TranSurVeyor: An improved database-free algorithm for finding non-reference transpositions in high-throughput sequencing data. Nucleic Acids Research, 46(20):e122, November 2018.

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

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

  • Conference Papers

    1. Pawel Gawrychowski, Gad M. Landau, Wing-Kin Sung, Oren Weimann. A faster construction of greedy consensus trees. Proceedings of 45th ICALP, article 63, Prague, Czech Republic, July 2018.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing Kin Sung. Fast, sensitive and accurate detection of virus integrations in cancer. Keynote at 8th International Conference on Bioscience, Biochemistry, and Bioinformatics (ICBBB), Tokyo, Japan, 18 - 20 January 2018

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

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

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

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

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

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

  2017

  • Books

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

    2. Wing-Kin Sung. Algorithms for Next-Generation Sequencing, CRC Press, Boca Raton, FL, April 2017. (346 pages)

  • Journal Papers

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

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

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

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

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

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

    7. Jesper Jansson, Ramesh Rajaby. A more practical algorithm for the rooted triplet distance. Journal of Computational Biology, 24(2):106-126, February 2017.

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

    9. Song Li, Chwee Tat Koe, Su Ting Tay, Angie Lay Keng Tan, Shenli Zhang, Yingjie Zhang, Patrick Tan, Wing-Kin Sung, Hongyan Wang. An intrinsic mechanism controls reactivation of neural stem cells by spindle matrix proteins. Nature Communications, 8:122, July 2017.

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

    11. Bing-Xin Lu, Louxin Zhang, Hon Wai Leong. A program to compute soft Robinson-Foulds distance between phylogenetic networks. BMC Genomics, 18(Suppl 2):111, March 2017.

    12. Felix H. Shek, Ruibang Luo, Brian Y. H, Lam, Wing-Kin Sung, Tak-Wah Lam, John M. Luk, Ming Sum Leung, Kin Tak Chan, Hector K. Wang, Chung Man Chan, Ronnie T. Poon, Nikki P. Lee. Serine peptidase inhibitor Kazal type 1 (SPINK1) as novel downstream effector of the cadherin-17/beta-catenin axis in hepatocellular carcinoma. Cellular Oncology, 40(5):443--456, October 2017.

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

    14. Chandana Tennakoon, Wing-Kin Sung. BATVI: Fast, sensitive, and accurate detection of virus integrations. BMC Bioinformatics, 18(Suppl 3):71, March 2017.

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

    16. Wanwipa Vongsangnak, Nachon Raethong, Warasinee Mujchariyakul, Nam Ninh Nguyen, Hon Wai Leong, Kobkul Laoteng. Genome-scale metabolic network of Cordyceps militaris useful for comparative analysis of entomopathogenic fungi. Gene, 626:132--139, August 2017.

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

  • Conference Papers

    1. Hayam Alamro, Mai Alzamel, Costas S. Iliopoulos, Solon P. Pissis, Steven Watts, Wing-Kin Sung. Efficient identification of k-closed strings. Proceedings of 18th International Conference on Engineering Applications of Neural Netowkrs (EANN), pages 583--595, Athens, Greece, August 2017.

    2. Mai Alzamel, Panagiotis Charalampopoulos, Costas S. Iliopoulos, Solon P. Pissis, Jakub Radoszewski, Wing-Kin Sung. Faster algorithms for 1-mappability of a sequence. Proceedings of 11th International Conference on Combinatorial Optimization and Applications (COCOA), part II, pages 109--121, Shanghai, China, December 2017.

    3. Jesper Jansson, Andrzej Lingas, Ramesh Rajaby, Wing-Kin Sung. Determining the consistency of resolved triplets and fan triplets. Proceedings of 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 82--98, Hong Kong, 7 May 2017.

    4. Jesper Jansson, Ramesh Rajaby, Wing-Kin Sung. An efficient algorithm for the rooted triplet distance between galled trees. Proceedings of 4th International Conference on Algorithms for Computational Biology (AlCoB), pages 115--126, Aveiro, Portugal, June 2017.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing Kin Sung. Issues on aligning short reads generated by next-generation sequencing. Invited talk at 3rd International Workshop on Innovative Algorithms for Big Data (IABD), Tokyo, Japan, 30 November 2017.

    2. Wing Kin Sung. Methods for constructing phylogenetic consensus tree. Invited talk at 25th London Stringology Days & London Algorithmic Workshop, London, UK, 9 - 10 February 2017.

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

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

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

  2016

  • Book chapters

    1. Jesper Jansson, Wing-Kin Sung. Algorithms for combining rooted triplets into a galled phylogenetic network. Encyclopedia of Algorithms, edited by Ming-Yang Kao, pages 48--52. Springer, 2016.

    2. Jesper Jansson, Wing-Kin Sung. Maximum agreement supertree. Encyclopedia of Algorithms, pages 1224--1227. Springer, 2016.

    3. Wing-Kin Sung. Indexed approximate string matching. Encyclopedia of Algorithms, edited by Ming-Yang Kao, pages 964--968. Springer, 2016.

  • Journal Papers

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

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

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

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

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

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

    7. Peiyong Guan, Wing-Kin Sung. Structural variation detection using next-generation sequencing data: A comparative technical review. Methods, 102:36--49, June 2016.

    8. Andreas D. M. Gunawan, Bingxin Lu, Louxin Zhang. A program for verification of phylogenetic network models. Bioinformatics, 32(17):i503--i510, September 2016.

    9. Jesper Jansson, Wing-Kin Sung, Hoa Vu, Siu-Ming Yiu. Faster algorithms for computing the R* consensus tree. Algorithmica, 76(4):1224--1244, December 2016.

    10. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung. Improved algorithms for constructing consensus trees. Journal of the ACM, 63(3):28, September 2016

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

    12. Bing-Xin Lu, Hon Wai Leong. Computational methods for predicting genomic islands in microbial genomes. Computational and Structural Biotechnology Journal>, 14(1):200--216, February 2016.

    13. Bing-Xin Lu, Hon Wai Leong. GI-SVM: A sensitive method for predicting genomic islands based on unannotated sequence of a single genome. Journal of Bioinformatics and Computational Biology, 14(1):1640003, February 2016.

    14. S. Maurer-Stroh, C. W. Lee, C. Patel, M. Lucero, H. Nohynek, W. K. Sung, C. Murad, J. Ma, M. L. Hibberd, C. W. Wong, E. A. Simões. Comparison of microarray-predicted closest genomes to sequencing for poliovirus vaccine strain similarity and influenza A phylogeny. Diagn Microbiol Infect Dis., 84(3):203--206, March 2016.

    15. Wing Kin Sung. Pan-omics analysis of biological data. Methods, 102:1--2, June 2016.

    16. Shuzhi Yu, Fanchang Hao, Hon Wai Leong. An O(n³) algorithm for sorting signed permutations by reversals, transpositions, transreversals, and block-interchanges. Journal of Bioinformatics and Computational Biology, 14(1):1640002, February 2016.

  • Conference Papers

    1. Jesper Jansson, Wing-Kin Sung. Minimal phylogenetic supertrees and local consensus trees. Proceedings of International Symposium on Foundations of Computer Science (MFCS), article 53, Krakow, Poland, August 2016.

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

  • Invited Keynotes, Talks, & Tutorials

    1. Hon Wai Leong. Algorithms for detecting protein complexes from whole-genome PPI networks, Talk at King's College London, London, UK, 16 June 2016.

    2. Hon Wai Leong. Big data community detection and its applications. Invited talk at 9th China-ASEAN Education Cooperation Week (CAECW), International Exchange Forum on Health Big Data and Green Medical Care, Guizhou Medical University, Guiyang, Guizhou, China, 1-3 August 2016.

    3. Wing-Kin Sung. Calling structural variations by next-generation sequencing. Keynote talk at 27th International Conference on Genome Informatics (GIW), Shanghai, China, 3-5 October 2016.

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

    5. Limsoon Wong. Enabling more sophisticated proteomic profile analysis. Invited talk at the St. Petersburg International Symposium on Systems Biology and Bioinformatics (SBBI2016), St. Petersburg, 30 June - 2 July 2016.

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

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

    8. Limsoon Wong. Improving coverage and consistency of MS-based proteomics. Invited keynote at 16th IEEE International Conference on Bioinformatics and Bioengineering (BIBE2016), Taichung, Taiwan, 31 October - 2 November 2016.

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

  2015

  • Journal Papers

    1. N. Buisine, X. Ruan, P. Bilesimo, A. Grimaldi, G. Alfama, P. Ariyaratne, F. Mulawadi, J. Chen, W. K. Sung, E. T. Liu, B. A. Demeneix, Y. Ruan, L. M. Sachs. Xenopus tropicalis genome re-scaffolding and re-annotation reach the resolution required for in vivo ChIA-PET analysis. PLoS One, 10(9):e0137526, September 2015.

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

    3. Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Linked dynamic tries with applications to LZ-compression in sublinear time and space. Algorithmica, 71(4):969--988, April 2015.

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

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

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

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

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

    9. Jing-Quan Lim, Chandana Tennakoon, Peiyong Guan, Wing-Kin Sung. BatAlign: An incremental method for accurate alignment of sequencing reads. Nucleic Acids Research, 43(16):e107, September 2015.

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

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

    12. Nam Ninh Nguyen, Sriganesh Srihari, Hon Wai Leong, Ket Fah Chong. EnzDP: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles. Journal of Bioinformatics and Computational Biology, 13(5):1543003, October 2015.

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

    14. Dhaval Patel, Wynne Hsu, Mong Li Lee. LinkNet: Capturing temporal dependencies among spatial regions. Distributed and Parallel Databases, 33(2):165--200, June 2015.

    15. S. Ribi, D. Baumhoer, K. Lee, Edison, A. S. M. Teo, B. Madan, K. Zhang, W. K. Kohlmann, F. Yao, W. H. Lee, Q. Hoi, S. Cai, X. Y. Woo, P. Tan, G. Jundt, J. Smida, M. Nathrath, W. K. Sung, J. D. Schiffman, D. M. Virshup, A. M. Hillmer. TP53 intron 1 hotspot rearrangements are specific to sporadic osteosarcoma and can cause Li-Fraumeni syndrome. Oncotarget, 6(10):7727--7740, April 2015.

    16. Wing-Kin Sung, Kunihiko Sadakane, Tetsuo Shibuya, Abha Belorkar, Iana Pyrogova. An O(m, log m)-time algorithm for detecting superbubbles. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12(4):770--777, August 2015.

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

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

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

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

    21. F. Yao, J. P. Kausalya, Y. Y. Sia, A. S. Teo, W. H. Lee, A. G. Ong, Z. Zhang, J. H. Tan, G. Li, D. Bertrand, X. Liu, H. M. Poh, P. Guan, F. Zhu, T. N. Pathiraja, P. N. Ariyaratne, J. Rao, X. Y. Woo, S. Cai, F. H. Mulawadi, W. T. Poh, L. Veeravalli, C. S. Chan, S. S. Lim, S. T. Leong, S. C. Neo, P. S. Choi, E. G. Chew, N. Nagarajan, P. E. Jacques, J. B. So, X. Ruan, K. G. Yeoh, P. Tan, W. K. Sung, W. Hunziker, Y. Ruan, A. M. Hillmer. Recurrent fusion genes in gastric cancer: CLDN18-ARHGAP26 induces loss of epithelial integrity. Cell Reports, 12(2):272--285, July 2015.

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

  • Conference Papers

    1. Jesper Jansson, Zhaoxian Li, Wing-Kin Sung. On finding the Adams consensus tree. Proceedings of 32nd Symposium on Theoretical Aspects of Computer Science (STACS), pages 487--499, Muenchen, Germany, 4-7 March 2015.

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

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Fast and accurate method for detecting virus integrations. Invited talk at 9th Asian Biophysics Association Symposium, Shangyu, China, 10 May 2015.

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

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

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

    5. Limsoon Wong. A novel principle for childhood ALL relapse prediction. Invited talk at 9th Asian Biophysics Association Symposium (ABA2015), Shangyu, China, 11 May 2015.

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

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

  2014

  • Book Chapters

    1. Qiangfeng Peter Lau, Mong Li Lee, Wynne Hsu, Tien Yin Wong. The Singapore eye vessel assessment system, Image Analysis and Modeling in Opthalmology, edited by Eddie Y. K. Ng, U. Rajendra Acharya, Jasjit S. Suri, Aurelio Campilho, chapter 8, pages 143--160, February 2014.

  • Journal Papers

    1. Sung-Min Ahn, Se Jin Jang, Ju Hyun Shim, Deokhoon Kim, Seung-Mo Hong, Chang Ohk Sung, Daehyun Baek, Farhan Haq, Adnan Ahmad Ansari, Sun Young Lee, Sung-Min Chun, Seongmin Choi, Hyun-Jeung Choi, Jongkyu Kim, Sukjun Kim, Shin Hwang, Young-Joo Lee, Jong-eun Lee, Wang-rim Jung, Hye Yoon Jang, Eunho Yang, Wing-Kin Sung, Nikki P. Lee, Mao Mao, Charles Lee, Jessica Zucman-Rossi, Eunsil Yu, Han Chu Lee, Gu Kong. Genomic portrait of resectable hepatocellular carcinomas: Implications of RB1 and FGF19 aberrations for patient stratification. Hepatology, 60(6):1972--1982, December 2014.
    2. Huy Hoang Do, Wing-Kin Sung. CWig: Compressed representation of Wiggle/BedGraph format. Bioinformatics, 30(18):2543--2550, September 2014.

    3. Huy Hoang Do, Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Fast relative Lempel-Ziv self-index for similar sequences. Theoretical Computer Science, 532:14--30, May 2014.

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

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

    6. Julio Fernandez-Banet, Nikki P. Lee, Kin Tak Chan, Huan Gao, Xiao Liu, Wing Kin Sung, Winnie Tan, Sheung Tat Fan, Ronnie T. Poon, Shiyong Li, Keith Ching, Paul Rejto, Mao Mao, Zhengyan Kan. Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma. Genomics, 103(2--3):189--203, February 2014.

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

    8. B. M. Gyori, G. Venkatachalam, P. S. Thiagarajan, D. Hsu, M. V. Clement. OpenComet: An automated tool for comet assay image analysis. Redox Biology, 2(2):457--465, January 2014.

    9. Reza Hassanzadeh, Changiz Eslahchi, Wing-Kin Sung. Do triplets have enough information to construct the multi-labeled phylogenetic tree?. PLoS ONE, 9(7):e103622, July 2014.

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

    11. Chwee Tat Koe, Song Li, Fabrizio Rossi, Jack Jing Lin Wong, Yan Wang, Zhizhuo Zhang, Keng Chen, Sherry Shiying Aw, Helena E Richardson, Paul Robson, Wing-Kin Sung, Fengwei Yu, Cayetano Gonzalez, Hongyan Wang. The Brm-HDAC3-Erm repressor complex suppresses dedifferentiation in Drosophila type II neuroblast lineages. eLife, 3:e01906, March 2014.

    12. Siew Hong Lam, Eei Yin Lui, Zhengjun Li, Shaojiang Cai, Wing-Kin Sung, Sinnakaruppan Mathavan, Toong Jin Lam and Yuen Kwong Ip. Differential transcriptomic analyses revealed genes and signaling pathways involved in iono-osmoregulation and cellular remodeling in the gills of euryhaline Mozambique tilapia, Oreochromis mossambicus. BMC Genomics, 15:921, October 2014.

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

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

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

    16. Nam Ninh Nguyen, Wanwipa Vongsangnak, Bairong Shen, Phi-Vu Nguyen, Hon Wai Leong. Megafiller: A retrofitted protein function predictor for filling gaps in metabolic networks. Journal of Proteomics & Bioinformatics, S9:003, June 2014.

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

    18. Sriganesh Srihari, Venkatesh Raman, Hon Wai Leong, Mark A. Ragan. Evolution and controllability of cancer networks: A Boolean perspective. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(1):83--94, January 2014.

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

    20. George N. Thomas, Shin-Yeu Ong, Yih Chung Tham, Wynne Hsu, Mong Li Lee, Qiangfeng Peter Lau, Wanting Tay, Jessica Alessi-Calandro, Lauren Hodgson, Ryo Kawasaki, Tien Yin Wong, Carol Y. Cheung. Measurement of macular fractal dimension using a computer-assisted program. Investigative Ophthalmology & Visual Science, 55(4):2237--2243, April 2014.

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

    22. Junjie Wang, Lisa Tucker-Kellogg, Inn Chuan Ng, Ruirui Jia, P. S. Thiagarajan, Jacob White, Hanry Yu. The self-limiting dynamics of TGF-beta signaling in silico and in vitro with negative feedback through PPM1A upregulation. PLoS Computational Biology, 10(6):e1003573, June 2014.

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

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

    25. Benedict Yan, Chik Hong Kuick, Malcolm Lim, Kavita Venkataraman, Chandana Tennakoon, Eva Loh, Derrick Lian, May Ying Leong, Manikandan Lakshmanan, Vinay Tergaonkar, Wing-Kin Sung, Shui Yen Soh, Kenneth T. E. Chang. Platform comparison for evaluation of ALK protein immunohistochemical expression, genomic copy number and hotspot mutation status in neuroblastomas. PLoS ONE, 9(9):e106575, September 2014.

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

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

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

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

  • Conference Papers

    1. Jesper Jansson, Wing-Kin Sung, Hoa Vu, Siu-Ming Yiu. Faster algorithms for computing the R* consensus tree. Proceedings of 25th International Symposium on Algorithms and Computation (ISAAC), pages 414--425, December 2014.

    2. Gilbert Lim, Mong Li Lee, Wynne Hsu, Tien Yin Wong. Transformed representations for convolutional neural networks in diabetic retinopathy screening. Proceedings of AAAI Workshop on Modern Artificial Intelligence for Health Analytics (MAIHA), pages 21--25, July 2014.

  • Invited Keynotes, Talks, & Tutorials

    1. Hon Wai Leong. Genome-wide metabolic network reconstruction and gap filling. Talk at Sino-US Translational BioInformatics Workshop (SU-TBIW-2013), Soochow University, Suzhou, China, 25-26 July 2014.

    2. Wing-Kin Sung. Finding collaborating transcription factors using ChIP-seq. Invited talk at 37th Annual Meeting of the Molecular Biology Society of Japan, Yokohama, Japan, 25-27 November 2014.

    3. Wing-Kin Sung. Structural variation identification and its application to identify recurrent HBV integrations in liver cancer. Invited talk at 73rd Annual Meeting of the Japanese Cancer Association, Yokohama, Japan, 27 September 2014.

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

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

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

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

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

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

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

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

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

  2013

  • Books

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

  • Book Chapters

    1. Hugo Willy, Wing-Kin Sung, See-Kiong Ng. Discovering interacting domains and motifs in protein-protein interactions. Data Mining for Systems Biology, edited by Hiroshi Mamitsuka, Charles DeLisi, and Kanehisa Minoru, chapter 2, pages 9--20, January 2013.

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

  • Journal Papers

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

    2. Huy Hoang Do, Wing-Kin Sung. Compressed directed acyclic word graph with application in local alignment. Algorithmica, 67(2): 125-141, October 2013.

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

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

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

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

    7. Jesper Jansson, Wing-Kin Sung. Constructing the R* Consensus Tree of Two Trees in Subcubic Time. Algorithmica, 66(2): 329--345, June 2013.

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

    9. Zhengyan Kan, Hancheng Zheng, Xiao Liu, Shuyu Li, Thomas Barber, Zhuolin Gong, Huan Gao, Ke Hao, Melinda D Willard, Jiangchun Xu, Robert Hauptschein, Paul A Rejto, Julio Fernandez, Guan Wang, Qinghui Zhang, Bo Wang, Ronghua Chen, Jian Wang, Nikki P Lee, Wei Zhou, Zhao Lin, Zhiyu Peng, Kang Yi, Shengpei Chen, Lin Li, Xiaomei Fan, Jie Yang, Rui Ye, Jia Ju, Kai Wang, Heather Estrella, Shibing Deng, Ping Wei, Ming Qiu, Isabella H Wulur, Jiangang Liu, Mariam E Ehsani, Chunsheng Zhang, Andrey Loboda, Wing Kin Sung, Amit Aggarwal, Ronnie T Poon, Sheung Tat Fan, James Hardwick, Jun Wang, Christoph Reinhard, Hongyue Dai, Yingrui Li, John M Luk, Mao Mao. Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma. Genome Research, 23(9):1422--1433, September 2013.

    10. Qiangfeng Peter Lau, Mong Li Lee, Wynne Hsu, Tien Yin Wong. Simultaneously Identifying All True Vessels from Segmented Retinal Images. IEEE Transactions on Biomedical Engineering, 60(7):1851--1858, July 2013.

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

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

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

    14. Phi-Vu Nguyen, Sriganesh Srihari, Hon Wai Leong. Identifying conserved protein complexes between species by constructing interolog networks. BMC Bioinformatics, 14(S16):S8, October 2013.

    15. Song Ling Poon, See-Tong Pang, John R. McPherson, Willie Yu, Kie Kyon Huang, Peiyong Guan, Wen-Hui Weng, Ee Yan Siew, Yujing Liu, Hong Lee Heng, Soo Ching Chong, Anna Gan, Su Ting Tay, Weng Khong Lim, Ioana Cutcutache, Dachuan Huang, Lian Dee Ler, Maarja-Liisa Nairismägi, Ming Hui Lee, Ying-Hsu Chang, Kai-Jie Yu, Waraporn Chan-on, Bin-Kui Li, Yun-Fei Yuan, Chao-Nan Qian, Kwai-Fong Ng, Ching-Fang Wu, Cheng-Lung Hsu, Ralph M. Bunte, Michael R. Stratton, P. Andrew Futreal, Wing-Kin Sung, Cheng-Keng Chuang, Choon Kiat Ong, Steven G. Rozen, Patrick Tan, Bin Tean Teh. Genome-Wide Mutational Signatures of Aristolochic Acid and Its Application as a Screening Tool. Science Translational Medicine, 5(197):197ra101, August 2013.

    16. Daniel Portal, Hufeng Zhou, Bo Zhao, Peter Kharchenko, Elizabeth Lowry, Limsoon Wong, John Quackenbush, Dustin Halloway, Sizun Jiang, Yong Lu, Elliott Kieff. Epstein-Barr Virus Nuclear Antigen Leader Protein localizes to promoters and enhancers with cell transcription factors and EBNA2. Proceedings of the National Academy of Sciences USA, 110(46):18537--18542, November 2013.

    17. E. A. Simoes, C. Patel, W. K. Sung, C. W. Lee, K. H. Loh, M. Lucero, H. Nohynek, G. Nai, P. L. Thien, C. W. Koh, Y. S. Chan, J. Ma, S. Maurer-Stroh, P. Carosone-Link, M. L. Hibberd, C. W. Wong; IVAC Consortium. Pathogen chip for respiratory tract infections. J Clin Microbiol, 51(3):945--953, March 2013.

    18. Sriganesh Srihari, Hon Wai Leong. A survey of computational methods for protein complex prediction from protein interaction networks. Journal of BioInformatics and Computational Biology, 11(2):1230002, April 2013.

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

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

    21. M. T. Weirauch, A. Cote, R. Norel, M. Annala, Y. Zhao, T. R. Riley, J. Saez-Rodriguez, T. Cokelaer, A. Vedenko, S. Talukder; DREAM5 Consortium, P. Agius, A. Arvey, P. Bucher, C. G. Callan Jr, C. W. Chang, C. Y. Chen, Y. S. Chen, Y. W. Chu, J. Grau, I. Grosse, V. Jagannathan, J. Keilwagen, S. M. Kielbasa, J. B. Kinney, H. Klein, M. B. Kursa, H. Lähdesmäki, K. Laurila, C. Lei, C. Leslie, C. Linhart, A. Murugan, A. Mysickova, W. S. Noble, M. Nykter, Y. Orenstein, S. Posch, J. Ruan, W. R. Rudnicki, C. D. Schmid, R. Shamir, W. K. Sung, M. Vingron, Z. Zhang, H. J. Bussemaker, Q. D. Morris, M. L. Bulyk, G. Stolovitzky, T. R. Hughes. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology, 31(2):126--134, January 2013.

    22. Yubo Zhang, Chee-Hong Wong, Ramon Y. Birnbaum, Guoliang Li, Rebecca Favaro, Chew Yee Ngan, Joanne Lim, Eunice Tai, Huay Mei Poh, Eleanor Wong, Fabianus Hendriyan Mulawadi, Wing-Kin Sung, Silvia Nicolis, Nadav Ahituv, Yijun Ruan, Chia-Lin Wei. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations, Nature, 504(7479):306--310, December 2013.

    23. Z. Zhang, C. W. Chang, W. Hugo, E. Cheung, W. K. Sung. Simultaneously learning DNA motif along with its position and sequence rank preferences through expectation maximization algorithm. Journal of Computational Biology, 20(3):237--248, March 2013.

    24. Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh, and Wing-Kin Sung. 3D chromosome modeling with semi-definite Ppogramming and Hi-C data. Journal of Computational Biology, 20(11):831--846, November 2013.

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

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

  • Conference Papers

    1. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung. Improved Algorithms for Constructing Consensus Trees. Proceedings of 24th Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 1800--1813, January 2013.

    2. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung. An Optimal Algorithm for Building the Majority Rule Consensus Tree. Proceedings of 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 88--99, April 2013.

    3. Jesper Jansson, Chuanqi Shen, Wing-Kin Sung. Algorithms for the Majority Rule (+) Consensus Tree and the Frequency Difference Consensus Tree. Proceedings of 13th International Workshop on Algorithms in Bioinformatics (WABI), pages 141-155, September 2013.

    4. Sucheendra K. Palaniappan, Benjamin M. Gyori, Bing Liu, David Hsu,\ P. S. Thiagarajan. Statistical model checking based calibration and analysis of bio-pathway models. Proceedings of 11th International Conference on Computational Methods in Systems Biology (CMSB), pages 120--134, September 2013.

    5. Hoa Vu, Francis Y. L. Chin, Wing-Kai Hon, Henry C. M. Leung, Kunihiko Sadakane, Ken Wing-Kin Sung, Siu-Ming Yiu. Reconstructing k-Reticulated Phylogenetic Network from a Set of Gene Trees. Proceedings of 9th International Symposium on Bioinformatics Research and Applications (ISBRA), pages 112-124, May 2013.

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

    7. Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh, Wing-Kin Sung. Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data. Proceedings of 17th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 317--332, April 2013.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Structural variation identification and its applications in decoding the cancer genome. Invited talk at 11th Korea-Singapore Workshop on Bioinformatics and Natural Language Processing, KAIST, Korea, 22 February 2013.

    2. P. S. Thiagarajan. Analysis of ODE models of bio-pathways using statistical model checking. Invited talk at 24th International Conference on Genome Informatics, Biopolis, Singapore, 17 December 2013.

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

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

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

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

    7. Limsoon Wong. Large-scale bio and medical data mining. Invited master class at UTS AAI Big Data Summer School, Sydney, Australia, 10 April 2013.

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

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

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

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

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

    13. Limsoon Wong. The use of context in gene expression and proteomic profile analysis. Invited master class at 2013 International Summer School on Trends in Computing (SSTiC2013), Tarragona, Spain, 22-26 July 2013.

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

    15. Limsoon Wong. Disease gene expression and proteomic profile analysis based on regulatory networks and systems. Invited master class at EMS Autumn School on Computational Aspects of Gene Regulation, Bedlewo, Poland, 13-19 October 2013.

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

  2012

  • Book Chapters

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

  • Journal Papers

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

    2. Ket Fah Chong, Hon Wai Leong. Tutorial on de novo peptide sequencing using MS/MS mass spectrometry. Journal of Bioinformatics and Computational Biology, 10(6):1231002, December 2012.

    3. Carol Cheung, George Thomas, Wanting Tay, Kamran Ikram, Wynne Hsu, Mong Li Lee, Qiangfeng Peter Lau, Tien Yin Wong. Retinal Vascular Fractal Dimension and its Relationship with Cardiovascular and Ocular Risk Factors. American Journal of Ophthalmology, 154(4):663--674, October 2012.

    4. Y. Cui, J. Jansson, W. K. Sung. Polynomial-Time Algorithms for Building a Consensus MUL-Tree. Journal of Computational Biology, 19(9):1073--1088, September 2012.

    5. A. Ghosh, G. Saginc, S. C. Leow, E. Khattar, E. M. Shin, T. D. Yan, M. Wong, Z. Zhang, G. Li, W. k. Sung, J. Zhou, W. J. Chng, S. Li, E. Liu, V. Tergaonkar. Telomerase directly regulates NF-kappa B-dependent transcription. Nat Cell Biol. 14(12):1270--1281, December 2012.

    6. B. Gipson, D. Hsu, L.E. Kavraki, and J.C. Latombe. Computational models of protein kinematics and dynamics: Beyond simulation. 5:273--291, July 2012.

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

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

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

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

    11. R. Hassanzadeh, C. Eslahchi, W. K. Sung. Constructing phylogenetic supernetworks based on simulated annealing. Molecular Phylogenetics and Evolution, 63(3):738--744, June 2012.

    12. J. Heisig, D. Weber, E. Englberger, A. Winkler, S. Kneitz, W. K. Sung, E. Wolf, M. Eilers, C. L. Wei, M. Gessler. Target gene analysis by microarrays and chromatin immunoprecipitation identifies HEY proteins as highly redundant bHLH repressors. PLoS Genetics, 8(5):e1002728, May 2012.

    13. Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Ultra-succinct representation of ordered trees with applications. Journal of Computer and System Sciences, 78(2):619--631, January 2012.

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

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

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

    17. G. Li, X. Ruan, R. K. Auerbach, K. S. Sandhu, M. Zheng, P. Wang, H. M. Poh, Y. Goh, J. Lim, J. Zhang, H. S. Sim, S. Q. Peh, F. H. Mulawadi, C. T. Ong, Y. L. Orlov, S. Hong, Z. Zhang, S. Landt, D. Raha, G. Euskirchen, C. L. Wei, W. Ge, H. Wang, C. Davis, K. I. Fisher-Aylor, A. Mortazavi, M. Gerstein, T. Gingeras, B. Wold, Y. Sun, M. J. Fullwood, E. Cheung, E. Liu, W. K. Sung, M. Snyder, Y. Ruan. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell, 148(1-2):84--98, January 2012.

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

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

    20. J. Q. Lim, C. Tennakoon, G. Li, E. Wong, Y. Ruan, C. L. Wei, W. K. Sung. BatMeth: Improved mapper for bisulfite sequencing reads on DNA methylation. Genome Biology, 13(10):R82, October 2012.

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

    22. Bing Liu, Andrei Hagiescu, Sucheendra K. Palaniappan, Bipasa Chattopadhyay, Zheng Cui, Weng Fai Wong, P.S. Thiagarajan. Approximate Probabilistic Analysis of Biopathway Dynamics. Bioinformatics, 28(11):1508--1516, June 2012.

    23. Bing Liu, P.S. Thiagarajan. Modeling and Analysis of Biopathways Dynamics. Journal of Bioinformatics and Computational Biology, 10(4):1231001, August 2012.

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

    25. K. P. Ng, A. M. Hillmer, C. T. Chuah, W. C. Juan, T. K. Ko, A. S. Teo, P. N. Ariyaratne, N. Takahashi, K. Sawada, Y. Fei, S. Soh, W. H. Lee, J. W. Huang, J. C. Allen Jr, X. Y. Woo, N. Nagarajan, V. Kumar, A. Thalamuthu, W. T. Poh, A. L. Ang, H. T. Mya, G. F. How, L. Y. Yang, L. P. Koh, B. Chowbay, C. T. Chang, V. S. Nadarajan, W. J. Chng, H. Than, L. C. Lim, Y. T. Goh, S. Zhang, D. Poh, P. Tan, J. E. Seet, M. K. Ang, N. M. Chau, Q. S. Ng, D. S. Tan, M. Soda, K. Isobe, M. M. Noethen, T. Y. Wong, A. Shahab, X. Ruan, V. Cacheux-Rataboul, W. K. Sung, E. H. Tan, Y. Yatabe, H. Mano, R. A. Soo, T. M. Chin, W. T. Lim, Y. Ruan, S. T. Ong. A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nature Medicine, 18(4):521--528, March 2012.

    26. N. Nagarajan, D. Bertrand, A. M. Hillmer, Z. J. Zang, F. Yao, P. E. Jacques, A. S. Teo, I. Cutcutache, Z. Zhang, W. H. Lee, Y. Y. Sia, S. Gao, P. N. Ariyaratne, A. Ho, X. Y. Woo, L. Veeravali, C. K. Ong, N. Deng, K. V. Desai, C. C. Khor, M. L. Hibberd, A. Shahab, J. Rao, M. Wu, M. Teh, F. Zhu, S. Y. Chin, B. Pang, J. B. So, G. Bourque, R. Soong, W. K. Sung, B. T. Teh, S. Rozen, X. Ruan, K. G. Yeoh, P. B. Tan, Y. Ruan. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biology, 13(12):R115, December 2012.

    27. Sucheendra K. Palaniappan, S. Akshay, Bing Liu, Blaise Genest, P. S. Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathway Application. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5):1352--1365, September 2012.

    28. Sriganesh Srihari, Hon Wai Leong. Employing functional interactions for characterization and detection of sparse complexes from yeast PPI networks. International Journal of Bioinformatics Research and Applications, 8(3/4):286--304, September 2012.

    29. Sriganesh Srihari, Hon Wai Leong. Temporal dynamics of protein complexes in PPI networks: A case study using yeast cell cycle dynamics. BMC Bioinformatics, 13(Suppl 17):S16, December 2012.

    30. Wing-Kin Sung. Bioinformatics applications in genomics. IEEE Computer, 45(6):57--63, June 2012.

    31. W. K. Sung, H. Zheng, S. Li, R. Chen, X. Liu, Y. Li, N. P. Lee, W. H. Lee, P. N. Ariyaratne, C. Tennakoon, F. H. Mulawadi, K. F. Wong, A. M. Liu, R. T. Poon, S. T. Fan, K. L. Chan, Z. Gong, Y. Hu, Z. Lin, G. Wang, Q. Zhang, T. D. Barber, W. C. Chou, A. Aggarwal, K. Hao, W. Zhou, C. Zhang, J. Hardwick, C. Buser, J. Xu, Z. Kan, H. Dai, M. Mao, G. Reinhard, J. Wang, J. M. Luk. Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nature Genetics, 44(7):765--769, May 2012.

    32. P. Y. Tan, C. W. Chang, K. R. Chng, K. D. Wansa, W. K. Sung, E. Cheung. Integration of Regulatory Networks by NKX3.1 Promotes Androgen-Dependent Prostate Cancer Survival. Mol Cell Biol, 32(2):399--414, January 2012.

    33. C. Tennakoon, R. W. Purbojati, W. K. Sung. BatMis: A fast algorithm for k-mismatch mapping. Bioinformatics, 28(16):2122--2128, August 2012.

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

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

    36. H. Xu, W. K. Sung. Identifying differential histone modification sites from ChIP-seq data. Methods in Molecular Biology, 802:293--303, January 2012.

    37. F. Yao, P. N. Ariyaratne, A. M. Hillmer, W. H. Lee, G. Li, A. S. Teo, X. Y. Woo, Z. Zhang, J. P. Chen, W. T. Poh, K. F. Zawack, C. S. Chan, S. T. Leong, S. C. Neo, P. S. Choi, S. Gao, N. Nagarajan, H. Thoreau, A. Shahab, X. Ruan, V. Cacheux-Rataboul, C. L. Wei, G. Bourque, W. K. Sung, E. T. Liu, Y. Ruan. Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations and Fusion-Point-Guided Reconstruction of Amplicons. PLoS One, 7(9):e46152, September 2012.

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

    39. J. Zhang, H. M. Poh, S. Q. Peh, Y. Y. Sia, G. Li, F. H. Mulawadi, Y. Goh, M. J. Fullwood, W. K. Sung, X. Ruan, Y. Ruan. ChIA-PET analysis of transcriptional chromatin interactions. Methods, 58(3):289--299, November 2012.

    40. Melvin Zhang, Hon Wai Leong. BBH-LS: An Algorithm for Computing Positional Homologs Using Sequence and Gene Context Similarities. BMC Systems Biology, 6(Suppl 1):S22, July 2012.

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

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

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

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

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

    46. Zhong Zhou, Melvin Zhang, FanChang Hao, Hon Wai Leong. On Two Variations of the Reversal Median Problem. International Journal of Modern Physics, 9:285-292, May 2012.

  • Conference Papers

    1. Huy Hoang Do, Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. Fast Relative Lempel-Ziv Self-index for Similar Sequences. Proceedings of Joint International Conference on Frontiers n Algorithmics and Algorithmic Aspects in Information and Management (FAW-AAIM), pages 291--302, Beijing, China, May 2012.

    2. Jesper Jansson, Kunihiko Sadakane, Wing-Kin Sung. CRAM: Compressed Random Access Memory. Proceedinsg of 39th International Colloquium on Automata, Languages, and Programming (ICALP), Part I, pages 510--521, July 2012.

    3. Yong San Gilbert Lim, Mong Li Lee, Wynne Hsu. Constrained-MSER Detection of Retinal Pathology. Proceedings of 21st International Conference on Pattern Recognition, pages ???--???, Japan, November 2012.

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

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

    6. Sriganesh Srihari, Hon Wai Leong. A Survey of Algorithms for Detecting Protein Complexes from Protein-Protein Interaction Networks. Proceedings of Asian Association for Algorithms and Computation (AAAC), pages ???--???, Shanghai, China, April 2012.

    7. ZhiZhuo Zhang, Cheng Wei Chang, Hugo Willy, Edwin Cheung, Wing-Kin Sung. Simultaneously Learning DNA Motif along with Its Position and Sequence Rank Preferences through EM Algorithm. Proceedings of 16th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 355--370, April 2012.

  • Invited Keynotes, Talks, & Tutorials

    1. Hon Wai Leong. Computational Methods for Detecting Protein Complexes from Protein-Protein Interaction Networks. Invited talk at Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Singapore, 27-28 February 2012.

    2. Hon Wai Leong. Detecting Protein Complexes from Large-Scale Protein-Protein Interaction Networks. Keynote talk at International Conference on Mathematical Applications in Engineering (ICMAE-2012), Kuala Lumpur, Malaysia, 3-5 July 2012.

    3. Sriganesh Srihari and Hon Wai Leong. Computational Methods for Protein Complex Prediction from Protein Interaction Networks. Tutorial given at International Conference on Bioinformatics (InCoB2012), Bangkok, Thailand, 2-5 October 2012.

    4. Bing Liu. Probabilistic Approximation Techniques for Biopathway Modeling. Invited talk at Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Singapore, 27-28 February 2012.

    5. Wing-Kin Sung. Sampling with Expectation Maximization for Motif Elicitation (SEME). Invited talk at Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Singapore, 27-28 February 2012.

    6. Wing-Kin Sung. Genome-Wide Survey of Recurrent HBV Integration in Hepatocellular Carcinoma. Invited talk at 2nd Bandung Biomolecular Medicine Conference, Bandung, Indonesia, 6 October 2012.

    7. Wing-Kin Sung. Extracting information from next-generation sequencing data. Invited master-class at International Summer School on Methods in Bioinformatics, Spain, 27-31 August 2012.

    8. P. S. Thiagarajan. Probabilistic Approximations of ODEs Dynamics of Signalling Pathways Dynamics. Invited talk at CMACS Workshop on Formal Methods and Systems Biology, New York University, Kimmel Center, 29-30 March 2012.

    9. P. S. Thiagarajan. Probabilistic Approximation and Analysis of Biopathways Dynamics. IEEE Distinguished Speaker series, EECS Dept, University of Central Florida, 11 May 2012.

    10. P. S. Thiagarajan. Probabilistic approximation of ODEs based Biopathways Dynamics. CMACS (Center for Mathematical Analysis of Complex Systems) Seminar, Carnegie-Mellon University, 25 May 2012.

    11. P. S. Thiagarajan. Approximate Analysis of ODEs based Bio-Pathways Dynamics. Invited talk at 4th International Conference on Computational and Systems Biology, Shanghai, China, 12-14 October 2012.

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

    13. Limsoon Wong. Analysis of Gene Expression and Proteomic Profiles based on Biological Networks. Tutorial at 10th Asia Pacific Bioinformatics Conference (APBC2012), Melbourne, Australia, 17-19 January 2012.

    14. Limsoon Wong. Using Biological Networks for Protein Function Prediction, Biomarker Identification, and Other Problems in Computational Biology. Invited master class at 2012 International Winter School in Methods in Bioinformatics (WSMBio 2012), Tarragona, Spain, 20-24 February 2012.

    15. Limsoon Wong. A Novel Contextualization Approach to Proteomic Profile Analysis. Invited talk at Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, Singapore, 27-28 February 2012.

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

    17. Limsoon Wong. Living with noise. Invited talk at SinFra 2012, UPMC, Paris, 15 October 2012.

    18. Limsoon Wong. A novel contextualization approach to proteomic profile analysis. Invited plenary talk at 2nd Biomarker Discovery Conference (BDC2012), Shoal Bay, Australia, 6 December 2012.

    19. Limsoon Wong. A novel principle for childhood ALL relapse prediction. Invited talk at Inaugural Post-BDC2012 Personalized Medicine Workshop, Hunter Medical Research Institute, University of Newcastle, Australia, 7 December 2012.

  2011

  • Book Chapters

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

  • Journal Papers

    1. Pramila Nuwantha Ariyaratne, Wing-Kin Sung. PE-Assembler: de novo assembler using short paired-end reads. Bioinformatics, 27(2): 167-174, January 2011.

    2. 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, 23(11):1735--1747, November 2011.

    3. Ho-Leung Chan, Tak Wah Lam, Wing-Kin Sung, Siu-Lung Tam, Swee-Seong Wong. A linear size index for approximate pattern matching. Journal of Discrete Algorithms, 9(4):358--364, December 2011.

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

    5. D. Earl, K. Bradnam, J. St John, A. Darling, D. Lin, J. Fass, H. O. Yu, V. Buffalo, D. R. Zerbino, M. Diekhans, N. Nguyen, P. N. Ariyaratne, W. K. Sung, Z. Ning, M. Haimel, J. T. Simpson, N. A. Fonseca, I. Birol, T. R. Docking, I. Y. Ho, D. S. Rokhsar, R. Chikhi, D. Lavenier, G. Chapuis, D. Naquin, N. Maillet, M. C. Schatz, D. R. Kelley, A. M. Phillippy, S. Koren, S. P. Yang, W. Wu, W. C. Chou, A. Srivastava, T. I. Shaw, J. G. Ruby, P. Skewes-Cox, M. Betegon, M. T. Dimon, V. Solovyev, I. Seledtsov, P. Kosarev, D. Vorobyev, R. Ramirez-Gonzalez, R. Leggett, D. Maclean, F. Xia, R. Luo, Z. Li, Y. Xie, B. Liu, S. Gnerre, I. Maccallum, D. Przybylski, F. J. Ribeiro, S. Yin, T. Sharpe, G. Hall, P. J. Kersey, R. Durbin, S. D. Jackman, J. A. Chapman, X. Huang, J. L. Derisi, M. Caccamo, Y. Li, D. B. Jaffe, R. E. Green, D. Haussler, I. Korf, B. Paten. Assemblathon 1: A competitive assessment of de novo short read assembly methods. Genome Research, 21(12):2224--2241, December 2011.

    6. M. J. Fullwood, J. Lee, L. Lin, G. Li, M. Huss, P. Ng, W. K. Sung, S. Shenolikar. Next-generation sequencing of apoptotic DNA breakpoints reveals association with actively transcribed genes and gene translocations. PLoS One, 6(11):e26054, November 2011.

    7. S. Gao, W. K. Sung, N. Nagarajan. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. Journal of Computational Biology, 18(11):1681--1691, November 2011.

    8. B. Gipson, D. Hsu, L. E. Kavraki, J. C. Latombe. Computational models of protein kinematics and dynamics: Beyond simulation. Annu. Rev. Anal. Chem, 5:273--291, July 2012.

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

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

    11. S. Guillemot, J. Jansson, W. K. Sung. Computing a Smallest Multi-labeled Phylogenetic Tree from Rooted Triplets. IEEE/ACM Trans Comput Biol Bioinform, 8(4):1141--1147, July 2011.

    12. L. Handoko, H. Xu, G. Li, C. Y. Ngan, E. Chew, M. Schnapp, C. W. Lee, C. Ye, J. L. Ping, F. Mulawadi, E. Wong, J. Sheng, Y. Zhang, T. Poh, C. S. Chan, G. Kunarso, A. Shahab, G. Bourque, V. Cacheux-Rataboul, W. K. Sung, Y. Ruan, C. L. Wei. CTCF-mediated functional chromatin interactome in pluripotent cells. Nature Genetics, 43(7):630--638, June 2011.

    13. A. M. Hillmer, F. Yao, K. Inaki, W. H. Lee, P. N. Ariyaratne, A. S. Teo, X. Y. Woo, Z. Zhang, H. Zhao, L. Ukil, J. P. Chen, F. Zhu, J. B. So, M. Salto-Tellez, W. T. Poh, K. F. Zawack, N. Nagarajan, S. Gao, G. Li, V. Kumar, H. P. Lim, Y. Y. Sia, C. S. Chan, S. T. Leong, S. C. Neo, P. S. Choi, H. Thoreau, P. B. Tan, A. Shahab, X. Ruan, J. Bergh, P. Hall, V. Cacheux-Rataboul, C. L. Wei, K. G. Yeoh, W. K. Sung, G. Bourque, E. T. Liu, Y. Ruan. Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome Research, 21(5):665--675, May 2011.

    14. Viet Tung Hoang, Wing-Kin Sung. Improved Algorithms for Maximum Agreement and Compatible Supertrees. Algorithmica, 59(2):195--214, February 2011.

    15. Wing-Kai Hon, Kunihiko Sadakane, Wing-Kin Sung. Succinct Data Structures for Searchable Partial Sums with Optimal Worst-Case Performance. Theoretical Computer Science, 412(39):5176-5186, September 2011.

    16. K. Inaki, A. M. Hillmer, L. Ukil, F. Yao, X. Y. Woo, L. A. Vardy, K. F. Zawack, C. W. Lee, P. N. Ariyaratne, Y. S. Chan, K. V. Desai, J. Bergh, P. Hall, T. C. Putti, W. L. Ong, A. Shahab, V. Cacheux-Rataboul, R. K. Karuturi, W. K. Sung, X. Ruan, G. Bourque, Y. Ruan, E. T. Liu. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Research, 21(5):676--687, May 2011.

    17. 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.

    18. Geoffrey Koh, David Hsu, P. S. Thiagarajan. Component-based construction of bio-pathway models: The parameter estimation problem. Theoretical Computer Science, 412(26):2840--2853, June 2011.

    19. S. L. Kong, G. Li, S. L. Loh, W. K. Sung, E. T. Liu. Cellular reprogramming by the conjoint action of ERalpha, FOXA1, and GATA3 to a ligand-indiucible growth state. Molecular Systems Biology, 7:526, August 2011.

    20. 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 hybrid functional Petri net with extension. Molecular Biosystems, 7(5):1576--1592, 2011.

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

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

    23. B. Liu, J. Zhang, P. Y. Tan, D. Hsu, A. Blom, B. Leong, S. Sethi, B. Ho, J. L. Ding, P. S. Thiagarajan. A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System. PLoS Computational Biology, 7(1):1--16, January 2011.

    24. Bing Liu, David Hsu, P. S. Thiagarajan. Probabilistic Approximations of ODEs based Bio-Pathway Dynamics. Theoretical Computer Science, 412(21):2188--2206, May 2011.

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

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

    27. Qian Liu, Steven C. H. Hoi, Chinh T. T. Su, Zhenhua Li, Chee-Keong Kwoh, Limsoon Wong, Jinyan Li. Structural analysis of the hot spots in the binding between H1N1 HA1 and the 2D1 antibody: Do mutations of H1N1 from 1918 to 2009 affect much on this binding?. Bioinformatics, 27(18):2529--2536, September 2011.

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

    29. Shlomo Moran, Sagi Snir, Wing-Kin Sung. Partial Convex Recolorings of Trees and Galled Networks: Tight Upper and Lower Bounds. ACM Transactions on Algorithms, 7(4):42, September 2011.

    30. Kang Ning and Hon Wai Leong. The Multiple Sequences Sets: Problem and Heuristic Algorithms. Journal of Combinatorial Optimization, 22(4):778-796, October 2011.

    31. 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, 5(6):611-625, December 2011.

    32. K. S. Sandhu, G. Li, W. K. Sung, Y. Ruan. Chromatin interaction networks and higher order architectures of eukaryotic genomes. J Cell Biochem, 112(9):2218--2221, September 2011.

    33. K. S. Sandhu, G. Li, H. M. Poh, Y. L. Quek, Y. Y. Sia, S. Q. Peh, F. H. Mulawadi, J. Lim, M. Sikic, F. Menghi, A. Thalamuthu, W. K. Sung, X. Ruan, M. J. Fullwood, E. Liu, P. Csermely, Y. Ruan. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep, 2(5):1207--1219, November 2012.

    34. Kelvin Sim, Guimei Liu, Vivekanand Gopalkrishnan, Jinyan Li. A case study on financial ratios via cross-graph quasi-bicliques. Information Science, 181(1):201--216, January 2011.

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

    36. S. K. Tan, Z. H. Lin, C. W. Chang, V. Varang, K. R. Chng, Y. F. Pan, E. L. Yong, W. K. Sung, E. Cheung. AP-2gamma regulates oestrogen receptor-mediated long-range chromatin interaction and gene transcription. EMBO Journal, 30(13):2569--2581, May 2011; EMBO Journal, 30(13):2750, July 2011.

    37. 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.

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

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

    40. 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.

    41. Hugo Willy, See Kiong Ng, Wing-Kin Sung. D-SLIMMER: Domain-SLiM Interaction Motifs Miner for Sequence-Based Protein-Protein Interaction Data. Journal of Proteome Research, 10(12):5285--5295, December 2011.

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

    43. T. K. Wong, T. W. Lam, W. K. Sung, B. W. Cheung, S. M. Yiu. Structural alignment of RNA with complex pseudoknot structure. Journal of Computational Biology, 18(1):97--108, January 2011.

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

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

    46. 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.

    47. Z. Zhang, C. W. Chang, W. L. Goh, W. K. Sung, E. Cheung. CENTDIST: Discovery of Co-Associated Factors by Motif Distribution. Nucleic Acids Research, 39(Suppl 2):W391--W399, July 2011.

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

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

  • Conference Papers

    1. Ket Fah Chong, Hon Wai Leong. MCPS: A Mono-Chromatic Peptide Sequencer for Multi-Charged Mass Spectra. Proceedings of RECOMB Satellite Conference on Computational Proteomics (RECOMB-CP), pages ???--???, San Diego, USA, March 2011.

    2. Yun Cui, Jesper Jansson, Wing-Kin Sung. Algorithms for Building Consensus MUL-trees. Proceedings of 22nd International Symposium on Algorithms and Computation (ISAAC), pages 744--753, Yokohama, Japan, December 2011.

    3. Huy Hoang Do, Wing-Kin Sung. Compressed Directed Acyclic Word Graph with Application in Local Alignment. Proceedings of 17th Annual International Conference on Computing and combinatorics (COCOON), pages 503--518, Dallas, TX, USA, August 2011.

    4. Song Gao, Niranjan Nagarajan, Wing-Kin Sung. Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences. Proceedings of 15th Annual International Conference on Research in Computational Biology (RECOMB), pages 437--451, Vancouver, Cananda, March 2011.

    5. Xiao Hang, Melvin Zhang, Axel Mosig, Hon Wai Leong. Dynamic Programming Algorithms for Efficiently Computing Cosegmentations between Biological Images. Proceedings of 11th Workshop on Bioinformatics Algorithms (WABI), pages 339--350, Saarbrucken, Germany, September 2011.

    6. Trong Dao Le, Melvin Zhang, Hon Wai Leong. Algorithms for Computing Bidirectional Best Hit r-Window Gene Clusters. Frontiers of Algorithmics and Algorithmic Aspects in Information and Management - Joint International Conference (FAW-AAIM), pages 275--286, Jinhua, China, May 2011.

    7. 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 745--756, Hannover, Germany, April 2011.

    8. Sucheendra K. Palaniappan, S. Akshay, Blaise Genest, P. S. Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Network Models of Biopathways. Proceedings of 9th International Conference on Computational Methods in Systems Biology (CMSB), pages 35--44, Paris, France, September 2011.

    9. Dhaval Patel, Wynne Hsu, Mong Li Lee. Discriminative Mutation Chains in Virus Sequences. Proceedings of 23rd IEEE International Conference on Tools with Artificial Intelligence, pages ???--???, Florida, USA, November 2011.

    10. HuiYi Tan, Hon Wai Leong. A Parent Mass Filter Algorithm for Peptide Sequencing from Tandem Mass Spectra. Proceedings of 5th International Conference on Bioinformatics and Biomedical Engineering (ICBBE), pages ???--???, Wuhan, China, May 2011.

    11. Melvin Zhang, Hon Wai Leong. Survey of Algorithms for Conserved Gene Cluster Discovery. Proceedings of 4th Annual Meeting of Asian Association for Algorithms and Computation (AAAC), page 23, NTHU, Hsinchu, Taiwan, April 2011.

    12. Melvin Zhang, Hon Wai Leong. Identifying Positional Homologs as Bidirectional Best Hits of Sequence and Gene Context Similarity. Proceedings of 2011 IEEE Conference on Systems Biology (ISB), pages 117--122, Zhuhai, China, September 2011.

    13. Zhong Zhou, Melvin Zhang, FanChang Hao, Hon Wai Leong. On Two Variations of the Reversal Median Problem. Proceedings of International Conference on Mathematical and Computational Biology (ICMCB), pages ???--???, Melaka, Malaysia, April 2011.

  • Invited Keynotes, Talks, & Tutorials

    1. Benjamin Gyori. Computational Modeling of DNA Damage Response Under Oxidative Stress. Talk at 3rd NUS-U. Tokyo Joint Workshop on Computational Systems Biology, School of Computing, NUS, Singapore, 19 April 2011.

    2. Hon Wai Leong. Algorithms for Analysis of PPI Networks. Invited talk at Center for Systems Biology, SooChow University, Suzhou, China, 27 May 2011.

    3. Hon Wai Leong. Algorithms for Conserved Gene Cluster Discovery. Invited talk at Center for Systems Biology, SooChow University, Suzhou, China, 27 May 2011.

    4. Hon Wai Leong. Algorithms for Conserved Gene Cluster Discovery. Seminar talk at Theoretical Computer Science Monthly Seminar Series, Xi'an JiaoTong-Liverpool University, Suzhou, China, 26 May 2011.

    5. Hon Wai Leong. Algorithms for Conserved Gene Cluster Discovery. Invited talk at East China Normal University, Shanghai, China, 24 May 2011.

    6. Bing Liu. A Platform-Aware GPU Realization of a Systems Biology Application. Talk at 3rd NUS-U. Tokyo Joint Workshop on Computational Systems Biology, School of Computing, NUS, Singapore, 19 April 2011.

    7. Sucheendra Kumar Palaniappan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks. Talk at 3rd NUS-U. Tokyo Joint Workshop on Computational Systems Biology, School of Computing, NUS, Singapore, 19 April 2011.

    8. Wing-Kin Sung. Assembly by Short Paired-End Reads. Talk at 2nd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 7 April 2011.

    9. Wing-Kin Sung. Analyzing ChIP-Seq Data. Talk at 2nd IPM-NUS Workshop on Computational Biology, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran, 7 April 2011.

    10. Wing-Kin Sung. Identifying Structural Variation Using Paired-End Reads. Invited talk at 22nd FAOBMB Conference, Biopolis, Singapore, 5 October 2011.

    11. Wing-Kin Sung. Application of next-generation sequencing to extract structural variations in our genomes. Invited talk at 5th Asian Young Researchers Conference on Computational and Omics Biology, Daejeon, Korea, 10 August 2011.

    12. P. S. Thiagarajan. Probabilistic Approximations of Biopathways Dynamics: Some Computational Aspects. Invited talk at VERIMAG Workshop on Toward Systems Biology, Grenoble, France, 30 May - 1 June 2011.

    13. P. S. Thiagarajan. TBA. Invited talk at 3rd International Conference on Computational and Systems Biology (ICCSB), Shanghai, China, 14 - 16 October 2011.

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

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

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

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

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

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

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

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

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

  2010

  • Books

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

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

  • Journal Papers

    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. Tsung-Han Chiang, David Hsu, Jean-Claude Latombe. Markov dynamic models for long-timescale protein motion. Bioinformatics, 26(12):i269-i277, July 2010. Special issue on ISMB2010.

    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. 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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    11. 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.

    12. 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.

    13. 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.

    14. 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.

    15. 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.

    16. V. Narang, A. Mittal, W. K. Sung. Localized Motif Discovery in Gene Regulatory Sequences. Bioinformatics, 26(9):1152--1159, May 2010.

    17. 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.

    18. 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.

    19. 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.

    20. 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.

    21. 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.

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

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

    24. 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.

    25. 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.

    26. 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.

    27. 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.

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

    29. 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.

    30. 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.

    31. Melvin Zhang, Hon Wai Leong. Bidirectional Best Hit r-Window Gene Clusters. BMC Bioinformatics, 11(Suppl 1):S63, January 2010.

    32. W. Zhang, L. Tucker-Kellogg, B. C. Narmada, L. Venkatraman, S. Chang, Y. Lu, N. Tan, J. K. White, R. Jia, S. S. Bhowmick, S. Shen, C. F. Dewey Jr, H. Yu. Cell-delivery therapeutics for liver regeneration, Adv Drug Deliv Rev, 62(7--8):814--826, June 2010.

    33. 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 (BIBM), 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. Geoffrey Koh, David Hsu, P.S. Thiagarajan. Incremental Signaling Pathway Modeling by Data Integration. Proceedings of 14th Annual International Conference on Research in Computational Molecular Biology (RECOMB), pages 281-296, Lisbon, Portugal, April 2010. (Conference postponed to August 2010)

    5. Louise Laurent, Eleanor Wong, Guoliang Li, Tien Huynh, Aristotelis Tsirigos, Chin Thing Ong, Hwee Meng Low, Ken Wing Kin Sung, Isidore Rigoutsos, Jeanne Loring, Chia-Lin Wei. Dynamic changes in the human methylome during differentiation. Genome Research, 20:320--331, 2010.
    6. 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 (BIBM), pages 280--283, Hong Kong, December 2010.

    7. 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.

    8. 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.

    9. 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.

    10. L. Venkatraman, H. Yu, S. S. Bhowmick, F. Dewey, L. Tucker-Kellogg. The steady states and dynamics of urokinase-mediated plasmin activation. Proceedings of Pacific Symposium on Biocomputing 2010 (PSB), pages 190--200, Big Island, Hawaii, January 2010.

    11. 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 (BIBM), pages 85--90, Hong Kong, December 2010.

    12. 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 (BIBM), pages 121--126, Hong Kong, December 2010.

  • Invited Keynotes, Talks, & Tutorials

    1. Wing-Kin Sung. Assembly by short paired-end reads and sequencing by hybridization. Invited talk at Hong Kong University, Hong Kong, 21 June 2010.

    2. Wing-Kin Sung. Genomic variation identification by resequencing. Invited talk at 1st PT-ERC International Symposium on Personalized Medicine, Chungbuk National University, Cheongju, Korea, 26 June 2010.

    3. Wing-Kin Sung. Bioinformatics Applications in Pathology. Invited talk at IEEE International Conference on Bioinformatics & Biomedicine (BIBM), Hong Kong, 18-21 December 2010.

    4. P. S. Thiagarajan. Probabilistic Approximation and Verification of Bio-Pathways Dynamics. Invited talk at Algebraic and Numeric Biology 2010, RISC, Castle of Hagenberg, Austria, 2 August 2010.

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

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

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

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

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

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

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

  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.

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

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

    4. Guimei Liu. Max-Pattern Mining. Encyclopedia of Database Systems, pages 1699--1702, 2009.

  • Journal Papers

    1. 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.

    2. 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.

    3. 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.

    4. 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.

    5. 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.

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

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

    12. 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.

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

    14. Kelvin Sim, Jinyan Li, Vivekanand Gopalkrishnan, Guimei Liu. Mining maximal quasi-bicliques: Novel algorithm and applications in the stock market and protein networks. Statistical Analysis and Data Mining, 2(4):255--273, November 2009.

    15. 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.

    16. 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.

    17. Xiaoling Wang, Jinfeng Luan, Guimei Liu, Aoying Zhou. Towards optimal workload-aware XML to relational schema mapping. Annals of Operations Research, 168(1):133--150, April 2009.

    18. 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.

    19. 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.

  • 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. Jurek Czyzowicz, Stefan Dobrev, Leszek Gasieniec, David Ilcinkas, Jesper Jansson, Ralf Klasing, Ioannis Lignos, Russell A. Martin, Kunihiko Sadakane, Wing-Kin Sung. More Efficient Periodic Traversal in Anonymous Undirected Graphs. Proceedings of 16th International Colloquium on Structural Information and Communication Complexity (SIROCCO), pages 167--181, Piran, Slovenia, May 2009.

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

    4. 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.

    5. 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.

    6. Hong Sang Low, Christopher J. O. Baker, Alexander Garcia, Markus R. Wenk. An OWL-DL Ontology for Classification of Lipids. Proceedings of International Conference on Biomedical Ontology, pages ???--???, Buffalo, NY, USA, 24-26 July 2009.

    7. Bing Liu, P. S. Thiagarajan, David Hsu. Probabilistic approximations of signaling pathways dynamics. Proc. 7th Conference on Computational Methods in Systems Biology (CMSB), pages 251--265, Bologna, Italy, 31 August - 1 September 2009.

    8. Yuan Shi, Simi M. Varghese, Sinong Huang, Jacob White, Shazib Pervaiz, Lisa Tucker-Kellogg. Computational Modeling of Pathway Dynamics for Detecting Drug Effects: Paradoxical Effects of LY303511 on Trail-Induced Apoptosis. Proceedings of 8th International Conference on Computational Systems Bioinformatics (CSB2009), pages ???--???, Stanford University, 10-12 August 2009.

    9. 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, 14-16 December 2009.

    10. 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.

    11. 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 Conf on Bioinformatics and Computational Biology (BICOB2009), pages 79--89, New Orleans, USA, 8-10 April 2009.

    12. Thomas K. F. Wong, Tak Wah Lam, Wing-Kin Sung, Siu-Ming Yiu. Structural Alignment of RNA with Complex Pseudoknot Structure. Proceedings of 9th International Workshop on Algorithms in Bioinformatics (WABI2009), pages 403--414, Philadelphia, PA, 12-13 September 2009.

    13. 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.

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

  • Invited Keynotes, Talks, & Tutorials

    1. Hon Wai Leong. Overview of Bioinformatics Research in NUS Computer Science Dept. Invited talk at 2nd Singapore-Hungary Joint Symposium, Institute of Microelectronics, Singapore, 23-24 April 2009.

    2. Wing-Kin Sung. The 2-interval Pattern Matching Problems and its Application to ncRNA Scanning. Invited keynote at 1st International Conf on Bioinformatics and Computational Biology (BICOB2009), New Orleans, USA, 8-10 April 2009.

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

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

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

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

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

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

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

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

    11. Melvin Zhang, Hon Wai Leong. Finding Gene Clusters. Invited talk at Mini-symposium on Gene Clustering Methodology, PICB, Shanghai, China, 3 Oct 2009.

    12. Melvin Zhang, Hon Wai Leong. Algorithms for Finding Gene Teams. Invited talk at 4th Intl Conf on Mathematics and Statistics, Lampung, Indonesia, 13-15 Aug 2009.

  2008

  • Books

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

    2. Hon Wai Leong, Wing-Kin Sung, Eleazar Eskin, editors. Proceedings of 3rd Annual RECOMB Workshop on Regulatory Genomics, Imperial College Press, London, December 2008. (130 pages)

  • Book chapters

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

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

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

  • Journal Papers

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

    2. 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.

    3. 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.

    4. 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.

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

    6. 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.

    7. 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.

    8. 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.

    9. 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.

    10. 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.

    11. 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.

    12. 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.

    13. 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.

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

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

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

    17. 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.

    18. 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.

    19. 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.

    20. 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.

  • Conference Papers

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

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

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

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

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

    6. 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

    7. Sriganesh Srihari, Hoong Kee Ng, Kang Ning, Hon Wai Leong. Detecting Hubs and Quasi Cliques in Scale-free Networks. Proceedings of 19th International Conference on Pattern Recognition (ICPR), pages 1--4, Tampa, Florida, USA, 8-11 December 2008.

    8. 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.

    9. 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.

    10. 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.

  • Invited Keynotes, Talks, & Tutorials

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  2007

  • Books

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

  • Book chapters

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

  • Journal Papers

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

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

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

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

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

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

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

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

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

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

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

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

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

    14. 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.

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

    16. 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.

    17. 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 Wen Bin Bin, Vladimir Kuznetsov, Atif Shahab, Wing-Kin Sung, Guillaume Bourque, Nallasivam Palanisamy, Chia-Lin Wei. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Research, 17(6):828-838, 2007.

    18. Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong. Enabling More Sophisticated Gene Expression Analysis for Understanding Diseases and Optimizing Treatments. ACM SIGKDD Explorations, 9(1):3-13, June 2007. (reviewed invited paper)

    19. 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.

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

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

  • Conference Papers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Invited Keynotes, Talks, & Tutorials

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

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

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

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

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

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

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

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

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

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

  2006

  • Books

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

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

  • Journal papers

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

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

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

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

    5. Rajesh Chowdhary, Sin Lam Tan, R. Ayesha Ali, Brent Boerlage, Limsoon Wong, and Vladimir B Bajic. Dragon Promoter Mapper (DPM): A Bayesian Framework for Modeling Promoter Structures. Bioinformatics, 22(18):2310--2312, 2006.

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

    7. Hon Nian Chua, Wing-Kin Sung, Limsoon Wong. Exploiting Indirect Neighbours and Topological Weight to Predict Protein Function from Protein-Protein Interactions. Bioinformatics, 22:1623--1630, 2006.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Conference papers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Invited Keynotes, Talks, & Tutorials

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  2005

  • Books

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

  • Book chapters

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

  • Journal papers

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

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

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

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

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

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

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

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

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

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

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

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

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

    14. Shao-Wu Meng, Zhuo Zhang, Limsoon Wong. A +1 Programmed Ribosomal Frameshifting in a Human C2H2 Zinc Finger Gene Discovered by Computational Analysis. Biotechnology, 4(4):316--324, 2005.

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

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

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

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

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

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

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

  • Conference papers

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  • Invited Keynotes, Talks, & Tutorials

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

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

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

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

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

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

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

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

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

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

  Selected Older Papers

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

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

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

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

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

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

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

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

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

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

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

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

  ---

  Lab Coordinator: Limsoon Wong / Last updated: 12 August 2023.