Department of Computer Science
School of Computing
National University of Singapore
Room CBL Lab, Building COM1, Law Link, Singapore 117590
Email: dongdife@comp.nus.edu.sg, dong.difeng@gmail.com (private)
Ph.D. Computer Science, National University of Singapore, Singapore, in progress,
Supervised by Prof. Limsoon Wong,
Thesis: Computational Techniques of Drug Pathway Identification and Treatment Optimization.
B.S. Computer Science, Fudan University, China, 2005,
Supervised by Dr. Xueqing Gong and Prof. Aoying Zhou,
Thesis: Applications of Self-Organized Map (SOM) Algorithm in Data Mining System.
Bioinformatics, Computational Biology, Knowledge Discovery in Cancer Research.
Drug Pathway Decipherer
Biological pathways have been incorporated into gene expression analysis to understand drug treatment response in disease population. However, existing methods fall short on several issues: 1) these works provide little information on the interplay between selected genes; 2) the collection of pathways that can be used, evaluated and ranked against the observed expression data is limited; 3) the generated hypotheses are still too general to guide further research and treatment. We have proposed a drug pathway identification system, which we called Drug Pathway Decipherer (Decipherer) to generate hypotheses of specific treatment responsive pathway. Decipherer takes in both pre- and post-treatment gene expression data, and evaluates known biological pathways on the data. In this talk, I will demonstrate a study case of applying Decipherer to two gene expression datasets of human nasopharyngeal carcinoma (NPC) treated with CYC202. As a result, we find the regulation of cell proliferation RAS-ERK pathway and anti-apoptosis PI3K-NFkB- IAP pathway are closely associated with treatment outcome...
W. Hsieh, R. Soo, B. Peh, T. Loh, D. Dong, D. Soh, L. Wong, S. Green, J. Chiao, C. Cui, Y. Lai, S. Lee, B. Mow, R. Soong, M. Salto-Tellez and B. Goh. Pharmacodynamic Effects of Seliciclib, an Orally Administered Cell Cycle Modulator, in Undifferentiated Nasopharyngeal Cancer. Clinical Cancer Research. (Submitted)
D. Soh, D. Dong, Y. Guo and L. Wong. Enabling More Sophisticated Gene Expression Analysis for Understanding Diseases and Optimizing Treatments. ACM SIGKDD Explorations, 9(1):3-14, June 2007. (Invited reviewed paper.)
D. Dong, C. Cui, B. Mow and L. Wong. Deciphering Drug Action and Escape Pathways: an Example on Nasopharyngeal Carcinoma. (Submitted)
W. Tan, D. Dong, M. Loh, L. Wong, R. Soo, I. Fichtner and R. Soong. Pathway Determinants of 5-Fluorouracil Activity. Poster presented at 20th EORTC-NCI-AACR symposium on "Molecular targets and Cancer Therapeutics". Geneva, Switzerland, 21-24 October 2008.
D. Dong, G. Liu and L. 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.
D. Dong and L.Wong. Using gene expression analysis for drug pathway identification: An example on nasopharyngeal carcinoma (NPC). Poster presented at 12th Annual International Conference on Research in Computational Molecular Biology (RECOMB'08), Singapore, 30 March-2 April 2008.