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Jagath C Rajapakse, PhD, FIEEE

Professor of Computer Engineering

School of Computer Science and Engineering

Nanyang Technological University

N4-2a06, 50 Nanyang Avenue

Singapore 639798

Email: asjagath[at]

Tel: +65 67905802; Fax: +65 67926559



Jagath Rajapakse is Professor of Computer Engineering at the School of Computer Science and Engieering at the Nanyang Technological University (NTU), Singapore. He obtained Ph.D. degrees in electrical and computer engineering from the University of Buffalo. He was Visiting Professor of Biological Engineering at the Massachusetts Institute of Technology, Visiting Scientist at the Max-Plank Institute of Cognitive and Brain Sciences (Leipzig), and Visiting Fellow at the National Institute of Health (USA).

His current research interests are in brain imaging, and computational and systems biology. Professor Rajapakse has published over 300 research papers in scientific journals and conferences.  He served as Associate Editor for the IEEE Transactions on Neural Networks and Learning Systems, the IEEE Transactions on Computational Biology and Bioinformatics, and the IEEE Transactions on Medical Imaging. He is a Fellow of Institute of Electrical and Electronics Engineering (IEEE).



CZ4041: Machine learning

CZ4042: Neural networks

CE7412: Computational and systems biology



Funded projects

      Post-doc positions

      Projects for Ph.D. students

Research Team

List of Publications



Selected Publications

A. Kumar, F. Lin, and J. C. Rajapakse, “Mixed spectrum analysis on fMRI time series,” IEEE Transactions on Medical Imaging, Vol. 35, No. 6, pp. 1555-62, 2016.

P. A. Mundra and J. C. Rajapakse, “Gene and sample selection with T-score with sample selection,” Journal of Biomedical Informatics, 59, pp. 31-41, 2016.

W. Liu, K. Miao, G. Li, K. Chang, J. Zheng, and J.C. Rajapakse, “Extracting rate changes in transcriptional regulation from MEDLINE abstracts,” BMC Bioinformatics, 2014, 15 (Suppl 2): S4

W. L. Au, J. Zhou, P. Palmes, Y.-Y. Sitoh,  L. C. Tan, and J. C. Rajapakse, “Levodopa and the feedback process on set-shifting in Parkinson’s disease,” Human Brain Mapping,33 (1), pp. 27-39, 2012 [pdf]

J. C. Rajapakse and P. A. Mundra, “Stability of building gene regulatory networks with sparse autoregressive models,” BMC Bioinformatics, 12, (Suppl. 13), S17, 2011 [pdf]

M. Veronica, R. E. Welsch, A. Ng, P. Matsudaira, and J.C. Rajapakse, “Correlation of cell membrane dynamics and cell motility,” BMC Bioinformatics, 12 (Suppl.13), S19, 2011 [pdf]

H. Q. Sun,  M. Y. H. Low, W. J. Hsu, C. W. Tan, and J. C. Rajapakse, “Tree-structured algorithm for long weak motif discovery,” Bioinformatics, Vol. 27, No. 19, pp. 2641 – 2647, 2011 [pdf]

M. N. Nguyen, J. M. Zurada, and J. C. Rajapakse, “Towards better understanding of protein secondary structure: extracting prediction rules,” IEEE Transactions on Computational Biology and Bioinformatics, Vol. 8, No. 3, pp. 858 – 864, 2011 [pdf]

I. Chaturvedi and J. C. Rajapakse, “Building gene networks with time-delayed regulations,” Pattern Recognition Letters, Vol. 31, Issue 14, pp. 2133 - 2137, Oct 15, 2010 [pdf]

P. A. Mundra and J. C. Rajapakse, “SVM-RFE with MRMR filter for gene selection,” IEEE Transactions on Nanobiosciences, Vol. 9, Issue 1, pp. 31 - 37, Mar 2010 [pdf]

M. Veronika, J. Evans, P. Matsudaira, R. Welsch, and J. C. Rajapakse, “Subpopulation analysis based on temporal features of high content images,” BMC Bioinformatics, 10: Suppl. 15, art. no. S4, Dec 2009 [pdf]

M. N. Nguyen, J. Ma, G. Fogel, and J. C. Rajapakse, “Di-codon usage for classification of genes,“ Biosystems, Vol. 98, Issue 1, pp. 1 - 6, Oct 2009 [pdf]

J. Cheng and J. C. Rajapakse, “Segmentation of clustered nuclei with shape markers and marking function,” IEEE Transactions on Biomedical Engineering, Vol. 56, Issue 3, pp. 741 - 748, Mar 2009 [pdf]

J. C. Rajapakse, “Computational techniques: Pattern discovery in bioinformatics,” IEEE Engineering in Medicine and Biology, Vol. 28, Issue 4, July 2009, pp. 19-24 [pdf]

Y. Zhang and J. C. Rajapakse (Eds.), Machine Learning in Bioinformatics, John Wiley and Sons Inc., 2009

J. Ma, M. N. Nguyen, and J. C. Rajapakse, “Gene classification using codon usage pattern analysis and support vector machines,” IEEE Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 1, Jan-March 2009, pp. 134-143 [pdf]

J. C. Rajapakse, W. Yang, X. Zheng, and J. Zhou, “Probabilistic framework for brain connectivity from functional MR images,” IEEE Transactions on Medical Imaging, Vol. 27, No. 6, pp. 825-833, 2008 [pdf]

J. C. Rajapakse and J. Zhou, “Modeling effective brain connectivity with dynamic Bayesian networks,” NeuroImage, Vol. 37, Issue 3, Sept 2007, pp. 749-760 [pdf]

N. Nguyen and J. C. Rajapakse, “Two stage support vector machines for protein secondary structure prediction,” International Journal of Data Mining and Bioinformatics, Vol. 1, No. 3, January 2007, pp. 248-269 [pdf]

W. Lu and J. C. Rajapakse, “ICA with Reference,” Neurocomputing, 69, Issues 16-19, Oct 2006, pp. 2244 – 2257 [pdf]

X. Zheng and J. C. Rajapakse, “Learning functional structure from fMR images,” NeuroImage, Vol. 31, No. 4, pp. 1601-1613, July 2006 [pdf]

Y. Wang and J. C. Rajapakse, “Contextual modeling of functional MR images with conditional random fields,” IEEE Transactions on Medical Imaging, Vol. 25, No. 6, pp. 804-812, June 2006 [pdf]

M. N. Nguyen and J. C. Rajapakse, “Two-stage support vector regression approach for predicting accessible surface areas of amino acids,” PROTIENS: Structure, Function, and Bioinformatics, 63: 542-550, May 2006 [pdf]

J. C. Rajapakse, C. L. Tan, X. Zheng, S. Mukhopadyay, and K. Yang, “Exploratory analysis of brain connectivity with ICA,” IEEE Engineering in Medicine and Biology Magazine, March/April Issue, Vol. 25, No. 2, 2006, pp. 102-111 [pdf]

R. G. N. Meegama and J. C. Rajapakse, “NURBS-based visualization of age-related diversity in cortical morphology,” Journal of Visualization, Vol. 9, No. 1, pp. 9-11, January 2006 [pdf]

R. Omondi and J. C. Rajapakse (Eds.) FPGA Implementations of Neural Networks, Springer-Verlag, 2006, Approx 365p, Hardcover, ISBN: 0-387-28485-0

J. Zhou and J. C. Rajapakse, “Segmentation of subcortical brain structures using fuzzy templates,” NeuroImage, Vol. 28, No. 4, Dec. 2005, pp. 927-936 [pdf]

W. W. P. Tham, S. J. R. Liow, J. C. Rajapakse, C. L. Tan, S. E. S. Ng, W. E. H. Lim, and L. G. Ho, “Phonological processing in Chinese-English bilingual biscriptals: an fMRI study, “, NeuroImage, Vol. 28, No. 3, Nov. 2005, pp. 579-587 [pdf]

J. C. Rajapakse, K. B. Duan, and W. K. Yeo, “Proteomic cancer classification with mass spectra data”, American Journal of Pharmacology, 5 (5), October 2005, pp. 228-234 [pdf]

K.-B. Duan, J. C. Rajapakse, H. Wang, and F. Azuaje, “Multiple SVM-RFE for gene selection in cancer classification with expression data,” IEEE Transactions on Nanobioscience, Vol. 4, No. 3, September 2005, pp. 228-234 [pdf]

J. C. Rajapakse and L. S. Ho, "Markov encoding for detecting signals in genomic sequences," IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 2, No. 2, April-June, 2005, pp. 131-142 [pdf]

M. N. Nguyen and J. C. Rajapakse, “Prediction of protein relative solvent accessibility with a two-stage SVM approach,” PROTIENS: Structure, Function, and Bioinformatics, Vol. 59, Issue 1, April 2005, pp. 30-37 [pdf]

W. Lu and J. C. Rajapakse, “Approach and applications of constrained ICA”, IEEE Transactions on Neural Networks, Vol. 16, No. 1, January, 2005, pp. 203-212 [pdf]



Last updated on 19/08/2016