jagath.jpgJagath C Rajapakse, PhD, FAIMBE, FIEEE

Professor of Computer Engineering

Director, BioInformatics Research Center

School of Computer Engineering

    Nanyang Technological University
    N4-2a06, 50 Nanyang Avenue
    Singapore 639798

Email: asjagath[at]ntu.edu.sg; jagath[at]mit.edu

   Tel: +65 67905802; Fax: +65 67926559



Jagath Rajapakse is Professor and Director of BioInformatics Research Center at the School of Computer Engineering, Nanyang Technological University (NTU). He is Visiting Professor of Biological Engineering at the Massachusetts Institute of Technology (MIT). He obtained B.Sc.(Eng) degree with First Class Honors from the University of Moratuwa (Sri Lanka) and M.S. and Ph.D. degrees in electrical and computer engineering from the University of Buffalo (USA). He was Visiting Fellow at the National Institute of Mental Health (USA) and Visiting Scientist at the Max-Planck-Institute of Brain and Cognitive Sciences (Germany).

His research interests are in the areas of cellular and brain imaging, computation and systems biology, and machine learning. Professor Rajapakse has made several fundamental contributions in his areas of research and was listed among the most cited scientists. He has published over 250 peer-reviewed journal and conference papers, and book chapters.  He serves presently as Associate Editor for the IEEE Transactions on Medical Imaging and the IEEE Transactions on Computational Biology and Bioinformatics, and has earlier served in editorial boards of several other journals. He is Fellow of American Institute of Medical and Biological Engineering (AIMBE) and Fellow of Institute of Electrical and Electronics Engineering (IEEE).



BI6103: Computational Biology 

BI6106: Algorithms in Bioinformatics

SMA 5303/MIT 15.077: Statistical learning and data mining in bioinformatics

CE/CZ 1007: Data Structures (tutorials)

CE 1005: Digital Logic (tutorials)

Previously offered courses



Research Page

Research Team


Research Grants

Invited Talks


▪ AMAP (IEEE Transactions on Medical Imaging, Vol. 16, No. 2, 1997, pp. 176-186) 

▪ BMAP (Image &Vision Computing, Vol. 16, No. 3, 1998, pp. 165-180)


Professional Activities

      Steering Committee, International Conference on Pattern Recognition in Bioinformatics (PRIB)

      Faculty Fellow, Computational and Systems Biology (CSB) program, Singapore-MIT Alliance

Faculty Fellow, Singapore-MIT Alliance for Science and Technology (SMART), Singapore

Associate Editor, IEEE Transactions on Medical Imaging

Associate Editor, IEEE Transactions on Computational Biology and Bioinformatics



Selected Publications

F. X. Ivan, J. C. Rajapakse, R. E. Welsch, S. G. Rozen, T. Narasaraju, G. M. Xiong, B. P. Engelward, and V. T. K. Chow,  “Differential pulmonary transcriptomic profiles in murine lungs infected with low and highly virulent influenza H3N2 viruses reveal dysregulation of TERM1 signaling, cytokines, and chemokines,” Functional and Integrative Genomics, (published on line) [pdf]

V. R. Singh, H. Choi, E. Y. S. Yew, D. Bhattacharya, L. Yuan, C. J. R. Sheppard, J. C. Rajapakse, G. Barbastathiis, P. So, “Improving signal-to-noise ratio of structured light microscopy based on photon reassignment,” Biomedical Optical Express, Vol. 3, No. 1, pp. 206 – 214, 2012 [pdf]

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]

R.G. N. Meegama and J. C. Rajapakse, "NURBS snakes," Image and Vision Computing, 21, 2003, pp. 551-562 [pdf]

J. C. Rajapakse and J. Piyaratna, "Bayesian approach to segmentation of statistical parametric maps," IEEE Transactions on Biomedical Engineering, Vol. 48, No. 10, Oct. 2001, pp.1186-1194 [pdf]

J. C. Rajapakse, "Random-grid stereologic volumetry of MR head scans", Journal of Magnetic Resonance Imaging, Vol. 12, 2000, pp. 833-841 [pdf]



Last updated on 7/3/2012