Jagath
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).
Teaching
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
Software:
▪ 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]
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]
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]
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Last updated on 7/3/2012