Text Box: Professor Jagath Rajapakse

Director, BioInformatics Research Center

Nanyang Technological University
50 Nanyang Avenue
Singapore 639798

 

Email: asjagath@ntu.edu.sg

          jagath.rajapakse@gmail.com

Tel: +65 67905802/67906608

Fax: +65 67926559/63162780

 

 

Jagath Rajapakse is a Professor of Computer Engineering and the Director of the BioInformatics Research Centre, Nanyang Technological University (NTU). He is also a Visiting Professor to the Department of Biological Engineering, Massachusetts Institute of Technology (MIT). He began his postgraduate studies at the University of Buffalo (USA) under the Fulbright Scholarship, where he received M.Sc. and Ph.D. degrees in Electrical and Computer Engineering. Before joining NTU (Singapore), he obtained his post-doctoral training at the Max-Planck-Institute of Cognitive and Brain Sciences (Germany) and the National Institute of Mental Health (USA).

 

Professor Rajapakse’s research expertise are in the areas of machine learning, brain imaging, and computational and systems biology. He has authored over 210 research papers in refereed journals, books, and conference proceedings. He serves as Associate Editor for IEEE Transactions on Medical Imaging, IEEE Transactions on Computational Biology and Bioinformatics, and IEEE Engineering in Medicine and Biology Magazine, and in editorial boards of several other journals.

 

  • Professional activities

o    Director, BioInformatics Research Centre (BIRC), NTU

o    R & D Committee, School of Computer Engineering (SCE), NTU

o    Fellow, Singapore-MIT Alliance, Computation and Systems Biology (CSB) program

o    Chair, IAPR Technical Committee on Pattern Recognition for Bioinformatics (IAPR-TC20)

o    Associate Editor, IEEE Transactions on Computational Biology and Bioinformatics (IEEE TCBB)

o    Associate Editor, IEEE Transactions on Medical Imaging (IEEE TMI)

o    Guest Editor, IEEE Engineering in Medicine and Biology Magazine (IEEE EMBM)

o    Editorial Board, International Journal of Computational Intelligence

o    Editorial Board, Neural Information Processing -- Letters and Reviews

o    Program Chair, Third IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2008)

o    Special Session Chair, 2008 IEEE World Congress of Computational Intelligence (WCCI-IJCNN 2008)

o    General Chair, Second IAPR International Workshop on Pattern Recognition in Bioinformatics (PRIB 2007)

o    General Co-Chair, 2007 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2007)

o    Program Co-Chair, 5th European Conference on Evolutionary Computation, Machine Learning, and Data Mining in Bioinformatics (EvoBIO 2007)

 

  • Teaching

o    CPE101: Electronics Principles

o    CPE/CSC103 Mathematics I / Foundation Mathematics

o    CPE104: Logic Circuits   

o    BI6103: Computational biology  

o    SMA 5301: Perspectives of Computational and Systems Biology

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

o   Previously taught courses

 

 

·         Research

    • Graduate students
    • Team
    • Software (kindly cite the publication if the software contributes to your research) : 

§  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)

o    Benchmarking of MR tissue segmentation algorithms

o    Edited books

 

 

·         Selected Publications

§  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 (in press)

§  C. Chen and J. C. Rajapakse, Grid-enabled BLASTZ: applications to comparative genomics,” Journal of VLSI Signal Processing Systems, (in press)

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

§  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, pp. 248-269, January 2007

§  W. Lu and J. C. Rajapakse, “ICA with Reference,” Neurocomputing, 69. pp. 2244 – 2257, Oct 2006

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

§  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

§  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

§  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

§  L. S. Ho, and J. C. Rajapakse, “Input encoding method for identifying transcription start sites in RNA polymerase II promoters by neural networks,” Soft Computing, Vol. 10, No. 4, pp. 331-337, February 2006

§  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, 2006, pp. 9-11, January 2006

§  Amos R. Omondi and Jagath 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

§  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

§  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

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

§  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. 

§  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

§  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