Bioinformatics and Computational Biology


Papers:  (Available as .pdf unless otherwise specified)

A New Phylogenetic Diversity Measure Generalizing the Shannon Index (with B. Allen and  Y. Bar Yam,  American Naturalist 174 (2009),236-243.


Ensemble machine methods for DNA binding (with Y. Fan, and C. DeLisi),  Machine Learning and Applications 7,  M. Wani, et al., eds.  IEEE, Washington (2008),709-716.  Algorithm available here.


Regulatory analysis for exploring human disease progression (with D. Holloway and C. DeLisi), Biology Direct 3:24, 2008. Algorithm available here.


Building transcription factor classifiers and discovering relevant biological features,  (with D. Holloway and C. DeLisi), BiologyDirect 3:22, 30 May 2008. Algorithm available here.


SVMMotif:  A machine learning motif algorithm (with Y. Fan, D.Holloway and C. DeLisi), International Conference on Machine Learning and Applications 6, 573-580, IEEE, Washington, 2007. Algorithm available here.


Learning methods for DNA binding in computational biology (with D. Holloway, et al.) International Joint Conference on Neural Networks,  20, IEEE, Los Alamitos 1605, 2007.


Machine learning for regulatory analysis and transcription factor target prediction in yeast (with D. Holloway and C. DeLisi), Systems and Synthetic Biology 1 (2006), 25-46.                                                                                                              


Approximating functions in reproducing kernel Hilbert spaces via statistical learning theory (with L. Raphael), in Splines and Wavelets, G. Chen and M.J. Lai, eds, (2006) 270-286

Machine learning methods for transcription data integration (with D. Holloway and C.DeLisi), IBM Journal of Research and Development 50(2006), 631-644 (Abstract only - Journal link is here)


Some Links:

BU Bioinformatics Program

Mathematical Biosciences Institute

Harvard Program for Evolutionary Dynamics

Harvard Mathematical and Computational Biology

MIT Computational Biology Group

MIT Computational and Systems Biology