Bioinformatics and Computational Biology
Papers:
(Available as .pdf unless otherwise
specified)
Software For Simulation of Wavelet Matrix Operations and Quantum
Transforms (with Zhiguo Zhang)
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:
Mathematical Biosciences Institute
Harvard Program for Evolutionary
Dynamics
Harvard Mathematical
and Computational Biology
MIT Computational Biology Group
MIT Computational and Systems Biology