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Scientist, Regenerative Medicine, Ottawa Hospital Research Institute
Research
Research in the Perkins lab spans bioinformatics, computational biology, mathematical biology and machine learning. Recent work includes theoretical and applied research on inferring gene regulatory networks; methods for dynamical model fitting, particularly for ordinary and partial differential equation models; analysis of information processing in biomolecular systems; and experiment design for network inference and combinatorial drug screening. More generally, members of the Perkins lab are interested in machine learning and statistical applications in molecular biology and health research.
Positions available
Dr. Perkins is presently recruiting students / fellows at all levels, from undergraduate to postdoctoral. If you are interested in joining the lab, email to Dr. Perkins using the address above.
Selected Publications
S. Mitra, S. Datta, T. Perkins and G. Michailidis (2008) Introduction to Machine Learning and Bioinformatics. Chapman & Hall/CRC Press.
S. Cory and T. J. Perkins (2008) Implementing Arithmetic and Other Analytic Operations by Transcriptional Regulation. PLoS Computational Biology, Vol. 4(4), e1000064.
E. Libby, T. J. Perkins, P. S. Swain (2007) Noisy information processing through transcriptional reegulation. Proceedings of the National Academy of Sciences, Vol. 104, No. 17, pp. 7151-7156.
T. J. Perkins, J. Jaeger, J. Reinitz, L. Glass (2006) Reverse Engineering the Gap Gene System of Drosophila Melanogaster. PLoS Computational Biology, Vol. 2, No. 5, e51.
N. Rosenfeld, T. J. Perkins, U. Alon, M. B. Elowitz, P. S. Swain (2006) A fluctuation method to quantify in vivo fluorescence data. Biophysical Journal, Vol. 91, No. 2, pp. 759-66.
M. Scott, T. J. Perkins, S. Bunnell, F. Pepin, D. Y. Thomas, M. Hallett (2005) Identifying Regulatory Subnetworks for a Distinguished Set of Genes. Molecular and Cellular Proteomics, Volume 4, Pages 683-692.
T. J. Perkins, M. Hallett and L. Glass (2004) Inferring Models of Gene Expression Dynamics. Journal of Theoretical Biology, Volume 230, pp. 289-299.
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