Theodore J. Perkins, Phd
Telephone: 613-737-8899 ext. 79795
Fax: 613-739-6294
Scientist, Regenerative Medicine Program, Ottawa Hospital Research Institute

Director, Ottawa Bioinformatics Core Facility
Member, Ottawa Methods Centre, Ottawa Hospital Research Institute
Assistant Professor, Department of Biochemistry, Microbiology and Immunology, University of Ottawa
Cross-appointed, School of Electrical Engineering and Computer Science, University of Ottawa
Adjunct Professor, School of Computer Science, McGill University

Research Interests

Research in the Perkins lab spans bioinformatics, computational biology, mathematical biology and machine learning. Our lab is located in the Sprott Center for Stem Cell Research at the Ottawa Hospital Research Institute. The Sprott Center is one of the top stem cell research centers in Canada, and one of the top muscle stem cell centers in the world. We do some basic theoretical and computational research, especially in the areas of dynamical and/or stochastic model fitting for molecular biological systems. We also work with a number of collaborators to analyze data and model specific biological systems, especially stem cell differentiation dynamics and gene regulatory networks in a variety of normal and diseased cell types. We also have pet interests in understanding information processing strategies exhibited by cells and their molecular implementations, and in high throughput drug screening. More generally, members of the Perkins lab are interested in bioinformatics, machine learning and statistical applications in molecular biology and health research.

Select Publications
(Note: A complete list of publications is available at

"Transcriptional Dominance of Pax7 in Adult Myogenesis Is Due to High-Affinity Recognition of Homeodomain Motifs" Developmental Cell, Vol. 22, Iss. 6, pp. 1208-1220, 2013. [Access On-Line]

"What Do Molecules Do When We're Not Looking? State Sequence Analysis for Stochastic Chemical Systems" Journal of the Royal Society Interface, Vol. 9, No. 77, pp. 3411-3425, 2013. [Access On-Line]

"Systematic Discovery of Rab GTPases with Synaptic Functions in Drosophila." Current Biology, Vol. 21, Iss. 20, pp. 1704-1715, 2011.[Access On-Line]

"Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data." PLoS Computational Biology Vol. 7, No. 5, Art. e1002048, 2011. [Access On-Line]

"Strategies for cellular decision-making." Molecular Systems Biology, Vol. 5, Article 326, 2009. [Access On-Line]

"Introduction to Machine Learning and Bioinformatics." Chapman & Hall/CRC Press, 2008. [At Amazon]

"Noisy information processing through transcriptional regulation." Proceedings of the National Academy of Sciences, Vol. 104, No. 17, pp. 7151-7156, 2007. [Access On-Line]

"Reverse Engineering the Gap Gene System of Drosophila Melanogaster." PLoS Computational Biology, Vol. 2, No. 5, e51, 2006.[Access On-Line]

"A fluctuation method to quantify in vivo fluorescence data." Biophysical Journal, Vol. 91, No. 2, pp. 759-66, 2006. [Access On-Line]

"Identifying Regulatory Subnetworks for a Distinguished Set of Genes." Molecular and Cellular Proteomics, Volume 4, pp. 683-692, 2005. [Access On-Line]

"Inferring Models of Gene Expression Dynamics." Journal of Theoretical Biology, Vol. 230, pp. 289-299, 2004. [Access On-Line]