Theodore J. Perkins / Perkins Lab
Note: I have moved to the Ottawa Hospital Research Institute as of January 2009, although I retain an Adjunct Professorship with the School of Computer Science at McGill. I can still be reached using my McGill email, or at my new email My new web page is here, or, for my OHRI page, try here. I do not expect to continue updating this web page.

Perkins Lab


About me: I am an assistant professor in the School of Computer Science at McGill University. I am also a member of the McGill Centre for Bioinformatics and the Centre for Nonlinear Dynamics in Physiology and Medicine.

Research summary: My research focuses on modeling dynamics and information processing in biochemical networks, elucidating their structure, and uncovering the principles upon which they operate. In particular, I am interested in using principles from probability theory, information theory, and control theory to identify and explain the structure and function of biochemical networks. I am interested in developing efficient algorithms for fitting differential equation models of time-series data and in understanding these fitting problems theoretically--issues which have not received nearly enough attention in the machine learning or statistics communities. More generally, I am interested in developing and applying machine learning and data mining algorithms for biological data sets.

Select recent publications:

Mitra, Datta, Perkins, Michailidis. Introduction to Machine Learning and Bioinformatics. Chapman & Hall/CRC Press (2008) [At Amazon]

Cory, Perkins "Implementing Arithmetic and Other Analytic Operations by Transcriptional Regulation" PLoS Computational Biology (2008) [On-Line]

Libby, Perkins, Swain, "Noisy information processing through transcriptional reegulation" Proceedings of the National Academy of Sciences (2007) [On-Line]

Perkins, Jaeger, Reinitz, Glass, "Reverse Engineering the Gap Gene Network of Drosophila melanogaster." PLoS Computational Biology (2006) [On-Line]

Rosenfeld, Perkins, Alon, Elowitz, Swain, "A fluctuation method to quantify in vivo fluorescence data." Biophysical Journal (2006) [On-Line]

Research keywords: computational biology, mathematical biology, bioinformatics, systems biology, machine learning, dynamical systems, genetic networks, development, Drosophila melanogaster, segmentation network.


Office: My office is in the McGill Centre for Bioinformatics, which is room 332 of the Lyman-Duff Medical Building.


Phone: (514) 398-5018

Fax: (514) 398-3387

Snail mail:

Prof. Theodore J. Perkins
McGill Centre for Bioinformatics
3775 University St.
Montreal, Quebec, H3A 2B4


Some miscellaneous invited lectures:

Student Advising

I am actively recruiting MSc and PhD students, and also enjoy working with undergraduates on honors/summer/research projects. If you think you might be interested in working with me and want to learn more, email me. Some (but not all) representative project areas in which I'm trying to recruit are: See also: Information for students interested in studying Computer Science or Software Engineering at McGill University.

See also: Undergraduate research project courses (open to all students in the Faculty of Science)


(In reverse chronological order.)