What we do:
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 (www.ohri.ca). 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 machine learning and statistical applications in molecular biology and health research.
Welcome! to Sharmin Nilufar, a new postdoctoral fellow who has joined the lab to work on advanced image processing and machine learning techniques for microscopy applications. (January 2012)
Congratulations! to Jeremie Lefebvre, who joined the lab as a postdoc last fall, and who has just been awarded an FQRNT Postdoctoral Fellowship. Good work, Jeremie! (June 2011)
"Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data" has just appread in PLoS Computational Biology [Access On-Line] (May 2011)
Publication update: In the past few months we've published five new papers in areas such as stochastic chemical kinetics, network inference, codon bias and filopodia organization. See our publications page for more info. (Dec 2010)
New lab members! We are very happy to welcome three new members to our lab this fall: Jeremie Lefebvre, a postdoc who did his PhD in physics on mathematical / computational neuroscience, Parameswaran Ramachandran, a postdoc who did his PhD in electrical engineering on genomic signal processing, and Pavel Levin, an MSc student with an honors applied math background from McGill. (Sep 2010)
"Estimating the Stochastic Bifurcation Structure of Cellular Networks" has just appeared in PLoS Computational Biology [Access On-Line] (Mar 2010)
"A trade-off between sample complexity and computational complexity in learning Boolean networks from time-series data" has just appeared in IEEE/ACM Transactions on Computational Biology and Bioinformatics [Access Online] (Feb 2010)
"Maximum likelihood trajectories for continuous-time Markov chains" appeared at NIPS-09 [Access Online] (Dec 2009)
"Strategies for Cellular Decision Making", coauthored with Peter Swain, has just appeared in Molecular Systems Biology [Access Online] (Nov 2009)
Recruitment: Dr. Perkins has finished recruiting for 2010. We expect one or more positions to be available at the graduate or postdoctoral level beginning in 2011. If you think you may be interested in joining the lab, see our Recruiting page for more information.