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Systems Biology

Welcome to the Systems Biology Training Program

A CIHR initiative (2009 - 2015)

We are no longer funding new students to our Program


***2015 Systems Biology Symposium***

Personalized Medicine of Cancer

May 28th, 2015, McGill University, Faculty Club and Conference Centre

For more information



Ph.D. Oral Defense
SPEAKER: Faiyaz Al Zamal

TITLE: Understanding the architectural basis of the robustness in transcriptional regulatory networks

DATE AND TIME:  Friday, May 1, 2015,    10:00 a.m.

PLACE: McConnell Eng. Bldg., room 103


Robustness to random mutations and environmental perturbations aids biological entities to survive and thrive under uncertainty. Empirical studies have uncovered the remarkable mutational and environmental robustness of transcriptional regulatory networks (TRN) in a variety of organisms. These transcriptional networks also exhibit distinct topological and parametric traits differentiating them from unconstrained random networks of similar size. A long-standing open problem in systems biology is to understand how these architectural traits of a TRN influence its robustness; which topological and parametric features can the striking robustness of TRNs be attributed to? This thesis presents three complete manuscripts describing computational and statistical methods we devised (i) to approach this open question concerning the architectural basis of the robustness of TRNs and (ii) to gain a comparative account of the relative contributions of different topological features to TRN robustness.

In the first article, we focus on the robustness contribution of a specific class of topological features: the first-order degree-based features of the TRNs. We devised a computational framework to compute and compare the robustness contributions of such features. Using it, we show that simple organizational principles such as limiting the number of regulatory TFs and suppressing the inter-regulatory connections (cross-talk) can significantly boost the robustness. In the second article, we use the same framework to estimate the contribution of sign-based parametric features and higher-order topological features to robustness. The study unearths a synergistic association between the topological and the sign-based features of TRNs for the attainment of robustness. Finally, in the third article, we introduce novel computational measures reflecting the robustness (or the lack thereof) against perturbations using only qualitative information about the transcriptional network. We f  ind that these measures, particularly the ones considering the interaction signs along with the network topology, carry a moderate, but definite signature of the real phenotypic impact of the perturbations.

On the whole, the thesis advances our understanding of the fundamental structural principles which make biochemical systems robust. We contribute a general framework enabling the comparison of the contributions of different features to robustness, uncover previously unreported architectural features of the transcriptional regulatory networks that are unlikely to appear in these networks by mere chance, and devise novel random network generation methods for selective retention or negation of these features.


Prof. J. Cheung (Chair/Deputy)                                  Prof. D. Ruths (Supervisor)

Prof. J. Waldispuhl (Internal Member)                   Prof. M. Blanchette (Internal Examiner)

Prof. G. Fussmann (External Member)                   Prof. TBA (Pro-Dean)    



Congratulations Doctor Sophia Kapchinsky!

Micro and Nanobioengineering Workshop

 Hands-on experience in several areas including photolithography, microfluidic immunoassays, and microcontact printing. This should be of particular interest to biomedical researchers, chemists, and physicists, as well as biomedical, mechanical, chemical, and materials engineers.

March 2-6, 2015 at McGill University

For further details

Congratulations to Systems Biology student Jan Gogarten (2012) for his involvement in tracking down the origins of the ebola outbreak.

Good job, Jan!

For further details

Fundamentals Montreal Light Microscopy Workshop

MLMC Fundamentals course March 2-6, 2015 at McGill University!
Lots of lectures and hands-on microscopy.
For more details




We are seeking a highly motivated post-doctoral researcher to work on the understanding of the molecular and cellular mechanisms that lead to the development of allergic asthma. Of interest to us is to characterize the genetics of the trait, which involve imprinting analysis, gene-gene and gene-environment interaction studies. The project includes genomics, genetics epigenetics and proteomics approaches on familial sample of 1250 persons from Saguenay–Lac-Saint-Jean include in a well characterize biobank in Canada. Actually we have accesses to respiratory phenotypes and genotyping data from GWAS, EWAS and we benefits to the strong collaboration in the context of national (example Respiratory Health Network of the FRSQ) and international research groups (as example AllerGen and GABRIEL).

The research program is supported by different sources of funding since ten years and it has recently been reconducted for seven additional years. The successful candidate will be encouraged to produce excellent data in order to send an application of this project to granting agencies.

Applicants should have a research formation in relevant fields of complex trait genetics, molecular biology, epidemiology genetics and/or functional genetics and also enthusiasm and motivation for basic biomedical research. Good communication skills in English are a prerequisite. Interested applicants should send a cover letter explaining their interests in the project, a curriculum vitae including previous publications and three reference letters.

This position is supported for a year. The successful applicant will be encouraged to apply for a fellowship for the next years.

Applications should be sent to:

Dr Catherine Laprise

Canada Research Chair on Genetic Determinants of Asthma

555 boulevard de l’Université

Chicoutimi, QC G7H 2B1

Tel: 418-545-5011 #5659

catherine [dot] laprise [at] uqac [dot] ca (catherine [dot] laprise [at] uqac [dot] ca)

Ph.D. Oral Defense
 SPEAKER: Mohamed Raef Smaoui
TITLE: Investigating the effect of mutations on the stability and toxicity of amyloid proteins for therapeutic benefit
DATE: Thursday, November 13, 2014
TIME: 11:30 a.m.
PLACE: McConnell Eng. Bldg., room 103

Amyloid aggregation is involved in the death of many cells and is believed to be the leading cause of neurodegenerative diseases such as Alzheimers, Parkinsons, Huntington, and Type II Diabetes. In order to counter their detrimental effects to the cell, it is crucial to first understand their intrinsic structural properties and their molecular dynamics. Although the topic of amyloid nucleation has been studied extensively, there are no computational studies modeling full aggregation of amyloid proteins into stable long fibril structures and analyzing their stability potentials. In addition to the computational complexity of these problems, there have been very few computational studies exploring the effect of sequence mutations on amyloid stability, amyloidegenicity and toxicity. In this thesis, we ultimately aim to construct these computational methods by modeling and simulating the dynamics of amyloid fibril build-up and assessing their sensitivity to sequence alterations. We present the tools we built to simulate the aggregation process of amyloid proteins into fibrils, explore the effect of sequence mutations on destabilizing amyloid fibrils, reveal the mutational landscape of the amylin amyloid protein involved in diabetes, and outline a novel method to construct a therapeutic agent to minimize the toxicity of amyloid oligomers in the pancreas of diabetes patients.

Prof. M. Maheswaran (Chair/Deputy)   Prof. J. Waldispuhl(Supervisor)
Prof. M. Blanchette (Internal Examiner)   Prof. N. Moitessier (Internal member)
Prof. P. Harrison (External member)   Prof. TBA (Pro-Dean) 


We are not currently funding any new students to our Program