graduate research opportunity in biomedical informatics

*Graduate Research Opportunity*

*Laboratory for Biomedical Knowledge Discovery*

*Carleton University in Ottawa, Canada*

The Laboratory for Biomedical Knowledge Discovery (
aims to develop semantics-aware computational methods towards increasing
our understanding of how living systems respond to chemical agents.

We are seeking three (3) MSc or PhD students in the following areas:

1) Metabolic Toxicology. The objective is to gain insight into
xenochemical-based toxicity using a novel semantic framework for
computational toxicology. The successful candidate will investigate aspects
of metabolic fate, enzymatic mechanism, molecular regulation and toxicity
prediction. This research will increase our ability to predict toxicity by
using increasing amounts of sophisticated knowledge and pave the way for
developing new regulatory protocols with Health Canada.

2) Cellular Dynamics. The objective is to investigate how the structure and
organization of molecular and cellular components affects cellular
dynamics. The successful candidate will further develop and undertake
studies using a novel a cell simulation framework, called BioThor, by
integrating its multi-scale hardware-accelerated engine with semantic
knowledge management.  This research may provide greater understanding of
the physical-chemical environment experienced by cellular systems.

3) Translational Medicine. The objective is to uncover chemical signatures
that elicit particular phenotypes. The successful candidate will design and
make use of formal ontologies to predict chemical associated phenotypes by
extending prior work with chemical and pathway knowledge, as well as known
side effects. This research could yield insight into the coordinated
targeting of pathways, which may form the basis for understanding adverse
drug events as complex phenotypes.


Deadline: Friday February 29, 2012 (yup, itís a leap year!)

The applicant should possess a strong background in biochemistry,
bioinformatics and/or computer science. The ideal applicant is able to
program and has a working knowledge of semantic web technologies. In order
to determine whether you would be a suitable candidate, please send the
following 3 documents to Dr. Michel Dumontier (

1 - Statement of Interest - briefly (1 page) describe a potential project
that you might undertake as supported by relevant scientific literature and
related to one of the three advertised areas of research

2 - Curriculum Vitae + 2 recommendation letters (1 from a thesis supervisor)

3 - University academic transcript

*** Note that successful applicants must satisfy and subsequently apply to
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Received on Wednesday, 8 February 2012 17:09:06 UTC