Fiona S. L. Brinkman, Associate Professor
Department of Molecular Biology and Biochemistry
Simon Fraser University
B.Sc., University of Waterloo
Ph.D., University of Ottawa
Office: SBB 7110
Phone: 778-782-5646
Email: brinkman@sfu.ca
Current Research Interests:
See the lab
website for more info.
Genomics and bioinformatics provide powerful new methods for the
study of microbes and microbial pathogenicity, hence the development of
a new field, Pathogenomics. I am forming an interdisciplinary "wet-lab"
and computer lab to investigate the following fundamental pathogenomics
questions:
How does a given pathogen and the property of pathogenicity
evolve?
What components of a bacterial genome sequence can be utilized to
predict the subcellular localization of proteins, particularly cell
surface-exposed proteins of relevance for pathogenicity?
What components of a genome sequence can be used to identify
virulence factors?
To investigate these questions, the laboratory will be performing
and developing computational analyses of genomes, individual proteins
and other laboratory data to facilitate the generation of new
hypotheses relevant to bacterial pathogenesis. These hypotheses will
then be tested in the laboratory using molecular genetic tools and
model host systems. Analyses include:
- Improved computational detection of horizontal gene transfer
through both codon usage bias and sequence similarity approaches, as
horizontal gene transfer appears to be an important mechanism in the
evolution of new pathogens. Laboratory confirmation of true cases of
horizontal gene transfer, leading to a more accurate evaluation of the
role horizontal gene transfer has played in the evolution of a new
pathogen (or the evolution of new pathogenic properties in an existing
pathogen).
- Analysis of a database of bacterial proteins of known subcellular
localization and development of an improved version of the program
PSORT to predict subcellular localization of bacterial proteins. The
focus is toward eventual prediction of surface-exposed regions of
proteins. Structural modeling and analysis of key surface-exposed
bacterial membrane proteins complements this work.
- Analysis of currently known and sequenced virulence factors in
all bacterial pathogens to identify sequence and structure commonalties
(particularly features of pathogenicity/genomic islands), functional
subgroupings, and their distributions within and between species.
Software development for these projects will focus primarily on
development of web-based applications and viewing tools. Some projects
are in collaboration with the Pathogenomics Project that I coordinate
(see link below). This laboratory endeavors to provide a stimulating
interdisciplinary research environment for students to learn about
bioinformatics, genomics, bacterial pathogenicity, molecular biology,
and microbiology.
space
Last updated 05/16/2006
