Flow Cytometry Bioinformatics
My group is focused on applying bioinformatics techniques to flow cytometry data. Flow cytometry is a technique
that is widely used within the biomedical community. New high throughput methods can generate up to a thousand
flow cytometry data files per day and each data file can consist of millions of multiparametric descriptions of
individual cells. However flow cytometry lacks data standards for fully representing both the methods used and
the data generated, hindering the handling, exchange and dissemination of scientific research. Consequently,
there are a variety of challenges to archiving, analyzing and reporting the results of high throughput flow cytometry
experiments. Furthermore, only rudimentary bioinformatics tools exist to manage and mine high throughput data. We
are leading an international effort to develop a systemic approach to modeling, capturing, analyzing and
disseminating flow cytometry data. Initial work is focused on developing a community-based standard for recording
and reporting flow cytometry data. Software implementations of this standard (UML, XML, SQL, Java) and an ontology
(Ontology for Biomedical Investigations) being created to facilitate data
exchange between both software components and collaborative groups. Statistics packages
(e.g., flowCore/flowUtils/flowClust) are also being developed to allow
users to implement analyses in a high throughput fashion, as well as exchange these analyses in more meaningful ways
then are currently available. We are also testing our high throughput analysis methods to analyze flow cytometry data
on datasets from the British Columbia Cancer Agency and the British Children's Hospital including developing methods
for the high throughput analysis of lymphoma, Graft versus Host Disease and innate immunity. We are also developing
user-friendly software that implements some of the new data analysis and visualization methods we and others have developed.
My research is supported by the NIH, CIHR, Genome Canada, Genome BC, The Michael Smith Foundation for Health Research and the
BC Cancer Agency.
Open Positions
Graduate Student and Postdoctoral
Positions
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Updated October 17, 2008