John Aitchison, Ph.D.
Understanding biological complexity in the context of modular cellular organization is the foundation of cellular systems biology and is the focus of the Aitchison lab. Specifically, the lab investigates conditions that induce peroxisomes.
The Aitchison Lab is highly collaborative and integrative. Experts on staff range from engineers to physicists. As they work together to develop and apply new technologies and methods in genomics, proteomics, genetics, and computational biology, they are beginning to identify and mathematically model aspects of complex cellular responses and gene expression that can be applied to infectious disease research.
Support
The National Institutes of Health, The National Institute for Allergy and Infectious Disease Research and the Canadian Institute for Health Research provide support for Aitchison’s current research.
Field of Study
Since joining the Institute for Systems Biology in 2000, my laboratory has been exploiting systems based assays and analyses to reveal and understand complex biological phenomena. Over the past ten years, we have focused on yeast as a model for developing systems biology approaches. Now a principal investigator (Member) at Seattle Biomedical Research Institute, my goal is to immerse my lab in an environment rich in infectious disease research to enhance our collective exposure to, and education in, research of infectious diseases. I've also kept my faculty position and a lab at the Institute of Systems Biology to maintain a position at the cutting edge of systems biology and to bring new developments to infectious disease research at Seattle BioMed.
Biography
Education
Ph.D. Biochemistry McMaster University
B.Sc. Biotechnology and genetic engineering McMaster University
Professional Experience
- Director of Integrative Biology and Full Member, Seattle Biomedical Research Institute, 2011-present
- Senior Vice President and Executive Director for Integrative Biology, Institute for Systems Biology, 2011-present
- Professor, Institute for Systems Biology, 2005-present
- Associate Director, Institute for Systems Biology, 2006-2011
- Affiliate Professor, Department of Biochemistry, University of Washington, 2003-present
- Adjunct Professor, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, 2002-present
- Adjunct Professor, Department of Cell Biology, Faculty of Medicine, University of Alberta, 2002-present
- Associate Professor, Institute for Systems Biology, 2000-2005
- Assistant Professor, Department of Cell Biology, faculty of Medicine, University of Alberta, 1997-2000
Select Honors & Awards
- Canadian Foundation for Innovation Research, 1998
- Alberta Heritage Foundation for Medical Research Scholarship, 1997
- Medical Research Council of Canada Scholarship, 1997
- Howard Hughes Medical Institute Research Associate Fellowship, 1995
- Medical Research Council of Canada Post Doctoral Fellowship, 1992
- Department of Biochemistry Scholarship, 1991
- Ontario Graduate Studies Scholarship, 1991
- Natural Sciences and Engineering Research Council of Canada Postgraduate Studentship, 1988
- Department of Biochemistry Scholarship, McMaster University, 1986
- Senate Scholarship, McMaster University, 1985
Publications
2011
2010
Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes
2009
2008
2007
2006
2005
Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae
2004
Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import
2003
2002
Improving the quality of kidneys from non-heart-beating donors, using streptokinase: an animal model
2001
2000
1999
1998
1997
1996
1995
1994
1992
1991
1990
1988
Staff
Abe Armstrong, Visiting Scientist
Anna Bran, Senior Project Coordinator
Lindsay Carpp, Postdoctoral Scientist
Sam Danziger, Bioinformatics Scientist
David Dilworth, Visiting Scientist
Arvind Jamakhandi, Postdoctoral Scientist
Song Li, Visiting Scientist
Leslie Miller, Visiting Scientist
Garrett Poshusta, Graduate Student
Alexander Ratushny, Staff Scientist
Rich Rogers, Visiting Scientist
Ramsey Saleem, Senior Scientist
Kate Sitko, Research Technician II
Accomplishments & Collaborations
Laboratory Accomplishments
- We used a quantitative mass spectrometry based analysis of the peroxisome, identifying both new static and dynamic components of the organelle, as well as mechanistic insight into the organization of actin at the peroxisome during biogenesis.
- Using a genome wide analysis of the signalome, we elucidated a signaling network governing responses to fatty acids, including the biogenesis of peroxisomes.
- Through both the characterization of a fatty acid responsive phosphoproteome and an integrative network approach, we were able to uncover key phosphorylation events regulating transcription factor activity during the peroxisome biogenesis process.
- We characterized the role of histone proteins and chromatin remodeling components in the regulation of oleate responsive promoter.
- We characterized cellular mechanisms of dynamic gene regulation in eukaryotic nuclei. Mechanisms include properties of regulatory network motifs as well as dynamic network structure to control and coordinate genetic and epigenetic responses to environmental stimuli.
- We have characterized mechanisms by which the nuclear pore complex and its associated factors contribute to the regulation of gene expression through chromatin organization.
Collaborations
- Institute for Systems Biology
- University of Washington
- University of Alberta
- The Rockefeller University
- University of British Columbia
- University of California, San Francisco
- ETH Zurich
- McGill University, Canada
- Institut Pasteur Korea
- University of Guelph