John Aitchison

John Aitchison

John Aitchison (Ph.D. McMaster University)

Adjunct Professor

Seattle Biomedical Research Institute/Institute for Systems Biology
Seattle, Washington
Phone: (206) 256-7470 / (206) 732-1344
Fax: (206) 256-7229 / (206) 732-1299 (fax)


  • CIHR Scholar
  • AHFMR Scholar

Systems Biology and Cellular Compartmentalization

The human genome project revolutionized how scientists view and practice biology. For the first time can see the entire genetic blueprint of an organism. The difficulty now is to understand how this blueprint is read to build a living organism. This challenge has catalyzed the development of new tools for high-throughput biological measurements, such as DNA microarrays, and large scale proteomic mass spectrometry. But sorting through the enormous amounts of information these techniques generate demands the integration of global analyses with computer science, mathematics, and statistics. This integration of technology, math and engineering with biology has spawned a new approach to studying biology, which is termed "systems biology". This approach holds the promise of being able to derive models that comprehensively represent the flow complex biological information in organisms, and to predict complex cellular behaviour.

Now, cell biologists have opportunities to exploit this revolution to its fullest to learn new fundamental biology. Our laboratories are located at Seattle Biomedical Research Institute and the Institute for Systems Biology in Seattle WA, and we work in close collaboration with the Rachubinski and Wozniak laboratories at the University of Alberta. Together we are using systems biology approaches to understand how compartmentalization regulates cellular function. In particular, we are using functional genomics, proteomics, computational biology, and molecular biology to understand nucleocytoplasmic transport and peroxisome biogenesis.

A more detailed description of our research can be found by clicking here.






Selected Publications

Dilworth, D.J., Saleem, R.A. Rogers, R.S., Mirzaei, H., Boyle, J., Aitchison, J.D. QTIPS: A novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. Journal of the American Society for Mass Spectrometry, (2010) Article in Press, Accepted Manuscript

Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD. (2010) Integrated phosphoproteomic analysis of a signaling network governing nutrient response and peroxisome induction, Mol Cell Proteomics. 2010 Apr 15. [Epub ahead of print].

Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT. (2010) GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome, Mol Syst Biol. 2010;6:353. Epub 2010 Mar 9. PMCID: PMC2858444

Jung, S., Marelli, M., Rachubinski, R. A., Goodlett, D. R. and Aitchison, J. D. (2010) Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress, J Biol Chem, 285: 6739-6749. PMCID: PMC2825468

Shmulevich, I. and Aitchison, J. D. (2009) Deterministic and stochastic models of genetic regulatory networks, Methods Enzymol, 467: 335-356

Wan, Y., Chiang, J. H., Lin, C. H., Arens, C. E., Saleem, R. A., Smith, J. J. and Aitchison, J. D. (2009) Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing, Nucleic Acids Res, 2010 Mar 1;38(5):1431-40. Epub 2009 Dec 14.. PMCID: PMC2836552

Smith, J. J. and Aitchison, J. D. (2009) Regulation of peroxisome dynamics, Curr Opin Cell Biol. Feb;21(1):119-26. Epub 2009 Jan 31.

Wan, Y., Saleem, R. A., Ratushny, A. V., Roda, O., Smith, J. J., Lin, C. H., Chiang, J. H. and Aitchison, J. D. (2009) Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes, Mol Cell Biol, 29: 2346-2358, PMCID: PMC2668375

Fagarasanu, A., Mast, F. D., Knoblach, B., Jin, Y., Brunner, M. J., Logan, M. R., Glover, J. N., Eitzen, G. A., Aitchison, J. D., Weisman, L. S. and Rachubinski, R. A. (2009) Myosin-driven peroxisome partitioning in S. cerevisiae, J Cell Biol, 186: 541-554. PMC2733749

Ptak, C., Anderson, A. M., Scott, R. J., Van de Vosse, D., Rogers, R. S., Sydorskyy, Y., Aitchison, J. D. and Wozniak, R. W. (2009) A role for the karyopherin Kap123p in microtubule stability, Traffic, 10: 1619-1634

Saleem RA, Aitchison JD. (2009) Quantitative Phosphoproteomics in Fatty Acid Stimulated Saccharomyces cerevisiae. J Vis Exp. 2009 Oct 12;(32). pii: 1474. doi: 10.3791/1474.

Gradolatto, A., Rogers, R. S., Lavender, H., Taverna, S. D., Allis, C. D., Aitchison, J. D. and Tackett, A. J. (2008) Saccharomyces cerevisiae Yta7 regulates histone gene expression, Genetics, 179: 291-304. PMCID: PMC2390607

Marelli, M., Nesvizhskii, A. I. and Aitchison, J. D. (2008) Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes, Methods Mol Biol, 432: 357-371

Ratushny, A. V., Ramsey, S. A., Roda, O., Wan, Y., Smith, J. J. and Aitchison, J. D. (2008) Control of transcriptional variability by overlapping feed-forward regulatory motifs, Biophys J, 95: 3715-3723

Saleem, R. A., Knoblach, B., Mast, F. D., Smith, J. J., Boyle, J., Dobson, C. M., Long-O'Donnell, R., Rachubinski, R. A. and Aitchison, J. D. (2008) Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis, J Cell Biol, 181: 281-292 

Graduate Student
Garrett Poshusta (University of Washington)
Postdoctoral Fellows
Lindsay Carpp
Fred Mast
Thurston Herricks 
Research Scientists
Song Li
Leslie Miller

Bioinformatics Scientist
Samuel Danziger

Senior Scientists 
Alex Ratushny
Jennifer Smith