Adjunct Professor (McMaster University) CIHR Scholar AHFMR Scholar Phone: 206-732-1344 Fax: 206-732-1299 Email: jaitchison@systemsbiology.org
Systems Biology and Cellular Compartmentalization The human genome project revolutionized how scientists view and practice biology. For the first time we 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 laboratory is located at 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

Fagarasanu, M., Fagarasanu, A., Tam, Y.-Y. C., Aitchison, J. D., and Rachubinski, R. A. (2005) Inp1p is a peroxisomal membrane protein required for peroxisomal inheritance in Saccharomyces cerevisiae, J. Cell Biol. In Press

Tackett, A. J., Dilworth, D. J., Davey, M. J., O'Donnell, M., Aitchison, J. D., Rout, M. P., and Chait, B. T. (2005) Proteomic and genomic characterization of chromatin complexes at a boundary, J Cell Biol 169, 35-47

Sydorskyy, Y., Dilworth, D. J., Halloran, B. P., Yi, E. C., Makhnevych, T. R., Wozniak, R. W., and Aitchison, J. D. (2005) Nop53p is a novel nucleolar 60S ribosomal biogenesis protein, Biochem J 388, 819-826  

Vizeacoumar, F. J., Torres-Guzman, J. C., Bouard, D., Aitchison, J. D., and Rachubinski, R. A. (2004) Pex30p, Pex31p, and Pex32p Form a Family of Peroxisomal Integral Membrane Proteins Regulating Peroxisome Size and Number in Saccharomyces cerevisiae, Mol Biol Cell 15, 665-677

Marelli, M., Smith, J. J., Jung, S., Yi, E., Nesvizhskii, A. I., Christmas, R. H., Saleem, R. A., Tam, Y. Y., Fagarasanu, A., Goodlett, D. R., Aebersold, R., Rachubinski, R. A., and Aitchison, J. D. (2004) Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane, J Cell Biol 167, 1099-1112

Leslie, D. M., Zhang, W., Timney, B. L., Chait, B. T., Rout, M. P., Wozniak, R. W., and Aitchison, J. D. (2004) Characterization of Karyopherin Cargoes Reveals Unique Mechanisms of Kap121p-Mediated Nuclear Import, Mol Cell Biol 2424(19):8487-8503

Lausted, C., Dahl, T., Warren, C., King, K., Smith, K., Johnson, M., Saleem, R., Aitchison, J., Hood, L., and Lasky, S. R. (2004) POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer, Genome Biol 5, R58

Vizeacoumar, F. J., Torres-Guzman, J. C., Tam, Y. Y., Aitchison, J. D., and Rachubinski, R. A. (2003) YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae, J Cell Biol 161, 321-332

Tam, Y. Y., Torres-Guzman, J. C., Vizeacoumar, F. J., Smith, J. J., Marelli, M., Aitchison, J. D., and Rachubinski, R. A. (2003) Pex11-related Proteins in Peroxisome Dynamics: A Role for the Novel Peroxin Pex27p in Controlling Peroxisome Size and Number in Saccharomyces cerevisiae, Mol Biol Cell 14, 4089-4102

Sydorskyy, Y., Dilworth, D. J., Yi, E. C., Goodlett, D. R., Wozniak, R. W., and Aitchison, J. D. (2003) Intersection of the Kap123p-mediated nuclear import and ribosome export pathways, Mol Cell Biol 23, 2042-2054

Steiner-Mosonyi, M., Leslie, D. M., Dehghani, H., Aitchison, J. D., and Mangroo, D. (2003) Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae, J Biol Chem 278, 32236-32245

Rout, M. P., Aitchison, J. D., Magnasco, M. O., and Chait, B. T. (2003) Virtual gating and nuclear transport: the hole picture, Trends Cell Biol 13, 622-628

Makhnevych, T., Lusk, C. P., Anderson, A. M., Aitchison, J. D., and Wozniak, R. W. (2003) Cell cycle regulated transport controlled by alterations in the nuclear pore complex, Cell 115, 813-823

Aitchison, J. D., and Galitski, T. (2003) Inventories to insights, J Cell Biol 161, 465-469

Aitchison, J., and Schwikowski, B. (2003) Systems biology and elephants, Nat Cell Biol 5, 285

Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R., Aitchison, J. D., and Goodlett, D. R. (2002) Approaching complete peroxisome characterization by gas-phase fractionation, Electrophoresis 23, 3205-3216

Smith, J. J., Marelli, M., Christmas, R. H., Vizeacoumar, F. J., Dilworth, D. J., Ideker, T., Galitski, T., Dimitrov, K., Rachubinski, R. A., and Aitchison, J. D. (2002) Transcriptome profiling to identify genes involved in peroxisome assembly and function, J Cell Biol 158, 259-271

Lusk, C. P., Makhnevych, T., Marelli, M., Aitchison, J. D., and Wozniak, R. W. (2002) Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes, J Cell Biol 159, 267-278

Leslie, D. M., Grill, B., Rout, M. P., Wozniak, R. W., and Aitchison, J. D. (2002) Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast, Mol Cell Biol 22, 2544-2555

Aitchison, J. D., and Rout, M. P. (2002) A tense time for the nuclear envelope, Cell 108, 301-304

Rout, M. P., and Aitchison, J. D. (2001) The nuclear pore complex as a transport machine, J Biol Chem 276, 16593-16596

Pariyarath, R., Wang, H., Aitchison, J. D., Ginsberg, H. N., Welch, W. J., Johnson, A. E., and Fisher, E. A. (2001) Co-translational interactions of apoprotein B with the ribosome and translocon during lipoprotein assembly or targeting to the proteasome, J Biol Chem 276, 541-550

Marelli, M., Lusk, C. P., Chan, H., Aitchison, J. D., and Wozniak, R. W. (2001) A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope, J Cell Biol 153, 709-724

Marelli, M., Dilworth, D. J., Wozniak, R. W., and Aitchison, J. D. (2001) The dynamics of karyopherin-mediated nuclear transport, Biochem Cell Biol 79, 603-612

Iouk, T. L., Aitchison, J. D., Maguire, S., and Wozniak, R. W. (2001) Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis, Mol Cell Biol 21, 1260-1271

Dilworth, D. J., Suprapto, A., Padovan, J. C., Chait, B. T., Wozniak, R. W., Rout, M. P., and Aitchison, J. D. (2001) Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex, J Cell Biol 153, 1465-1478

Aitchison, J. D., and Rout, M. P. (2001) in The Encyclopedia of Genetics (Brenner, S., and Miller, J. H., eds), pp. 1352-1356, Academic Press

Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism, J Cell Biol 148, 635-651

Rout, M. P., and Aitchison, J. D. (2000) Pore relations: nuclear pore complexes and nucleocytoplasmic exchange, Essays Biochem 36, 75-88

Aitchison, J. D., and Rout, M. P. (2000) The road to ribosomes. Filling potholes in the export pathway, J Cell Biol 151, F23-26

Graduate Students

Sun Hee Jung

Nicole Quenneville (Collaboration; UBC)

Student Intern

Rose Long-O’Donnell

Postdoctoral Fellows

Alexander Ratushny

Oriol Roda

Ramsey Saleem

Yakun Wan

Senior Scientists

John Boyle

Jennifer Smith

Research Associate

Mark Fuller