John Aitchison, PhD


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Dr. John Aitchison is a Professor and founding faculty member at the Institute for Systems Biology. He also holds an appointment at Center for Infectious Disease Research as Director of Integrative Biology and Principal Investigator. As a student, he studied biochemistry, specializing in biotechnology and genetic engineering, at McMaster University in Ontario, Canada. There, in the laboratory of Dr. Richard Rachubinski, he investigated the molecular mechanisms responsible for sorting proteins into peroxisomes. After receiving his PhD, Dr. Aitchison performed his postdoctoral work in the l aboratory of Nobel Laureate Dr. Günter Blobel at Rockefeller University. In Dr. Blobel’s lab, Dr. Aitchison applied classic cell biology techniques and yeast genetics to the study of protein import into the nucleus. During this time, he began to apply large-scale proteomics to the problem, which he continued as an Assistant Professor in the Faculty of Medicine and Dentistry at the University of Alberta until joining the ISB in 2000. Dr. Aitchison also holds affiliate appointments at the University of Washington, University of Alberta, and University of British Columbia. He is a member of the Molecular and Cellular Biology and Biomolecular Structural Design Graduate Programs at the University of Washington. Since joining ISB in 2000, his laboratory has been exploiting systems based assays and analyses to reveal and understand complex biological phenomena. Over the past ten years, his lab has focused on yeast as a model for developing systems biology approaches. He recently, took a Principal Investigator position at Center for Infectious Disease Research to immerse his lab in an environment rich in infectious-disease research to enhance our collective exposure to, and education in, research of infectious diseases. With his current position and lab at ISB, he will remain at the cutting-edge of systems biology while bringing new developments to infectious disease research at CID Research.

PhD, Biochemistry McMaster University, Ontario, Canada, 1992

Systems Cell Biology, Organelle Biogenesis, Host-pathogen Interactions


Wurtmann EJ, Ratushny AV, Pan M, Beer K.D, Aitchison JD, Baliga NS.  2014.  An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Molecular microbiology. 92:369-82.

Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2014.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic acids research. 42:1442-60.

Ptak C, Aitchison JD, Wozniak RW.  2014.  The multifunctional nuclear pore complex: a platform for controlling gene expression. Current opinion in cell biology. 28C:46-53.

Holden JM, Koreny L., Obado S., Ratushny AV, Chen WM, Chiang JH, Kelly S., Chait BT, Aitchison JD, Rout MP et al..  2014.  Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity. Molecular biology of the cell. 25:1421-36.

Schoggins J.W, Macduff D.A, Imanaka N., Gainey M.D, Shrestha B., Eitson J.L, Mar K.B, Richardson R.B, Ratushny AV, Litvak V et al..  2014.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature. 505:691-5.

Carpp L.N, Rogers RS, Moritz RL, Aitchison JD.  2014.  Quantitative proteomic analysis of host-virus interactions reveals a role for GBF1 in dengue infection. Molecular & cellular proteomics : MCP.


Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.  2013.  Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics. 12:1421-35.

Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.  2013.  Metallochaperones regulate intracellular copper levels. PLoS computational biology. 9:e1002880.

Danziger S.A, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH et al..  2013.  Molecular mechanisms of system responses to novel stimuli are predictable from public data. Nucleic Acids Res.

Schoggins J.W, Macduff D.A, Imanaka N., Gainey M.D, Shrestha B., Eitson J.L, Mar K.B, Richardson R.B, Ratushny AV, Litvak V et al..  2013.  Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity. Nature.

Smith JJ, Aitchison JD.  2013.  Peroxisomes take shape. Nat Rev Mol Cell Biol. 14:803-17.
Chen WM, Danziger S.A, Chiang JH, Aitchison JD.  2013.  PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. Bioinformatics. 29:2435-44.

Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.  2013.  A role for the nucleoporin nup170p in chromatin structure and gene silencing. Cell. 152:969-83.

Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD et al..  2013.  Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proceedings of the National Academy of Sciences of the United States of America. 110:3645-50.


Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD.  2012.  Asymmetric positive feedback loops reliably control biological responses. Molecular systems biology. 8:577.

Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.  2012.  A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses. Nature.

Dubois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD et al..  2012.  NUP-1 Is a Large Coiled-Coil Nucleoskeletal Protein in Trypanosomes with Lamin-Like Functions. PLoS biology. 10:e1001287.

Aitchison JD, Rout MP.  2012.  The yeast nuclear pore complex and transport through it. Genetics. 190:855-83.


Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD.  2011.  Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol. 7:455.

Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.  2011.  Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. 83:2250-7.

Ratushny AV, Ramsey SA, Aitchison JD.  2011.  Mathematical modeling of biomolecular network dynamics. Methods in molecular biology. 781:415-33.

Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.  2011.  Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Molecular & cellular proteomics : MCP.

Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA.  2011.  The Peroxin Pex34p Functions with the Pex11 Family of Peroxisomal Divisional Proteins to Regulate the Peroxisome Population in Yeast. Mol Biol Cell.

Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.  2011.  A regression model approach to enable cell morphology correction in high-throughput flow cytometry. Molecular systems biology. 7:531.

Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.  2011.  Role of the nuclear envelope in genome organization and gene expression. Wiley Interdiscip Rev Syst Biol Med. 3:147-66.

Smith JJ, Saleem RA, Aitchison JD.  2011.  Statistical analysis of dynamic transcriptional regulatory network structure. Methods in molecular biology. 781:337-52.

Ratushny AV, Shmulevich I, Aitchison JD.  2011.  Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues. PLoS computational biology. 7:e1002091.


Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.  2010.  Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem. 285:6739-49.

Vinh DB, Ko DC, Rachubinski RA, Aitchison JD, Miller SI.  2010.  Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes. Mol Biol Cell. 21:3567-77.

Saleem RA, Long-O’Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemisto A, Boyle J, Rachubinski RA et al..  2010.  Genome-wide analysis of effectors of peroxisome biogenesis. PLoS OnePLoS ONE. 5

Sekedat MD, Fenyo 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. 6:353.

Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD.  2010.  Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing. Nucleic Acids Res. 38:1431-40.

Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon P, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA et al..  2010.  Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction. Mol Cell Proteomics. 9:2076-88.

Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.  2010.  QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments. J Am Soc Mass Spectrom. 21:1417-22.

Saleem RA, Aitchison JD.  2010.  Systems cell biology of the mitotic spindle. J Cell Biol. 188:7-9.


Shmulevich I, Aitchison JD.  2009.  Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol. 467:335-56.

Fagarasanu A, Mast FD, Knoblach B, Jin Y, Brunner MJ, Logan MR, Glover JN, Eitzen GA, Aitchison JD, Weisman LS et al..  2009.  Myosin-driven peroxisome partitioning in S. cerevisiae. J Cell Biol. 186:541-54.

Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD et al..  2009.  A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity. Mol Cell Biol. 29:4604-11.

Saleem RA, Aitchison JD.  2009.  Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae. J Vis Exp.

Smith JJ, Aitchison JD.  2009.  Regulation of peroxisome dynamics. Curr Opin Cell Biol. 21:119-26.

Ptak C, Anderson AM, Scott RJ, Van de Vosse D, Rogers RS, Sydorskyy Y, Aitchison JD, Wozniak RW.  2009.  A role for the karyopherin Kap123p in microtubule stability. Traffic. 10:1619-34.

Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD.  2009.  Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. Mol Cell Biol. 29:2346-58.


Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.  2008.  Control of transcriptional variability by overlapping feed-forward regulatory motifs. Biophys J. 95:3715-23.

Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O’Donnell R, Rachubinski RA, Aitchison JD.  2008.  Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis. J Cell Biol. 181:281-92.

Marelli M, Nesvizhskii AI, Aitchison JD.  2008.  Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes. Methods Mol Biol. 432:357-71.

Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ.  2008.  Saccharomyces cerevisiae Yta7 regulates histone gene expression. Genetics. 179:291-304.

Hood L, Rowen L, Galas DJ, Aitchison JD.  2008.  Systems biology at the Institute for Systems Biology. Brief Funct Genomic Proteomic. 7:239-48.


Aitchison JD, Wozniak RW.  2007.  Cell biology: pore puzzle. Nature. 450:621-2.
Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP.  2007.  Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods. 4:951-6.

Niemisto A, Korpelainen T, Saleem R, Yli-Harja O, Aitchison JD, Shmulevich I.  2007.  A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy. Conf Proc IEEE Eng Med Biol Soc. 2007:5559-62.

Makhnevych T, Ptak C, Lusk CP, Aitchison JD, Wozniak RW.  2007.  The role of karyopherins in the regulated sumoylation of septins. J Cell Biol. 177:39-49.

Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD.  2007.  Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol Syst Biol. 3:115.


Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison JD, Matunis M, Aebersold R.  2006.  Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software. Nat Methods. 3:533-9.

Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.  2006.  Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet. 38:1082-7.

Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. J Biol Chem. 281:12817-23.

Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD.  2006.  Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism. Mol Syst Biol. 2:20060009.

Niemisto A, Selinummi J, Saleem R, Shmulevich I, Aitchison JD, Yli-Harja O.  2006.  Extraction of the number of peroxisomes in yeast cells by automated image analysis. Conf Proc IEEE Eng Med Biol Soc. 1:2353-6.

Kowalewska J, Smith KD, Hudkins KL, Chang A, Fogo AB, Houghton D, Leslie D, Aitchison JD, Nicosia RF, Alpers CE.  2006.  Membranous glomerulopathy with spherules: an uncommon variant with obscure pathogenesis. Am J Kidney Dis. 47:983-92.

Fagarasanu A, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae. Dev Cell. 10:587-600.

Vizeacoumar FJ, Vreden WN, Aitchison JD, Rachubinski RA.  2006.  Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals. J Biol Chem. 281:14805-12.

Saleem RA, Smith JJ, Aitchison JD.  2006.  Proteomics of the peroxisome. Biochim Biophys Acta. 1763:1541-51.

Leslie DM, Timney B, Rout MP, Aitchison JD.  2006.  Studying nuclear protein import in yeast. Methods. 39:291-308.

Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT et al..  2006.  Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell. 24:785-96.


Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF et al..  2005.  A data integration methodology for systems biology. Proc Natl Acad Sci U S A. 102:17296-301.

Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD et al..  2005.  A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A. 102:17302-7.

Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA.  2005.  Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. J Cell Biol. 169:765-75.

Scott RJ, Lusk CP, Dilworth DJ, Aitchison JD, Wozniak RW.  2005.  Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae. Mol Biol Cell. 16:4362-74.

Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD.  2005.  The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control. J Cell Biol. 171:955-65.

Sydorskyy Y, Dilworth DJ, Halloran B, Yi EC, Makhnevych T, Wozniak RW, Aitchison JD.  2005.  Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein. Biochem J. 388:819-26.

Tackett AJ, Dilworth DJ, Davey MJ, O’Donnell M, Aitchison JD, Rout MP, Chait BT.  2005.  Proteomic and genomic characterization of chromatin complexes at a boundary. J Cell Biol. 169:35-47.


Leslie DM, Zhang W, Timney BL, Chait BT, Rout MP, Wozniak RW, Aitchison JD.  2004.  Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import. Mol Cell Biol. 24:8487-503.

Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA.  2004.  Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae. Mol Biol Cell. 15:665-77.

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

Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR et al..  2004.  Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol. 167:1099-112.


Makhnevych T, Lusk CP, Anderson AM, Aitchison JD, Wozniak RW.  2003.  Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell. 115:813-23.

Sydorskyy Y, Dilworth DJ, Yi EC, Goodlett DR, Wozniak RW, Aitchison JD.  2003.  Intersection of the Kap123p-mediated nuclear import and ribosome export pathways. Mol Cell Biol. 23:2042-54.

Aitchison JD, Galitski T.  2003.  Inventories to insights. J Cell Biol. 161:465-9.

Tam YY, Torres-Guzman JC, Vizeacoumar FJ, Smith JJ, Marelli M, Aitchison JD, Rachubinski RA.  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. 14:4089-102.

Aitchison JD.  2003.  Systems biology and elephants. Nature Cell Biology. 5:285.
Steiner-Mosonyi M, Leslie DM, Dehghani H, Aitchison JD, Mangroo D.  2003.  Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae. J Biol Chem. 278:32236-45.

Rout MP, Aitchison JD, Magnasco MO, Chait BT.  2003.  Virtual gating and nuclear transport: the hole picture. Trends Cell Biol. 13:622-8.

Vizeacoumar FJ, Torres-Guzman JC, Tam YY, Aitchison JD, Rachubinski RA.  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. 161:321-32.


Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR.  2002.  Approaching complete peroxisome characterization by gas-phase fractionation. Electrophoresis. 23:3205-16.

Leslie DM, Grill B, Rout MP, Wozniak RW, Aitchison JD.  2002.  Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast. Mol Cell Biol. 22:2544-55.

Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW.  2002.  Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes. J Cell Biol. 159:267-78.

Aitchison JD, Rout MP.  2002.  A tense time for the nuclear envelope. Cell. 108:301-4.

Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD.  2002.  Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 158:259-71.


Pariyarath R, Wang H, Aitchison JD, Ginsberg HN, Welch WJ, Johnson AE, Fisher EA.  2001.  Co-translational interactions of apoprotein B with the ribosome and translocon during lipoprotein assembly or targeting to the proteasome. J Biol Chem. 276:541-50.

Marelli M, Dilworth DJ, Wozniak RW, Aitchison JD.  2001.  The dynamics of karyopherin-mediated nuclear transport. Biochem Cell Biol. 79:603-12.

Marelli M, Lusk CP, Chan H, Aitchison JD, Wozniak RW.  2001.  A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope. J Cell Biol. 153:709-24.

Rout MP, Aitchison JD.  2001.  The nuclear pore complex as a transport machine. J Biol Chem. 276:16593-6.

Dilworth DJ, Suprapto A, Padovan JC, Chait BT, Wozniak RW, Rout MP, Aitchison JD.  2001.  Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex. J Cell Biol. 153:1465-78.

Iouk TL, Aitchison JD, Maguire S, Wozniak RW.  2001.  Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis. Mol Cell Biol. 21:1260-71.


Aitchison JD, Rout MP.  2000.  The road to ribosomes. Filling potholes in the export pathway. J Cell Biol. 151:F23-6.