John Aitchison, PhD

John Aitchison, PhD

Infectious Disease Research

Children's Title: Principal Investigator, Supervisor, Center for Global Infectious Disease Research

Academic Title: Professor

Research Center: Center for Global Infectious Disease Research

  • Biography

    John Aitchison is co-director of the Center for Global Infectious Disease at Seattle Children’s Research Institute. Dr. Aitchison received his PhD in Biochemistry from McMaster University, Canada. He performed postdoctoral research in the Laboratory of Cell Biology at The Rockefeller University under the guidance of Professor Gunter Blobel (Nobel Laureate, 1999). Dr. Aitchison is a founding faculty member at the Institute for Systems Biology where he served as senior vice president and executive director of Integrative Biology. Professor Aitchison holds part-time, adjunct or affiliate faculty positions at Institute for Systems Biology, University of Washington (Biochemistry), University of Alberta (Cell Biology) and University of British Columbia (Biochemistry). Outside of the lab, John enjoys spending time with his family, playing squash, and racing sailboats.

    Memberships:

    • American Society for Cell Biology
    • American Society for Microbiology
    • Biophysical Society
    • AAAS

    Research Interests:

    1. Systems based approaches to reveal and understand complex biological phenomena focusing on yeast as a model for developing systems biology approaches to infectious disease research. Understanding cellular function from this perspective is essential to developing strategies for intervention when these functions go awry, causing diseases (such as neuropathologies or cancer) or are usurped in the cases of infection by pathogens.
    2. The molecular mechanisms responsible for sorting proteins to peroxisomes – an organelle in the cytoplasm of cells that is responsible for metabolizing fatty acids. Defects in peroxisomal functions have been associated with neuropathologies, diabetes, obesity, metabolic syndrome, cancer and aging.
    3. The development of innovative and dramatically new approaches for the detection, isolation, and analysis of macromolecular complexes that will enable scientists to realize the full potential of the revolution brought about by genomics, interdisciplinary research, and proteomics technologies.

    Research Funding

    Dr. Aitchison is funded by the National Institutes of Health and graciously acknowledges funding from generous donors.

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  • Awards and Honors

    Award Name Award Description Awarded By Award Date
    Researcher Canadian Foundation for Innovation 1998
    Scholar Alberta Heritage Foundation for Medical Research 1997 - 2000
    Scholar Medical Research Council of Canada 1997 - 2000
    Research Associate Fellow Award Howard Hughes Medical Institute 1995 - 1997
    Post Doctoral Fellow Award Medical Research Council of Canada 1992 - 1995
    Graduate Studentship Award Ontario Graduate Studies 1990 - 1991
    Postgraduate Student Award 1988 - 1990
    Scholar Department of Biochemistry, McMaster University 1986
    Senate Scholar McMaster University 1985

  • Publications

    Manuscripts in Refereed Journals

    • Vijayan K, Cestari I, Mast FD, Glennon EKK, McDermott SM, Kain HS, Brokaw AM, Aitchison JD, Stuart K, Kaushansky A.
      Plasmodium Secretion Induces Hepatocyte Lysosome Exocytosis and Promotes Parasite Entry.
      31731198 iScience, 2019 Nov 22 : 21603-611.
      https://www.ncbi.nlm.nih.gov/pubmed/31731198
    • Regier MC, Olszewski E, Carter CC, Aitchison JD, Kaushansky A, Davis J, Berthier E, Beebe DJ, Stevens KR.
      Spatial presentation of biological molecules to cells by localized diffusive transfer.
      31111131 Lab on a chip, 2019 Jun 11 : 19(12)2114-2126. PMCID:PMC6755031
      https://www.ncbi.nlm.nih.gov/pubmed/31111131
    • Duffy F, Bernabeu M, Babar PH, Kessler A, Wang CW, Vaz M, Chery L, Mandala WL, Rogerson SJ, Taylor TE, Seydel KB, Lavstsen T, Gomes E, Kim K, Lusingu J, Rathod PK, Aitchison JD, Smith JD.
      Meta-analysis of Plasmodium falciparum var Signatures Contributing to Severe Malaria in African Children and Indian Adults.
      31040236 mBio, 2019 Apr 30 : 10(2) PMCID:PMC6495371
      https://www.ncbi.nlm.nih.gov/pubmed/31040236
    • Glennon EKK, Austin LS, Arang N, Kain HS, Mast FD, Vijayan K, Aitchison JD, Kappe SHI, Kaushansky A.
      Alterations in Phosphorylation of Hepatocyte Ribosomal Protein S6 Control Plasmodium Liver Stage Infection.
      30893610 Cell reports, 2019 Mar 19 : 26(12)3391-3399.e4. PMCID:PMC6447308
      https://www.ncbi.nlm.nih.gov/pubmed/30893610
    • Mast FD, Herricks T, Strehler KM, Miller LR, Saleem RA, Rachubinski RA, Aitchison JD.
      ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum.
      29588378 The Journal of cell biology, 2018 Jun 4 : 217(6)2087-2102. PMCID:PMC5987711
      https://www.ncbi.nlm.nih.gov/pubmed/29588378
    • Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC.
      Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes.
      29496964 Molecular biology of the cell, 2018 May 1 : 29(9)1100-1110. PMCID:PMC5921576
      https://www.ncbi.nlm.nih.gov/pubmed/29496964
    • Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP.
      Integrative structure and functional anatomy of a nuclear pore complex.
      29539637 Nature, 2018 Mar 22 : 555(7697)475-482. PMCID:PMC6022767
      https://www.ncbi.nlm.nih.gov/pubmed/29539637
    • Kessler A, Dankwa S, Bernabeu M, Harawa V, Danziger SA, Duffy F, Kampondeni SD, Potchen MJ, Dambrauskas N, Vigdorovich V, Oliver BG, Hochman SE, Mowrey WB, MacCormick IJC, Mandala WL, Rogerson SJ, Sather DN, Aitchison JD, Taylor TE, Seydel KB, Smith JD, Kim K.
      Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria.
      29107642 Cell host & microbe, 2017 Nov 8 : 22(5)601-614.e5. PMCID:PMC5783720
      https://www.ncbi.nlm.nih.gov/pubmed/29107642
    • Herricks T, Mast FD, Li S, Aitchison JD.
      ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth.
      28715382 Journal of visualized experiments : JoVE, 2017 Jul 3 : (125) PMCID:PMC5608540
      https://www.ncbi.nlm.nih.gov/pubmed/28715382
    • López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS.
      Adaptive Prediction Emerges Over Short Evolutionary Time Scales.
      28854640 Genome biology and evolution, 2017 Jun 1 : 9(6)1616-1623. PMCID:PMC5570091
      https://www.ncbi.nlm.nih.gov/pubmed/28854640
    • Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND.
      Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast.
      28520713 PLoS computational biology, 2017 May : 13(5)e1005489. PMCID:PMC5453602
      https://www.ncbi.nlm.nih.gov/pubmed/28520713
    • Herricks T, Dilworth DJ, Mast FD, Li S, Smith JJ, Ratushny AV, Aitchison JD.
      One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!
      27856698 G3 (Bethesda, Md.), 2017 Jan 5 : 7(1)279-288. PMCID:PMC5217116
      https://www.ncbi.nlm.nih.gov/pubmed/27856698
    • Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ.
      An indicator cell assay for blood-based diagnostics.
      28594877 PloS one, 2017 : 12(6)e0178608. PMCID:PMC5464608
      https://www.ncbi.nlm.nih.gov/pubmed/28594877
    • Maishman L, Obado SO, Alsford S, Bart JM, Chen WM, Ratushny AV, Navarro M, Horn D, Aitchison JD, Chait BT, Rout MP, Field MC.
      Co-dependence between trypanosome nuclear lamina components in nuclear stability and control of gene expression.
      27625397 Nucleic acids research, 2016 Dec 15 : 44(22)10554-10570. PMCID:PMC5159534
      https://www.ncbi.nlm.nih.gov/pubmed/27625397
    • Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.
      Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
      27453469 Cell, 2016 Jul 28 : 166(3)766-778. PMCID:PMC5245710
      https://www.ncbi.nlm.nih.gov/pubmed/27453469
    • Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD.
      Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum.
      27129769 The Journal of biological chemistry, 2016 Jul 22 : 291(30)15408-27. PMCID:PMC4957030
      https://www.ncbi.nlm.nih.gov/pubmed/27129769
    • Bernabeu M, Danziger SA, Avril M, Vaz M, Babar PH, Brazier AJ, Herricks T, Maki JN, Pereira L, Mascarenhas A, Gomes E, Chery L, Aitchison JD, Rathod PK, Smith JD.
      Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.
      27185931 Proceedings of the National Academy of Sciences of the United States of America, 2016 Jun 7 : 113(23)E3270-9. PMCID:PMC4988613
      https://www.ncbi.nlm.nih.gov/pubmed/27185931
    • Aitchison JD, Rout MP.
      The interactome challenge.
      26572620 The Journal of cell biology, 2015 Nov 23 : 211(4)729-32. PMCID:PMC4657177
      https://www.ncbi.nlm.nih.gov/pubmed/26572620
    • Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM.
      Corrigendum: Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.
      26153856 Nature, 2015 Sep 3 : 525(7567)144.
      https://www.ncbi.nlm.nih.gov/pubmed/26153856
    • Hakhverdyan Z, Domanski M, Hough LE, Oroskar AA, Oroskar AR, Keegan S, Dilworth DJ, Molloy KR, Sherman V, Aitchison JD, Fenyö D, Chait BT, Jensen TH, Rout MP, LaCava J.
      Rapid, optimized interactomic screening.
      25938370 Nature methods, 2015 June : 12(6)553-60. PMCID:PMC4449307
      https://www.ncbi.nlm.nih.gov/pubmed/25938370
    • Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.
      Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions.
      25881257 BMC systems biology, 2015 : 9 Suppl 2S1. PMCID:PMC4407105
      https://www.ncbi.nlm.nih.gov/pubmed/25881257
    • Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR.
      Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.
      26962293 Journal of proteomics & bioinformatics, 2015 : 8(10)231-239. PMCID:PMC4780416
      https://www.ncbi.nlm.nih.gov/pubmed/26962293
    • Carpp LN, Rogers RS, Moritz RL, Aitchison JD.
      Quantitative proteomic analysis of host-virus interactions reveals a role for Golgi brefeldin A resistance factor 1 (GBF1) in dengue infection.
      24855065 Molecular & cellular proteomics : MCP, 2014 Nov. : 13(11)2836-54. PMCID:PMC4223476
      https://www.ncbi.nlm.nih.gov/pubmed/24855065
    • Finney OC, Danziger SA, Molina DM, Vignali M, Takagi A, Ji M, Stanisic DI, Siba PM, Liang X, Aitchison JD, Mueller I, Gardner MJ, Wang R.
      Predicting antidisease immunity using proteome arrays and sera from children naturally exposed to malaria.
      25023128 Molecular & cellular proteomics : MCP, 2014 Oct. : 13(10)2646-60. PMCID:PMC4188993
      https://www.ncbi.nlm.nih.gov/pubmed/25023128
    • Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC.
      Nuclear pore complex evolution: a trypanosome Mlp analogue functions in chromosomal segregation but lacks transcriptional barrier activity.
      24600046 Molecular biology of the cell, 2014 May : 25(9)1421-36. PMCID:PMC4004592
      https://www.ncbi.nlm.nih.gov/pubmed/24600046
    • Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS.
      An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation.
      24612392 Molecular microbiology, 2014 April : 92(2)369-82. PMCID:PMC4060883
      https://www.ncbi.nlm.nih.gov/pubmed/24612392
    • Danziger SA, Ratushny AV, Smith JJ, Saleem RA, Wan Y, Arens CE, Armstrong AM, Sitko K, Chen WM, Chiang JH, Reiss DJ, Baliga NS, Aitchison JD.
      Molecular mechanisms of system responses to novel stimuli are predictable from public data.
      24185701 Nucleic acids research, 2014 Feb. : 42(3)1442-60. PMCID:PMC3919619
      https://www.ncbi.nlm.nih.gov/pubmed/24185701
    • Schoggins JW, MacDuff DA, Imanaka N, Gainey MD, Shrestha B, Eitson JL, Mar KB, Richardson RB, Ratushny AV, Litvak V, Dabelic R, Manicassamy B, Aitchison JD, Aderem A, Elliott RM, García-Sastre A, Racaniello V, Snijder EJ, Yokoyama WM, Diamond MS, Virgin HW, Rice CM.
      Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.
      24284630 Nature, 2014 Jan 30 : 505(7485)691-5. PMCID:PMC4077721
      https://www.ncbi.nlm.nih.gov/pubmed/24284630
    • Cooney LA, Gupta M, Thomas S, Mikolajczak S, Choi KY, Gibson C, Jang IK, Danziger S, Aitchison J, Gardner MJ, Kappe SH, Wang R.
      Short-lived effector CD8 T cells induced by genetically attenuated malaria parasite vaccination express CD11c.
      23980113 Infection and immunity, 2013 Nov. : 81(11)4171-81. PMCID:PMC3811835
      https://www.ncbi.nlm.nih.gov/pubmed/23980113
    • Chen WM, Danziger SA, Chiang JH, Aitchison JD.
      PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data.
      23832245 Bioinformatics (Oxford, England), 2013 Oct 1 : 29(19)2435-44. PMCID:PMC3777105
      https://www.ncbi.nlm.nih.gov/pubmed/23832245
    • Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.
      Global analysis of condition-specific subcellular protein distribution and abundance.
      23349476 Molecular & cellular proteomics : MCP, 2013 May : 12(5)1421-35 PMCID:PMC3650349
      https://www.ncbi.nlm.nih.gov/pubmed/23349476
    • Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.
      A role for the nucleoporin Nup170p in chromatin structure and gene silencing.
      23452847 Cell, 2013 Feb 28 : 152(5)969-83. PMCID:PMC3690833
      https://www.ncbi.nlm.nih.gov/pubmed/23452847
    • Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J.
      Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.
      23388641 Proceedings of the National Academy of Sciences of the United States of America, 2013 Feb 26 : 110(9)3645-50 PMCID:PMC3587231
      https://www.ncbi.nlm.nih.gov/pubmed/23388641
    • Sundaravaradan V, Saleem R, Micci L, Gasper MA, Ortiz AM, Else J, Silvestri G, Paiardini M, Aitchison JD, Sodora DL.
      Multifunctional double-negative T cells in sooty mangabeys mediate T-helper functions irrespective of SIV infection.
      23825945 PLoS pathogens, 2013 : 9(6)e1003441. PMCID:PMC3694849
      https://www.ncbi.nlm.nih.gov/pubmed/23825945
    • Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.
      Metallochaperones regulate intracellular copper levels.
      23349626 PLoS computational biology, 2013 : 9(1)e1002880. PMCID:PMC3551603
      https://www.ncbi.nlm.nih.gov/pubmed/23349626
    • Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A
      A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.
      22982991 Nature, 2012 Oct 18 : 490(7420)421-5 PMCID:PMC3556990
      https://www.ncbi.nlm.nih.gov/pubmed/22982991
    • Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD.
      Asymmetric positive feedback loops reliably control biological responses.
      22531117 Molecular systems biology, 2012 Apr 24 : 8577. PMCID:PMC3361002
      https://www.ncbi.nlm.nih.gov/pubmed/22531117
    • Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.
      Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests.
      22186714 Molecular & cellular proteomics : MCP, 2012 April : 11(4)M111.014985. PMCID:PMC3322575
      https://www.ncbi.nlm.nih.gov/pubmed/22186714
    • Aitchison JD, Rout MP.
      The yeast nuclear pore complex and transport through it.
      22419078 Genetics, 2012 March : 190(3)855-83. PMCID:PMC3296253
      https://www.ncbi.nlm.nih.gov/pubmed/22419078
    • DuBois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD, Navarro M, Horn D, Aitchison JD, Rout MP, Field MC.
      NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.
      22479148 PLoS biology, 2012 : 10(3)e1001287. PMCID:PMC3313915
      https://www.ncbi.nlm.nih.gov/pubmed/22479148
    • Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.
      A regression model approach to enable cell morphology correction in high-throughput flow cytometry.
      21952134 Molecular systems biology, 2011 Sep 27 : 7531. PMCID:PMC3202802
      https://www.ncbi.nlm.nih.gov/pubmed/21952134
    • Ratushny AV, Shmulevich I, Aitchison JD.
      Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.
      21738459 PLoS computational biology, 2011 June : 7(6)e1002091. PMCID:PMC3127798
      https://www.ncbi.nlm.nih.gov/pubmed/21738459
    • Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA.
      The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast.
      21441307 Molecular biology of the cell, 2011 May 15 : 22(10)1727-38. PMCID:PMC3093324
      https://www.ncbi.nlm.nih.gov/pubmed/21441307
    • Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.
      Faster, quantitative, and accurate precursor acquisition independent from ion count.
      21341720 Analytical chemistry, 2011 Mar 15 : 83(6)2250-7 PMCID:PMC3217585
      https://www.ncbi.nlm.nih.gov/pubmed/21341720
    • Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD.
      Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing.
      21206489 Molecular systems biology, 2011 Jan 4 : 7455 PMCID:PMC3049408
      https://www.ncbi.nlm.nih.gov/pubmed/21206489
    • Smith JJ, Saleem RA, Aitchison JD.
      Statistical analysis of dynamic transcriptional regulatory network structure.
      21877289 Methods in molecular biology (Clifton, N.J.), 2011 : 781337-52.
      https://www.ncbi.nlm.nih.gov/pubmed/21877289
    • Ratushny AV, Ramsey SA, Aitchison JD.
      Mathematical modeling of biomolecular network dynamics.
      21877294 Methods in molecular biology (Clifton, N.J.), 2011 : 781415-33. PMCID:PMC4482237
      https://www.ncbi.nlm.nih.gov/pubmed/21877294
    • Vinh DB, Ko DC, Rachubinski RA, Aitchison JD, Miller SI.
      Expression of the Salmonella spp. virulence factor SifA in yeast alters Rho1 activity on peroxisomes.
      20739463 Molecular biology of the cell, 2010 Oct 15 : 21(20)3567-77. PMCID:PMC2954121
      https://www.ncbi.nlm.nih.gov/pubmed/20739463
    • Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD.
      Integrated phosphoproteomics analysis of a signaling network governing nutrient response and peroxisome induction.
      20395639 Molecular & cellular proteomics : MCP, 2010 Sept. : 9(9)2076-88. PMCID:PMC2938103
      https://www.ncbi.nlm.nih.gov/pubmed/20395639
    • Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemistö A, Boyle J, Rachubinski RA, Shmulevich I, Aitchison JD.
      Genome-wide analysis of effectors of peroxisome biogenesis.
      20694151 PloS one, 2010 Aug 4 : 5(8)e11953. PMCID:PMC2915925
      https://www.ncbi.nlm.nih.gov/pubmed/20694151
    • Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.
      QTIPS: a novel method of unsupervised determination of isotopic amino acid distribution in SILAC experiments.
      20451407 Journal of the American Society for Mass Spectrometry, 2010 Aug. : 21(8)1417-22. PMCID:PMC2914207
      https://www.ncbi.nlm.nih.gov/pubmed/20451407
    • Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD.
      Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing.
      20008511 Nucleic acids research, 2010 March : 38(5)1431-40. PMCID:PMC2836552
      https://www.ncbi.nlm.nih.gov/pubmed/20008511
    • Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.
      Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress.
      20026609 The Journal of biological chemistry, 2010 Feb 26 : 285(9)6739-49 PMCID:PMC2825468
      https://www.ncbi.nlm.nih.gov/pubmed/20026609
    • Saleem RA, Aitchison JD.
      Systems cell biology of the mitotic spindle.
      20065087 The Journal of cell biology, 2010 Jan 11 : 188(1)7-9 PMCID:PMC2812858
      https://www.ncbi.nlm.nih.gov/pubmed/20065087
    • Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT.
      GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.
      20212525 Molecular systems biology, 2010 : 6353 PMCID:PMC2858444
      https://www.ncbi.nlm.nih.gov/pubmed/20212525
    • Ptak C, Anderson AM, Scott RJ, Van de Vosse D, Rogers RS, Sydorskyy Y, Aitchison JD, Wozniak RW
      A role for the karyopherin Kap123p in microtubule stability.
      19761543 Traffic (Copenhagen, Denmark), 2009 Nov. : 10(11)1619-34.
      https://www.ncbi.nlm.nih.gov/pubmed/19761543
    • Saleem RA, Aitchison JD.
      Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae.
      19823167 Journal of visualized experiments : JoVE, 2009 Oct 12 : (32) PMCID:PMC2865974
      https://www.ncbi.nlm.nih.gov/pubmed/19823167
    • Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD, Tackett AJ
      A noncanonical bromodomain in the AAA ATPase protein Yta7 directs chromosomal positioning and barrier chromatin activity.
      19581291 Molecular and cellular biology, 2009 Sept. : 29(17)4604-11 PMCID:PMC2725702
      https://www.ncbi.nlm.nih.gov/pubmed/19581291
    • Fagarasanu A, Mast FD, Knoblach B, Jin Y, Brunner MJ, Logan MR, Glover JN, Eitzen GA, Aitchison JD, Weisman LS, Rachubinski RA
      Myosin-driven peroxisome partitioning in S. cerevisiae.
      19687257 The Journal of cell biology, 2009 Aug 24 : 186(4)541-54. PMCID:PMC2733749
      https://www.ncbi.nlm.nih.gov/pubmed/19687257
    • Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD.
      Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes.
      19273605 Molecular and cellular biology, 2009 May : 29(9)2346-58. PMCID:PMC2668375
      https://www.ncbi.nlm.nih.gov/pubmed/19273605
    • Shmulevich I, Aitchison JD.
      Deterministic and stochastic models of genetic regulatory networks.
      19897099 Methods in enzymology, 2009 : 467335-356. PMCID:PMC3230268
      https://www.ncbi.nlm.nih.gov/pubmed/19897099
    • Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.
      Control of transcriptional variability by overlapping feed-forward regulatory motifs.
      18621837 Biophysical journal, 2008 Oct. : 95(8)3715-23. PMCID:PMC2553142
      https://www.ncbi.nlm.nih.gov/pubmed/18621837
    • Hood L, Rowen L, Galas DJ, Aitchison JD.
      Systems biology at the Institute for Systems Biology.
      18579616 Briefings in functional genomics & proteomics, 2008 July : 7(4)239-48
      https://www.ncbi.nlm.nih.gov/pubmed/18579616
    • Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ.
      Saccharomyces cerevisiae Yta7 regulates histone gene expression.
      18493054 Genetics, 2008 May : 179(1)291-304 PMCID:PMC2390607
      https://www.ncbi.nlm.nih.gov/pubmed/18493054
    • Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD.
      Genome-wide analysis of signaling networks regulating fatty acid-induced gene expression and organelle biogenesis.
      18426976 The Journal of cell biology, 2008 Apr 21 : 181(2)281-92 PMCID:PMC2315675
      https://www.ncbi.nlm.nih.gov/pubmed/18426976
    • Marelli M, Nesvizhskii AI, Aitchison JD.
      Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions : an example in peroxisomes.
      18370030 Methods in molecular biology (Clifton, N.J.), 2008 : 432357-71
      https://www.ncbi.nlm.nih.gov/pubmed/18370030
    • Aitchison JD, Wozniak RW.
      Cell biology: pore puzzle.
      18046388 Nature, 2007 Nov 29 : 450(7170)621-2
      https://www.ncbi.nlm.nih.gov/pubmed/18046388
    • Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP.
      Comprehensive analysis of diverse ribonucleoprotein complexes.
      17922018 Nature methods, 2007 Nov 1 : 4(11)951-6.
      https://www.ncbi.nlm.nih.gov/pubmed/17922018
    • Makhnevych T, Ptak C, Lusk CP, Aitchison JD, Wozniak RW.
      The role of karyopherins in the regulated sumoylation of septins.
      17403926 The Journal of cell biology, 2007 Apr 9 : 177(1)39-49. PMCID:PMC2064105
      https://www.ncbi.nlm.nih.gov/pubmed/17403926
    • Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD.
      Transcriptional responses to fatty acid are coordinated by combinatorial control.
      17551510 Molecular systems biology, 2007 : 3115. PMCID:PMC1911199
      https://www.ncbi.nlm.nih.gov/pubmed/17551510
    • Taverna SD, Ilin S, Rogers RS, Tanny JC, Lavender H, Li H, Baker L, Boyle J, Blair LP, Chait BT, Patel DJ, Aitchison JD, Tackett AJ, Allis CD.
      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.
      17157260 Molecular cell, 2006 Dec 8 : 24(5)785-796. PMCID:PMC4690528
      https://www.ncbi.nlm.nih.gov/pubmed/17157260
    • Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.
      Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.
      16936734 Nature genetics, 2006 Sept. : 38(9)1082-7.
      https://www.ncbi.nlm.nih.gov/pubmed/16936734
    • Leslie DM, Timney B, Rout MP, Aitchison JD.
      Studying nuclear protein import in yeast.
      16979507 Methods (San Diego, Calif.), 2006 Aug. : 39(4)291-308.
      https://www.ncbi.nlm.nih.gov/pubmed/16979507
    • Vizeacoumar FJ, Vreden WN, Aitchison JD, Rachubinski RA.
      Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals.
      16551610 The Journal of biological chemistry, 2006 May 26 : 281(21)14805-12.
      https://www.ncbi.nlm.nih.gov/pubmed/16551610
    • Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.
      The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner.
      16520372 The Journal of biological chemistry, 2006 May 5 : 281(18)12817-23. PMCID:https://www.ncbi.nlm.nih.gov/pubmed/16520372
    • Fagarasanu A, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.
      The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae.
      16678774 Developmental cell, 2006 May : 10(5)587-600
      https://www.ncbi.nlm.nih.gov/pubmed/16678774
    • Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD.
      Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism.
      16738555 Molecular systems biology, 2006 : 22006.0009 PMCID:PMC1681483
      https://www.ncbi.nlm.nih.gov/pubmed/16738555
    • Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD.
      The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control.
      16365162 The Journal of cell biology, 2005 Dec 19 : 171(6)955-65. PMCID:PMC2171315
      https://www.ncbi.nlm.nih.gov/pubmed/16365162
    • Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H
      A data integration methodology for systems biology.
      16301537 Proceedings of the National Academy of Sciences of the United States of America, 2005 Nov 29 : 102(48)17296-301. PMCID:PMC1297682
      https://www.ncbi.nlm.nih.gov/pubmed/16301537
    • Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, Hood L.
      A data integration methodology for systems biology: experimental verification.
      Proc Natl Acad Sci USA, 2005 Nov 29 : 102(48)17302-7. PMCID:PMC1297683
      https://www.ncbi.nlm.nih.gov/pubmed/?term=16301536
    • Scott RJ, Lusk CP, Dilworth DJ, Aitchison JD, Wozniak RW.
      Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae.
      16000377 Molecular biology of the cell, 2005 Sept. : 16(9)4362-74. PMCID:PMC1196344
      https://www.ncbi.nlm.nih.gov/pubmed/16000377
    • Sydorskyy Y, Dilworth DJ, Halloran B, Yi EC, Makhnevych T, Wozniak RW, Aitchison JD.
      Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.
      15686447 The Biochemical journal, 2005 Jun 15 : 388(Pt 3)819-26. PMCID:PMC1183461
      https://www.ncbi.nlm.nih.gov/pubmed/15686447
    • Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA.
      Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae.
      15928207 The Journal of cell biology, 2005 Jun 6 : 169(5)765-75. PMCID:PMC2171609
      https://www.ncbi.nlm.nih.gov/pubmed/15928207
    • Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT.
      Proteomic and genomic characterization of chromatin complexes at a boundary.
      15824130 The Journal of cell biology, 2005 Apr 11 : 169(1)35-47. PMCID:PMC2171912
      https://www.ncbi.nlm.nih.gov/pubmed/15824130
    • Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD.
      Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane.
      15596542 The Journal of cell biology, 2004 Dec 20 : 167(6)1099-112. PMCID:PMC2172632
      https://www.ncbi.nlm.nih.gov/pubmed/15596542
    • Leslie DM, Zhang W, Timney BL, Chait BT, Rout MP, Wozniak RW, Aitchison JD.
      Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import.
      15367670 Molecular and cellular biology, 2004 Oct. : 24(19)8487-503. PMCID:PMC516728
      https://www.ncbi.nlm.nih.gov/pubmed/15367670
    • Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA.
      Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae.
      14617799 Molecular biology of the cell, 2004 Feb. : 15(2)665-77. PMCID:PMC329287
      https://www.ncbi.nlm.nih.gov/pubmed/14617799
    • Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison J, Hood L, Lasky SR.
      POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.
      15287980 Genome biology, 2004 : 5(8)R58 PMCID:PMC507883
      https://www.ncbi.nlm.nih.gov/pubmed/?term=15287980
    • Makhnevych T, Lusk CP, Anderson AM, Aitchison JD, Wozniak RW.
      Cell cycle regulated transport controlled by alterations in the nuclear pore complex.
      14697200 Cell, 2003 Dec 26 : 115(7)813-23.
      https://www.ncbi.nlm.nih.gov/pubmed/14697200
    • Tam YY, Torres-Guzman JC, Vizeacoumar FJ, Smith JJ, Marelli M, Aitchison JD, Rachubinski RA.
      Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae.
      14517321 Molecular biology of the cell, 2003 Oct. : 14(10)4089-102. PMCID:PMC207002
      https://www.ncbi.nlm.nih.gov/pubmed/14517321
    • Steiner-Mosonyi M, Leslie DM, Dehghani H, Aitchison JD, Mangroo D.
      Utp8p is an essential intranuclear component of the nuclear tRNA export machinery of Saccharomyces cerevisiae.
      12794079 The Journal of biological chemistry, 2003 Aug 22 : 278(34)32236-45.
      https://www.ncbi.nlm.nih.gov/pubmed/12794079
    • Vizeacoumar FJ, Torres-Guzman JC, Tam YY, Aitchison JD, Rachubinski RA.
      YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae.
      12707309 The Journal of cell biology, 2003 Apr 28 : 161(2)321-32. PMCID:PMC2172915
      https://www.ncbi.nlm.nih.gov/pubmed/12707309
    • Sydorskyy Y, Dilworth DJ, Yi EC, Goodlett DR, Wozniak RW, Aitchison JD.
      Intersection of the Kap123p-mediated nuclear import and ribosome export pathways.
      Mol Cell Biol., 2003 March : 23(6)2042-54. PMCID:PMC149464
      https://www.ncbi.nlm.nih.gov/pubmed/?term=12612077
    • Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW.
      Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes.
      12403813 The Journal of cell biology, 2002 Oct 28 : 159(2)267-78. PMCID:PMC2173048
      https://www.ncbi.nlm.nih.gov/pubmed/12403813
    • Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR.
      Approaching complete peroxisome characterization by gas-phase fractionation.
      12298092 Electrophoresis, 2002 Sept. : 23(18)3205-16.
      https://www.ncbi.nlm.nih.gov/pubmed/12298092
    • Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD.
      Transcriptome profiling to identify genes involved in peroxisome assembly and function.
      12135984 The Journal of cell biology, 2002 Jul 22 : 158(2)259-71 PMCID:PMC2173120
      https://www.ncbi.nlm.nih.gov/pubmed/12135984
    • Leslie DM, Grill B, Rout MP, Wozniak RW, Aitchison JD.
      Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast.
      11909949 Molecular and cellular biology, 2002 April : 22(8)2544-55 PMCID:PMC133723
      https://www.ncbi.nlm.nih.gov/pubmed/11909949

    Other Publications

    • Mast FD, Aitchison JD.
      Characterization of Peroxisomal Regulation Networks.
      30378032 Sub-cellular biochemistry, 2018 : 89367-382. Review.
      https://www.ncbi.nlm.nih.gov/pubmed/30378032
    • Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A.
      The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria.
      29201016 Frontiers in microbiology, 2017 : 82183. Review. PMCID:PMC5696578
      https://www.ncbi.nlm.nih.gov/pubmed/29201016
    • Mast FD, Rachubinski RA, Aitchison JD.
      Signaling dynamics and peroxisomes.
      26042681 Current opinion in cell biology, 2015 Aug. : 35131-6. Review. PMCID:PMC4529763
      https://www.ncbi.nlm.nih.gov/pubmed/26042681
    • Mast FD, Ratushny AV, Aitchison JD.
      Systems cell biology.
      25225336 The Journal of cell biology, 2014 Sep 15 : 206(6)695-706. Review. PMCID:PMC4164942
      https://www.ncbi.nlm.nih.gov/pubmed/25225336
    • Ptak C, Aitchison JD, Wozniak RW.
      The multifunctional nuclear pore complex: a platform for controlling gene expression.
      24657998 Current opinion in cell biology, 2014 June : 2846-53. Review. PMCID:PMC4061258
      https://www.ncbi.nlm.nih.gov/pubmed/24657998
    • Smith JJ, Aitchison JD.
      Peroxisomes take shape.
      24263361 Nature reviews. Molecular cell biology, 2013 Dec. : 14(12)803-17. Review. PMCID:PMC4060825
      https://www.ncbi.nlm.nih.gov/pubmed/24263361
    • Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.
      Role of the nuclear envelope in genome organization and gene expression.
      21305702 Wiley interdisciplinary reviews. Systems biology and medicine, 2011 March : 3(2)147-66. Review. PMCID:PMC3050641
      https://www.ncbi.nlm.nih.gov/pubmed/21305702
    • Smith JJ, Aitchison JD.
      Regulation of peroxisome dynamics.
      19188056 Current opinion in cell biology, 2009 Feb. : 21(1)119-26. Review. PMCID:PMC2681484
      https://www.ncbi.nlm.nih.gov/pubmed/19188056
    • Niemistö A, Korpelainen T, Saleem R, Yli-Harja O, Aitchison J, Shmulevich I.
      A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy.
      18003272 Conf Proc IEEE Eng Med Biol Soc., 2007 : 20075559-62
      https://www.ncbi.nlm.nih.gov/pubmed/18003272
    • Rout MP, Aitchison JD, Magnasco MO, Chait BT.
      Virtual gating and nuclear transport: the hole picture.
      14624840 Trends in cell biology., 2003 Dec. : 13(12)622-8. Review.
      https://www.ncbi.nlm.nih.gov/pubmed/14624840
    • Aitchison JD, Rout MP.
      A tense time for the nuclear envelope.
      11853664 Cell, 2002 Feb 8 : 108(3)301-4. Review..
      https://www.ncbi.nlm.nih.gov/pubmed/11853664

Overview

Research Description

The Aitchison Lab is focused on the development and application of systems biology approaches to infectious diseases. We combine high-throughput quantitative ‘omics technologies (e.g. proteomics, transcriptomics) with computational biology to interrogate, map, and model pathogens, host responses, and the interface between hosts and pathogens. Read more about the Aitchison Lab.

Learn about partnering opportunities with Dr. Aitchison:

Research Focus Area

Big Data, Biotechnology, Computational Biology, Data Analysis, Genetic Engineering, Genetics, Genomics, Global Health, HIV/AIDS, Host-Pathogen Interaction, Immunology, Infectious Disease, Influenza (Flu), OMICS, Predictive Analytics, Proteomics, Systems Biology