faculty
John Aitchison
john.aitchison@seattlechildrens.org
Professor
Seattle Childrens Research Institute
Computational Biology
Gene Expression, Cell Cycle & Chromosome Biology
Microbiology, Infection & Immunity
Systems Cell Biology, Organelle biogenesis, and host-pathogen interactions
Faculty Contact Information
Building: Seattle Children's Research Institute, 307 Westlake Ave N
Room: 5th floor
Box: 307W
https://www.seattlechildrens.org/directory/john-aitchison/
Research Summary
My laboratory is focused on developing and applying systems approaches to reveal systems levels insights into cell biology and infectious disease processes. We develop and build on advances in high throughput technologies and computational biology (including mass spectrometry, next generation DNA sequencing, high throughput microscopy, and integrative modeling of structures and networks) to gain fundamental insights into cell biology of organelle biogenesis and responses to infection.
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Publications
The following publications were retrieved from PubMed:
Autophagy as a Mechanism for Adaptive Prediction-Mediated Emergence of Drug Resistance.
Nivedita N, Aitchison JD, Baliga NS.
Front Microbiol. 2021; (12)712631
Determinants of brain swelling in pediatric and adult cerebral malaria.
Sahu PK, Duffy FJ, Dankwa S, Vishnyakova M, Majhi M, Pirpamer L, Vigdorovich V, Bage J, Maharana S, Mandala W, Rogerson SJ, Seydel KB, Taylor TE, Kim K, Sather DN, Mohanty A, Mohanty RR, Mohanty A, Pattnaik R, Aitchison JD, Hoffman A, Mohanty S, Smith JD, Bernabeu M, Wassmer SC.
JCI Insight. 2021 Sep 22; 18(6)
Duffy FJ, Du Y, Carnes J, Epstein JE, Hoffman SL, Abdulla S, Jongo S, Mpina M, Daubenberger C, Aitchison JD, Stuart K.
Malar J. 2021 Jul 9; 1(20)308
Herricks T, Donczew M, Sherman DR, Aitchison JD.
Bio Protoc. 2021 May 20; 10(11)e4027
Nazitto R, Amon LM, Mast FD, Aitchison JD, Aderem A, Johnson JS, Diercks AH.
J Immunol. 2021 May 24;
Nanobody Repertoires for Exposing Vulnerabilities of SARS-CoV-2.
Mast FD, Fridy PC, Ketaren NE, Wang J, Jacobs EY, Olivier JP, Sanyal T, Molloy KR, Schmidt F, Rutkowska M, Weisblum Y, Rich LM, Vanderwall ER, Dambrauskas N, Vigdorovich V, Keegan S, Jiler JB, Stein ME, Olinares PDB, Hatziioannou T, Sather DN, Debley JS, Fenyö D, Sali A, Bieniasz PD, Aitchison JD, Chait BT, Rout MP.
bioRxiv. 2021 Apr 10;
Duffy FJ, Olson GS, Gold ES, Jahn A, Aderem A, Aitchison J, Rothchild AC, Diercks AH, Nemeth J.
J Infect Dis. 2021 Mar 10;
A systems-level gene regulatory network model for Plasmodium falciparum.
Neal ML, Wei L, Peterson E, Arrieta-Ortiz ML, Danziger SA, Baliga NS, Kaushansky A, Aitchison JD.
Nucleic Acids Res. 2021 May 21; 9(49)4891-4906
Dissecting the Structural Dynamics of the Nuclear Pore Complex.
Hakhverdyan Z, Molloy KR, Keegan S, Herricks T, Lepore DM, Munson M, Subbotin RI, Fenyö D, Aitchison JD, Fernandez-Martinez J, Chait BT, Rout MP.
Mol Cell. 2021 Jan 7; 1(81)153-165.e7
Viral protein engagement of GBF1 induces host cell vulnerability through synthetic lethality.
Navare AT, Mast FD, Olivier JP, Bertomeu T, Neal M, Carpp LN, Kaushansky A, Coulombe-Huntington J, Tyers M, Aitchison JD.
bioRxiv. 2020 Nov 6;
Plumlee CR, Duffy FJ, Gern BH, Delahaye JL, Cohen SB, Stoltzfus CR, Rustad TR, Hansen SG, Axthelm MK, Picker LJ, Aitchison JD, Sherman DR, Ganusov VV, Gerner MY, Zak DE, Urdahl KB.
Cell Host Microbe. 2021 Jan 13; 1(29)68-82.e5
Defining the proteolytic landscape during enterovirus infection.
Saeed M, Kapell S, Hertz NT, Wu X, Bell K, Ashbrook AW, Mark MT, Zebroski HA, Neal ML, Flodström-Tullberg M, MacDonald MR, Aitchison JD, Molina H, Rice CM.
PLoS Pathog. 2020 Sep; 9(16)e1008927
Crippling life support for SARS-CoV-2 and other viruses through synthetic lethality.
Mast FD, Navare AT, van der Sloot AM, Coulombe-Huntington J, Rout MP, Baliga NS, Kaushansky A, Chait BT, Aderem A, Rice CM, Sali A, Tyers M, Aitchison JD.
J Cell Biol. 2020 Oct 5; 10(219)
Herricks T, Donczew M, Mast FD, Rustad T, Morrison R, Sterling TR, Sherman DR, Aitchison JD.
Elife. 2020 May 13; (9)
Peroxisome prognostications: Exploring the birth, life, and death of an organelle.
Mast FD, Rachubinski RA, Aitchison JD.
J Cell Biol. 2020 Mar 2; 3(219)
Recruitment of an Activated Gene to the Yeast Nuclear Pore Complex Requires Sumoylation.
Saik NO, Park N, Ptak C, Adames N, Aitchison JD, Wozniak RW.
Front Genet. 2020; (11)174
Plasmodium Secretion Induces Hepatocyte Lysosome Exocytosis and Promotes Parasite Entry.
Vijayan K, Cestari I, Mast FD, Glennon EKK, McDermott SM, Kain HS, Brokaw AM, Aitchison JD, Stuart K, Kaushansky A.
iScience. 2019 Nov 22; (21)603-611
Spatial presentation of biological molecules to cells by localized diffusive transfer.
Regier MC, Olszewski E, Carter CC, Aitchison JD, Kaushansky A, Davis J, Berthier E, Beebe DJ, Stevens KR.
Lab Chip. 2019 Jun 11; 12(19)2114-2126
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.
mBio. 2019 Apr 30; 2(10)
Glennon EKK, Austin LS, Arang N, Kain HS, Mast FD, Vijayan K, Aitchison JD, Kappe SHI, Kaushansky A.
Cell Rep. 2019 Mar 19; 12(26)3391-3399.e4
Characterization of Peroxisomal Regulation Networks.
Mast FD, Aitchison JD.
Subcell Biochem. 2018; (89)367-382
ESCRT-III is required for scissioning new peroxisomes from the endoplasmic reticulum.
Mast FD, Herricks T, Strehler KM, Miller LR, Saleem RA, Rachubinski RA, Aitchison JD.
J Cell Biol. 2018 Jun 4; 6(217)2087-2102
Integrative structure and functional anatomy of a nuclear pore complex.
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.
Nature. 2018 Mar 22; 7697(555)475-482
Involvement in surface antigen expression by a moonlighting FG-repeat nucleoporin in trypanosomes.
Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Bart JM, Navarro M, Chait BT, Aitchison JD, Rout MP, Field MC.
Mol Biol Cell. 2018 May 1; 9(29)1100-1110
The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria.
Zuck M, Austin LS, Danziger SA, Aitchison JD, Kaushansky A.
Front Microbiol. 2017; (8)2183
Linking EPCR-Binding PfEMP1 to Brain Swelling in Pediatric Cerebral Malaria.
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.
Cell Host Microbe. 2017 Nov 8; 5(22)601-614.e5
Adaptive Prediction Emerges Over Short Evolutionary Time Scales.
López García de Lomana A, Kaur A, Turkarslan S, Beer KD, Mast FD, Smith JJ, Aitchison JD, Baliga NS.
Genome Biol Evol. 2017 Jun 1; 6(9)1616-1623
ODELAY: A Large-scale Method for Multi-parameter Quantification of Yeast Growth.
Herricks T, Mast FD, Li S, Aitchison JD.
J Vis Exp. 2017 Jul 3; 125
An indicator cell assay for blood-based diagnostics.
Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ.
PLoS One. 2017; 6(12)e0178608
Wang Z, Danziger SA, Heavner BD, Ma S, Smith JJ, Li S, Herricks T, Simeonidis E, Baliga NS, Aitchison JD, Price ND.
PLoS Comput Biol. 2017 May; 5(13)e1005489
One-Cell Doubling Evaluation by Living Arrays of Yeast, ODELAY!
Herricks T, Dilworth DJ, Mast FD, Li S, Smith JJ, Ratushny AV, Aitchison JD.
G3 (Bethesda). 2017 Jan 5; 1(7)279-288
Maishman L, Obado SO, Alsford S, Bart JM, Chen WM, Ratushny AV, Navarro M, Horn D, Aitchison JD, Chait BT, Rout MP, Field MC.
Nucleic Acids Res. 2016 Dec 15; 22(44)10554-10570
Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.
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.
Cell. 2016 Jul 28; 3(166)766-778
Severe adult malaria is associated with specific PfEMP1 adhesion types and high parasite biomass.
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.
Proc Natl Acad Sci U S A. 2016 Jun 7; 23(113)E3270-9
Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD.
J Biol Chem. 2016 Jul 22; 30(291)15408-27
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.
Nature. 2015 Sep 3; 7567(525)144
Signaling dynamics and peroxisomes.
Mast FD, Rachubinski RA, Aitchison JD.
Curr Opin Cell Biol. 2015 Aug; (35)131-6
Rapid, optimized interactomic screening.
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.
Nat Methods. 2015 Jun; 6(12)553-60
Danziger SA, Reiss DJ, Ratushny AV, Smith JJ, Plaisier CL, Aitchison JD, Baliga NS.
BMC Syst Biol. 2015; (9 Suppl 2)S1
Systematic Analysis of Yeast Proteome Reveals Peptide Detectability Factors for Mass Spectrometry.
Jung S, Danziger SA, Panchaud A, von Haller P, Aitchison JD, Goodlett DR.
J Proteomics Bioinform. 2015; 10(8)231-239
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.
Mol Cell Proteomics. 2014 Oct; 10(13)2646-60
Carpp LN, Rogers RS, Moritz RL, Aitchison JD.
Mol Cell Proteomics. 2014 Nov; 11(13)2836-54
The multifunctional nuclear pore complex: a platform for controlling gene expression.
Ptak C, Aitchison JD, Wozniak RW.
Curr Opin Cell Biol. 2014 Jun; (28)46-53
Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS.
Mol Microbiol. 2014 Apr; 2(92)369-82
Holden JM, Koreny L, Obado S, Ratushny AV, Chen WM, Chiang JH, Kelly S, Chait BT, Aitchison JD, Rout MP, Field MC.
Mol Biol Cell. 2014 May; 9(25)1421-36
Pan-viral specificity of IFN-induced genes reveals new roles for cGAS in innate immunity.
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.
Nature. 2014 Jan 30; 7485(505)691-5
Molecular mechanisms of system responses to novel stimuli are predictable from public data.
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.
Nucleic Acids Res. 2014 Feb; 3(42)1442-60
Cooney LA, Gupta M, Thomas S, Mikolajczak S, Choi KY, Gibson C, Jang IK, Danziger S, Aitchison J, Gardner MJ, Kappe SH, Wang R.
Infect Immun. 2013 Nov; 11(81)4171-81
Chen WM, Danziger SA, Chiang JH, Aitchison JD.
Bioinformatics. 2013 Oct 1; 19(29)2435-44
Sundaravaradan V, Saleem R, Micci L, Gasper MA, Ortiz AM, Else J, Silvestri G, Paiardini M, Aitchison JD, Sodora DL.
PLoS Pathog. 2013; 6(9)e1003441
A role for the nucleoporin Nup170p in chromatin structure and gene silencing.
Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.
Cell. 2013 Feb 28; 5(152)969-83
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.
Proc Natl Acad Sci U S A. 2013 Feb 26; 9(110)3645-50
Metallochaperones regulate intracellular copper levels.
Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS.
PLoS Comput Biol. 2013; 1(9)e1002880
Global analysis of condition-specific subcellular protein distribution and abundance.
Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD.
Mol Cell Proteomics. 2013 May; 5(12)1421-35
A FOXO3-IRF7 gene regulatory circuit limits inflammatory sequelae of antiviral responses.
Litvak V, Ratushny AV, Lampano AE, Schmitz F, Huang AC, Raman A, Rust AG, Bergthaler A, Aitchison JD, Aderem A.
Nature. 2012 Oct 18; 7420(490)421-5
Asymmetric positive feedback loops reliably control biological responses.
Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD.
Mol Syst Biol. 2012 Apr 24; (8)577
NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.
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.
PLoS Biol. 2012; 3(10)e1001287
The yeast nuclear pore complex and transport through it.
Aitchison JD, Rout MP.
Genetics. 2012 Mar; 3(190)855-83
Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL.
Mol Cell Proteomics. 2012 Apr; 4(11)M111.014985
A regression model approach to enable cell morphology correction in high-throughput flow cytometry.
Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.
Mol Syst Biol. 2011 Sep 27; (7)531
Mathematical modeling of biomolecular network dynamics.
Ratushny AV, Ramsey SA, Aitchison JD.
Methods Mol Biol. 2011; (781)415-33
Statistical analysis of dynamic transcriptional regulatory network structure.
Smith JJ, Saleem RA, Aitchison JD.
Methods Mol Biol. 2011; (781)337-52
Ratushny AV, Shmulevich I, Aitchison JD.
PLoS Comput Biol. 2011 Jun; 6(7)e1002091
Tower RJ, Fagarasanu A, Aitchison JD, Rachubinski RA.
Mol Biol Cell. 2011 May 15; 10(22)1727-38
Faster, quantitative, and accurate precursor acquisition independent from ion count.
Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR.
Anal Chem. 2011 Mar 15; 6(83)2250-7
Role of the nuclear envelope in genome organization and gene expression.
Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.
Wiley Interdiscip Rev Syst Biol Med. 2011 Mar-Apr; 2(3)147-66
Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing.
Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD.
Mol Syst Biol. 2011 Jan 4; (7)455
Vinh DB, Ko DC, Rachubinski RA, Aitchison JD, Miller SI.
Mol Biol Cell. 2010 Oct 15; 20(21)3567-77
Genome-wide analysis of effectors of peroxisome biogenesis.
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.
PLoS One. 2010 Aug 4; 8(5)e11953
Dilworth DJ, Saleem RA, Rogers RS, Mirzaei H, Boyle J, Aitchison JD.
J Am Soc Mass Spectrom. 2010 Aug; 8(21)1417-22
Saleem RA, Rogers RS, Ratushny AV, Dilworth DJ, Shannon PT, Shteynberg D, Wan Y, Moritz RL, Nesvizhskii AI, Rachubinski RA, Aitchison JD.
Mol Cell Proteomics. 2010 Sep; 9(9)2076-88
GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome.
Sekedat MD, Fenyö D, Rogers RS, Tackett AJ, Aitchison JD, Chait BT.
Mol Syst Biol. 2010; (6)353
Systems cell biology of the mitotic spindle.
Saleem RA, Aitchison JD.
J Cell Biol. 2010 Jan 11; 1(188)7-9
Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress.
Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.
J Biol Chem. 2010 Feb 26; 9(285)6739-49
Histone chaperone Chz1p regulates H2B ubiquitination and subtelomeric anti-silencing.
Wan Y, Chiang JH, Lin CH, Arens CE, Saleem RA, Smith JJ, Aitchison JD.
Nucleic Acids Res. 2010 Mar; 5(38)1431-40
Deterministic and stochastic models of genetic regulatory networks.
Shmulevich I, Aitchison JD.
Methods Enzymol. 2009; (467)335-356
Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae.
Saleem RA, Aitchison JD.
J Vis Exp. 2009 Oct 12; 32
A role for the karyopherin Kap123p in microtubule stability.
Ptak C, Anderson AM, Scott RJ, Van de Vosse D, Rogers RS, Sydorskyy Y, Aitchison JD, Wozniak RW.
Traffic. 2009 Nov; 11(10)1619-34
Myosin-driven peroxisome partitioning in S. cerevisiae.
Fagarasanu A, Mast FD, Knoblach B, Jin Y, Brunner MJ, Logan MR, Glover JN, Eitzen GA, Aitchison JD, Weisman LS, Rachubinski RA.
J Cell Biol. 2009 Aug 24; 4(186)541-54
Gradolatto A, Smart SK, Byrum S, Blair LP, Rogers RS, Kolar EA, Lavender H, Larson SK, Aitchison JD, Taverna SD, Tackett AJ.
Mol Cell Biol. 2009 Sep; 17(29)4604-11
Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD.
Mol Cell Biol. 2009 May; 9(29)2346-58
Regulation of peroxisome dynamics.
Smith JJ, Aitchison JD.
Curr Opin Cell Biol. 2009 Feb; 1(21)119-26
Control of transcriptional variability by overlapping feed-forward regulatory motifs.
Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD.
Biophys J. 2008 Oct; 8(95)3715-23
Systems biology at the Institute for Systems Biology.
Hood L, Rowen L, Galas DJ, Aitchison JD.
Brief Funct Genomic Proteomic. 2008 Jul; 4(7)239-48
Saccharomyces cerevisiae Yta7 regulates histone gene expression.
Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ.
Genetics. 2008 May; 1(179)291-304
Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM, Long-O'Donnell R, Rachubinski RA, Aitchison JD.
J Cell Biol. 2008 Apr 21; 2(181)281-92
Marelli M, Nesvizhskii AI, Aitchison JD.
Methods Mol Biol. 2008; (432)357-71
Niemistö A, Korpelainen T, Saleem R, Yli-Harja O, Aitchison J, Shmulevich I.
Annu Int Conf IEEE Eng Med Biol Soc. 2007; (2007)5559-62
Extraction of the number of peroxisomes in yeast cells by automated image analysis.
Niemistö A, Selinummi J, Saleem R, Shmulevich I, Aitchison J, Yli-Harja O.
Conf Proc IEEE Eng Med Biol Soc. 2006; (2006)2353-6
Comprehensive analysis of diverse ribonucleoprotein complexes.
Oeffinger M, Wei KE, Rogers R, DeGrasse JA, Chait BT, Aitchison JD, Rout MP.
Nat Methods. 2007 Nov; 11(4)951-6
Transcriptional responses to fatty acid are coordinated by combinatorial control.
Smith JJ, Ramsey SA, Marelli M, Marzolf B, Hwang D, Saleem RA, Rachubinski RA, Aitchison JD.
Mol Syst Biol. 2007; (3)115
The role of karyopherins in the regulated sumoylation of septins.
Makhnevych T, Ptak C, Lusk CP, Aitchison JD, Wozniak RW.
J Cell Biol. 2007 Apr 9; 1(177)39-49
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.
Mol Cell. 2006 Dec 8; 5(24)785-796
Studying nuclear protein import in yeast.
Leslie DM, Timney B, Rout MP, Aitchison JD.
Methods. 2006 Aug; 4(39)291-308
Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast.
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.
Nat Genet. 2006 Sep; 9(38)1082-7
Pedrioli PG, Raught B, Zhang XD, Rogers R, Aitchison J, Matunis M, Aebersold R.
Nat Methods. 2006 Jul; 7(3)533-9
Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism.
Smith JJ, Sydorskyy Y, Marelli M, Hwang D, Bolouri H, Rachubinski RA, Aitchison JD.
Mol Syst Biol. 2006; (2)2006.0009
Membranous glomerulopathy with spherules: an uncommon variant with obscure pathogenesis.
Kowalewska J, Smith KD, Hudkins KL, Chang A, Fogo AB, Houghton D, Leslie D, Aitchison J, Nicosia RF, Alpers CE.
Am J Kidney Dis. 2006 Jun; 6(47)983-92
Fagarasanu A, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.
Dev Cell. 2006 May; 5(10)587-600
Vizeacoumar FJ, Vreden WN, Aitchison JD, Rachubinski RA.
J Biol Chem. 2006 May 26; 21(281)14805-12
Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.
J Biol Chem. 2006 May 5; 18(281)12817-23
Dilworth DJ, Tackett AJ, Rogers RS, Yi EC, Christmas RH, Smith JJ, Siegel AF, Chait BT, Wozniak RW, Aitchison JD.
J Cell Biol. 2005 Dec 19; 6(171)955-65
A data integration methodology for systems biology.
Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF, Bolouri H.
Proc Natl Acad Sci U S A. 2005 Nov 29; 48(102)17296-301
A data integration methodology for systems biology: experimental verification.
Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD, Hood L.
Proc Natl Acad Sci U S A. 2005 Nov 29; 48(102)17302-7
Scott RJ, Lusk CP, Dilworth DJ, Aitchison JD, Wozniak RW.
Mol Biol Cell. 2005 Sep; 9(16)4362-74
Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA.
J Cell Biol. 2005 Jun 6; 5(169)765-75
Proteomic and genomic characterization of chromatin complexes at a boundary.
Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT.
J Cell Biol. 2005 Apr 11; 1(169)35-47
Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein.
Sydorskyy Y, Dilworth DJ, Halloran B, Yi EC, Makhnevych T, Wozniak RW, Aitchison JD.
Biochem J. 2005 Jun 15; Pt 3(388)819-26
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.
J Cell Biol. 2004 Dec 20; 6(167)1099-112
Leslie DM, Zhang W, Timney BL, Chait BT, Rout MP, Wozniak RW, Aitchison JD.
Mol Cell Biol. 2004 Oct; 19(24)8487-503
POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer.
Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison J, Hood L, Lasky SR.
Genome Biol. 2004; 8(5)R58
Cell cycle regulated transport controlled by alterations in the nuclear pore complex.
Makhnevych T, Lusk CP, Anderson AM, Aitchison JD, Wozniak RW.
Cell. 2003 Dec 26; 7(115)813-23
Virtual gating and nuclear transport: the hole picture.
Rout MP, Aitchison JD, Magnasco MO, Chait BT.
Trends Cell Biol. 2003 Dec; 12(13)622-8
Vizeacoumar FJ, Torres-Guzman JC, Bouard D, Aitchison JD, Rachubinski RA.
Mol Biol Cell. 2004 Feb; 2(15)665-77
Tam YY, Torres-Guzman JC, Vizeacoumar FJ, Smith JJ, Marelli M, Aitchison JD, Rachubinski RA.
Mol Biol Cell. 2003 Oct; 10(14)4089-102
Steiner-Mosonyi M, Leslie DM, Dehghani H, Aitchison JD, Mangroo D.
J Biol Chem. 2003 Aug 22; 34(278)32236-45
Vizeacoumar FJ, Torres-Guzman JC, Tam YY, Aitchison JD, Rachubinski RA.
J Cell Biol. 2003 Apr 28; 2(161)321-32
Lusk CP, Makhnevych T, Marelli M, Aitchison JD, Wozniak RW.
J Cell Biol. 2002 Oct 28; 2(159)267-78
Approaching complete peroxisome characterization by gas-phase fractionation.
Yi EC, Marelli M, Lee H, Purvine SO, Aebersold R, Aitchison JD, Goodlett DR.
Electrophoresis. 2002 Sep; 18(23)3205-16
Transcriptome profiling to identify genes involved in peroxisome assembly and function.
Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD.
J Cell Biol. 2002 Jul 22; 2(158)259-71
Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast.
Leslie DM, Grill B, Rout MP, Wozniak RW, Aitchison JD.
Mol Cell Biol. 2002 Apr; 8(22)2544-55
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Lab Information
Location: Seattle Children's Research Institute
Building: 307 Westlake
https://www.seattlechildrens.org/research/centers-programs/global-infectious-disease-research/research-areas-and-labs/aitchison-lab/
Building: 307 Westlake
https://www.seattlechildrens.org/research/centers-programs/global-infectious-disease-research/research-areas-and-labs/aitchison-lab/