Publications

Found 94 results
Filters: Author is Aitchison, J. D.  [Clear All Filters]
2013
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.
2011
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.
2010
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.
2006
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.
2005
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.