Publications

Found 1186 results
2009
Yan W, Aebersold R, Raines EW.  2009.  Evolution of organelle-associated protein profiling. J Proteomics. 72:4-11.
Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I.  2009.  Fewer permutations, more accurate P-values. Bioinformatics. 25:i161-8.
Picotti P, Bodenmiller B, Mueller LN, Domon B, Aebersold R.  2009.  Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell. 138:795-806.
Litvak V, Ramsey SA, Rust AG, Zak DE, Kennedy KA, Lampano AE, Nykter M, Shmulevich I, Aderem A.  2009.  Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals. Nat Immunol. 10:437-43.
Pascal LE, Goo YA, Vencio RZ, Page LS, Chambers AA, Liebeskind ES, Takayama TK, True LD, Liu AY.  2009.  Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes. BMC Cancer. 9:317.
Pascal LE, Vencio RZ, Page LS, Liebeskind ES, Shadle CP, Troisch P, Marzolf B, True LD, Hood LE, Liu AY.  2009.  Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes. BMC Cancer. 9:452.
Ghosh D, Yan X, Tian Q.  2009.  Gene regulatory networks in embryonic stem cells and brain development. Birth Defects Res C Embryo Today. 87:182-91.
Hawn TR, Scholes D, Wang H, Li SS, Stapleton AE, Janer M, Aderem A, Stamm WE, Zhao LP, Hooton TM.  2009.  Genetic variation of the human urinary tract innate immune response and asymptomatic bacteriuria in women. PLoS OnePLoS ONE. 4:e8300.
Glusman G, Smit A.  2009.  Genome organization. Encyclopedia of Complexity and Systems Science. 4:4160-4178.
Eisenacher M, Martens L, Hardt T, Kohl M, Barsnes H, Helsens K, Hakkinen J, Levander F, Aebersold R, Vandekerckhove J et al..  2009.  Getting a grip on proteomics data - Proteomics Data Collection (ProDaC). Proteomics. 9:3928-33.
Mirzaei H, Brusniak MY, Mueller LN, Letarte S, Watts J, Aebersold R.  2009.  Halogenated peptides as internal standards (H-PINS): introduction of an MS-based internal standard set for liquid chromatography-mass spectrometry. Mol Cell Proteomics. 8:1934-46.
Anderson NL, Anderson NG, Pearson TW, Borchers CH, Paulovich AG, Patterson SD, Gillette M, Aebersold R, Carr SA.  2009.  A human proteome detection and quantitation project. Mol Cell Proteomics. 8:883-6.
Bell AW, Deutsch EW, Au CE, Kearney RE, Beavis R, Sechi S, Nilsson T, Bergeron JJ.  2009.  A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat Methods. 6:423-30.
Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E et al..  2009.  Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biol. 7:e1000236.
Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE et al..  2009.  Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS OnePLoS ONE. 4:e6589.
Glatter T, Wepf A, Aebersold R, Gstaiger M.  2009.  An integrated workflow for charting the human interaction proteome: insights into the PP2A system. Mol Syst Biol. 5:237.
Nana-Sinkam SP, Hunter MG, Nuovo GJ, Schmittgen TD, Gelinas R, Galas DJ, Marsh CB.  2009.  Integrating the MicroRNome into the study of lung disease. Am J Respir Crit Care Med. 179:4-10.
Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, Pe'er D, Koller D.  2009.  Learning a prior on regulatory potential from eQTL data. PLoS Genet. 5:e1000358.
Wang K, Zhang S, Weber J, Baxter D, Galas DJ.  2009.  Mammalian cells in culture actively export specific microRNAs. Nature Precedings. :hdl:10101/npre.2009.3718.1.
Killcoyne S, Boyle J.  2009.  Managing Chaos: Lessons Learned Developing Software in the Life Sciences. IEEE Design & Test. 11:20-29.
Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N et al..  2009.  MaRiMba: a software application for spectral library-based MRM transition list assembly. J Proteome Res. 8:4396-405.
Pan S, Aebersold R, Chen R, Rush J, Goodlett DR, McIntosh MW, Zhang J, Brentnall TA.  2009.  Mass spectrometry based targeted protein quantification: methods and applications. J Proteome Res. 8:787-97.
Wollscheid B, Bausch-Fluck D, Henderson C, O'Brien R, Bibel M, Schiess R, Aebersold R, Watts J.  2009.  Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins. Nat Biotechnol. 27:378-86.
Carter GW, Galas DJ, Galitski T.  2009.  Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol. 5:e1000347.
Kutlu B, Kayali AG, Jung S, Parnaud G, Baxter D, Glusman G, Goodman N, Behie LA, Hayek A, Hood L.  2009.  Meta-analysis of gene expression in human pancreatic islets after in vitro expansion. Physiol Genomics. 39:72-81.
Diercks AH, Ozinsky A, Hansen CL, Spotts JM, Rodriguez DJ, Aderem A.  2009.  A microfluidic device for multiplexed protein detection in nano-liter volumes. Anal Biochem. 386:30-5.
Fu E, Nelson KE, Ramsey SA, Foley JO, Helton K, Yager P.  2009.  Modeling of a competitive microfluidic heterogeneous immunoassay: sensitivity of the assay response to varying system parameters. Anal Chem. 81:3407-13.
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.
Heath JR, Davis ME, Hood L.  2009.  Nanomedicine targets cancer. Sci Am. 300:44-51.
Hemmi H, Idoyaga J, Suda K, Suda N, Kennedy K, Noda M, Aderem A, Steinman RM.  2009.  A new triggering receptor expressed on myeloid cells (Trem) family member, Trem-like 4, binds to dead cells and is a DNAX activation protein 12-linked marker for subsets of mouse macrophages and dendritic cells. J Immunol. 182:1278-86.
Hu L, Hittelman W, Lu T, Ji P, Arlinghaus R, Shmulevich I, Hamilton SR, Zhang W.  2009.  NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells. Lab Invest. 89:531-48.
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.
Gillespie MA, Le Grand F, Scime A, Kuang S, von Maltzahn J, Seale V, Cuenda A, Ranish J, Rudnicki MA.  2009.  p38-{gamma}-dependent gene silencing restricts entry into the myogenic differentiation program. J Cell Biol. 187:991-1005.
Huttenhain R, Malmstrom J, Picotti P, Aebersold R.  2009.  Perspectives of targeted mass spectrometry for protein biomarker verification. Curr Opin Chem Biol. 13:518-25.
Su YH, Li E, Geiss GK, Longabaugh W, Kramer A, Davidson EH.  2009.  A perturbation model of the gene regulatory network for oral and aboral ectoderm specification in the sea urchin embryo. Dev Biol. 329:410-21.
Liu Y, Warfield L, Zhang C, Luo J, Allen J, Lang WH, Ranish J, Shokat KM, Hahn S.  2009.  Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol. 29:4852-63.
Bochud PY, Sinsimer D, Aderem A, Siddiqui MR, Saunderson P, Britton S, Abraham I, Tadesse Argaw A, Janer M, Hawn TR et al..  2009.  Polymorphisms in Toll-like receptor 4 (TLR4) are associated with protection against leprosy. Eur J Clin Microbiol Infect Dis. 28:1055-65.
Goudreault M, D'Ambrosio LM, Kean MJ, Mullin MJ, Larsen BG, Sanchez A, Chaudhry S, Chen GI, Sicheri F, Nesvizhskii AI et al..  2009.  A PP2A phosphatase high density interaction network identifies a novel striatin-interacting phosphatase and kinase complex linked to the cerebral cavernous malformation 3 (CCM3) protein. Mol Cell Proteomics. 8:157-71.
Gehlenborg N, Yan W, Lee I, Yoo H, Nieselt K, Hwang D, Aebersold R, Hood L.  2009.  Prequips--an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data. Bioinformatics. 25:682-3.
Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY et al..  2009.  Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 5:285.
Gehlenborg N, Hwang D, Lee I, Yoo H, Baxter D, Petritis B, Pitstick R, Marzolf B, Dearmond SJ, Carlson GA et al..  2009.  The Prion Disease Database: a comprehensive transcriptome resource for systems biology research in prion diseases. Database : the journal of biological databases and curation. 2009:bap011.
Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R.  2009.  Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol Cell Proteomics. 8:2405-17.
Brentnall TA, Pan S, Bronner MP, Crispin DA, Mirzaei H, Cooke K, Tamura Y, Nikolskaya T, Jebailey L, Goodlett DR et al..  2009.  Proteins That Underlie Neoplastic Progression of Ulcerative Colitis. Proteomics Clin Appl. 3:1326-1337.
Urwyler S, Nyfeler Y, Ragaz C, Lee H, Mueller LN, Aebersold R, Hilbi H.  2009.  Proteome analysis of Legionella vacuoles purified by magnetic immunoseparation reveals secretory and endosomal GTPases. Traffic. 10:76-87.
Claassen M, Aebersold R, Buhmann JM.  2009.  Proteome coverage prediction with infinite Markov models. Bioinformatics. 25:i154-60.
Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, Rode M, Yamada T, Maier T, Bader S, Beltran-Alvarez P et al..  2009.  Proteome organization in a genome-reduced bacterium. Science. 326:1235-40.
Malmstrom J, Beck M, Schmidt A, Lange V, Deutsch EW, Aebersold R.  2009.  Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature. 460:762-5.
Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB.  2009.  Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J Proteome Res. 8:1415-22.
Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M.  2009.  Quantitative interaction proteomics using mass spectrometry. Nat Methods. 6:203-5.
Saleem RA, Aitchison JD.  2009.  Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae. J Vis Exp.
Akiyoshi B, Nelson CR, Ranish J, Biggins S.  2009.  Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. Genes Dev. 23:2887-99.
Pan S, Cheng L, White JT, Lu W, Utleg AG, Yan X, Urban ND, Drescher CW, Hood L, Lin B.  2009.  Quantitative proteomics analysis integrated with microarray data reveals that extracellular matrix proteins, catenins, and p53 binding protein 1 are important for chemotherapy response in ovarian cancers. OMICS. 13:345-54.
Teckchandani A, Toida N, Goodchild J, Henderson C, Watts J, Wollscheid B, Cooper JA.  2009.  Quantitative proteomics identifies a Dab2/integrin module regulating cell migration. J Cell Biol. 186:99-111.
Miles GP, Samuel MA, Ranish J, Donohoe SM, Sperrazzo GM, Ellis BE.  2009.  Quantitative proteomics identifies oxidant-induced, AtMPK6-dependent changes in Arabidopsis thaliana protein profiles. Plant Signal Behav. 4:497-505.
Pan S, Chen R, Reimel BA, Crispin DA, Mirzaei H, Cooke K, Coleman JF, Lane Z, Bronner MP, Goodlett DR et al..  2009.  Quantitative proteomics investigation of pancreatic intraepithelial neoplasia. Electrophoresis. 30:1132-44.
Sherwood CA, Eastham A, Lee LW, Risler J, Mirzaei H, Falkner JA, Martin DB.  2009.  Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets. J Proteome Res. 8:3746-51.
Smith JJ, Aitchison JD.  2009.  Regulation of peroxisome dynamics. Curr Opin Cell Biol. 21:119-26.
Sumara G, Formentini I, Collins S, Sumara I, Windak R, Bodenmiller B, Ramracheya R, Caille D, Jiang H, Platt KA et al..  2009.  Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis. Cell. 136:235-48.
Eddy JA, Geman D, Price ND.  2009.  Relative expression analysis for identifying perturbed pathways. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2009:5456-9.
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J et al..  2009.  Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 3:9-17.
Diercks A, Kostner H, Ozinsky A.  2009.  Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS OnePLoS ONE. 4:e6326.
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.
Koide T, Pang WL, Baliga NS.  2009.  The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol. 7:297-305.
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.
Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS.  2009.  A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 5:282.
Lausted C, Hu Z, Hood L, Campbell CT.  2009.  SPR imaging for high throughput, label-free interaction analysis. Comb Chem High Throughput Screen. 12:741-51.
Aebersold R.  2009.  A stress test for mass spectrometry-based proteomics. Nat Methods. 6:411-2.
Carapito C, Klemm C, Aebersold R, Domon B.  2009.  Systematic LC-MS analysis of labile post-translational modifications in complex mixtures. J Proteome Res. 8:2608-14.
Hwang D, Lee I, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D et al..  2009.  A systems approach to prion disease. Molecular systems biology. 5:252.
Galas DJ, Hood L.  2009.  Systems biology and emerging technologies will catalyze the transition from reactive medicine to predictive, personalized, preventive and participatory (P4) medicine. Interdisciplinary Bio Central. 1:0006.
Price ND, Edelman LB, Lee I, Yoo H, Hwang D, Carlson G, Galas DJ, Heath JR, Hood L.  2009.  Systems biology and the emergence of systems medicine. Genomic and Personalized Medicine: From Principles to Practice.
Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B et al..  2009.  Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol. 10:116-25.
Zak DE, Aderem A.  2009.  Systems biology of innate immunity. Immunol Rev. 227:264-82.
Carter GW, Dudley AM.  2009.  Systems Genetics and Complex Traits. Encyclopedia of Complexity and Systems Science.
Auffray C, Chen Z, Hood L.  2009.  Systems medicine: the future of medical genomics and healthcare. Genome Med. 1:2.
Zak DE, Aderem A.  2009.  A systems view of host defense. Nat Biotechnol. 27:999-1001.
Schiess R, Wollscheid B, Aebersold R.  2009.  Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol. 3:33-44.
Tu LC, Foltz G, Lin E, Hood L, Tian Q.  2009.  Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther. 4:147-53.
Pascal LE, Vencio RZ, Goo YA, Page LS, Shadle CP, Liu AY.  2009.  Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells. Prostate. 69:1353-65.
Fulton DL, Sundararajan S, Badis G, Hughes TR, Wasserman WW, Roach J, Sladek R.  2009.  TFCat: the curated catalog of mouse and human transcription factors. Genome Biol. 10:R29.
Hawn TR, Scholes D, Li SS, Wang H, Yang Y, Roberts PL, Stapleton AE, Janer M, Aderem A, Stamm WE et al..  2009.  Toll-like receptor polymorphisms and susceptibility to urinary tract infections in adult women. PLoS OnePLoS ONE. 4:e5990.
Bollyky PL, Bice JB, Sweet IR, Falk BA, Gebe JA, Clark AE, Gersuk VH, Aderem A, Hawn TR, Nepom GT.  2009.  The toll-like receptor signaling molecule Myd88 contributes to pancreatic beta-cell homeostasis in response to injury. PLoS OnePLoS ONE. 4:e5063.
David-Fung ES, Butler R, Buzi G, Yui MA, Diamond RA, Anderson MK, Rowen L, Rothenberg EV.  2009.  Transcription factor expression dynamics of early T-lymphocyte specification and commitment. Dev Biol. 325:444-67.
Edelman L.B, Toia G., Geman D, Zhang W, Price ND.  2009.  Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. BMC genomics. 10:583.
Leidel S, Pedrioli PG, Bucher T, Brost R, Costanzo M, Schmidt A, Aebersold R, Boone C, Hofmann K, Peter M.  2009.  Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature. 458:228-32.
Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I.  2009.  Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst Biol. 3:20.
Di Paolo NC, Miao EA, Iwakura Y, Murali-Krishna K, Aderem A, Flavell RA, Papayannopoulou T, Shayakhmetov DM.  2009.  Virus binding to a plasma membrane receptor triggers interleukin-1 alpha-mediated proinflammatory macrophage response in vivo. Immunity. 31:110-21.
Beck M, Malmstrom JA, Lange V, Schmidt A, Deutsch EW, Aebersold R.  2009.  Visual proteomics of the human pathogen Leptospira interrogans. Nat Methods. 6:817-23.
Longabaugh W, Davidson EH, Bolouri H.  2009.  Visualization, documentation, analysis, and communication of large-scale gene regulatory networks. Biochim Biophys Acta. 1789:363-74.
2008
Gilchrist M, Henderson, W. R. J., Clark AE, Simmons RM, Ye X, Smith KD, Aderem A.  2008.  Activating transcription factor 3 is a negative regulator of allergic pulmonary inflammation. J Exp Med. 205:2349-57.
Lee WW, Cui D, Czesnikiewicz-Guzik M, Vencio RZ, Shmulevich I, Aderem A, Weyand CM, Goronzy JJ.  2008.  Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling. Rejuvenation Res. 11:1001-11.
Aderem A.  2008.  Alan Aderem: from molecules to megabytes. Interviewed by Nicole LeBrasseur. J Cell Biol. 180:252-3.
Mueller LN, Brusniak MY, Mani DR, Aebersold R.  2008.  An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J Proteome Res. 7:51-61.
Qi Y, Ranish J, Zhu X, Krones A, Zhang J, Aebersold R, Rose DW, Rosenfeld MG, Carriere C.  2008.  Atbf1 is required for the Pit1 gene early activation. Proc Natl Acad Sci U S A. 105:2481-6.
Rosenberger CM, Clark AE, Treuting PM, Johnson CD, Aderem A.  2008.  ATF3 regulates MCMV infection in mice by modulating IFN-gamma expression in natural killer cells. Proc Natl Acad Sci U S A. 105:2544-9.
Lam H, Deutsch EW, Eddes JS, Eng JK, Stein SE, Aebersold R.  2008.  Building consensus spectral libraries for peptide identification in proteomics. Nat Methods. 5:873-5.
Ao P, Galas DJ, Hood L, Zhu X.  2008.  Cancer as robust intrinsic state of endogenous molecular-cellular network shaped by evolution. Med Hypotheses. 70:678-84.
Yamazaki T, Yang XO, Chung Y, Fukunaga A, Nurieva R, Pappu B, Martin-Orozco N, Kang HS, Ma L, Panopoulos AD et al..  2008.  CCR6 regulates the migration of inflammatory and regulatory T cells. J Immunol. 181:8391-401.
Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A et al..  2008.  Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A. 105:10513-8.
Mirzaei H, McBee JK, Watts J, Aebersold R.  2008.  Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics. Mol Cell Proteomics. 7:813-23.

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