Publications

Found 305 results
Filters: Author is Aebersold, R.  [Clear All Filters]
2012
Bislev SL, Deutsch EW, Sun Z, Farrah T, Aebersold R, Moritz RL, Bendixen E, Codrea MC.  2012.  A Bovine PeptideAtlas of milk and mammary gland proteomes. Proteomics.
Paik YK, Jeong SK, Omenn GS, Uhlen M, Hanash S, Cho SY, Lee HJ, Na K, Choi EY, Yan F et al..  2012.  The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome. Nature biotechnology. 30:221-3.
Hood LE, Omenn GS, Moritz RL, Aebersold R, K YR, Amos M, Hunter-Cevera J, Locascio L.  2012.  New and improved proteomics technologies for understanding complex biological systems: Addressing a grand challenge in the life sciences. Proteomics.
Farrah T, Deutsch EW, Kreisberg R, Sun Z, Campbell DS, Mendoza L, Kusebauch U, Brusniak MY, Huttenhain R, Schiess R et al..  2012.  PASSEL: The PeptideAtlas SRM Experiment Library. Proteomics.
Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Rontved CM, Aebersold R, Moritz RL, Bendixen E.  2012.  Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis. Journal of proteome research. 11:1832-43.
Huttenhain R, Soste M, Selevsek N, Rost H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL et al..  2012.  Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science translational medicine. 4:142ra94.
Deutsch EW, Chambers M, Neumann S, Levander F, Binz PA, Shofstahl J, Campbell DS, Mendoza L, Ovelleiro D, Helsens K et al..  2012.  TraML--A Standard Format for Exchange of Selected Reaction Monitoring Transition Lists. Molecular & cellular proteomics : MCP. 11:R111015040.
2011
Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J et al..  2011.  ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics. 12:78.
Legrain P, Aebersold R, Archakov A, Bairoch A, Bala K, Beretta L, Bergeron J, Borchers C, Corthals GL, Costello CE et al..  2011.  The human proteome project: Current state and future direction. Mol Cell Proteomics.
Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J.  2011.  Index-ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures. Mol Cell Proteomics. 10:M110005611.
Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI.  2011.  iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Molecular & cellular proteomics : MCP.
Reiter L, Rinner O, Picotti P, Huttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.  2011.  mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat Methods.
Ramos H, Shannon P, Brusniak MY, Kusebauch U, Moritz RL, Aebersold R.  2011.  The Protein Information and Property Explorer 2: Gaggle-like exploration of biological proteomic data within one webpage. Proteomics. 11:154-8.
Farrah T, Deutsch EW, Aebersold R.  2011.  Using the Human Plasma PeptideAtlas to Study Human Plasma Proteins. Methods Mol Biol. 728:349-74.
2009
Omenn GS, Aebersold R, Paik YK.  2009.  7(th) HUPO World Congress of Proteomics: launching the second phase of the HUPOPlasma Proteome Project (PPP-2) 16-20 August 2008, Amsterdam, The Netherlands. Proteomics. 9:4-6.
Schiess R, Mueller LN, Schmidt A, Mueller M, Wollscheid B, Aebersold R.  2009.  Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Mol Cell Proteomics. 8:624-38.
Gstaiger M, Aebersold R.  2009.  Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet. 10:617-27.
Jeong SK, Kwon MS, Lee EY, Lee HJ, Cho SY, Kim H, Yoo JS, Omenn GS, Aebersold R, Hanash S et al..  2009.  BiomarkerDigger: a versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers. Proteomics. 9:3729-40.
Huber A, Bodenmiller B, Uotila A, Stahl M, Wanka S, Gerrits B, Aebersold R, Loewith R.  2009.  Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes Dev. 23:1929-43.
Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jorgensen C, Bader GD, Aebersold R, Pawson T, Linding R.  2009.  Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci Signal. 2:ra39.
Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmstrom J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE et al..  2009.  Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 7:e48.
Theis M, Slabicki M, Junqueira M, Paszkowski-Rogacz M, Sontheimer J, Kittler R, Heninger AK, Glatter T, Kruusmaa K, Poser I et al..  2009.  Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J. 28:1453-65.
Ulintz PJ, Yocum AK, Bodenmiller B, Aebersold R, Andrews PC, Nesvizhskii AI.  2009.  Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. J Proteome Res. 8:887-99.
Schmidt A, Claassen M, Aebersold R.  2009.  Directed mass spectrometry: towards hypothesis-driven proteomics. Curr Opin Chem Biol. 13:510-7.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase C, Aebersold R, Hafen E.  2009.  The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics. 10:59.
Domon B, Bodenmiller B, Carapito C, Hao Z, Huehmer A, Aebersold R.  2009.  Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. J Proteome Res. 8:2633-9.
Yan W, Aebersold R, Raines EW.  2009.  Evolution of organelle-associated protein profiling. J Proteomics. 72:4-11.
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.
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.
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.
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.
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.
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.
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.
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.
Wepf A, Glatter T, Schmidt A, Aebersold R, Gstaiger M.  2009.  Quantitative interaction proteomics using mass spectrometry. Nat Methods. 6:203-5.
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.
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.
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.
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.
Schiess R, Wollscheid B, Aebersold R.  2009.  Targeted proteomic strategy for clinical biomarker discovery. Mol Oncol. 3:33-44.
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.
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.
2008
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.
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.
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.
Brusniak MY, Bodenmiller B, Campbell D, Cooke K, Eddes J, Garbutt A, Lau H, Letarte S, Mueller LN, Sharma V et al..  2008.  Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics. 9:542.
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish J, Krumm A.  2008.  CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A. 105:8309-14.
Deutsch EW, Lam H, Aebersold R.  2008.  Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics. 33:18-25.
Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R.  2008.  A database of mass spectrometric assays for the yeast proteome. Nat Methods. 5:913-4.
Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS et al..  2008.  Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics. 4:105.
Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, Huhmer A, Kussmann M, Lilley K et al..  2008.  Guidelines for reporting the use of mass spectrometry in proteomics. Nat Biotechnol. 26:860-1.
Chi Y, Welcker M, Hizli AA, Posakony JJ, Aebersold R, Clurman BE.  2008.  Identification of CDK2 substrates in human cell lysates. Genome Biol. 9:R149.
Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R.  2008.  Identification of cross-linked peptides from large sequence databases. Nat Methods. 5:315-8.
Schmidt A, Gehlenborg N, Bodenmiller B, Mueller LN, Campbell D, Mueller M, Aebersold R, Domon B.  2008.  An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Mol Cell Proteomics. 7:2138-50.
Ulintz PJ, Bodenmiller B, Andrews PC, Aebersold R, Nesvizhskii AI.  2008.  Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Mol Cell Proteomics. 7:71-87.
Gavin AC, Aebersold R, Heck AJ.  2008.  Meeting report on the 7th World Congress of the Human Proteome Organization (HUPO) in Amsterdam: Proteome Biology. Mol Cell Proteomics. 7:2288-91.
Zhang Q, Menon R, Deutsch EW, Pitteri SJ, Faca VM, Wang H, Newcomb LF, Depinho RA, Bardeesy N, Dinulescu D et al..  2008.  A mouse plasma peptide atlas as a resource for disease proteomics. Genome Biol. 9:R93.
Hwang D, Zhang N, Lee H, Yi E, Zhang H, Lee I, Hood L, Aebersold R.  2008.  MS-BID: a Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics. 24:2641-2.
Soltermann A, Ossola R, Kilgus-Hawelski S, von Eckardstein A, Suter T, Aebersold R, Moch H.  2008.  N-glycoprotein profiling of lung adenocarcinoma pleural effusions by shotgun proteomics. Cancer. 114:124-33.
Deutsch EW, Lam H, Aebersold R.  2008.  PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9:429-34.
Bodenmiller B, Campbell D, Gerrits B, Lam H, Jovanovic M, Picotti P, Schlapbach R, Aebersold R.  2008.  PhosphoPep--a database of protein phosphorylation sites in model organisms. Nat Biotechnol. 26:1339-40.
Ramos H, Shannon P, Aebersold R.  2008.  The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data. Bioinformatics. 24:2110-1.
Tress ML, Bodenmiller B, Aebersold R, Valencia A.  2008.  Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome Biol. 9:R162.
Pflieger D, Junger MA, Muller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R.  2008.  Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Mol Cell Proteomics. 7:326-46.
Yan W, Hwang D, Aebersold R.  2008.  Quantitative proteomic analysis to profile dynamic changes in the spatial distribution of cellular proteins. Methods Mol Biol. 432:389-401.
Lange V, Picotti P, Domon B, Aebersold R.  2008.  Selected reaction monitoring for quantitative proteomics: a tutorial. Mol Syst Biol. 4:222.
Klimek J, Eddes JS, Hohmann L, Jackson J, Peterson A, Letarte S, Gafken PR, Katz JE, Mallick P, Lee H et al..  2008.  The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. J Proteome Res. 7:96-103.
Zou Z, Ibisate M, Zhou Y, Aebersold R, Xia Y, Zhang H.  2008.  Synthesis and evaluation of superparamagnetic silica particles for extraction of glycopeptides in the microtiter plate format. Anal Chem. 80:1228-34.
Lange V, Malmstrom JA, Didion J, King NL, Johansson BP, Schafer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY et al..  2008.  Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring. Mol Cell Proteomics. 7:1489-500.
2007
Lu Y, Bottari P, Aebersold R, Turecek F, Gelb MH.  2007.  Absolute quantification of specific proteins in complex mixtures using visible isotope-coded affinity tags. Methods Mol Biol. 359:159-76.
Demers C, Chaturvedi CP, Ranish J, Juban G, Lai P, Morle F, Aebersold R, Dilworth FJ, Groudine M, Brand M.  2007.  Activator-mediated recruitment of the MLL2 methyltransferase complex to the beta-globin locus. Mol Cell. 27:573-84.
Malmstrom J, Lee H, Aebersold R.  2007.  Advances in proteomic workflows for systems biology. Curr Opin Biotechnol. 18:378-84.
Nesvizhskii AI, Vitek O, Aebersold R.  2007.  Analysis and validation of proteomic data generated by tandem mass spectrometry. Nat Methods. 4:787-97.
Gingras AC, Gstaiger M, Raught B, Aebersold R.  2007.  Analysis of protein complexes using mass spectrometry. Nat Rev Mol Cell Biol. 8:645-54.
Prakash A, Piening B, Whiteaker J, Zhang H, Shaffer SA, Martin D, Hohmann L, Cooke K, Olson JM, Hansen S et al..  2007.  Assessing bias in experiment design for large scale mass spectrometry-based quantitative proteomics. Mol Cell Proteomics. 6:1741-8.
Chen R, Pan S, Cooke K, Moyes KW, Bronner MP, Goodlett DR, Aebersold R, Brentnall TA.  2007.  Comparison of pancreas juice proteins from cancer versus pancreatitis using quantitative proteomic analysis. Pancreas. 34:70-9.
Mallick P, Schirle M, Chen SS, Flory MR, Lee H, Martin D, Ranish J, Raught B, Schmitt R, Werner T et al..  2007.  Computational prediction of proteotypic peptides for quantitative proteomics. Nat Biotechnol. 25:125-31.

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