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Publications for Aebersold, R

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Number of items: 72.

2017

Zhong, Qing; Guo, Tiannan; Rechsteiner, Markus; Rüschoff, Jan H; Rupp, Niels; Fankhauser, Christian; Saba, Karim; Mortezavi, Ashkan; Poyet, Cédric; Hermanns, Thomas; Zhu, Yi; Moch, Holger; Aebersold, Ruedi; Wild, Peter J (2017). A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients. Scientific Data, 4:170014.

Nemeth, Johannes; Vongrad, Valentina; Metzner, Karin J; Strouvelle, Victoria P; Weber, Rainer; Pedrioli, Patrick G A; Aebersold, Ruedi; Günthard, Huldrych F; Collins, Ben C (2017). In vivo and in vitro proteome analysis of Human Immunodeficiency Virus (HIV)-1-infected, human CD4(+) T cells. Molecular & Cellular Proteomics, 16(4 suppl 1):S108-S123.

2016

Röst, Hannes L; Sachsenberg, Timo; Aiche, Stephan; Bielow, Chris; Weisser, Hendrik; Aicheler, Fabian; Andreotti, Sandro; Ehrlich, Hans-Christian; Gutenbrunner, Petra; Kenar, Erhan; Liang, Xiao; Nahnsen, Sven; Nilse, Lars; Pfeuffer, Julianus; Rosenberger, George; Rurik, Marc; Schmitt, Uwe; Veit, Johannes; Walzer, Mathias; Wojnar, David; Wolski, Witold E; Schilling, Oliver; Choudhary, Jyoti S; Malmström, Lars; Aebersold, Ruedi; Reinert, Knut; Kohlbacher, Oliver (2016). OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods, 13(9):741-748.

Groner, Anna C; Cato, Laura; de Tribolet-Hardy, Jonas; Bernasocchi, Tiziano; Janouskova, Hana; Melchers, Diana; Houtman, René; Cato, Andrew C B; Tschopp, Patrick; Gu, Lei; Corsinotti, Andrea; Zhong, Qing; Fankhauser, Christian; Fritz, Christine; Poyet, Cédric; Wagner, Ulrich; Guo, Tiannan; Aebersold, Ruedi; Garraway, Levi A; Wild, Peter J; Theurillat, Jean-Philippe; Brown, Myles (2016). TRIM24 is an oncogenic transcriptional activator in prostate cancer. Cancer Cell, 29(6):846-858.

Williams, Evan G; Wu, Yibo; Jha, Pooja; Dubuis, Sébastien; Blattmann, Peter; Argmann, Carmen A; Houten, Sander M; Amariuta, Tiffany; Wolski, Witold; Zamboni, Nicola; Aebersold, Ruedi; Auwerx, Johan (2016). Systems proteomics of liver mitochondria function. Science, 352(6291):aad0189.

Greber, Basil Johannes; Gerhardy, Stefan; Leitner, Alexander; Leibundgut, Marc; Salem, Michèle; Boehringer, Daniel; Leulliot, Nicolas; Aebersold, Ruedi; Panse, Vikram Govind; Ban, Nenad (2016). Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation. Cell, 164(1-2):91-102.

2015

Subasic, Deni; Brümmer, Anneke; Wu, Yibo; Pinto, Sérgio Morgado; Imig, Jochen; Keller, Martin; Jovanovic, Marko; Lightfoot, Helen Louise; Nasso, Sara; Goetze, Sandra; Brunner, Erich; Hall, Jonathan; Aebersold, Ruedi; Zavolan, Mihaela; Hengartner, Michael O (2015). Cooperative target mRNA destabilization and translation inhibition by miR-58 microRNA family inC. elegans. Genome Research, 25(11):1680-1691.

Hofmann, Andreas; Thiesler, Thore; Gerrits, Bertran; Behnke, Silvia; Sobotzki, Nadine; Omasits, Ulrich; Bausch-Fluck, Damaris; Bock, Thomas; Aebersold, Ruedi; Moch, Holger; Tinguely, Marianne; Wollscheid, Bernd (2015). Surfaceome of classical Hodgkin and non-Hodgkin lymphoma. Proteomics. Clinical applications, 9(7-8):661-670.

Selevsek, Nathalie; Chang, Ching-Yun; Gillet, Ludovic C; Navarro, Pedro; Bernhardt, Oliver M; Reiter, Lukas; Cheng, Lin-Yang; Vitek, Olga; Aebersold, Ruedi (2015). Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry. Molecular & Cellular Proteomics, 14(3):739-749.

Bausch-Fluck, Damaris; Hofmann, Andreas; Bock, Thomas; Frei, Andreas P; Cerciello, Ferdinando; Jacobs, Andrea; Moest, Hansjoerg; Omasits, Ulrich; Gundry, Rebekah L; Yoon, Charles; Schiess, Ralph; Schmidt, Alexander; Mirkowska, Paulina; Härtlová, Anetta; Van Eyk, Jennifer E; Bourquin, Jean-Pierre; Aebersold, Ruedi; Boheler, Kenneth R; Zandstra, Peter; Wollscheid, Bernd (2015). A mass spectrometric-derived cell surface protein atlas. PLoS ONE, 10(3):e0121314.

Lebert, Dorothée; Louwagie, Mathilde; Goetze, Sandra; Picard, Guillaume; Ossola, Reto; Duquesne, Caroline; Basler, Konrad; Ferro, Myriam; Rinner, Oliver; Aebersold, Ruedi; Garin, Jérôme; Mouz, Nicolas; Brunner, Erich; Brun, Virginie (2015). DIGESTIF: A universal quality standard for the control of bottom-up proteomics experiments. Journal of Proteome Research, 14(2):787-803.

2013

Wippich, Frank; Bodenmiller, Bernd; Trajkovska, Maria Gustafsson; Wanka, Stefanie; Aebersold, Ruedi; Pelkmans, Lucas (2013). Dual specificity kinase DYRK3 couples stress granule condensation/dissolution to mTORC1 signaling. Cell, 152(4):791-805.

Bontron, Séverine; Jaquenoud, Malika; Vaga, Stefania; Talarek, Nicolas; Bodenmiller, Bernd; Aebersold, Ruedi; De Virgilio, Claudio (2013). Yeast endosulfines control entry into quiescence and chronological life span by inhibiting protein phosphatase 2A. Cell Reports, 3(1):16-22.

Picotti, Paola; Bodenmiller, Bernd; Aebersold, Ruedi (2013). Proteomics meets the scientific method. Nature Methods, 10(1):24-27.

Weisser, Hendrik; Nahnsen, Sven; Grossmann, Jonas; Nilse, Lars; Quandt, Andreas; Brauer, Hendrik; Sturm, Marc; Kenar, Erhan; Kohlbacher, Oliver; Aebersold, Ruedi; Malmström, Lars (2013). An automated pipeline for high-throughput label-free quantitative proteomics. Journal of Proteome Research, 12(4):1628-1644.

Berti, Matteo; Chaudhuri, Arnab Ray; Thangavel, Saravanabhavan; Gomathinayagam, Shivasankari; Kenig, Sasa; Vujanovic, Marko; Odreman, Federico; Glatter, Timo; Graziano, Simona; Mendoza-Maldonado, Ramiro; Marino, Francesca; Lucic, Bojana; Biasin, Valentina; Gstaiger, Matthias; Aebersold, Ruedi; Sidorova, Julia M; Monnat, Raymond J; Lopes, Massimo; Vindigni, Alessandro (2013). Human RECQ1 promotes restart of replication forks reversed by DNA topoisomerase I inhibition. Nature Structural & Molecular Biology, 20(3):347-354.

Cerciello, Ferdinando; Choi, Meena; Nicastri, Annalisa; Bausch-Fluck, Damaris; Ziegler, Annemarie; Vitek, Olga; Felley-Bosco, Emanuela; Stahel, Rolf; Aebersold, Ruedi; Wollscheid, Bernd (2013). Identification of a seven glycopeptide signature for malignant pleural mesothelioma in human serum by selected reaction monitoring. Clinical Proteomics, 10:16.

Templeton, Arnoud J; Dutoit, Valérie; Cathomas, Richard; Rothermundt, Christian; Bärtschi, Daniela; Dröge, Cornelia; Gautschi, Oliver; Borner, Markus; Fechter, Eva; Stenner, Frank; Winterhalder, Ralph; Müller, Beat; Schiess, Ralph; Wild, Peter J; Rüschoff, Jan H; Thalmann, George; Dietrich, Pierre-Yves; Aebersold, Ruedi; Klingbiel, Dirk; Gillessen, Silke (2013). Phase 2 trial of single-agent everolimus in chemotherapy-naive patients with castration-resistant prostate cancer (SAKK 08/08). European Urology, 64(1):150-158.

Zampar, Guillermo G; Kümmel, Anne; Ewald, Jennifer; Jol, Stefan; Niebel, Bastian; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2013). Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast. Molecular Systems Biology, 9:online.

Varjosalo, Markku; Keskitalo, Salla; Van Drogen, Audrey; Nurkkala, Helka; Vichalkovski, Anton; Aebersold, Ruedi; Gstaiger, Matthias (2013). The protein interaction landscape of the human CMGC kinase group. Cell Reports, 3(4):1306-20.

2012

Bock, T; Moest, H; Omasits, Ulrich; Dolski, S; Lundberg, E; Frei, A; Hofman, A; Bausch-Fluck, D; Jacobs, A H; Krayenbühl, N; Uhlen, M; Aebersold, R; Frei, K; Wollscheid, B (2012). Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines. Journal of Proteome Research, 11(10):4885-4893.

Frei, Andreas P; Jeon, Ock-Youm; Kilcher, Samuel; Moest, Hansjoerg; Henning, Lisa M; Jost, Christian; Plückthun, Andreas; Mercer, Jason; Aebersold, Ruedi; Carreira, Erick M; Wollscheid, Bernd (2012). Direct identification of ligand-receptor interactions on living cells and tissues. Nature biotechnology, 30(10):997-1001.

Danzer, C; Eckhardt, K; Schmidt, A; Fankhauser, N; Ribrioux, S; Wollscheid, B; Müller, L; Schiess, R; Zuellig, R; Lehmann, R; Spinas, G; Aebersold, R; Krek, W (2012). A comprehensive description of the N-glycoproteome of mouse pancreatic β-cells and human islets. Journal of Proteome Research, 11(3):1598-1608.

Claassen, M; Reiter, L; Hengartner, M O; Buhmann, J M; Aebersold, R (2012). Generic comparison of protein inference engines. Molecular & Cellular Proteomics, 11(4):O110.007088.

Kohli, Bernhard M; Pflieger, Delphine; Mueller, Lukas N; Carbonetti, Giovanni; Aebersold, Ruedi; Nitsch, Roger M; Konietzko, Uwe (2012). Interactome of the amyloid precursor protein APP in brain reveals a protein network involved in synaptic vesicle turnover and a close association with Synaptotagmin-1. Journal of Proteome Research, 11(8):4075-4090.

Jovanovic, Marko; Reiter, Lukas; Clark, Alejandra; Weiss, Manuel; Picotti, Paola; Rehrauer, Hubert; Frei, Andreas; Neukomm, Lukas; Kaufman, Ethan; Wollscheid, Bernd; Simard, Martin J; Miska, Eric; Aebersold, Ruedi; Gerber, Andre P; Hengartner, Michael O (2012). RIPchipSRM, a new combinatorial large scale approach identifies a set of translationally regulated bantam/miR58 targets in C. elegans. Genome Research, 22(7):1360-1371.

Oliveira, Ana Paula; Ludwig, Christina; Picotti, Paola; Kogadeeva, Maria; Aebersold, Ruedi; Sauer, Uwe (2012). Regulation of yeast central metabolism by enzyme phosphorylation. Molecular Systems Biology, 8:online.

Jones, A M E; Aebersold, R; Ahrens, C H; Apweiler, R; Baerenfaller, K; Baker, M; Bendixen, E; Briggs, S; Brownridge, P; Brunner, E; Daube, M; Deutsch, E W; Grossniklaus, U; Heazlewood, J L; Hengartner, M O; Hermjakob, H; Jovanovic, M; Lawless, C; Lochnit, G; Martens, L; Ravnsborg, C; Schrimpf, S P; Shim, Y H; Subasic, D; Tholey, A; van Wijk, K; von Mering, C; Weiss, M; Zheng, X (2012). The HUPO initiative on Model Organism Proteomes, iMOP. Proteomics, 12(3):340-345.

2011

Wiedl, T; Arni, S; Roschitzki, B; Grossmann, J; Collaud, S; Soltermann, A; Hillinger, S; Aebersold, R; Weder, W (2011). Activity-based proteomics: identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma. Journal of Proteomics, 74(10):1884-1894.

Esterházy, D; Stützer, I; Wang, H; Rechsteiner, M P; Beauchamp, J; Döbeli, H; Hilpert, H; Matile, H; Prummer, M; Schmidt, A; Lieske, N; Boehm, B; Marselli, L; Bosco, D; Kerr-Conte, J; Aebersold, R; Spinas, G A; Moch, H; Migliorini, C; Stoffel, M (2011). Bace2 is a β cell-enriched protease that regulates pancreatic β cell function and mass. Cell Metabolism, 14(3):365-377.

Cima, I; Schiess, R; Wild, P; Kaelin, M; Schüffler, P; Lange, V; Picotti, P; Ossola, R; Templeton, A; Schubert, O; Fuchs, T; Leippold, T; Wyler, S; Zehetner, J; Jochum, W; Buhmann, J M; Cerny, T; Moch, H; Gillessen, S; Aebersold, R; Krek, W (2011). Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 108(8):3342-3347.

Costenoble, Roeland; Picotti, Paola; Reiter, Lukas; Stallmach, Robert; Heinemann, Matthias; Sauer, Uwe; Aebersold, Ruedi (2011). Comprehensive quantitative analysis of central carbon and amino-acid metabolism in Saccharomyces cerevisiae under multiple conditions by targeted proteomics. Molecular Systems Biology, 7:464.

Glatter, Timo; Schittenhelm, Ralf B; Rinner, Oliver; Roguska, Katarzyna; Wepf, Alexander; Jünger, Martin A; Köhler, Katja; Jevtov, Irena; Choi, Hyungwon; Schmidt, Alexander; Nesvizhskii, Alexey I; Stocker, Hugo; Hafen, Ernst; Aebersold, Ruedi; Gstaiger, Matthias (2011). Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Molecular Systems Biology, 7:547.

Kälin, M; Cima, I; Schiess, R; Fankhauser, N; Powles, T; Wild, P; Templeton, A; Cerny, T; Aebersold, R; Krek, W; Gillessen, S (2011). Novel prognostic markers in the serum of patients with castration-resistant prostate cancer derived from quantitative analysis of the pten conditional knockout mouse proteome. European Urology, 60(6):1235-1243.

Surinova, Silvia; Schiess, Ralph; Hüttenhain, Ruth; Cerciello, Ferdinando; Wollscheid, Bernd; Aebersold, Ruedi (2011). On the development of plasma protein biomarkers. Journal of Proteome Research, 10(1):5-16.

Bodenmiller, Bernd; Aebersold, Ruedi (2011). Phosphoproteome resource for systems biology research. Methods in Molecular Biology, 694:307-322.

Laurell, Eva; Beck, Katja; Krupina, Ksenia; Theerthagiri, Gandhi; Bodenmiller, Bernd; Horvath, Peter; Aebersold, Ruedi; Antonin, Wolfram; Kutay, Ulrike (2011). Phosphorylation of Nup98 by multiple kinases is crucial for NPC disassembly during mitotic entry. Cell, 144(4):539-550.

Reiter, L; Rinner, O; Picotti, P; Hüttenhain, R; Beck, M; Brusniak, M Y; Hengartner, M O; Aebersold, R (2011). mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nature Methods, 8(5):430-435.

2010

Ahrens, C H; Brunner, E; Qeli, E; Basler, K; Aebersold, R (2010). Generating and navigating proteome maps using mass spectrometry. Nature Reviews. Molecular Cell Biology, 11(11):789-801.

Jovanovic, M; Reiter, L; Picotti, P; Lange, V; Bogan, E; Hurschler, B A; Blenkiron, C; Lehrbach, N J; Ding, X C; Weiss, M; Schrimpf, S P; Miska, E A; Grosshans, H; Aebersold, R; Hengartner, M O (2010). A quantitative targeted proteomics approach to validate predicted microRNA targets in C. elegans. Nature Methods, 7(10):837-842.

Kümmel, Anne; Ewald, Jennifer Christina; Fendt, Sarah-Maria; Jol, Stefan Jasper; Picotti, Paola; Aebersold, Ruedi; Sauer, Uwe; Zamboni, Nicola; Heinemann, Matthias (2010). Differential glucose repression in common yeast strains in response to HXK2 deletion. FEMS Yeast Research, 10(3):322-332.

Breslow, David K; Collins, Sean R; Bodenmiller, Bernd; Aebersold, Ruedi; Simons, Kai; Shevchenko, Andrej; Ejsing, Christer S; Weissman, Jonathan S (2010). Orm family proteins mediate sphingolipid homeostasis. Nature, 463(7284):1048-1053.

Bodenmiller, B; Wanka, S; Kraft, C; Urban, J; Campbell, D; Pedrioli, P G; Gerrits, B; Picotti, P; Lam, H; Vitek, O; Brusniak, M Y; Roschitzki, B; Zhang, C; Shokat, K M; Schlapbach, R; Colman-Lerner, A; Nolan, G P; Nesvizhskii, A I; Peter, M; Loewith, R; von Mering, C; Aebersold, R (2010). Phosphoproteomic analysis reveals interconnected system-wide responses to perturbations of kinases and phosphatases in yeast. Science Signaling, 3(153):rs4.

Hofmann, A; Gerrits, B; Schmidt, A; Bock, T; Bausch-Fluck, D; Aebersold, R; Wollscheid, B (2010). Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116(13):e26-34.

Bodenmiller, Bernd; Aebersold, Ruedi (2010). Quantitative analysis of protein phosphorylation on a system-wide scale by mass spectrometry-based proteomics. Methods in enzymology, 470:317-334.

Bandyopadhyay, Sourav; Mehta, Monika; Kuo, Dwight; Sung, Min-Kyung; Chuang, Ryan; Jaehnig, Eric J; Bodenmiller, Bernd; Licon, Katherine; Copeland, Wilbert; Shales, Michael; Fiedler, Dorothea; Dutkowski, Janusz; Guénolé, Aude; van Attikum, Haico; Shokat, Kevan M; Kolodner, Richard D; Huh, Won-Ki; Aebersold, Ruedi; Keogh, Michael-Christopher; Krogan, Nevan J; Ideker, Trey (2010). Rewiring of genetic networks in response to DNA damage. Science, 330(6009):1385-1389.

2009

Reiter, L; Claassen, M; Schrimpf, S P; Jovanovic, M; Schmidt, A; Buhmann, J M; Hengartner, M O; Aebersold, R (2009). Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular & Cellular Proteomics, 8(11):2405-2417.

Tan, C S H; Bodenmiller, B; Pasculescu, A; Jovanovic, M; Hengartner, M O; Jørgensen, C; Bader, G D; Aebersold, R; Pawson, T; Linding, R (2009). Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Science Signaling, 2(81):ra39.

Huber, Alexandre; Bodenmiller, Bernd; Uotila, Aino; Stahl, Michael; Wanka, Stefanie; Gerrits, Bertran; Aebersold, Ruedi; Loewith, Robbie (2009). Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis. Genes and Development, 23(16):1929-1943.

Schrimpf, S P; Weiss, M; Reiter, L; Ahrens, C H; Jovanovic, M; Malmström, J; Brunner, E; Mohanty, S; Lercher, M J; Hunziker, P E; Aebersold, R; von Mering, C; Hengartner, M O (2009). Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biology, 7(3):e48.

Ulintz, Peter J; Yocum, Anastasia K; Bodenmiller, Bernd; Aebersold, Ruedi; Andrews, Philip C; Nesvizhskii, Alexey I (2009). Comparison of MS(2)-only, MSA, and MS(2)/MS(3) methodologies for phosphopeptide identification. Journal of Proteome Research, 8(2):887-899.

Domon, Bruno; Bodenmiller, Bernd; Carapito, Christine; Hao, Zhiqi; Huehmer, Andreas; Aebersold, Ruedi (2009). Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. Journal of Proteome Research, 8(6):2633-2639.

Picotti, Paola; Bodenmiller, Bernd; Mueller, Lukas N; Domon, Bruno; Aebersold, Ruedi (2009). Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell, 138(4):795-806.

Goetze, S; Qeli, E; Mosimann, C; Staes, A; Gerrits, B; Roschitzki, B; Mohanty, S; Niederer, E M; Laczko, E; Timmerman, E; Lange, V; Hafen, E; Aebersold, R; Vandekerckhove, J; Basler, K; Ahrens, C H; Gevaert, K; Brunner, E (2009). Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. PLoS Biology, 7(11):e1000236.

Sumara, Grzegorz; Formentini, Ivan; Collins, Stephan; Sumara, Izabela; Windak, Renata; Bodenmiller, Bernd; Ramracheya, Reshma; Caille, Dorothée; Jiang, Huiping; Platt, Kenneth A; Meda, Paolo; Aebersold, Rudolf; Rorsman, Patrik; Ricci, Romeo (2009). Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis. Cell, 136(2):235-248.

2008

Schmidt, Alexander; Gehlenborg, Nils; Bodenmiller, Bernd; Mueller, Lukas N; Campbell, Dave; Mueller, Markus; Aebersold, Ruedi; Domon, Bruno (2008). An integrated, directed mass spectrometric approach for in-depth characterization of complex peptide mixtures. Molecular & Cellular Proteomics, 7(11):2138-2150.

Brusniak, Mi-Youn; Bodenmiller, Bernd; Campbell, David; Cooke, Kelly; Eddes, James; Garbutt, Andrew; Lau, Hollis; Letarte, Simon; Mueller, Lukas N; Sharma, Vagisha; Vitek, Olga; Zhang, Ning; Aebersold, Ruedi; Watts, Julian D (2008). Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics, 9:542.

Ulintz, Peter J; Bodenmiller, Bernd; Andrews, Philip C; Aebersold, Ruedi; Nesvizhskii, Alexey I (2008). Investigating MS2/MS3 matching statistics: a model for coupling consecutive stage mass spectrometry data for increased peptide identification confidence. Molecular & Cellular Proteomics, 7(1):71-87.

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(2):124-133.

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. Nature Biotechnology, 26(12):1339-1340.

Tress, Michael L; Bodenmiller, Bernd; Aebersold, Ruedi; Valencia, Alfonso (2008). Proteomics studies confirm the presence of alternative protein isoforms on a large scale. Genome biology, 9(11):R162.

Pflieger, D; Jünger, M A; Müller, M; Rinner, O; Lee, H; Gehrig, P M; Gstaiger, M; Aebersold, R (2008). Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation. Molecular and Cellular Proteomics, 7(2):326-346.

2007

Brunner, E; Ahrens, C H; Mohanty, S; Baetschmann, H; Loevenich, S; Potthast, F; Deutsch, E W; Panse, C; de Lichtenberg, U; Rinner, O; Lee, H; Pedrioli, P G A; Malmstrom, J; Koehler, K; Schrimpf, S; Krijgsveld, J; Kregenow, F; Heck, A J R; Hafen, E; Schlapbach, R; Aebersold, R (2007). A high-quality catalog of the Drosophila melanogaster proteome. Nature Biotechnology, 25(5):576-583.

Bodenmiller, Bernd; Mueller, Lukas N; Pedrioli, Patrick G A; Pflieger, Delphine; Jünger, Martin A; Eng, Jimmy K; Aebersold, Ruedi; Tao, W Andy (2007). An integrated chemical, mass spectrometric and computational strategy for (quantitative) phosphoproteomics: application to Drosophila melanogaster Kc167 cells. Molecular Biosystems, 3(4):275-286.

Bodenmiller, B; Malmstrom, J; Gerrits, B; Campbell, D; Lam, H; Schmidt, A; Rinner, O; Mueller, L N; Shannon, P T; Pedrioli, P G; Panse, C; Lee, H K; Schlapbach, R; Aebersold, R (2007). PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology, 3:139.

Bodenmiller, Bernd; Mueller, Lukas N; Mueller, Markus; Domon, Bruno; Aebersold, Ruedi (2007). Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nature Methods, 4(3):231-237.

Mueller, Lukas N; Rinner, Oliver; Schmidt, Alexander; Letarte, Simon; Bodenmiller, Bernd; Brusniak, Mi-Youn; Vitek, Olga; Aebersold, Ruedi; Müller, Markus (2007). SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics, 7(19):3470-3480.

2006

Nesvizhskii, A I; Roos, F F; Grossmann, J; Vogelzang, M; Eddes, J S; Gruissem, W; Baginsky, S; Aebersold, R (2006). Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Molecular and Cellular Proteomics, 5(4):652-670.

2005

Gingras, A C; Caballero, M; Zarske, M; Sanchez, Amy; Hazbun, T R; Fields, S; Sonenberg, N; Hafen, E; Raught, B; Aebersold, R (2005). A novel, evolutionarily conserved protein phosphatase complex involved in cisplatin sensitivity. Molecular & Cellular Proteomics, 4(11):1725-1740.

Schrimpf, S P; Meskenaite, V; Brunner, E; Rutishauser, D; Walther, P; Eng, J K; Aebersold, R; Sonderegger, P (2005). Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics, 5(10):2531-2541.

Desiere, F; Deutsch, E W; Nesvizhskii, A I; Mallick, P; King, N L; Eng, J K; Aderem, A; Boyle, R; Brunner, E; Donohoe, S; Fausto, N; Hafen, E; Hood, L; Katze, M G; Kennedy, K A; Kregenow, F; Lee, H; Lin, B; Martin, D; Ranish, J A; Rawlings, D J; Samelson, L E; Shiio, Y; Watts, J D; Wollscheid, B; Wright, M E; Yan, W; Yang, L; Yi, E C; Zhang, H; Aebersold, R (2005). Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biology, 6:R9.

Tao, W Andy; Wollscheid, Bernd; O'Brien, Robert; Eng, Jimmy K; Li, Xiao-jun; Bodenmiller, Bernd; Watts, Julian D; Hood, Leroy; Aebersold, Ruedi (2005). Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry. Nature Methods, 2(8):591-598.

This list was generated on Wed Dec 13 18:21:38 2017 CET.