Items where Author is "Aebersold, Ruedi"

Article

Mori, Matteo and Zhang, Zhongge and Banaei-Esfahani, Amir and Lalanne, Jean-Benoît and Okano, Hiroyuki and Collins, Ben C. and Schmidt, Alexander and Schubert, Olga T. and Lee, Deok-Sun and Li, Gene-Wei and Aebersold, Ruedi and Hwa, Terence and Ludwig, Christina. (2021) From coarse to fine: the absolute Escherichia coli proteome under diverse growth conditions. Molecular systems biology, 17 (5). e9536.

Sendoel, Ataman and Subasic, Deni and Ducoli, Luca and Keller, Martin and Michel, Erich and Kohler, Ines and Singh, Kapil Dev and Zheng, Xue and Brümmer, Anneke and Imig, Jochen and Kishore, Shivendra and Wu, Yibo and Kanitz, Alexander and Kaech, Andres and Mittal, Nitish and Matia-González, Ana M. and Gerber, André P. and Zavolan, Mihaela and Aebersold, Ruedi and Hall, Jonathan and Allain, Frédéric H.-T. and Hengartner, Michael O.. (2019) MINA-1 and WAGO-4 are part of regulatory network coordinating germ cell death and RNAi in C. elegans. Cell Death & Differentiation subscription, 26 (10). pp. 2157-2178.

Liu, Yansheng and Mi, Yang and Mueller, Torsten and Kreibich, Saskia and Williams, Evan G. and Van Drogen, Audry and Borel, Christelle and Frank, Max and Germain, Pierre-Luc and Bludau, Isabell and Mehnert, Martin and Seifert, Michael and Emmenlauer, Mario and Sorg, Isabel and Bezrukov, Fedor and Sloan Bena, Frederique and Zhou, Hu and Dehio, Christoph and Testa, Giuseppe and Saez-Rodriguez, Julio and Antonarakis, Stylianos E. and Hardt, Wolf-Dietrich and Aebersold, Ruedi. (2019) Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology, 37 (3). pp. 314-322.

Schmidt, Alexander and Kochanowski, Karl and Vedelaar, Silke and Ahrné, Erik and Volkmer, Benjamin and Callipo, Luciano and Knoops, Kèvin and Bauer, Manuel and Aebersold, Ruedi and Heinemann, Matthias. (2016) The quantitative and condition-dependent Escherichia coli proteome. Nature biotechnology, 34 (1). pp. 104-110.

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

Sjöström, Martin and Ossola, Reto and Breslin, Thomas and Rinner, Oliver and Malmström, Lars and Schmidt, Alexander and Aebersold, Ruedi and Malmström, Johan and Niméus, Emma. (2015) A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Journal of Proteome Research, 14 (7). pp. 2807-2818.

Fengos, Georgios and Schmidt, Alexander and Martin, Katrin and Fluri, Erika and Aebersold, Ruedi and Iber, Dagmar and Pertz, Olivier. (2014) Spatial proteomic and phospho-proteomic organization in three prototypical cell migration modes. Proteome science, Vol. 12. p. 23.

Picotti, Paola and Clément-Ziza, Mathieu and Lam, Henry and Campbell, David S. and Schmidt, Alexander and Deutsch, Eric W. and Röst, Hannes and Sun, Zhi and Rinner, Oliver and Reiter, Lukas and Shen, Qin and Michaelson, Jacob J. and Frei, Andreas and Alberti, Simon and Kusebauch, Ulrike and Wollscheid, Bernd and Moritz, Robert L. and Beyer, Andreas and Aebersold, Ruedi. (2013) A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature, Vol. 494, H. 7436. pp. 266-270.

Gunaratne, Jayantha and Schmidt, Alexander and Quandt, Andreas and Neo, Suat Peng and Saraç, Omer Sinan and Gracia, Tannia and Loguercio, Salvatore and Ahrné, Erik and Xia, Rachel Li Hai and Tan, Keng Hwa and Lössner, Christopher and Bähler, Jürg and Beyer, Andreas and Blackstock, Walter and Aebersold, Ruedi. (2013) Extensive mass spectrometry-based analysis of the fission yeast proteome : the Schizosaccharomyces pombe Peptide Atlas. Molecular & cellular proteomics, Vol. 12, H. 6. pp. 1741-1751.

von Meyenn, Ferdinand and Porstmann, Thomas and Gasser, Emanuel and Selevsek, Nathalie and Schmidt, Alexander and Aebersold, Ruedi and Stoffel, Markus. (2013) Glucagon-Induced Acetylation of Foxa2 Regulates Hepatic Lipid Metabolism. Cell metabolism, Vol. 17, H. 3. pp. 436-447.

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

Wong, Catherine C. L. and Cociorva, Daniel and Miller, Christine A. and Schmidt, Alexander and Monell, Craig and Aebersold, Ruedi and Yates, John R.. (2013) Proteomics of Pyrococcus furiosus (Pfu) : Identification of Extracted Proteins by Three Independent Methods. Journal of Proteome Research, Vol. 12, H. 2. pp. 763-770.

Stützer, Ina and Selevsek, Nathalie and Esterhazy, Daria and Schmidt, Alexander and Aebersold, Ruedi and Stoffel, Markus. (2013) Systematic proteomic analysis identifies beta-site amyloid precursor protein cleaving enzyme 2 and 1 (BACE2 and BACE1) substrates in pancreatic beta-cells. Journal of biological chemistry, Vol. 288, H. 15. pp. 10536-10547.

Hausser, Jean and Syed, Afzal Pasha and Selevsek, Nathalie and van Nimwegen, Erik and Jaskiewicz, Lukasz and Aebersold, Ruedi and Zavolan, Mihaela. (2013) Timescales and bottlenecks in miRNA-dependent gene regulation. Molecular systems biology, Vol. 9 , 711.

Ludwig, Christina and Claassen, Manfred and Schmidt, Alexander and Aebersold, Ruedi. (2012) Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Molecular and Cellular Proteomics, 11 (3). M111.013987.

Glatter, Timo and Ludwig, Christina and Ahrné, Erik and Aebersold, Ruedi and Heck, Albert J. R. and Schmidt, Alexander. (2012) Large-Scale Quantitative Assessment of Different In-Solution Protein Digestion Protocols Reveals Superior Cleavage Efficiency of Tandem Lys-C/Trypsin Proteolysis over Trypsin Digestion. Journal of proteome research, Vol. 11, H. 11. pp. 5145-5156.

Marguerat, Samuel and Schmidt, Alexander and Codlin, Sandra and Chen, Wei and Aebersold, Ruedi and Bähler, Jürg. (2012) Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells. Cell, Vol. 151, H. 3. pp. 671-683.

Esterházy, Daria and Stützer, Ina and Wang, Haiyan and Rechsteiner, Markus P. and Beauchamp, Jeremy and Döbeli, Heinz and Hilpert, Hans and Matile, Hugues and Prummer, Michael and Schmidt, Alexander and Lieske, Nora and Boehm, Bernhard and Marselli, Lorella and Bosco, Domenico and Kerr-Conte, Julie and Aebersold, Ruedi and Spinas, Giatgen Andreia and Moch, Holger and Migliorini, Cristiano and Stoffel, Markus. (2011) Bace2 Is a Beta-Cell-Enriched Protease that Regulates Pancreatic Beta-Cell Function and Mass. Cell Metabolism, 14 (3). pp. 365-377.

Cima, Igor and Schiess, Ralph and Wild, Peter and Kaelin, Martin and Schüffler, Peter and Lange, Vinzenz and Picotti, Paola and Ossola, Reto and Templeton, Arnoud and Schubert, Olga and Fuchs, Thomas and Leippold, Thomas and Wyler, Stephen and Zehetner, Jens and Jochum, Wolfram and Buhmann, Joachim and Cerny, Thomas and Moch, Holger and Gillessen, Silke and Aebersold, Ruedi and Krek, Wilhelm. (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, Vol. 108, H. 8. pp. 3342-3347.

Higdon, Roger and Reiter, Lukas and Hather, Gregory and Haynes, Winston and Kolker, Natali and Stewart, Elizabeth and Bauman, Andrew T. and Picotti, Paola and Schmidt, Alexander and van Belle, Gerald and Aebersold, Ruedi and Kolker, Eugene. (2011) IPM: An integrated protein model for false discovery rate estimation and identification in high-throughput proteomics. Journal of Proteomics , 75 (1). pp. 116-121.

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

Maier, Tobias and Schmidt, Alexander and Güell, Marc and Kühner, Sebastian and Gavin, Anne-Claude and Aebersold, Ruedi and Serrano, Luis . (2011) Quantification of mRNA and protein and integration with protein turnover in a bacterium. Molecular Systems Biology, 7. p. 511.

Beck, Martin and Schmidt, Alexander and Malmstroem, Johan and Claassen, Manfred and Ori, Alessandro and Szymborska, Anna and Herzog, Franz and Rinner, Oliver and Ellenberg, Jan and Aebersold, Ruedi. (2011) The quantitative proteome of a human cell line. Molecular Systems Biology, Vol. 7 , 549.

Bensimon, Ariel and Schmidt, Alexander and Ziv, Yael and Elkon, Ran and Wang, Shih-Ya and Chen, David J. and Aebersold, Ruedi and Shiloh, Yosef . (2010) ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage. Science Signaling, 3 (151). rs3.

Schiess, Ralph and Mueller, Lukas N. and Schmidt, Alexander and Mueller, Markus and Wollscheid, Bernd and Aebersold, Ruedi . (2009) Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry. Molecular and Cellular Proteomics, 8 (4). pp. 624-638.

Schmidt, Alexander and Claassen, Manfred and Aebersold, Ruedi. (2009) Directed mass spectrometry: towards hypothesis-driven proteomics. Current Opinion in Chemical Biology, 13 (5-6). pp. 510-517.

Reiter, Lukas and Claassen, Manfred and Schrimpf, Sabine P. and Jovanovic, Marko and Schmidt, Alexander and Buhmann, Joachim M. and Hengartner, Michael O. and Aebersold, Ruedi . (2009) Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Molecular and Cellular Proteomics, 8 (11). pp. 2405-2417.

Kühner, Sebastian and van Noort, Vera and Betts, Matthew J. and Leo-Macias, Alejandra and Batisse, Claire and Rode, Michaela and Yamada, Takuji and Maier, Tobias and Bader, Samuel and Beltran-Alvarez, Pedro and Castaño-Diez, Daniel and Chen, Wei-Hua and Devos, Damien and Güell, Marc and Norambuena, Tomas and Racke, Ines and Rybin, Vladimir and Schmidt, Alexander and Yus, Eva and Aebersold, Ruedi and Herrmann, Richard and Böttcher, Bettina and Frangakis, Achilleas S. and Russell, Robert B. and Serrano, Luis and Bork, Peer and Gavin, Anne-Claude. (2009) Proteome organization in a genome-reduced bacterium. Science, 326 (5957). pp. 1235-1240.

Malmström, Johan and Beck, Martin and Schmidt, Alexander and Lange, Vinzenz and Deutsch, Eric W. and Aebersold, Ruedi . (2009) Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans. Nature, 460 (7256). pp. 762-765.

Wepf, Alexander and Glatter, Timo and Schmidt, Alexander and Aebersold, Ruedi and Gstaiger, Matthias . (2009) Quantitative interaction proteomics using mass spectrometry. Nature Methods, 6 (3). pp. 203-205.

Leidel, Sebastian and Pedrioli, Patrick G. A. and Bucher, Tamara and Brost, Renée and Costanzo, Michael and Schmidt, Alexander and Aebersold, Ruedi and Boone, Charles and Hofmann, Kay and Peter, Matthias . (2009) Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature, 458 (7235). pp. 228-232.

Beck, Martin and Malmström, Johan A. and Lange, Vinzenz and Schmidt, Alexander and Deutsch, Eric W. and Aebersold, Ruedi . (2009) Visual proteomics of the human pathogen Leptospira interrogans. Nature Methods, 6 (11). pp. 817-823.

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

Letarte, Simon and Brusniak, Mi-Youn and Campbell, David and Eddes, James and Kemp, Christopher J. and Lau, Hollis and Mueller, Lukas and Schmidt, Alexander and Shannon, Paul and Kelly-Spratt, Karen S. and Vitek, Olga and Zhang, Hui and Aebersold, Ruedi and Watts, Julian D.. (2008) Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clinical Proteomics, 4 (3-4). p. 105.

Rinner, Oliver and Seebacher, Jan and Walzthoeni, Thomas and Mueller, Lukas N. and Beck, Martin and Schmidt, Alexander and Mueller, Markus and Aebersold, Ruedi. (2008) Identification of cross-linked peptides from large sequence databases. Nature methods, 5 (4). pp. 315-318.

Klimek, John and Eddes, James S. and Hohmann, Laura and Jackson, Jennifer and Peterson, Amelia and Letarte, Simon and Gafken, Philip R. and Katz, Jonathan E. and Mallick, Parag and Lee, Hookeun and Schmidt, Alexander and Ossola, Reto and Eng, Jimmy K. and Aebersold, Ruedi and Martin, Daniel B. . (2008) The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. Journal of Proteome Research, 7 (1). pp. 96-103.

Bodenmiller, Bernd and Malmstrom, Johan and Gerrits, Bertran and Campbell, David and Lam, Henry and Schmidt, Alexander and Rinner, Oliver and N. Mueller, Lukas and T. Shannon, Paul and G. Pedrioli, Patrick and Panse, Christian and Lee, Hoo-Keun and Schlapbach, Ralph and Aebersold, Ruedi . (2007) PhosphoPep-a phosphoproteome resource for systems biology research in Drosophila Kc167 cells. Molecular Systems Biology, 3 (1). p. 139.

Djouder, Nabil and Christian Metzler, Stefan and Schmidt, Alexander and Wirbelauer, Christiane and Gstaiger, Matthias and Aebersold, Ruedi and Hess, Daniel and Krek, Wilhelm. (2007) S6K1-mediated disassembly of mitochondrial URI/PP1gamma complexes activates a negative feedback program that counters S6K1 survival signaling. Molecular Cell, 28 (1). pp. 28-40.

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

Schmidt, Alexander and Aebersold, Ruedi. (2006) High-accuracy proteome maps of human body fluids. Genome Biology, 7 (11). p. 242.