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Items where Division is "05 Faculty of Science > Departement Biozentrum > Services Biozentrum > Proteomics (Schmidt)"

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Number of items at this level: 62.

January 2016

Oettinghaus, Bjorn and Schulz, J. M. and Restelli, L. M. and Licci, M. and Savoia, C. and Schmidt, Alexander and Schmitt, K. and Grimm, A. and Morè, L. and Hench, J. and Tolnay, M. and Eckert, A. and D'Adamo, P. and Franken, P. and Ishihara, N. and Mihara, K. and Bischofberger, J. and Scorrano, L. and Frank, Stephan. (2016) Synaptic dysfunction, memory deficits and hippocampal atrophy due to ablation of mitochondrial fission in adult forebrain neurons. Cell death and differentiation, 23 (1). pp. 18-28.

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.

2016

Ahrné, Erik and Glatter, Timo and Viganò, Cristina and Schubert, Conrad von and Nigg, Erich A. and Schmidt, Alexander. (2016) Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. Journal of Proteome Research, 15 (8). pp. 2537-2547.

Gumienny, Rafal and Jedlinski, Dominik J. and Schmidt, Alexander and Gypas, Foivos and Martin, Georges and Vina-Vilaseca, Arnau and Zavolan, Mihaela. (2016) High-throughput identification of C/D box snoRNA targets with CLIP and RiboMeth-seq. Nucleic Acids Research, 45 (5). pp. 2341-2353.

Radzikowski, Jakub Leszek and Vedelaar, Silke and Siegel, David and Ortega, Álvaro Dario and Schmidt, Alexander and Heinemann, Matthias. (2016) Bacterial persistence is an active σS stress response to metabolic flux limitation. Molecular Systems Biology, 12 (9). p. 882.

1 December 2015

Janssens, Georges E. and Meinema, Anne C. and González, Javier and Wolters, Justina C. and Schmidt, Alexander and Guryev, Victor and Bischoff, Rainer and Wit, Ernst C. and Veenhoff, Liesbeth M. and Heinemann, Matthias. (2015) Protein biogenesis machinery is a driver of replicative aging in yeast. eLife, 4. e08527 .

November 2015

Glatter, Timo and Ahrné, Erik and Schmidt, Alexander. (2015) Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. Journal of Proteome Research, 14 (11). pp. 4472-4485.

1 September 2015

Ahrné, Erik and Martinez-Segura, Amalia and Syed, Afzal Pasha and Vina-Vilaseca, Arnau and Gruber, Andreas J. and Marguerat, Samuel and Schmidt, Alexander. (2015) Exploiting the multiplexing capabilities of tandem mass tags for high-throughput estimation of cellular protein abundances by mass spectrometry. Methods, 85. pp. 100-107.

July 2015

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.

2014

Bauer, Manuel and Ahrné, Erik and Baron, Anna P. and Glatter, Timo and Fava, Luca L. and Santamaria, Anna and Nigg, Erich A. and Schmidt, Alexander. (2014) Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. Journal of proteome research, Vol. 13, H. 12. S. 5973-5988.

Clément-Ziza, Mathieu and Marsellach, Francesc X. and Codlin, Sandra and Papadakis, Manos A. and Reinhardt, Susanne and Rodríguez-López, María and Martin, Stuart and Marguerat, Samuel and Schmidt, Alexander and Lee, Eunhye and Workman, Christopher T. and Bähler, Jürg and Beyer, Andreas. (2014) Natural genetic variation impacts expression levels of coding, non-coding, and antisense transcripts in fission yeast. Molecular systems biology, Vol. 10, H. 11. S. 764.

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. S. 23.

Pieles, Kathrin and Glatter, Timo and Harms, Alexander and Schmidt, Alexander and Dehio, Christoph. (2014) An experimental strategy for the identification of AMPylation targets from complex protein samples. Proteomics, 14 (9). pp. 1048-1052.

2013

Ahrné, Erik and Molzahn, Lars and Glatter, Timo and Schmidt, Alexander. (2013) Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Proteomics, Vol. 13, H. 17. S. 2567-2578.

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.

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. S. 1741-1751.

Kochanowski, Karl and Volkmer, Benjamin and Gerosa, Luca and Haverkorn van Rijsewijk, Bart R. and Schmidt, Alexander and Heinemann, Matthias. (2013) Functioning of a metabolic flux sensor in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America, Vol. 110, H. 3. S. 1130-1135.

Lehtinen, Sonja and Marsellach, Francesc Xavier and Codlin, Sandra and Schmidt, Alexander and Clément-Ziza, Mathieu and Beyer, Andreas and Bähler, Jürg and Orengo, Christine and Pancaldi, Vera. (2013) Stress induces remodelling of yeast interaction and co-expression networks. Molecular biosystems, Vol. 9, H. 7. S. 1697-1707.

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. S. 266-270.

Québatte, Maxime and Dick, Mathias S. and Kaever, Volkhard and Schmidt, Alexander and Dehio, Christoph. (2013) Dual input control : activation of the Bartonella henselae VirB/D4 type IV secretion system by the stringent sigma factor RpoH1 and the BatR/BatS two-component system. Molecular microbiology, Vol. 90, H. 4. S. 756-775.

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. S. 10536-10547.

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. S. 763-770.

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. S. 436-447.

2012

Danzer, Carsten and Eckhardt, Katrin and Schmidt, Alexander and Fankhauser, Niklaus and Ribrioux, Sebastien and Wollscheid, Bernd and Müller, Lukas and Schiess, Ralph and Züllig, Richard and Lehmann, Roger and Spinas, Giatgen and Aebersold, Rudolf and Krek, Wilhelm. (2012) Comprehensive description of the N-glycoproteome of mouse pancreatic ?-cells and human islets. Journal of Proteome Research, 11 (3). pp. 1598-1608.

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. S. 5145-5156.

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.

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. S. 671-683.

Nesper, J. and Reinders, A. and Glatter, T. and Schmidt, A. and Jenal, U.. (2012) A novel capture compound for the identification and analysis of cyclic di-GMP binding proteins. Journal of Proteomics, 75 (15). pp. 4874-4878.

2011

Alexander Schmidt, and Martin Beck, and Johan Malmström, and Henry Lam, and Manfred Claassen, and David Campbell, and Ruedi Aebersold, . (2011) Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Molecular Systems Biology, Vol. 7 , 510.

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.

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.

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.

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.

Iijima, Takatoshi and Wu, Karen and Witte, Harald and Hanno-Iijima, Yoko and Glatter, Timo and Richard, Stéphane and Scheiffele, Peter. (2011) SAM68 regulates neuronal activity-dependent alternative splicing of Neurexin-1. Cell, Vol. 147, H. 7. S. 1601-1614.

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.

Santamaria, A. and Wang, B. and Elowe, S. and Malik, R. and Zhang, F. and Bauer, M. and Schmidt, A. and Sillje, H. H. and Koerner, R. and Nigg, E. A.. (2011) The Plk1-dependent phosphoproteome of the early mitotic spindle. Molecular & cellular proteomics, Vol. 10, H. 1 , M110.004457.

Strübbe, Gero and Popp, Christian and Schmidt, Alexander and Pauli, Andrea and Ringrose, Leonie and Beisel, Christian and Paro, Renato . (2011) Polycomb purification by in vivo biotinylation tagging reveals cohesin and Trithorax group proteins as interaction partners. Proceedings of the National Academy of Sciences, 108 (14). pp. 5572-5577.

2010

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.

Hofmann, Andreas and Gerrits, Bertran and Schmidt, Alexander and Bock, Thomas and Bausch-Fluck, Damaris and Aebersold, Rudolf and Wollscheid, Bernd . (2010) Proteomic cell surface phenotyping of differentiating acute myeloid leukemia cells. Blood, 116 (13). e26-34.

2009

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.

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.

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.

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.

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.

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 Bisle, Birgit and Kislinger, Thomas . (2009) Quantitative peptide and protein profiling by mass spectrometry. Methods in Molecular Biology, 492. pp. 21-38.

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.

Tebbe, Andreas and Schmidt, Alexander and Konstantinidis, Kosta and Falb, Michaela and Bisle, Birgit and Klein, Christian and Aivaliotis, Michalis and Kellermann, Josef and Siedler, Frank and Pfeiffer, Friedhelm and Lottspeich, Friedrich and Oesterhelt, Dieter . (2009) Life-style changes of a halophilic archaeon analyzed by quantitative proteomics. Proteomics, 9 (15). pp. 3843-3855.

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.

2008

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.

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.

Meltretter, Jasmin and Schmidt, Alexander and Humeny, Andreas and Becker, Cord-Michael and Pischetsrieder, Monika . (2008) Analysis of the peptide profile of milk and its changes during thermal treatment and storage. Journal of Agricultural and Food Chemistry, 56 (9). pp. 2899-2906.

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.

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.

2007

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.

2006

Bisle, Birgit and Schmidt, Alexander and Scheibe, Burghardt and Klein, Christian and Tebbe, Andreas and Kellermann, Joseph and Siedler, Frank and Pfeiffer, Friedhelm and Lottspeich, Friedrich and Oesterhelt, Dieter . (2006) Quantitative profiling of the membrane proteome in a halophilic archaeon. Molecular and Cellular Proteomics, 5 (9). pp. 1543-1558.

Sarioglu, Hakan and Brandner, Stefanie and Jacobsen, Carola and Meindl, Thomas and Schmidt, Alexander and Kellermann, Josef and Lottspeich, Friedrich and Andrae, Ulrich . (2006) Quantitative analysis of 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics, 6 (8). pp. 2407-2421.

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

2005

Hochleitner, Elisabeth O. and Kastner, Berthold and Fröhlich, Thomas and Schmidt, Alexander and Lührmann, Reinhard and Arnold, Georg and Lottspeich, Friedrich. (2005) Protein stoichiometry of a multiprotein complex, the human spliceosomal U1 small nuclear ribonucleoprotein: absolute quantification using isotope-coded tags and mass spectrometry. Journal of Biological Chemistry, 280 (4). pp. 2536-2542.

Schmidt, Alexander and Kellermann, Josef and Lottspeich, Friedrich. (2005) A novel strategy for quantitative proteomics using isotope-coded protein labels. Proteomics, 5 (1). pp. 4-15.

This list was generated on Sat Dec 16 03:48:48 2017 CET.