Selected Publications

Quantitative proteomics: A central technology for systems biology. Ahrens CH, Brunner E, Basler K. J Proteomics. 2010 Feb;73(4):820-827. Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Weiss M, Schrimpf S, Hengartner MO, Lercher MJ, von Mering C. Proteomics. 2010 Jan 13. [Epub ahead of print]. Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster. Goetze S, Qeli E, Mosimann C, Staes A, Gerrits B, Roschitzki B, Mohanty S, Niederer EM, Laczko E, Timmerman E, Lange V, Hafen E, Aebersold R, Vandekerckhove J, Basler K, Ahrens CH, Gevaert K, Brunner E. PLoS Biol. 2009 Nov;7(11):e1000236. Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Reiter L, Claassen M, Schrimpf SP, Jovanovic M, Schmidt A, Buhmann JM, Hengartner MO, Aebersold R. Mol Cell Proteomics. 2009 Nov;8(11):2405-17. Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function. Grobei MA, Qeli E, Brunner E, Rehrauer H, Zhang R, Roschitzki B, Basler K, Ahrens CH, Grossniklaus U. Genome Res. 2009 Oct 19(10):1786-1800. A combined proteomic and genetic analysis identifies a role for the lipid desaturase Desat1 in starvation-induced autophagy in Drosophila. Köhler K, Brunner E, Guan XL, Boucke K, Greber UF, Mohanty S, Barth JM, Wenk MR, Hafen E. Autophagy. 2009 Oct;5(7):980-90. Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes. Schrimpf SP, Weiss M, Reiter L, Ahrens CH, Jovanovic M, Malmström J, Brunner E, Mohanty S, Lercher MJ, Hunziker PE, Aebersold R, von Mering C, Hengartner MO. PLoS Biol. 2009 Mar;7(3):e48. The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE; FlyBase Consortium, Aebersold R, Hafen E. BMC Bioinformatics. 2009 Feb;10:59. Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics. Baerenfaller K, Grossmann J, Grobei MA, Hull R, Hirsch-Hoffmann M, Yalovsky S, Zimmermann P, Grossniklaus U, Gruissem W, Baginsky S. Science. 2008 May;320(5878):938-41. PepSplice: Cache-Efficient Search Algorithms for Comprehensive Identification of Tandem Mass Spectra. Roos FF, Jacob R, Grossmann J, Fischer B, Buhmann JM, Gruissem W, Baginsky S, Widmayer P. Bioinformatics 2007 Nov;23(22):3016-3023. A Proteome Catalog of Drosophila melanogaster: An Essential Resource for Targeted Quantitative Proteomics. Ahrens CH, Brunner E, Hafen E, Aebersold R, Basler K. Fly 2007 May/June;1(3):182-186. A high-quality catalog of the Drosophila melanogaster proteome. Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R. Nat Biotechnol. 2007 May;25(5):576-83. Semi-supervised LC/MS alignment for differential proteomics. Fischer B, Grossmann J, Roth V, Gruissem W, Baginsky S, Buhmann JM. Bioinformatics. 2006 Jul;22(14):e132-40.

[18.01.2010]