Publications

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Ulysse MG, Di Tommaso P, Nahnsen S. The nf-Core Framework for Community-Curated Bioinformatics Pipelines. Nat Biotechnol 2020;38:276–278.Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walzer M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 2016;13:741-748.Löffler MW, Chandran PA, Laske K, Schroeder C, Bonzheim I, Walzer M, Hilke FJ, Trautwein N, Kowalewski DJ, Schuster H, Günder M, Carcamo Yañez VA, Mohr C, Sturm M, Nguyen HP, Riess O, Bauer P, Nahnsen S, Nadalin S, Zieker D, Glatzle J, Thiel K, Schneiderhan-Marra N, Clasen S, Bösmüller H, Fend F, Kohlbacher O, Gouttefangeas C, Stevanović S, Königsrainer A, Rammensee HG. Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient. J Hepatol 2016;S0168-8278(16)30323-3.Dammeier S*, Nahnsen S*, Veit J*, Wehner F, Ueffing M, Kohlbacher O. Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence. J Proteome Res 2016;15:182-192.Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaino JA, Hermjakob H, Kohlbacher O, Martens L. qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics 2014;13:1905-1913.Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmstrom L. An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics. J Proteome Res. 2013;15(12),4686-4695.Nahnsen S, Sachsenberg T, Kohlbacher O. PTMeta: Increasing identification rates of modified peptides using modification prescanning and meta-analysis. Proteomics 2013;13:1042-1051.Nahnsen S, Kohlbacher O. In silico design of targeted SRM-based experiments. BMC Bioinformatics 2012;13 Suppl 16:S8.Nahnsen S, Bielow C, Reinert K, Kohlbacher O. Computational tools for label-free peptide quantification. Mol Cell Proteomics 2012;12:549-556.Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O. Probabilistic consensus scoring improves tandem mass spectrometry peptide identification. J Proteome Res 2011;10:3332-3343.