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Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.
Breckels LM, Holden SB, Wojnar D, Mulvey CM, Christoforou A, Groen A, Trotter MW, Kohlbacher O, Lilley KS, Gatto L. Breckels LM, et al. Among authors: kohlbacher o. PLoS Comput Biol. 2016 May 13;12(5):e1004920. doi: 10.1371/journal.pcbi.1004920. eCollection 2016 May. PLoS Comput Biol. 2016. PMID: 27175778 Free PMC article.
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics.
Walzer M, Qi D, Mayer G, Uszkoreit J, Eisenacher M, Sachsenberg T, Gonzalez-Galarza FF, Fan J, Bessant C, Deutsch EW, Reisinger F, Vizcaíno JA, Medina-Aunon JA, Albar JP, Kohlbacher O, Jones AR. Walzer M, et al. Among authors: kohlbacher o. Mol Cell Proteomics. 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506. Epub 2013 Apr 18. Mol Cell Proteomics. 2013. PMID: 23599424 Free PMC article.
qcML: an exchange format for quality control metrics from mass spectrometry experiments.
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, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L. Walzer M, et al. Among authors: kohlbacher o. Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23. Mol Cell Proteomics. 2014. PMID: 24760958 Free PMC article.
The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.
Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H. Griss J, et al. Among authors: kohlbacher o. Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30. Mol Cell Proteomics. 2014. PMID: 24980485 Free PMC article.
Testing and Validation of Computational Methods for Mass Spectrometry.
Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Gatto L, et al. Among authors: kohlbacher o. J Proteome Res. 2016 Mar 4;15(3):809-14. doi: 10.1021/acs.jproteome.5b00852. Epub 2015 Nov 17. J Proteome Res. 2016. PMID: 26549429 Free PMC article.
OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
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. Röst HL, et al. Among authors: kohlbacher o. Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959. Nat Methods. 2016. PMID: 27575624
OpenMS - A platform for reproducible analysis of mass spectrometry data.
Pfeuffer J, Sachsenberg T, Alka O, Walzer M, Fillbrunn A, Nilse L, Schilling O, Reinert K, Kohlbacher O. Pfeuffer J, et al. Among authors: kohlbacher o. J Biotechnol. 2017 Nov 10;261:142-148. doi: 10.1016/j.jbiotec.2017.05.016. Epub 2017 May 27. J Biotechnol. 2017. PMID: 28559010 Free article. Review.
qPortal: A platform for data-driven biomedical research.
Mohr C, Friedrich A, Wojnar D, Kenar E, Polatkan AC, Codrea MC, Czemmel S, Kohlbacher O, Nahnsen S. Mohr C, et al. Among authors: kohlbacher o. PLoS One. 2018 Jan 19;13(1):e0191603. doi: 10.1371/journal.pone.0191603. eCollection 2018. PLoS One. 2018. PMID: 29352322 Free PMC article.
253 results