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A proteomics sample metadata representation for multiomics integration and big data analysis.
Dai C, Füllgrabe A, Pfeuffer J, Solovyeva EM, Deng J, Moreno P, Kamatchinathan S, Kundu DJ, George N, Fexova S, Grüning B, Föll MC, Griss J, Vaudel M, Audain E, Locard-Paulet M, Turewicz M, Eisenacher M, Uszkoreit J, Van Den Bossche T, Schwämmle V, Webel H, Schulze S, Bouyssié D, Jayaram S, Duggineni VK, Samaras P, Wilhelm M, Choi M, Wang M, Kohlbacher O, Brazma A, Papatheodorou I, Bandeira N, Deutsch EW, Vizcaíno JA, Bai M, Sachsenberg T, Levitsky LI, Perez-Riverol Y. Dai C, et al. Among authors: pfeuffer j. Nat Commun. 2021 Oct 6;12(1):5854. doi: 10.1038/s41467-021-26111-3. Nat Commun. 2021. PMID: 34615866 Free PMC article. Review.
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: pfeuffer j. Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959. Nat Methods. 2016. PMID: 27575624
BioContainers: an open-source and community-driven framework for software standardization.
da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. da Veiga Leprevost F, et al. Among authors: pfeuffer j. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. Bioinformatics. 2017. PMID: 28379341 Free PMC article.
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. 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.
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: pfeuffer j. Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106. Nucleic Acids Res. 2019. PMID: 30395289 Free PMC article.
EPIFANY: A Method for Efficient High-Confidence Protein Inference.
Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. Pfeuffer J, et al. J Proteome Res. 2020 Mar 6;19(3):1060-1072. doi: 10.1021/acs.jproteome.9b00566. Epub 2020 Feb 13. J Proteome Res. 2020. PMID: 31975601 Free PMC article.
124 results