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Items: 23

1.

The Draft Whole-Genome Sequence of the Antibiotic Producer Empedobacter haloabium ATCC 31962 Provides Indications for Its Taxonomic Reclassification.

Miess H, Arlt P, Apel AK, Weber T, Nieselt K, Hanssen F, Czemmel S, Nahnsen S, Gross H.

Microbiol Resour Announc. 2019 Nov 7;8(45). pii: e01120-19. doi: 10.1128/MRA.01120-19.

2.

Challenges of big data integration in the life sciences.

Fillinger S, de la Garza L, Peltzer A, Kohlbacher O, Nahnsen S.

Anal Bioanal Chem. 2019 Oct;411(26):6791-6800. doi: 10.1007/s00216-019-02074-9. Epub 2019 Aug 28.

PMID:
31463515
3.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma.

Löffler MW, Mohr C, Bichmann L, Freudenmann LK, Walzer M, Schroeder CM, Trautwein N, Hilke FJ, Zinser RS, Mühlenbruch L, Kowalewski DJ, Schuster H, Sturm M, Matthes J, Riess O, Czemmel S, Nahnsen S, Königsrainer I, Thiel K, Nadalin S, Beckert S, Bösmüller H, Fend F, Velic A, Maček B, Haen SP, Buonaguro L, Kohlbacher O, Stevanović S, Königsrainer A; HEPAVAC Consortium, Rammensee HG.

Genome Med. 2019 Apr 30;11(1):28. doi: 10.1186/s13073-019-0636-8.

4.

Ring1b-dependent epigenetic remodelling is an essential prerequisite for pancreatic carcinogenesis.

Benitz S, Straub T, Mahajan UM, Mutter J, Czemmel S, Unruh T, Wingerath B, Deubler S, Fahr L, Cheng T, Nahnsen S, Bruns P, Kong B, Raulefs S, Ceyhan GO, Mayerle J, Steiger K, Esposito I, Kleeff J, Michalski CW, Regel I.

Gut. 2019 Nov;68(11):2007-2018. doi: 10.1136/gutjnl-2018-317208. Epub 2019 Apr 6.

PMID:
30954952
5.

Measles Virus-Based Treatments Trigger a Pro-inflammatory Cascade and a Distinctive Immunopeptidome in Glioblastoma.

Rajaraman S, Canjuga D, Ghosh M, Codrea MC, Sieger R, Wedekink F, Tatagiba M, Koch M, Lauer UM, Nahnsen S, Rammensee HG, Mühlebach MD, Stevanovic S, Tabatabai G.

Mol Ther Oncolytics. 2018 Dec 31;12:147-161. doi: 10.1016/j.omto.2018.12.010. eCollection 2019 Mar 29.

6.

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.

PLoS One. 2018 Jan 19;13(1):e0191603. doi: 10.1371/journal.pone.0191603. eCollection 2018.

7.

Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states.

Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS.

J Proteomics. 2018 May 30;180:11-24. doi: 10.1016/j.jprot.2017.11.008. Epub 2017 Nov 15.

PMID:
29155090
8.

Platforms and Pipelines for Proteomics Data Analysis and Management.

Codrea MC, Nahnsen S.

Adv Exp Med Biol. 2016;919:203-215. Review.

PMID:
27975218
9.

Erratum to "Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient".

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.

J Hepatol. 2017 Jan;66(1):252-253. doi: 10.1016/j.jhep.2016.10.021. Epub 2016 Nov 15. No abstract available.

PMID:
27863814
10.

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.

Nat Methods. 2016 Aug 30;13(9):741-8. doi: 10.1038/nmeth.3959.

PMID:
27575624
11.

Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient.

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.

J Hepatol. 2016 Oct;65(4):849-855. doi: 10.1016/j.jhep.2016.06.027. Epub 2016 Jul 7. Erratum in: J Hepatol. 2017 Jan;66(1):252-253.

12.

Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

Dammeier S, Nahnsen S, Veit J, Wehner F, Ueffing M, Kohlbacher O.

J Proteome Res. 2016 Jan 4;15(1):182-92. doi: 10.1021/acs.jproteome.5b00704. Epub 2015 Dec 8.

PMID:
26593679
13.

Intuitive web-based experimental design for high-throughput biomedical data.

Friedrich A, Kenar E, Kohlbacher O, Nahnsen S.

Biomed Res Int. 2015;2015:958302. doi: 10.1155/2015/958302. Epub 2015 Apr 14.

14.

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.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

15.

An automated pipeline for high-throughput label-free quantitative proteomics.

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmström L.

J Proteome Res. 2013 Apr 5;12(4):1628-44. doi: 10.1021/pr300992u. Epub 2013 Feb 22.

PMID:
23391308
16.

PTMeta: increasing identification rates of modified peptides using modification prescanning and meta-analysis.

Nahnsen S, Sachsenberg T, Kohlbacher O.

Proteomics. 2013 Mar;13(6):1042-51. doi: 10.1002/pmic.201200315.

PMID:
23335442
17.

Tools for label-free peptide quantification.

Nahnsen S, Bielow C, Reinert K, Kohlbacher O.

Mol Cell Proteomics. 2013 Mar;12(3):549-56. doi: 10.1074/mcp.R112.025163. Epub 2012 Dec 17. Review.

18.

In silico design of targeted SRM-based experiments.

Nahnsen S, Kohlbacher O.

BMC Bioinformatics. 2012;13 Suppl 16:S8. doi: 10.1186/1471-2105-13-S16-S8. Epub 2012 Nov 5.

19.

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

Nahnsen S, Bertsch A, Rahnenführer J, Nordheim A, Kohlbacher O.

J Proteome Res. 2011 Aug 5;10(8):3332-43. doi: 10.1021/pr2002879. Epub 2011 Jun 23.

PMID:
21644507
20.

Alterations of primary fatty acid amides in serum of patients with severe mental illness.

Schwarz E, Whitfield P, Nahnsen S, Wang L, Major H, Leweke FM, Koethe D, Lio P, Bahn S.

Front Biosci (Elite Ed). 2011 Jan 1;3:308-14.

PMID:
21196311
21.

Mass spectrometry at the interface of proteomics and genomics.

Krug K, Nahnsen S, Macek B.

Mol Biosyst. 2011 Feb;7(2):284-91. doi: 10.1039/c0mb00168f. Epub 2010 Oct 21. Review.

PMID:
20967315
22.

Suppression of casein kinase 1alpha in melanoma cells induces a switch in beta-catenin signaling to promote metastasis.

Sinnberg T, Menzel M, Kaesler S, Biedermann T, Sauer B, Nahnsen S, Schwarz M, Garbe C, Schittek B.

Cancer Res. 2010 Sep 1;70(17):6999-7009. doi: 10.1158/0008-5472.CAN-10-0645. Epub 2010 Aug 10.

23.

Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics.

Bertsch A, Jung S, Zerck A, Pfeifer N, Nahnsen S, Henneges C, Nordheim A, Kohlbacher O.

J Proteome Res. 2010 May 7;9(5):2696-704. doi: 10.1021/pr1001803.

PMID:
20201589

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