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Items: 24

1.

mzTab-M: A Data Standard for Sharing Quantitative Results in Mass Spectrometry Metabolomics.

Hoffmann N, Rein J, Sachsenberg T, Hartler J, Haug K, Mayer G, Alka O, Dayalan S, Pearce JTM, Rocca-Serra P, Qi D, Eisenacher M, Perez-Riverol Y, Vizcaíno JA, Salek RM, Neumann S, Jones AR.

Anal Chem. 2019 Mar 5;91(5):3302-3310. doi: 10.1021/acs.analchem.8b04310. Epub 2019 Feb 13.

PMID:
30688441
2.

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.

Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106.

3.

Expanding the Use of Spectral Libraries in Proteomics.

Deutsch EW, Perez-Riverol Y, Chalkley RJ, Wilhelm M, Tate S, Sachsenberg T, Walzer M, Käll L, Delanghe B, Böcker S, Schymanski EL, Wilmes P, Dorfer V, Kuster B, Volders PJ, Jehmlich N, Vissers JPC, Wolan DW, Wang AY, Mendoza L, Shofstahl J, Dowsey AW, Griss J, Salek RM, Neumann S, Binz PA, Lam H, Vizcaíno JA, Bandeira N, Röst H.

J Proteome Res. 2018 Dec 7;17(12):4051-4060. doi: 10.1021/acs.jproteome.8b00485. Epub 2018 Oct 11.

4.

Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients.

Kahles A, Lehmann KV, Toussaint NC, Hüser M, Stark SG, Sachsenberg T, Stegle O, Kohlbacher O, Sander C; Cancer Genome Atlas Research Network, Rätsch G.

Cancer Cell. 2018 Aug 13;34(2):211-224.e6. doi: 10.1016/j.ccell.2018.07.001. Epub 2018 Aug 2.

5.

Differential Enzymatic 16O/18O Labeling for the Detection of Cross-Linked Nucleic Acid-Protein Heteroconjugates.

Flett FJ, Sachsenberg T, Kohlbacher O, Mackay CL, Interthal H.

Anal Chem. 2017 Nov 7;89(21):11208-11213. doi: 10.1021/acs.analchem.7b01625. Epub 2017 Oct 13.

6.

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.

J Biotechnol. 2017 Nov 10;261:142-148. doi: 10.1016/j.jbiotec.2017.05.016. Epub 2017 May 27. Review.

7.

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.

Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192.

8.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
9.

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
10.

LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer.

Veit J, Sachsenberg T, Chernev A, Aicheler F, Urlaub H, Kohlbacher O.

J Proteome Res. 2016 Sep 2;15(9):3441-8. doi: 10.1021/acs.jproteome.6b00407. Epub 2016 Aug 10.

PMID:
27476824
11.

Ten Simple Rules for Taking Advantage of Git and GitHub.

Perez-Riverol Y, Gatto L, Wang R, Sachsenberg T, Uszkoreit J, Leprevost Fda V, Fufezan C, Ternent T, Eglen SJ, Katz DS, Pollard TJ, Konovalov A, Flight RM, Blin K, Vizcaíno JA.

PLoS Comput Biol. 2016 Jul 14;12(7):e1004947. doi: 10.1371/journal.pcbi.1004947. eCollection 2016 Jul. No abstract available. Erratum in: PLoS Comput Biol. 2019 Jun 14;15(6):e1007142.

12.

Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions.

Zaman U, Richter FM, Hofele R, Kramer K, Sachsenberg T, Kohlbacher O, Lenz C, Urlaub H.

Mol Cell Proteomics. 2015 Dec;14(12):3196-210. doi: 10.1074/mcp.M115.052795. Epub 2015 Oct 8.

13.

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry.

Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RH, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H.

Methods. 2015 Nov 1;89:138-48. doi: 10.1016/j.ymeth.2015.06.005. Epub 2015 Jun 10.

PMID:
26071038
14.

Workflows for automated downstream data analysis and visualization in large-scale computational mass spectrometry.

Aiche S, Sachsenberg T, Kenar E, Walzer M, Wiswedel B, Kristl T, Boyles M, Duschl A, Huber CG, Berthold MR, Reinert K, Kohlbacher O.

Proteomics. 2015 Apr;15(8):1443-7. doi: 10.1002/pmic.201400391. Epub 2015 Feb 14.

15.

MetaProSIP: automated inference of stable isotope incorporation rates in proteins for functional metaproteomics.

Sachsenberg T, Herbst FA, Taubert M, Kermer R, Jehmlich N, von Bergen M, Seifert J, Kohlbacher O.

J Proteome Res. 2015 Feb 6;14(2):619-27. doi: 10.1021/pr500245w. Epub 2014 Dec 1.

PMID:
25412983
16.

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins.

Kramer K, Sachsenberg T, Beckmann BM, Qamar S, Boon KL, Hentze MW, Kohlbacher O, Urlaub H.

Nat Methods. 2014 Oct;11(10):1064-70. doi: 10.1038/nmeth.3092. Epub 2014 Aug 31.

17.

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.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

18.

On comparison of SimTandem with state-of-the-art peptide identification tools, efficiency of precursor mass filter and dealing with variable modifications.

Novák J, Sachsenberg T, Hoksza D, Skopal T, Kohlbacher O.

J Integr Bioinform. 2013 Nov 14;10(3):228. doi: 10.2390/biecoll-jib-2013-228.

PMID:
24231142
19.

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.

Mol Cell Proteomics. 2013 Aug;12(8):2332-40. doi: 10.1074/mcp.O113.028506. Epub 2013 Apr 18.

20.

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
21.

Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome.

Laubinger S, Zeller G, Henz SR, Buechel S, Sachsenberg T, Wang JW, Rätsch G, Weigel D.

Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17466-73. doi: 10.1073/pnas.1012891107. Epub 2010 Sep 24.

22.

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays.

Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rätsch G, Weigel D, Laubinger S.

Plant J. 2009 Jun;58(6):1068-82. doi: 10.1111/j.1365-313X.2009.03835.x. Epub 2009 Feb 13. Erratum in: Plant J. 2009 Dec;60(5):929.

23.

At-TAX: a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana.

Laubinger S, Zeller G, Henz SR, Sachsenberg T, Widmer CK, Naouar N, Vuylsteke M, Schölkopf B, Rätsch G, Weigel D.

Genome Biol. 2008;9(7):R112. doi: 10.1186/gb-2008-9-7-r112. Epub 2008 Jul 9.

24.

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana.

Laubinger S, Sachsenberg T, Zeller G, Busch W, Lohmann JU, Rätsch G, Weigel D.

Proc Natl Acad Sci U S A. 2008 Jun 24;105(25):8795-800. doi: 10.1073/pnas.0802493105. Epub 2008 Jun 12.

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