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Items: 26

1.

Proteotype profiling unmasks a viral signalling network essential for poxvirus assembly and transcriptional competence.

Novy K, Kilcher S, Omasits U, Bleck CKE, Beerli C, Vowinckel J, Martin CK, Syedbasha M, Maiolica A, White I, Mercer J, Wollscheid B.

Nat Microbiol. 2018 May;3(5):588-599. doi: 10.1038/s41564-018-0142-6. Epub 2018 Apr 9.

PMID:
29632367
2.

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.

Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH.

Genome Res. 2017 Dec;27(12):2083-2095. doi: 10.1101/gr.218255.116. Epub 2017 Nov 15.

3.

Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation.

Čuklina J, Hahn J, Imakaev M, Omasits U, Förstner KU, Ljubimov N, Goebel M, Pessi G, Fischer HM, Ahrens CH, Gelfand MS, Evguenieva-Hackenberg E.

BMC Genomics. 2016 Apr 23;17:302. doi: 10.1186/s12864-016-2602-9.

4.

Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms.

Turnbull L, Toyofuku M, Hynen AL, Kurosawa M, Pessi G, Petty NK, Osvath SR, Cárcamo-Oyarce G, Gloag ES, Shimoni R, Omasits U, Ito S, Yap X, Monahan LG, Cavaliere R, Ahrens CH, Charles IG, Nomura N, Eberl L, Whitchurch CB.

Nat Commun. 2016 Apr 14;7:11220. doi: 10.1038/ncomms11220.

5.

Quantitative proteomic analysis of Shigella flexneri and Shigella sonnei Generalized Modules for Membrane Antigens (GMMA) reveals highly pure preparations.

Maggiore L, Yu L, Omasits U, Rossi O, Dougan G, Thomson NR, Saul A, Choudhary JS, Gerke C.

Int J Med Microbiol. 2016 Feb;306(2):99-108. doi: 10.1016/j.ijmm.2015.12.003. Epub 2015 Dec 23.

6.

A Peptidomimetic Antibiotic Targets Outer Membrane Proteins and Disrupts Selectively the Outer Membrane in Escherichia coli.

Urfer M, Bogdanovic J, Lo Monte F, Moehle K, Zerbe K, Omasits U, Ahrens CH, Pessi G, Eberl L, Robinson JA.

J Biol Chem. 2016 Jan 22;291(4):1921-32. doi: 10.1074/jbc.M115.691725. Epub 2015 Dec 1.

7.

Surfaceome of classical Hodgkin and non-Hodgkin lymphoma.

Hofmann A, Thiesler T, Gerrits B, Behnke S, Sobotzki N, Omasits U, Bausch-Fluck D, Bock T, Aebersold R, Moch H, Tinguely M, Wollscheid B.

Proteomics Clin Appl. 2015 Aug;9(7-8):661-70. doi: 10.1002/prca.201400146.

8.

A mass spectrometric-derived cell surface protein atlas.

Bausch-Fluck D, Hofmann A, Bock T, Frei AP, Cerciello F, Jacobs A, Moest H, Omasits U, Gundry RL, Yoon C, Schiess R, Schmidt A, Mirkowska P, Härtlová A, Van Eyk JE, Bourquin JP, Aebersold R, Boheler KR, Zandstra P, Wollscheid B.

PLoS One. 2015 Apr 20;10(3):e0121314. doi: 10.1371/journal.pone.0121314. eCollection 2015.

9.

σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111.

Lardi M, Aguilar C, Pedrioli A, Omasits U, Suppiger A, Cárcamo-Oyarce G, Schmid N, Ahrens CH, Eberl L, Pessi G.

Appl Environ Microbiol. 2015 Jun 15;81(12):4077-89. doi: 10.1128/AEM.00694-15. Epub 2015 Apr 3.

10.

Improved prediction of peptide detectability for targeted proteomics using a rank-based algorithm and organism-specific data.

Qeli E, Omasits U, Goetze S, Stekhoven DJ, Frey JE, Basler K, Wollscheid B, Brunner E, Ahrens CH.

J Proteomics. 2014 Aug 28;108:269-83. doi: 10.1016/j.jprot.2014.05.011. Epub 2014 May 27.

PMID:
24878426
11.

Proteome-wide identification of predominant subcellular protein localizations in a bacterial model organism.

Stekhoven DJ, Omasits U, Quebatte M, Dehio C, Ahrens CH.

J Proteomics. 2014 Mar 17;99:123-37. doi: 10.1016/j.jprot.2014.01.015. Epub 2014 Jan 28.

PMID:
24486812
12.

A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum.

Koch M, Delmotte N, Ahrens CH, Omasits U, Schneider K, Danza F, Padhi B, Murset V, Braissant O, Vorholt JA, Hennecke H, Pessi G.

Appl Environ Microbiol. 2014 Apr;80(7):2094-101. doi: 10.1128/AEM.03314-13. Epub 2014 Jan 24.

13.

Combine and conquer: surfactants, solvents, and chaotropes for robust mass spectrometry based analyses of membrane proteins.

Waas M, Bhattacharya S, Chuppa S, Wu X, Jensen DR, Omasits U, Wollscheid B, Volkman BF, Noon KR, Gundry RL.

Anal Chem. 2014 Feb 4;86(3):1551-9. doi: 10.1021/ac403185a. Epub 2014 Jan 21.

14.

Protter: interactive protein feature visualization and integration with experimental proteomic data.

Omasits U, Ahrens CH, Müller S, Wollscheid B.

Bioinformatics. 2014 Mar 15;30(6):884-6. doi: 10.1093/bioinformatics/btt607. Epub 2013 Oct 24.

15.

Response of Burkholderia cenocepacia H111 to micro-oxia.

Pessi G, Braunwalder R, Grunau A, Omasits U, Ahrens CH, Eberl L.

PLoS One. 2013 Sep 2;8(9):e72939. doi: 10.1371/journal.pone.0072939. eCollection 2013.

16.

Proteomics analysis of Psychotria leaf nodule symbiosis: improved genome annotation and metabolic predictions.

Carlier AL, Omasits U, Ahrens CH, Eberl L.

Mol Plant Microbe Interact. 2013 Nov;26(11):1325-33. doi: 10.1094/MPMI-05-13-0152-R.

17.

Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome.

Omasits U, Quebatte M, Stekhoven DJ, Fortes C, Roschitzki B, Robinson MD, Dehio C, Ahrens CH.

Genome Res. 2013 Nov;23(11):1916-27. doi: 10.1101/gr.151035.112. Epub 2013 Jul 22.

18.

The hemolymph proteome of fed and starved Drosophila larvae.

Handke B, Poernbacher I, Goetze S, Ahrens CH, Omasits U, Marty F, Simigdala N, Meyer I, Wollscheid B, Brunner E, Hafen E, Lehner CF.

PLoS One. 2013 Jun 20;8(6):e67208. doi: 10.1371/journal.pone.0067208. Print 2013.

19.

The AHL- and BDSF-dependent quorum sensing systems control specific and overlapping sets of genes in Burkholderia cenocepacia H111.

Schmid N, Pessi G, Deng Y, Aguilar C, Carlier AL, Grunau A, Omasits U, Zhang LH, Ahrens CH, Eberl L.

PLoS One. 2012;7(11):e49966. doi: 10.1371/journal.pone.0049966. Epub 2012 Nov 20.

20.

Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.

Bock T, Moest H, Omasits U, Dolski S, Lundberg E, Frei A, Hofmann A, Bausch-Fluck D, Jacobs A, Krayenbuehl N, Uhlen M, Aebersold R, Frei K, Wollscheid B.

J Proteome Res. 2012 Oct 5;11(10):4885-93. doi: 10.1021/pr300360a. Epub 2012 Aug 31.

PMID:
22909291
21.

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

Knapp B, Lederer N, Omasits U, Schreiner W.

J Comput Chem. 2010 Dec;31(16):2868-73. doi: 10.1002/jcc.21581.

PMID:
20928849
22.

A comparative approach linking molecular dynamics of altered peptide ligands and MHC with in vivo immune responses.

Knapp B, Omasits U, Schreiner W, Epstein MM.

PLoS One. 2010 Jul 19;5(7):e11653. doi: 10.1371/journal.pone.0011653.

23.

jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability.

Roopra S, Knapp B, Omasits U, Schreiner W.

J Chem Inf Model. 2009 Oct;49(10):2412-7. doi: 10.1021/ci900248f.

PMID:
19852516
24.

3-Layer-based analysis of peptide-MHC interaction: in silico prediction, peptide binding affinity and T cell activation in a relevant allergen-specific model.

Knapp B, Omasits U, Bohle B, Maillere B, Ebner C, Schreiner W, Jahn-Schmid B.

Mol Immunol. 2009 May;46(8-9):1839-44. doi: 10.1016/j.molimm.2009.01.009. Epub 2009 Feb 15.

PMID:
19232439
25.

A critical cross-validation of high throughput structural binding prediction methods for pMHC.

Knapp B, Omasits U, Frantal S, Schreiner W.

J Comput Aided Mol Des. 2009 May;23(5):301-7. doi: 10.1007/s10822-009-9259-2. Epub 2009 Feb 5.

PMID:
19194661
26.

Side chain substitution benchmark for peptide/MHC interaction.

Knapp B, Omasits U, Schreiner W.

Protein Sci. 2008 Jun;17(6):977-82. doi: 10.1110/ps.073402508. Epub 2008 Apr 23.

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