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Items: 42

1.

Analysis of 1508 Plasma Samples by Capillary-Flow Data-Independent Acquisition Profiles Proteomics of Weight Loss and Maintenance.

Bruderer R, Muntel J, Müller S, Bernhardt OM, Gandhi T, Cominetti O, Macron C, Carayol J, Rinner O, Astrup A, Saris WHM, Hager J, Valsesia A, Dayon L, Reiter L.

Mol Cell Proteomics. 2019 Jun;18(6):1242-1254. doi: 10.1074/mcp.RA118.001288. Epub 2019 Apr 4.

2.

Next-generation Proteomics from an Industrial Perspective.

Rinner O.

Chimia (Aarau). 2016 Dec 21;70(12):860-863. doi: 10.2533/chimia.2016.860.

PMID:
28661357
3.

Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.

Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL.

Cell. 2016 Jul 28;166(3):766-778. doi: 10.1016/j.cell.2016.06.041. Epub 2016 Jul 21.

4.

A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery.

Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E.

J Proteome Res. 2015 Jul 2;14(7):2807-18. doi: 10.1021/acs.jproteome.5b00315. Epub 2015 Jun 5.

PMID:
25944384
5.

Extending the limits of quantitative proteome profiling with data-independent acquisition and application to acetaminophen-treated three-dimensional liver microtissues.

Bruderer R, Bernhardt OM, Gandhi T, Miladinović SM, Cheng LY, Messner S, Ehrenberger T, Zanotelli V, Butscheid Y, Escher C, Vitek O, Rinner O, Reiter L.

Mol Cell Proteomics. 2015 May;14(5):1400-10. doi: 10.1074/mcp.M114.044305. Epub 2015 Feb 27.

6.

DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments.

Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V.

J Proteome Res. 2015 Feb 6;14(2):787-803. doi: 10.1021/pr500834z. Epub 2014 Dec 30.

PMID:
25495225
7.

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines.

Ori A, Banterle N, Iskar M, Andrés-Pons A, Escher C, Khanh Bui H, Sparks L, Solis-Mezarino V, Rinner O, Bork P, Lemke EA, Beck M.

Mol Syst Biol. 2013;9:648. doi: 10.1038/msb.2013.4.

8.

N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications.

Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, Aebersold R.

Mol Cell Proteomics. 2013 Apr;12(4):1005-16. doi: 10.1074/mcp.O112.026617. Epub 2013 Feb 13.

9.

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis.

Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R.

Nature. 2013 Feb 14;494(7436):266-70. doi: 10.1038/nature11835. Epub 2013 Jan 20.

10.

Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics.

Hüttenhain R, Soste M, Selevsek N, Röst H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL, Niméus-Malmström E, Rinner O, Aebersold R.

Sci Transl Med. 2012 Jul 11;4(142):142ra94. doi: 10.1126/scitranslmed.3003989.

11.

Using iRT, a normalized retention time for more targeted measurement of peptides.

Escher C, Reiter L, MacLean B, Ossola R, Herzog F, Chilton J, MacCoss MJ, Rinner O.

Proteomics. 2012 Apr;12(8):1111-21. doi: 10.1002/pmic.201100463.

12.

The quantitative proteome of a human cell line.

Beck M, Schmidt A, Malmstroem J, Claassen M, Ori A, Szymborska A, Herzog F, Rinner O, Ellenberg J, Aebersold R.

Mol Syst Biol. 2011 Nov 8;7:549. doi: 10.1038/msb.2011.82.

13.

Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome.

Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Jünger MA, Köhler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M.

Mol Syst Biol. 2011 Nov 8;7:547. doi: 10.1038/msb.2011.79.

14.

The oxygen sensor PHD3 limits glycolysis under hypoxia via direct binding to pyruvate kinase.

Chen N, Rinner O, Czernik D, Nytko KJ, Zheng D, Stiehl DP, Zamboni N, Gstaiger M, Frei C.

Cell Res. 2011 Jun;21(6):983-6. doi: 10.1038/cr.2011.66. Epub 2011 Apr 12. No abstract available.

15.

Biomarker validation in blood specimens by selected reaction monitoring mass spectrometry of N-glycosites.

Ossola R, Schiess R, Picotti P, Rinner O, Reiter L, Aebersold R.

Methods Mol Biol. 2011;728:179-94. doi: 10.1007/978-1-61779-068-3_11.

PMID:
21468948
16.

mProphet: automated data processing and statistical validation for large-scale SRM experiments.

Reiter L, Rinner O, Picotti P, Hüttenhain R, Beck M, Brusniak MY, Hengartner MO, Aebersold R.

Nat Methods. 2011 May;8(5):430-5. doi: 10.1038/nmeth.1584. Epub 2011 Mar 20.

PMID:
21423193
17.

Combined functional genomic and proteomic approaches identify a PP2A complex as a negative regulator of Hippo signaling.

Ribeiro PS, Josué F, Wepf A, Wehr MC, Rinner O, Kelly G, Tapon N, Gstaiger M.

Mol Cell. 2010 Aug 27;39(4):521-34. doi: 10.1016/j.molcel.2010.08.002.

18.

Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics.

Leitner A, Walzthoeni T, Kahraman A, Herzog F, Rinner O, Beck M, Aebersold R.

Mol Cell Proteomics. 2010 Aug;9(8):1634-49. doi: 10.1074/mcp.R000001-MCP201. Epub 2010 Mar 31. Review.

19.

High-throughput generation of selected reaction-monitoring assays for proteins and proteomes.

Picotti P, Rinner O, Stallmach R, Dautel F, Farrah T, Domon B, Wenschuh H, Aebersold R.

Nat Methods. 2010 Jan;7(1):43-6. doi: 10.1038/nmeth.1408. Epub 2009 Dec 6.

PMID:
19966807
20.

Identification of cross-linked peptides from large sequence databases.

Rinner O, Seebacher J, Walzthoeni T, Mueller LN, Beck M, Schmidt A, Mueller M, Aebersold R.

Nat Methods. 2008 Apr;5(4):315-8. doi: 10.1038/nmeth.1192. Epub 2008 Mar 9. Erratum in: Nat Methods. 2008 Aug;5(8):748.

21.

The zebrafish mutant lbk/vam6 resembles human multisystemic disorders caused by aberrant trafficking of endosomal vesicles.

Schonthaler HB, Fleisch VC, Biehlmaier O, Makhankov Y, Rinner O, Bahadori R, Geisler R, Schwarz H, Neuhauss SC, Dahm R.

Development. 2008 Jan;135(2):387-99. Epub 2007 Dec 12.

22.

Quantitative proteomic analysis of protein complexes: concurrent identification of interactors and their state of phosphorylation.

Pflieger D, Jünger MA, Müller M, Rinner O, Lee H, Gehrig PM, Gstaiger M, Aebersold R.

Mol Cell Proteomics. 2008 Feb;7(2):326-46. Epub 2007 Oct 23.

23.

PhosphoPep--a phosphoproteome resource for systems biology research in Drosophila Kc167 cells.

Bodenmiller B, Malmstrom J, Gerrits B, Campbell D, Lam H, Schmidt A, Rinner O, Mueller LN, Shannon PT, Pedrioli PG, Panse C, Lee HK, Schlapbach R, Aebersold R.

Mol Syst Biol. 2007;3:139. Epub 2007 Oct 16. Review.

24.

Epitope mapping on bovine prion protein using chemical cross-linking and mass spectrometry.

Pimenova T, Nazabal A, Roschitzki B, Seebacher J, Rinner O, Zenobi R.

J Mass Spectrom. 2008 Feb;43(2):185-95.

PMID:
17924399
25.

Evidence for RPE65-independent vision in the cone-dominated zebrafish retina.

Schonthaler HB, Lampert JM, Isken A, Rinner O, Mader A, Gesemann M, Oberhauser V, Golczak M, Biehlmaier O, Palczewski K, Neuhauss SC, von Lintig J.

Eur J Neurosci. 2007 Oct;26(7):1940-9. Epub 2007 Sep 14.

26.

SuperHirn - a novel tool for high resolution LC-MS-based peptide/protein profiling.

Mueller LN, Rinner O, Schmidt A, Letarte S, Bodenmiller B, Brusniak MY, Vitek O, Aebersold R, Müller M.

Proteomics. 2007 Oct;7(19):3470-80.

PMID:
17726677
27.

A high-quality catalog of the Drosophila melanogaster proteome.

Brunner E, Ahrens CH, Mohanty S, Baetschmann H, Loevenich S, Potthast F, Deutsch EW, Panse C, de Lichtenberg U, Rinner O, Lee H, Pedrioli PG, Malmstrom J, Koehler K, Schrimpf S, Krijgsveld J, Kregenow F, Heck AJ, Hafen E, Schlapbach R, Aebersold R.

Nat Biotechnol. 2007 May;25(5):576-83. Epub 2007 Apr 22.

PMID:
17450130
28.

An integrated mass spectrometric and computational framework for the analysis of protein interaction networks.

Rinner O, Mueller LN, Hubálek M, Müller M, Gstaiger M, Aebersold R.

Nat Biotechnol. 2007 Mar;25(3):345-52. Epub 2007 Feb 25.

PMID:
17322870
29.

Oculomotor instabilities in zebrafish mutant belladonna: a behavioral model for congenital nystagmus caused by axonal misrouting.

Huang YY, Rinner O, Hedinger P, Liu SC, Neuhauss SC.

J Neurosci. 2006 Sep 27;26(39):9873-80.

30.

The Zebrafish fade out mutant: a novel genetic model for Hermansky-Pudlak syndrome.

Bahadori R, Rinner O, Schonthaler HB, Biehlmaier O, Makhankov YV, Rao P, Jagadeeswaran P, Neuhauss SC.

Invest Ophthalmol Vis Sci. 2006 Oct;47(10):4523-31.

31.
32.

Duplicated genes with split functions: independent roles of protocadherin15 orthologues in zebrafish hearing and vision.

Seiler C, Finger-Baier KC, Rinner O, Makhankov YV, Schwarz H, Neuhauss SC, Nicolson T.

Development. 2005 Feb;132(3):615-23. Epub 2005 Jan 5.

33.

Contrast sensitivity, spatial and temporal tuning of the larval zebrafish optokinetic response.

Rinner O, Rick JM, Neuhauss SC.

Invest Ophthalmol Vis Sci. 2005 Jan;46(1):137-42.

34.

AGenDA: gene prediction by cross-species sequence comparison.

Taher L, Rinner O, Garg S, Sczyrba A, Morgenstern B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W305-8.

35.

An inexpensive device for non-invasive electroretinography in small aquatic vertebrates.

Makhankov YV, Rinner O, Neuhauss SC.

J Neurosci Methods. 2004 May 30;135(1-2):205-10.

36.

Retinal function and morphology in two zebrafish models of oculo-renal syndromes.

Bahadori R, Huber M, Rinner O, Seeliger MW, Geiger-Rudolph S, Geisler R, Neuhauss SC.

Eur J Neurosci. 2003 Sep;18(6):1377-86.

PMID:
14511318
37.

AGenDA: homology-based gene prediction.

Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B.

Bioinformatics. 2003 Aug 12;19(12):1575-7.

PMID:
12912840
38.

AGenDA: gene prediction by comparative sequence analysis.

Rinner O, Morgenstern B.

In Silico Biol. 2002;2(3):195-205.

PMID:
12542405
39.

Cone contributions to colour constancy.

Rinner O, Gegenfurtner KR.

Perception. 2002;31(6):733-46.

PMID:
12092799
40.

Exon discovery by genomic sequence alignment.

Morgenstern B, Rinner O, Abdeddaïm S, Haase D, Mayer KF, Dress AW, Mewes HW.

Bioinformatics. 2002 Jun;18(6):777-87.

PMID:
12075013
41.

The colors seen behind transparent filters.

D'Zmura M, Rinner O, Gegenfurtner KR.

Perception. 2000;29(8):911-26.

PMID:
11145083
42.

Time course of chromatic adaptation for color appearance and discrimination.

Rinner O, Gegenfurtner KR.

Vision Res. 2000;40(14):1813-26.

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