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Items: 41

1.

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.

Griss J, Stanek F, Hudecz O, Dürnberger G, Perez-Riverol Y, Vizcaíno JA, Mechtler K.

J Proteome Res. 2019 Apr 5;18(4):1477-1485. doi: 10.1021/acs.jproteome.8b00377. Epub 2019 Mar 22.

2.

IsoProt: A Complete and Reproducible Workflow To Analyze iTRAQ/TMT Experiments.

Griss J, Vinterhalter G, Schwämmle V.

J Proteome Res. 2019 Apr 5;18(4):1751-1759. doi: 10.1021/acs.jproteome.8b00968. Epub 2019 Mar 20.

3.

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.

4.

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.

5.

Future Prospects of Spectral Clustering Approaches in Proteomics.

Perez-Riverol Y, Vizcaíno JA, Griss J.

Proteomics. 2018 Jul;18(14):e1700454. doi: 10.1002/pmic.201700454.

6.

Response to "Comparison and Evaluation of Clustering Algorithms for Tandem Mass Spectra".

Griss J, Perez-Riverol Y, The M, Käll L, Vizcaíno JA.

J Proteome Res. 2018 May 4;17(5):1993-1996. doi: 10.1021/acs.jproteome.7b00824. Epub 2018 Apr 25.

PMID:
29682973
7.

Digital image analysis improves precision of PD-L1 scoring in cutaneous melanoma.

Koelzer VH, Gisler A, Hanhart JC, Griss J, Wagner SN, Willi N, Cathomas G, Sachs M, Kempf W, Thommen DS, Mertz KD.

Histopathology. 2018 Sep;73(3):397-406. doi: 10.1111/his.13528. Epub 2018 Jun 5.

PMID:
29660160
8.

Tumor-associated B-cells induce tumor heterogeneity and therapy resistance.

Somasundaram R, Zhang G, Fukunaga-Kalabis M, Perego M, Krepler C, Xu X, Wagner C, Hristova D, Zhang J, Tian T, Wei Z, Liu Q, Garg K, Griss J, Hards R, Maurer M, Hafner C, Mayerhöfer M, Karanikas G, Jalili A, Bauer-Pohl V, Weihsengruber F, Rappersberger K, Koller J, Lang R, Hudgens C, Chen G, Tetzlaff M, Wu L, Frederick DT, Scolyer RA, Long GV, Damle M, Ellingsworth C, Grinman L, Choi H, Gavin BJ, Dunagin M, Raj A, Scholler N, Gross L, Beqiri M, Bennett K, Watson I, Schaider H, Davies MA, Wargo J, Czerniecki BJ, Schuchter L, Herlyn D, Flaherty K, Herlyn M, Wagner SN.

Nat Commun. 2017 Sep 19;8(1):607. doi: 10.1038/s41467-017-00452-4.

9.

Molecular classification of tumour cells in a patient with intravascular large B-cell lymphoma.

Bauer WM, Aichelburg MC, Griss J, Skrabs C, Simonitsch-Klupp I, Schiefer AI, Kittler H, Jäger U, Zeyda M, Knobler R, Stingl G.

Br J Dermatol. 2018 Jan;178(1):215-221. doi: 10.1111/bjd.15841. Epub 2017 Dec 29.

PMID:
28733977
10.

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.

11.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, Del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Dec 15;44(22):11033. Epub 2016 Sep 28. No abstract available.

12.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.

Nat Methods. 2016 Aug;13(8):651-656. Epub 2016 Jun 27.

13.

Greazy: Open-Source Software for Automated Phospholipid Tandem Mass Spectrometry Identification.

Kochen MA, Chambers MC, Holman JD, Nesvizhskii AI, Weintraub ST, Belisle JT, Islam MN, Griss J, Tabb DL.

Anal Chem. 2016 Jun 7;88(11):5733-41. doi: 10.1021/acs.analchem.6b00021. Epub 2016 May 24.

14.

Tumor-associated B cells in cutaneous primary melanoma and improved clinical outcome.

Garg K, Maurer M, Griss J, Brüggen MC, Wolf IH, Wagner C, Willi N, Mertz KD, Wagner SN.

Hum Pathol. 2016 Aug;54:157-64. doi: 10.1016/j.humpath.2016.03.022. Epub 2016 Apr 21.

PMID:
27107457
15.

Cleaning out the Litterbox of Proteomic Scientists' Favorite Pet: Optimized Data Analysis Avoiding Trypsin Artifacts.

Schittmayer M, Fritz K, Liesinger L, Griss J, Birner-Gruenberger R.

J Proteome Res. 2016 Apr 1;15(4):1222-9. doi: 10.1021/acs.jproteome.5b01105. Epub 2016 Mar 22.

16.

Spectral library searching in proteomics.

Griss J.

Proteomics. 2016 Mar;16(5):729-40. doi: 10.1002/pmic.201500296. Epub 2016 Feb 9. Review.

PMID:
26616598
17.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

18.

2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.

19.

A rare bullous variant of dermatitis herpetiformis.

Griss J, Stingl G, Schmidt E, Bangert C.

Br J Dermatol. 2016 Jan;174(1):231-3. doi: 10.1111/bjd.13941. Epub 2015 Oct 26. No abstract available.

PMID:
26042658
20.

Autoantibody Levels and Clinical Disease Severity in Patients with Pemphigus: Comparison of Aggregated Anti-desmoglein ELISA Values and Indirect Immunofluorescence Titres.

Weiss D, Ristl R, Griss J, Bangert C, Foedinger D, Stingl G, Brunner PM.

Acta Derm Venereol. 2015 May;95(5):559-64. doi: 10.2340/00015555-2023.

21.

Identifying novel biomarkers through data mining-a realistic scenario?

Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics Clin Appl. 2015 Apr;9(3-4):437-43. doi: 10.1002/prca.201400107. Epub 2015 Jan 12. Review.

22.

Analysis of the tryptic search space in UniProt databases.

Alpi E, Griss J, da Silva AW, Bely B, Antunes R, Zellner H, Ríos D, O'Donovan C, Vizcaíno JA, Martin MJ.

Proteomics. 2015 Jan;15(1):48-57. doi: 10.1002/pmic.201400227. Epub 2014 Dec 3.

23.

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.

24.

Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma.

Maurer M, Müller AC, Parapatics K, Pickl WF, Wagner C, Rudashevskaya EL, Breitwieser FP, Colinge J, Garg K, Griss J, Bennett KL, Wagner SN.

J Proteome Res. 2014 Jun 6;13(6):2830-45. doi: 10.1021/pr401270y. Epub 2014 May 6.

PMID:
24803318
25.

jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Jun;14(11):1328-32. doi: 10.1002/pmic.201300560. Epub 2014 Apr 29.

26.

Functional classification of cellular proteome profiles support the identification of drug resistance signatures in melanoma cells.

Paulitschke V, Haudek-Prinz V, Griss J, Berger W, Mohr T, Pehamberger H, Kunstfeld R, Gerner C.

J Proteome Res. 2013 Jul 5;12(7):3264-76. doi: 10.1021/pr400124w. Epub 2013 Jun 19.

27.

PRIDE Cluster: building a consensus of proteomics data.

Griss J, Foster JM, Hermjakob H, Vizcaíno JA.

Nat Methods. 2013 Feb;10(2):95-6. doi: 10.1038/nmeth.2343. No abstract available.

28.

The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013.

Vizcaíno JA, Côté RG, Csordas A, Dianes JA, Fabregat A, Foster JM, Griss J, Alpi E, Birim M, Contell J, O'Kelly G, Schoenegger A, Ovelleiro D, Pérez-Riverol Y, Reisinger F, Ríos D, Wang R, Hermjakob H.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29.

29.

The PRoteomics IDEntification (PRIDE) Converter 2 framework: an improved suite of tools to facilitate data submission to the PRIDE database and the ProteomeXchange consortium.

Côté RG, Griss J, Dianes JA, Wang R, Wright JC, van den Toorn HW, van Breukelen B, Heck AJ, Hulstaert N, Martens L, Reisinger F, Csordas A, Ovelleiro D, Perez-Rivevol Y, Barsnes H, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4.

30.

Proteome signatures of inflammatory activated primary human peripheral blood mononuclear cells.

Haudek-Prinz VJ, Klepeisz P, Slany A, Griss J, Meshcheryakova A, Paulitschke V, Mitulovic G, Stöckl J, Gerner C.

J Proteomics. 2012 Dec 5;76 Spec No.:150-62. doi: 10.1016/j.jprot.2012.07.012. Epub 2012 Jul 16.

31.

jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats.

Griss J, Reisinger F, Hermjakob H, Vizcaíno JA.

Proteomics. 2012 Mar;12(6):795-8. doi: 10.1002/pmic.201100578.

32.

The mzIdentML data standard for mass spectrometry-based proteomics results.

Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D.

Mol Cell Proteomics. 2012 Jul;11(7):M111.014381. doi: 10.1074/mcp.M111.014381. Epub 2012 Feb 27.

33.

PRIDE Inspector: a tool to visualize and validate MS proteomics data.

Wang R, Fabregat A, Ríos D, Ovelleiro D, Foster JM, Côté RG, Griss J, Csordas A, Perez-Riverol Y, Reisinger F, Hermjakob H, Martens L, Vizcaíno JA.

Nat Biotechnol. 2012 Feb 8;30(2):135-7. doi: 10.1038/nbt.2112. No abstract available.

34.

Consequences of the discontinuation of the International Protein Index (IPI) database and its substitution by the UniProtKB "complete proteome" sets.

Griss J, Martín M, O'Donovan C, Apweiler R, Hermjakob H, Vizcaíno JA.

Proteomics. 2011 Nov;11(22):4434-8. doi: 10.1002/pmic.201100363. Epub 2011 Oct 17.

35.

Published and perished? The influence of the searched protein database on the long-term storage of proteomics data.

Griss J, Côté RG, Gerner C, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2011 Sep;10(9):M111.008490. doi: 10.1074/mcp.M111.008490. Epub 2011 Jun 23.

36.

A posteriori quality control for the curation and reuse of public proteomics data.

Foster JM, Degroeve S, Gatto L, Visser M, Wang R, Griss J, Apweiler R, Martens L.

Proteomics. 2011 Jun;11(11):2182-94. doi: 10.1002/pmic.201000602. Epub 2011 May 2.

PMID:
21538885
37.

GPDE: A biological proteomic database for biomarker discovery and evaluation.

Griss J, Haudek-Prinz V, Gerner C.

Proteomics. 2011 Mar;11(5):1000-4. doi: 10.1002/pmic.201000507. Epub 2011 Jan 27.

PMID:
21337704
38.

Introducing the CPL/MUW proteome database: interpretation of human liver and liver cancer proteome profiles by referring to isolated primary cells.

Wimmer H, Gundacker NC, Griss J, Haudek VJ, Stättner S, Mohr T, Zwickl H, Paulitschke V, Baron DM, Trittner W, Kubicek M, Bayer E, Slany A, Gerner C.

Electrophoresis. 2009 Jun;30(12):2076-89. doi: 10.1002/elps.200900072.

PMID:
19582709
39.

Introducing a new parameter for quality control of proteome profiles: consideration of commonly expressed proteins.

Slany A, Haudek VJ, Gundacker NC, Griss J, Mohr T, Wimmer H, Eisenbauer M, Elbling L, Gerner C.

Electrophoresis. 2009 Apr;30(8):1306-28. doi: 10.1002/elps.200800440.

PMID:
19382132
40.

Cytoplasmic proteome and secretome profiles of differently stimulated human dendritic cells.

Gundacker NC, Haudek VJ, Wimmer H, Slany A, Griss J, Bochkov V, Zielinski C, Wagner O, Stöckl J, Gerner C.

J Proteome Res. 2009 Jun;8(6):2799-811. doi: 10.1021/pr8011039.

PMID:
19351150
41.

Orally administered rapamycin, dacarbazine or both for treatment of human melanoma evaluated in severe combined immunodeficiency mice.

Thallinger C, Skorjanec S, Soleiman A, Tzaneva S, Griss J, Rous W, Poeppl W, Weinlich G, Karimian-Teherani D, Joukhadar C.

Pharmacology. 2008;82(3):233-8. doi: 10.1159/000156490. Epub 2008 Sep 23.

PMID:
18810248

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