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Items: 1 to 20 of 33


BioContainers: An open-source and community-driven framework for software standardization.

Leprevost FD, 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 Mar 30. doi: 10.1093/bioinformatics/btx192. [Epub ahead of print]


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.


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.


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.


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.


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.


Spectral library searching in proteomics.

Griss J.

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


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.

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