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Items: 7

1.

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.

2.

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.

3.

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.

4.

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.

5.

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.

6.

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.

7.

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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