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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. Vizcaíno JA, et al. Among authors: wang r. Nucleic Acids Res. 2016 Dec 15;44(22):11033. doi: 10.1093/nar/gkw880. Epub 2016 Sep 28. Nucleic Acids Res. 2016. PMID: 27683222 Free PMC article. 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. Vizcaíno JA, et al. Among authors: wang r. Nucleic Acids Res. 2013 Jan;41(Database issue):D1063-9. doi: 10.1093/nar/gks1262. Epub 2012 Nov 29. Nucleic Acids Res. 2013. PMID: 23203882 Free PMC article.
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. Vizcaíno JA, et al. Among authors: wang r. Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2. Nucleic Acids Res. 2016. PMID: 26527722 Free PMC article.
PRIDE: quality control in a proteomics data repository.
Csordas A, Ovelleiro D, Wang R, Foster JM, Ríos D, Vizcaíno JA, Hermjakob H. Csordas A, et al. Among authors: wang r. Database (Oxford). 2012 Mar 20;2012:bas004. doi: 10.1093/database/bas004. Print 2012. Database (Oxford). 2012. PMID: 22434838 Free PMC article.
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. Côté RG, et al. Among authors: wang r. Mol Cell Proteomics. 2012 Dec;11(12):1682-9. doi: 10.1074/mcp.O112.021543. Epub 2012 Sep 4. Mol Cell Proteomics. 2012. PMID: 22949509 Free PMC article.
From Peptidome to PRIDE: public proteomics data migration at a large scale.
Csordas A, Wang R, Ríos D, Reisinger F, Foster JM, Slotta DJ, Vizcaíno JA, Hermjakob H. Csordas A, et al. Among authors: wang r. Proteomics. 2013 May;13(10-11):1692-5. doi: 10.1002/pmic.201200514. Epub 2013 Apr 20. Proteomics. 2013. PMID: 23533138 Free PMC article.
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. Perez-Riverol Y, et al. Among authors: wang r. Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6. Mol Cell Proteomics. 2016. PMID: 26545397 Free PMC article.
jmzTab: a java interface to the mzTab data standard.
Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA. Xu QW, et al. Among authors: wang r. Proteomics. 2014 Jun;14(11):1328-32. doi: 10.1002/pmic.201300560. Epub 2014 Apr 29. Proteomics. 2014. PMID: 24659499 Free PMC article.
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. Vizcaíno JA, et al. Among authors: wang r. Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. Nat Biotechnol. 2014. PMID: 24727771 Free PMC article. No abstract available.
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