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Results: 13

1.

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.

2.

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.

3.

Improvements in the Protein Identifier Cross-Reference service.

Wein SP, Côté RG, Dumousseau M, Reisinger F, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W276-80. doi: 10.1093/nar/gks338. Epub 2012 Apr 27.

4.

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.

5.

Critical amino acid residues in proteins: a BioMart integration of Reactome protein annotations with PRIDE mass spectrometry data and COSMIC somatic mutations.

Ndegwa N, Côté RG, Ovelleiro D, D'Eustachio P, Hermjakob H, Vizcaíno JA, Croft D.

Database (Oxford). 2011 Oct 23;2011:bar047. doi: 10.1093/database/bar047. Print 2011.

6.

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.

7.

jmzML, an open-source Java API for mzML, the PSI standard for MS data.

Côté RG, Reisinger F, Martens L.

Proteomics. 2010 Apr;10(7):1332-5. doi: 10.1002/pmic.200900719.

PMID:
20127693
8.

OLS dialog: an open-source front end to the ontology lookup service.

Barsnes H, Côté RG, Eidhammer I, Martens L.

BMC Bioinformatics. 2010 Jan 17;11:34. doi: 10.1186/1471-2105-11-34.

9.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

Côté RG, Jones P, Martens L, Apweiler R, Hermjakob H.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W372-6. doi: 10.1093/nar/gkn252. Epub 2008 May 8.

10.

PRIDE: new developments and new datasets.

Jones P, Côté RG, Cho SY, Klie S, Martens L, Quinn AF, Thorneycroft D, Hermjakob H.

Nucleic Acids Res. 2008 Jan;36(Database issue):D878-83. Epub 2007 Nov 22.

11.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

Côté RG, Jones P, Martens L, Kerrien S, Reisinger F, Lin Q, Leinonen R, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2007 Oct 18;8:401.

12.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Côté RG, Jones P, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2006 Feb 28;7:97.

13.

PRIDE: a public repository of protein and peptide identifications for the proteomics community.

Jones P, Côté RG, Martens L, Quinn AF, Taylor CF, Derache W, Hermjakob H, Apweiler R.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D659-63.

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