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Results: 1 to 20 of 23

1.

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group.

Database (Oxford). 2013 Mar 12;2013:bat009. doi: 10.1093/database/bat009. Print 2013.

2.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19. Review.

3.

Mutation of plasma membrane Ca2+ ATPase isoform 3 in a family with X-linked congenital cerebellar ataxia impairs Ca2+ homeostasis.

Zanni G, Calì T, Kalscheuer VM, Ottolini D, Barresi S, Lebrun N, Montecchi-Palazzi L, Hu H, Chelly J, Bertini E, Brini M, Carafoli E.

Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14514-9. doi: 10.1073/pnas.1207488109. Epub 2012 Aug 21.

4.

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens.

Panni S, Montecchi-Palazzi L, Kiemer L, Cabibbo A, Paoluzi S, Santonico E, Landgraf C, Volkmer-Engert R, Bachi A, Castagnoli L, Cesareni G.

Proteomics. 2011 Jan;11(1):128-43. doi: 10.1002/pmic.201000030. Epub 2010 Dec 6.

PMID:
21182200
5.

mzML--a community standard for mass spectrometry data.

Martens L, Chambers M, Sturm M, Kessner D, Levander F, Shofstahl J, Tang WH, Römpp A, Neumann S, Pizarro AD, Montecchi-Palazzi L, Tasman N, Coleman M, Reisinger F, Souda P, Hermjakob H, Binz PA, Deutsch EW.

Mol Cell Proteomics. 2011 Jan;10(1):R110.000133. doi: 10.1074/mcp.R110.000133. Epub 2010 Aug 17.

6.

The IntAct molecular interaction database in 2010.

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C, Feuermann M, Ghanbarian AT, Kerrien S, Khadake J, Kerssemakers J, Leroy C, Menden M, Michaut M, Montecchi-Palazzi L, Neuhauser SN, Orchard S, Perreau V, Roechert B, van Eijk K, Hermjakob H.

Nucleic Acids Res. 2010 Jan;38(Database issue):D525-31. doi: 10.1093/nar/gkp878. Epub 2009 Oct 22.

7.

The PSI semantic validator: a framework to check MIAPE compliance of proteomics data.

Montecchi-Palazzi L, Kerrien S, Reisinger F, Aranda B, Jones AR, Martens L, Hermjakob H.

Proteomics. 2009 Nov;9(22):5112-9. doi: 10.1002/pmic.200900189.

8.

A community standard format for the representation of protein affinity reagents.

Gloriam DE, Orchard S, Bertinetti D, Björling E, Bongcam-Rudloff E, Borrebaeck CA, Bourbeillon J, Bradbury AR, de Daruvar A, Dübel S, Frank R, Gibson TJ, Gold L, Haslam N, Herberg FW, Hiltke T, Hoheisel JD, Kerrien S, Koegl M, Konthur Z, Korn B, Landegren U, Montecchi-Palazzi L, Palcy S, Rodriguez H, Schweinsberg S, Sievert V, Stoevesandt O, Taussig MJ, Ueffing M, Uhlén M, van der Maarel S, Wingren C, Woollard P, Sherman DJ, Hermjakob H.

Mol Cell Proteomics. 2010 Jan;9(1):1-10. doi: 10.1074/mcp.M900185-MCP200. Epub 2009 Aug 11.

9.

The Protein Feature Ontology: a tool for the unification of protein feature annotations.

Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM.

Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20.

10.

The PSI-MOD community standard for representation of protein modification data.

Montecchi-Palazzi L, Beavis R, Binz PA, Chalkley RJ, Cottrell J, Creasy D, Shofstahl J, Seymour SL, Garavelli JS.

Nat Biotechnol. 2008 Aug;26(8):864-6. doi: 10.1038/nbt0808-864. No abstract available.

PMID:
18688235
11.

iSPOT: a web tool for the analysis and recognition of protein domain specificity.

Brannetti B, Zanzoni A, Montecchi-Palazzi L, Cesareni G, Helmer-Citterich M.

Comp Funct Genomics. 2001;2(5):314-8. doi: 10.1002/cfg.104.

12.

Progress in Establishing Common Standards for Exchanging Proteomics Data: The Second Meeting of the HUPO Proteomics Standards Initiative.

Orchard S, Kersey P, Zhu W, Montecchi-Palazzi L, Hermjakob H, Apweiler R.

Comp Funct Genomics. 2003;4(2):203-6. doi: 10.1002/cfg.279.

13.

InteroPORC: automated inference of highly conserved protein interaction networks.

Michaut M, Kerrien S, Montecchi-Palazzi L, Chauvat F, Cassier-Chauvat C, Aude JC, Legrain P, Hermjakob H.

Bioinformatics. 2008 Jul 15;24(14):1625-31. doi: 10.1093/bioinformatics/btn249. Epub 2008 May 28.

14.

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions.

Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stümpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H.

BMC Biol. 2007 Oct 9;5:44.

15.

The minimum information required for reporting a molecular interaction experiment (MIMIx).

Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stümpflen V, Ceol A, Chatr-aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, De Las Rivas J, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H.

Nat Biotechnol. 2007 Aug;25(8):894-8. Review.

PMID:
17687370
16.

IntAct--open source resource for molecular interaction data.

Kerrien S, Alam-Faruque Y, Aranda B, Bancarz I, Bridge A, Derow C, Dimmer E, Feuermann M, Friedrichsen A, Huntley R, Kohler C, Khadake J, Leroy C, Liban A, Lieftink C, Montecchi-Palazzi L, Orchard S, Risse J, Robbe K, Roechert B, Thorneycroft D, Zhang Y, Apweiler R, Hermjakob H.

Nucleic Acids Res. 2007 Jan;35(Database issue):D561-5. Epub 2006 Dec 1.

17.
18.

Selectivity and promiscuity in the interaction network mediated by protein recognition modules.

Castagnoli L, Costantini A, Dall'Armi C, Gonfloni S, Montecchi-Palazzi L, Panni S, Paoluzi S, Santonico E, Cesareni G.

FEBS Lett. 2004 Jun 1;567(1):74-9. Review.

19.

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R.

Nat Biotechnol. 2004 Feb;22(2):177-83.

PMID:
14755292
20.

Protein interaction networks by proteome peptide scanning.

Landgraf C, Panni S, Montecchi-Palazzi L, Castagnoli L, Schneider-Mergener J, Volkmer-Engert R, Cesareni G.

PLoS Biol. 2004 Jan;2(1):E14. Epub 2004 Jan 20.

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