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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.

PMID:
23482073
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
23429179
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
22912398
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
20716697
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19850723
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
19834897
[PubMed - indexed for MEDLINE]
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.

PMID:
19674966
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
18936051
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
18629248
[PubMed]
Free PMC Article
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.

PMID:
18629121
[PubMed]
Free PMC Article
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.

PMID:
18508856
[PubMed - indexed for MEDLINE]
Free Article
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.

PMID:
17925023
[PubMed - indexed for MEDLINE]
Free PMC Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
17145710
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The use of common ontologies and controlled vocabularies to enable data exchange and deposition for complex proteomic experiments.

Orchard S, Montecchi-Palazzi L, Hermjakob H, Apweiler R.

Pac Symp Biocomput. 2005:186-96.

PMID:
15759625
[PubMed - indexed for MEDLINE]
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.

PMID:
15165896
[PubMed - indexed for MEDLINE]
Free Article
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
[PubMed - indexed for MEDLINE]
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.

PMID:
14737190
[PubMed - indexed for MEDLINE]
Free PMC Article

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