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Results: 20

1.

Capturing cooperative interactions with the PSI-MI format.

Van Roey K, Orchard S, Kerrien S, Dumousseau M, Ricard-Blum S, Hermjakob H, Gibson TJ.

Database (Oxford). 2013 Sep 25;2013:bat066. doi: 10.1093/database/bat066. Print 2013.

PMID:
24067240
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium.

Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H.

Nat Methods. 2012 Apr;9(4):345-50. doi: 10.1038/nmeth.1931. Erratum in: Nat Methods. 2012 Jun;9(6):626. Brinkman, Fiona [corrected to Brinkman, Fiona S L]; Hancock, Robert [corrected to Hancock, Robert E W].

PMID:
22453911
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The IntAct molecular interaction database in 2012.

Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H.

Nucleic Acids Res. 2012 Jan;40(Database issue):D841-6. doi: 10.1093/nar/gkr1088. Epub 2011 Nov 24.

PMID:
22121220
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

PMID:
22027554
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

PSICQUIC and PSISCORE: accessing and scoring molecular interactions.

Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H.

Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637. No abstract available.

PMID:
21716279
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Molecular interactions and data standardisation.

Orchard S, Kerrien S.

Methods Mol Biol. 2010;604:309-18. doi: 10.1007/978-1-60761-444-9_21.

PMID:
20013380
[PubMed - indexed for MEDLINE]
7.

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
8.

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]
9.

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
10.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data.

Chatr-aryamontri A, Kerrien S, Khadake J, Orchard S, Ceol A, Licata L, Castagnoli L, Costa S, Derow C, Huntley R, Aranda B, Leroy C, Thorneycroft D, Apweiler R, Cesareni G, Hermjakob H.

Genome Biol. 2008;9 Suppl 2:S5. doi: 10.1186/gb-2008-9-s2-s5. Epub 2008 Sep 1.

PMID:
18834496
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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
12.

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.

Chiang T, Li N, Orchard S, Kerrien S, Hermjakob H, Gentleman R, Huber W.

Bioinformatics. 2008 Apr 15;24(8):1100-1. Epub 2007 Nov 7.

PMID:
17989096
[PubMed - indexed for MEDLINE]
Free Article
13.

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.

PMID:
17945017
[PubMed - indexed for MEDLINE]
Free PMC 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.

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.

Proteomics. 2007 Sep;7 Suppl 1:28-34.

PMID:
17893861
[PubMed - indexed for MEDLINE]
16.

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]
17.

The implications of alternative splicing in the ENCODE protein complement.

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.

PMID:
17372197
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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
19.

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia.

Camargo LM, Collura V, Rain JC, Mizuguchi K, Hermjakob H, Kerrien S, Bonnert TP, Whiting PJ, Brandon NJ.

Mol Psychiatry. 2007 Jan;12(1):74-86. Epub 2006 Oct 17.

PMID:
17043677
[PubMed - indexed for MEDLINE]
20.

IntAct: an open source molecular interaction database.

Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5.

PMID:
14681455
[PubMed - indexed for MEDLINE]
Free PMC Article

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