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Items: 1 to 20 of 93

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.

2.

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.

4.

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.

Krallinger M, Leitner F, Vazquez M, Salgado D, Marcelle C, Tyers M, Valencia A, Chatr-aryamontri A.

Database (Oxford). 2012 Mar 21;2012:bas017. doi: 10.1093/database/bas017. Print 2012.

5.

Common interchange standards for proteomics data: Public availability of tools and schema.

Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R.

Proteomics. 2004 Feb;4(2):490-1.

PMID:
14760721
6.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
7.

Meeting new challenges: The 2014 HUPO-PSI/COSMOS Workshop: 13-15 April 2014, Frankfurt, Germany.

Orchard S, Albar JP, Binz PA, Kettner C, Jones AR, Salek RM, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2014 Nov;14(21-22):2363-8. doi: 10.1002/pmic.201470164. Epub 2014 Oct 9.

PMID:
25297050
8.

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
9.

Ontological visualization of protein-protein interactions.

Drabkin HJ, Hollenbeck C, Hill DP, Blake JA.

BMC Bioinformatics. 2005 Feb 11;6:29.

10.

The Biomolecular Interaction Network Database in PSI-MI 2.5.

Isserlin R, El-Badrawi RA, Bader GD.

Database (Oxford). 2011 Jan 12;2011:baq037. doi: 10.1093/database/baq037. Print 2011.

11.

Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK.

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H.

Proteomics. 2013 Oct;13(20):2931-7. doi: 10.1002/pmic.201370166.

PMID:
24108681
12.

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
13.

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.

14.

Further steps in standardisation. Report of the second annual Proteomics Standards Initiative Spring Workshop (Siena, Italy 17-20th April 2005).

Orchard S, Hermjakob H, Taylor CF, Potthast F, Jones P, Zhu W, Julian RK Jr, Apweiler R.

Proteomics. 2005 Sep;5(14):3552-5.

PMID:
16167370
15.

PIMWalker: visualising protein interaction networks using the HUPO PSI molecular interaction format.

Meil A, Durand P, Wojcik J.

Appl Bioinformatics. 2005;4(2):137-9.

PMID:
16128615
16.

Molecular interaction databases.

Orchard S.

Proteomics. 2012 May;12(10):1656-62. doi: 10.1002/pmic.201100484. Review.

PMID:
22611057
17.

AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis.

Li P, Zang W, Li Y, Xu F, Wang J, Shi T.

Nucleic Acids Res. 2011 Jan;39(Database issue):D1130-3. doi: 10.1093/nar/gkq959. Epub 2010 Oct 29.

18.

ConsensusPathDB--a database for integrating human functional interaction networks.

Kamburov A, Wierling C, Lehrach H, Herwig R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D623-8. doi: 10.1093/nar/gkn698. Epub 2008 Oct 21.

19.

Navigating the global protein-protein interaction landscape using iRefWeb.

Turinsky AL, Razick S, Turner B, Donaldson IM, Wodak SJ.

Methods Mol Biol. 2014;1091:315-31. doi: 10.1007/978-1-62703-691-7_22.

PMID:
24203342
20.

Visualization of protein interaction networks: problems and solutions.

Agapito G, Guzzi PH, Cannataro M.

BMC Bioinformatics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2105-14-S1-S1. Epub 2013 Jan 14.

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