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Items: 1 to 20 of 109

1.

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

Sivade Dumousseau M, Alonso-López D, Ammari M, Bradley G, Campbell NH, Ceol A, Cesareni G, Combe C, De Las Rivas J, Del-Toro N, Heimbach J, Hermjakob H, Jurisica I, Koch M, Licata L, Lovering RC, Lynn DJ, Meldal BHM, Micklem G, Panni S, Porras P, Ricard-Blum S, Roechert B, Salwinski L, Shrivastava A, Sullivan J, Thierry-Mieg N, Yehudi Y, Van Roey K, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):134. doi: 10.1186/s12859-018-2118-1.

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.

3.

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
4.

JAMI: a Java library for molecular interactions and data interoperability.

Sivade Dumousseau M, Koch M, Shrivastava A, Alonso-López D, De Las Rivas J, Del-Toro N, Combe CW, Meldal BHM, Heimbach J, Rappsilber J, Sullivan J, Yehudi Y, Orchard S.

BMC Bioinformatics. 2018 Apr 11;19(1):133. doi: 10.1186/s12859-018-2119-0.

5.

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.

6.

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
7.

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
8.

Enabling BioSharing - a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H.

Proteomics. 2011 Nov;11(22):4284-90. doi: 10.1002/pmic.201190117.

9.

Proteomics Standards Initiative: Fifteen Years of Progress and Future Work.

Deutsch EW, Orchard S, Binz PA, Bittremieux W, Eisenacher M, Hermjakob H, Kawano S, Lam H, Mayer G, Menschaert G, Perez-Riverol Y, Salek RM, Tabb DL, Tenzer S, Vizcaíno JA, Walzer M, Jones AR.

J Proteome Res. 2017 Dec 1;16(12):4288-4298. doi: 10.1021/acs.jproteome.7b00370. Epub 2017 Sep 15.

10.

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
11.

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.

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.

Molecular interaction databases.

Orchard S.

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

PMID:
22611057
14.

From proteomics data representation to public data flow: a report on the HUPO-PSI workshop September 2011, Geneva, Switzerland.

Orchard S, Albar JP, Deutsch EW, Eisenacher M, Binz PA, Martinez-Bartolomé S, Vizcaíno JA, Hermjakob H.

Proteomics. 2012 Feb;12(3):351-5. doi: 10.1002/pmic.201290016.

PMID:
22290802
15.

Managing the data explosion. A report on the HUPO-PSI Workshop. August 2008, Amsterdam, The Netherlands.

Orchard S, Hoogland C, Bairoch A, Eisenacher M, Kraus HJ, Binz PA.

Proteomics. 2009 Feb;9(3):499-501. doi: 10.1002/pmic.200800838.

PMID:
19132688
16.

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
17.

CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination.

Perfetto L, Acencio ML, Bradley G, Cesareni G, Del Toro N, Fazekas D, Hermjakob H, Korcsmaros T, Kuiper M, Lægreid A, Lo Surdo P, Lovering RC, Orchard S, Porras P, Thomas PD, Touré V, Zobolas J, Licata L.

Bioinformatics. 2019 Oct 1;35(19):3779-3785. doi: 10.1093/bioinformatics/btz132.

PMID:
30793173
18.

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.

19.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

Perez-Riverol Y, Xu QW, Wang R, Uszkoreit J, Griss J, Sanchez A, Reisinger F, Csordas A, Ternent T, Del-Toro N, Dianes JA, Eisenacher M, Hermjakob H, Vizcaíno JA.

Mol Cell Proteomics. 2016 Jan;15(1):305-17. doi: 10.1074/mcp.O115.050229. Epub 2015 Nov 6.

20.

Proteomics and Beyond: a report on the 3rd Annual Spring Workshop of the HUPO-PSI 21-23 April 2006, San Francisco, CA, USA.

Orchard S, Apweiler R, Barkovich R, Field D, Garavelli JS, Horn D, Jones A, Jones P, Julian R, McNally R, Nerothin J, Paton N, Pizarro A, Seymour S, Taylor C, Wiemann S, Hermjakob H.

Proteomics. 2006 Aug;6(16):4439-43.

PMID:
16897683

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