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Results: 1 to 20 of 185

1.

Shared resources, shared costs-leveraging biocuration resources.

Orchard S, Hermjakob H.

Database (Oxford). 2015 Mar 16;2015. pii: bav009. doi: 10.1093/database/bav009. Print 2015.

2.

Expression data analysis with reactome.

Jupe S, Fabregat A, Hermjakob H.

Curr Protoc Bioinformatics. 2015 Mar 9;49:8.20.1-9. doi: 10.1002/0471250953.bi0820s49.

PMID:
25754994
3.

Development of data representation standards by the human proteome organization proteomics standards initiative.

Deutsch EW, Albar JP, Binz PA, Eisenacher M, Jones AR, Mayer G, Omenn GS, Orchard S, Vizcaíno JA, Hermjakob H.

J Am Med Inform Assoc. 2015 Feb 28. pii: ocv001. doi: 10.1093/jamia/ocv001. [Epub ahead of print] Review.

4.

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Villaveces JM, Jiménez RC, Porras P, Del-Toro N, Duesbury M, Dumousseau M, Orchard S, Choi H, Ping P, Zong NC, Askenazi M, Habermann BH, Hermjakob H.

Database (Oxford). 2015 Feb 4;2015. pii: bau131. doi: 10.1093/database/bau131. Print 2015.

5.

A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology.

Porras P, Duesbury M, Fabregat A, Ueffing M, Orchard S, Gloeckner CJ, Hermjakob H.

Proteomics. 2015 Feb 3. doi: 10.1002/pmic.201400390. [Epub ahead of print]

PMID:
25648416
6.

SPARQL-enabled identifier conversion with Identifiers.org.

Wimalaratne SM, Bolleman J, Juty N, Katayama T, Dumontier M, Redaschi N, Le Novère N, Hermjakob H, Laibe C.

Bioinformatics. 2015 Jan 31. pii: btv064. [Epub ahead of print]

7.

A public repository for mass spectrometry imaging data.

Römpp A, Wang R, Albar JP, Urbani A, Hermjakob H, Spengler B, Vizcaíno JA.

Anal Bioanal Chem. 2015 Mar;407(8):2027-33. doi: 10.1007/s00216-014-8357-8. No abstract available.

8.

Open source libraries and frameworks for biological data visualisation: A guide for developers.

Wang R, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Dec 5. doi: 10.1002/pmic.201400377. [Epub ahead of print]

PMID:
25475079
9.

BioModels: ten-year anniversary.

Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C.

Nucleic Acids Res. 2015 Jan;43(Database issue):D542-8. doi: 10.1093/nar/gku1181. Epub 2014 Nov 20.

10.

Identifying novel biomarkers through data mining-A realistic scenario?

Griss J, Perez-Riverol Y, Hermjakob H, Vizcaíno JA.

Proteomics Clin Appl. 2014 Oct 28. doi: 10.1002/prca.201400107. [Epub ahead of print]

PMID:
25347964
11.

The complex portal--an encyclopaedia of macromolecular complexes.

Meldal BH, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S.

Nucleic Acids Res. 2015 Jan;43(Database issue):D479-84. doi: 10.1093/nar/gku975. Epub 2014 Oct 13.

12.

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
13.

BioModels linked dataset.

Wimalaratne SM, Grenon P, Hermjakob H, Le Novère N, Laibe C.

BMC Syst Biol. 2014 Aug 15;8(1):91. [Epub ahead of print]

14.

Making proteomics data accessible and reusable: Current state of proteomics databases and repositories.

Perez-Riverol Y, Alpi E, Wang R, Hermjakob H, Vizcaíno JA.

Proteomics. 2015 Mar;15(5-6):930-50. doi: 10.1002/pmic.201400302.

15.

BioJS: an open source standard for biological visualisation - its status in 2014.

Corpas M, Jimenez R, Carbon SJ, García A, Garcia L, Goldberg T, Gomez J, Kalderimis A, Lewis SE, Mulvany I, Pawlik A, Rowland F, Salazar G, Schreiber F, Sillitoe I, Spooner WH, Thanki AS, Villaveces JM, Yachdav G, Hermjakob H.

F1000Res. 2014 Feb 13;3:55. doi: 10.12688/f1000research.3-55.v1. eCollection 2014.

16.

How to submit MS proteomics data to ProteomeXchange via the PRIDE database.

Ternent T, Csordas A, Qi D, Gómez-Baena G, Beynon RJ, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Oct;14(20):2233-41. doi: 10.1002/pmic.201400120. Epub 2014 Aug 21.

17.

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience.

Griss J, Jones AR, Sachsenberg T, Walzer M, Gatto L, Hartler J, Thallinger GG, Salek RM, Steinbeck C, Neuhauser N, Cox J, Neumann S, Fan J, Reisinger F, Xu QW, Del Toro N, Pérez-Riverol Y, Ghali F, Bandeira N, Xenarios I, Kohlbacher O, Vizcaíno JA, Hermjakob H.

Mol Cell Proteomics. 2014 Oct;13(10):2765-75. doi: 10.1074/mcp.O113.036681. Epub 2014 Jun 30.

18.

qcML: an exchange format for quality control metrics from mass spectrometry experiments.

Walzer M, Pernas LE, Nasso S, Bittremieux W, Nahnsen S, Kelchtermans P, Pichler P, van den Toorn HW, Staes A, Vandenbussche J, Mazanek M, Taus T, Scheltema RA, Kelstrup CD, Gatto L, van Breukelen B, Aiche S, Valkenborg D, Laukens K, Lilley KS, Olsen JV, Heck AJ, Mechtler K, Aebersold R, Gevaert K, Vizcaíno JA, Hermjakob H, Kohlbacher O, Martens L.

Mol Cell Proteomics. 2014 Aug;13(8):1905-13. doi: 10.1074/mcp.M113.035907. Epub 2014 Apr 23.

19.

ProteomeXchange provides globally coordinated proteomics data submission and dissemination.

Vizcaíno JA, Deutsch EW, Wang R, Csordas A, Reisinger F, Ríos D, Dianes JA, Sun Z, Farrah T, Bandeira N, Binz PA, Xenarios I, Eisenacher M, Mayer G, Gatto L, Campos A, Chalkley RJ, Kraus HJ, Albar JP, Martinez-Bartolomé S, Apweiler R, Omenn GS, Martens L, Jones AR, Hermjakob H.

Nat Biotechnol. 2014 Mar;32(3):223-6. doi: 10.1038/nbt.2839. No abstract available.

20.

jmzTab: a java interface to the mzTab data standard.

Xu QW, Griss J, Wang R, Jones AR, Hermjakob H, Vizcaíno JA.

Proteomics. 2014 Jun;14(11):1328-32. doi: 10.1002/pmic.201300560. Epub 2014 Apr 29.

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