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Items: 1 to 20 of 198


Gene regulation knowledge commons: community action takes care of DNA binding transcription factors.

Tripathi S, Vercruysse S, Chawla K, Christie KR, Blake JA, Huntley RP, Orchard S, Hermjakob H, Thommesen L, Lægreid A, Kuiper M.

Database (Oxford). 2016 Jun 5;2016. pii: baw088. doi: 10.1093/database/baw088. Print 2016.


The evolution of standards and data management practices in systems biology.

Stanford NJ, Wolstencroft K, Golebiewski M, Kania R, Juty N, Tomlinson C, Owen S, Butcher S, Hermjakob H, Le Novère N, Mueller W, Snoep J, Goble C.

Mol Syst Biol. 2015 Dec 23;11(12):851. doi: 10.15252/msb.20156053. No abstract available.


The Reactome pathway Knowledgebase.

Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351. Epub 2015 Dec 9.


Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences.

Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y.

Bioinformatics. 2016 Mar 15;32(6):821-7. doi: 10.1093/bioinformatics/btv674. Epub 2015 Nov 14.


Testing and Validation of Computational Methods for Mass Spectrometry.

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.

J Proteome Res. 2016 Mar 4;15(3):809-14. doi: 10.1021/acs.jproteome.5b00852. Epub 2015 Nov 17.


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.


2016 update of the PRIDE database and its related tools.

Vizcaíno JA, Csordas A, del-Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perez-Riverol Y, Reisinger F, Ternent T, Xu QW, Wang R, Hermjakob H.

Nucleic Acids Res. 2016 Jan 4;44(D1):D447-56. doi: 10.1093/nar/gkv1145. Epub 2015 Nov 2.


Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

Swat MJ, Moodie S, Wimalaratne SM, Kristensen NR, Lavielle M, Mari A, Magni P, Smith MK, Bizzotto R, Pasotti L, Mezzalana E, Comets E, Sarr C, Terranova N, Blaudez E, Chan P, Chard J, Chatel K, Chenel M, Edwards D, Franklin C, Giorgino T, Glont M, Girard P, Grenon P, Harling K, Hooker AC, Kaye R, Keizer R, Kloft C, Kok JN, Kokash N, Laibe C, Laveille C, Lestini G, Mentré F, Munafo A, Nordgren R, Nyberg HB, Parra-Guillen ZP, Plan E, Ribba B, Smith G, Trocóniz IF, Yvon F, Milligan PA, Harnisch L, Karlsson M, Hermjakob H, Le Novère N.

CPT Pharmacometrics Syst Pharmacol. 2015 Jun;4(6):316-9. doi: 10.1002/psp4.57. Epub 2015 Jun 15.


BioModels: Content, Features, Functionality, and Use.

Juty N, Ali R, Glont M, Keating S, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V.

CPT Pharmacometrics Syst Pharmacol. 2015 Feb;4(2):e3. doi: 10.1002/psp4.3. Epub 2015 Feb 26.


ms-data-core-api: an open-source, metadata-oriented library for computational proteomics.

Perez-Riverol Y, Uszkoreit J, Sanchez A, Ternent T, Del Toro N, Hermjakob H, Vizcaíno JA, Wang R.

Bioinformatics. 2015 Sep 1;31(17):2903-5. doi: 10.1093/bioinformatics/btv250. Epub 2015 Apr 24.


Introducing the PRIDE Archive RESTful web services.

Reisinger F, del-Toro N, Ternent T, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2015 Jul 1;43(W1):W599-604. doi: 10.1093/nar/gkv382. Epub 2015 Apr 22.


Proteomics data visualisation.

Vizcaíno JA, Barsnes H, Hermjakob H.

Proteomics. 2015 Apr;15(8):1339-40. doi: 10.1002/pmic.201570063. No abstract available.


Harnessing the heart of big data.

Scruggs SB, Watson K, Su AI, Hermjakob H, Yates JR 3rd, Lindsey ML, Ping P.

Circ Res. 2015 Mar 27;116(7):1115-9. doi: 10.1161/CIRCRESAHA.115.306013. No abstract available.


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.


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.


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 May;22(3):495-506. doi: 10.1093/jamia/ocv001. Epub 2015 Feb 28. Review.


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.


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 Apr;15(8):1390-404. doi: 10.1002/pmic.201400390. Epub 2015 Mar 21. Review.


SPARQL-enabled identifier conversion with

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

Bioinformatics. 2015 Jun 1;31(11):1875-7. doi: 10.1093/bioinformatics/btv064. Epub 2015 Jan 31.


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.

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