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Items: 1 to 50 of 219

1.

Interleukins and their signaling pathways in the Reactome biological pathway database.

Jupe S, Ray K, Duenas Roca C, Varusai T, Shamovsky V, Stein L, D'Eustachio P, Hermjakob H.

J Allergy Clin Immunol. 2018 Jan 25. pii: S0091-6749(18)30114-3. doi: 10.1016/j.jaci.2017.12.992. [Epub ahead of print]

PMID:
29378288
2.

Reactome graph database: Efficient access to complex pathway data.

Fabregat A, Korninger F, Viteri G, Sidiropoulos K, Marin-Garcia P, Ping P, Wu G, Stein L, D'Eustachio P, Hermjakob H.

PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan.

3.

Integrated omics dissection of proteome dynamics during cardiac remodeling.

Lau E, Cao Q, Lam MPY, Wang J, Ng DCM, Bleakley BJ, Lee JM, Liem DA, Wang D, Hermjakob H, Ping P.

Nat Commun. 2018 Jan 9;9(1):120. doi: 10.1038/s41467-017-02467-3.

4.

Reactome diagram viewer: Data structures and strategies to boost performance.

Fabregat A, Sidiropoulos K, Viteri G, Marin-Garcia P, Ping P, Stein L, D'Eustachio P, Hermjakob H.

Bioinformatics. 2017 Nov 23. doi: 10.1093/bioinformatics/btx752. [Epub ahead of print]

PMID:
29186351
5.

The Reactome Pathway Knowledgebase.

Fabregat A, Jupe S, Matthews L, Sidiropoulos K, Gillespie M, Garapati P, Haw R, Jassal B, Korninger F, May B, Milacic M, Roca CD, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Viteri G, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P.

Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132.

6.

BioModels: expanding horizons to include more modelling approaches and formats.

Glont M, Nguyen TVN, Graesslin M, Hälke R, Ali R, Schramm J, Wimalaratne SM, Kothamachu VB, Rodriguez N, Swat MJ, Eils J, Eils R, Laibe C, Malik-Sheriff RS, Chelliah V, Le Novère N, Hermjakob H.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1248-D1253. doi: 10.1093/nar/gkx1023.

7.

Reactome enhanced pathway visualization.

Sidiropoulos K, Viteri G, Sevilla C, Jupe S, Webber M, Orlic-Milacic M, Jassal B, May B, Shamovsky V, Duenas C, Rothfels K, Matthews L, Song H, Stein L, Haw R, D'Eustachio P, Ping P, Hermjakob H, Fabregat A.

Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441.

PMID:
29077811
8.

ComplexViewer: visualization of curated macromolecular complexes.

Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J.

Bioinformatics. 2017 Nov 15;33(22):3673-3675. doi: 10.1093/bioinformatics/btx497.

PMID:
29036573
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.

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data.

McMurry JA, Juty N, Blomberg N, Burdett T, Conlin T, Conte N, Courtot M, Deck J, Dumontier M, Fellows DK, Gonzalez-Beltran A, Gormanns P, Grethe J, Hastings J, Hériché JK, Hermjakob H, Ison JC, Jimenez RC, Jupp S, Kunze J, Laibe C, Le Novère N, Malone J, Martin MJ, McEntyre JR, Morris C, Muilu J, Müller W, Rocca-Serra P, Sansone SA, Sariyar M, Snoep JL, Soiland-Reyes S, Stanford NJ, Swainston N, Washington N, Williams AR, Wimalaratne SM, Winfree LM, Wolstencroft K, Goble C, Mungall CJ, Haendel MA, Parkinson H.

PLoS Biol. 2017 Jun 29;15(6):e2001414. doi: 10.1371/journal.pbio.2001414. eCollection 2017 Jun.

11.

Discovering and linking public omics data sets using the Omics Discovery Index.

Perez-Riverol Y, Bai M, da Veiga Leprevost F, Squizzato S, Park YM, Haug K, Carroll AJ, Spalding D, Paschall J, Wang M, Del-Toro N, Ternent T, Zhang P, Buso N, Bandeira N, Deutsch EW, Campbell DS, Beavis RC, Salek RM, Sarkans U, Petryszak R, Keays M, Fahy E, Sud M, Subramaniam S, Barbera A, Jiménez RC, Nesvizhskii AI, Sansone SA, Steinbeck C, Lopez R, Vizcaíno JA, Ping P, Hermjakob H.

Nat Biotechnol. 2017 May 9;35(5):406-409. doi: 10.1038/nbt.3790. No abstract available.

PMID:
28486464
12.

Reactome pathway analysis: a high-performance in-memory approach.

Fabregat A, Sidiropoulos K, Viteri G, Forner O, Marin-Garcia P, Arnau V, D'Eustachio P, Stein L, Hermjakob H.

BMC Bioinformatics. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2.

13.

The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions.

Lloret-Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V.

CPT Pharmacometrics Syst Pharmacol. 2017 Feb;6(2):73-86. doi: 10.1002/psp4.12155. Epub 2017 Jan 7. Review.

14.

Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome.

Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P.

Handb Exp Pharmacol. 2017;240:377-401. doi: 10.1007/164_2016_93. Review.

PMID:
27995389
15.

AAgAtlas 1.0: a human autoantigen database.

Wang D, Yang L, Zhang P, LaBaer J, Hermjakob H, Li D, Yu X.

Nucleic Acids Res. 2017 Jan 4;45(D1):D769-D776. doi: 10.1093/nar/gkw946. Epub 2016 Oct 19.

16.

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition.

Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1100-D1106. doi: 10.1093/nar/gkw936. Epub 2016 Oct 18.

17.

Open Targets: a platform for therapeutic target identification and validation.

Koscielny G, An P, Carvalho-Silva D, Cham JA, Fumis L, Gasparyan R, Hasan S, Karamanis N, Maguire M, Papa E, Pierleoni A, Pignatelli M, Platt T, Rowland F, Wankar P, Bento AP, Burdett T, Fabregat A, Forbes S, Gaulton A, Gonzalez CY, Hermjakob H, Hersey A, Jupe S, Kafkas Ş, Keays M, Leroy C, Lopez FJ, Magarinos MP, Malone J, McEntyre J, Munoz-Pomer Fuentes A, O'Donovan C, Papatheodorou I, Parkinson H, Palka B, Paschall J, Petryszak R, Pratanwanich N, Sarntivijal S, Saunders G, Sidiropoulos K, Smith T, Sondka Z, Stegle O, Tang YA, Turner E, Vaughan B, Vrousgou O, Watkins X, Martin MJ, Sanseau P, Vamathevan J, Birney E, Barrett J, Dunham I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29.

18.

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS.

J Proteome Res. 2016 Nov 4;15(11):3961-3970. Epub 2016 Aug 24.

19.

In-depth analysis of protein inference algorithms using multiple search engines and well-defined metrics.

Audain E, Uszkoreit J, Sachsenberg T, Pfeuffer J, Liang X, Hermjakob H, Sanchez A, Eisenacher M, Reinert K, Tabb DL, Kohlbacher O, Perez-Riverol Y.

J Proteomics. 2017 Jan 6;150:170-182. doi: 10.1016/j.jprot.2016.08.002. Epub 2016 Aug 4.

PMID:
27498275
20.

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 Dec 15;44(22):11033. Epub 2016 Sep 28. No abstract available.

21.

Recognizing millions of consistently unidentified spectra across hundreds of shotgun proteomics datasets.

Griss J, Perez-Riverol Y, Lewis S, Tabb DL, Dianes JA, Del-Toro N, Rurik M, Walzer MW, Kohlbacher O, Hermjakob H, Wang R, Vizcaíno JA.

Nat Methods. 2016 Aug;13(8):651-656. Epub 2016 Jun 27.

22.

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.

23.

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.

24.

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.

25.

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.

PMID:
26568629
26.

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.

27.

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.

28.

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. Erratum in: Nucleic Acids Res. 2016 Dec 15;44(22):11033.

29.

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.

30.

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.

31.

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.

32.

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.

33.

Proteomics data visualisation.

Vizcaíno JA, Barsnes H, Hermjakob H.

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

PMID:
25854789
34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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

41.

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.

42.

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

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

Proteomics. 2015 Apr;15(8):1356-74. doi: 10.1002/pmic.201400377. Epub 2015 Feb 5. Review.

43.

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.

44.

Identifying novel biomarkers through data mining-a realistic scenario?

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

Proteomics Clin Appl. 2015 Apr;9(3-4):437-43. doi: 10.1002/prca.201400107. Epub 2015 Jan 12. Review.

45.

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.

46.

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
47.

BioModels linked dataset.

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

BMC Syst Biol. 2014 Aug 15;8:91. doi: 10.1186/s12918-014-0091-5.

48.

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):930-49. doi: 10.1002/pmic.201400302. Review.

49.

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.

50.

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.

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