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Items: 1 to 20 of 164

1.

Integrative annotation and knowledge discovery of kinase post-translational modifications and cancer-associated mutations through federated protein ontologies and resources.

Huang LC, Ross KE, Baffi TR, Drabkin H, Kochut KJ, Ruan Z, D'Eustachio P, McSkimming D, Arighi C, Chen C, Natale DA, Smith C, Gaudet P, Newton AC, Wu C, Kannan N.

Sci Rep. 2018 Apr 25;8(1):6518. doi: 10.1038/s41598-018-24457-1.

2.

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

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

J Allergy Clin Immunol. 2018 Apr;141(4):1411-1416. doi: 10.1016/j.jaci.2017.12.992. Epub 2018 Feb 21.

3.

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.

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. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752.

5.

Gramene 2018: unifying comparative genomics and pathway resources for plant research.

Tello-Ruiz MK, Naithani S, Stein JC, Gupta P, Campbell M, Olson A, Wei S, Preece J, Geniza MJ, Jiao Y, Lee YK, Wang B, Mulvaney J, Chougule K, Elser J, Al-Bader N, Kumari S, Thomason J, Kumar V, Bolser DM, Naamati G, Tapanari E, Fonseca N, Huerta L, Iqbal H, Keays M, Munoz-Pomer Fuentes A, Tang A, Fabregat A, D'Eustachio P, Weiser J, Stein LD, Petryszak R, Papatheodorou I, Kersey PJ, Lockhart P, Taylor C, Jaiswal P, Ware D.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. doi: 10.1093/nar/gkx1111.

6.

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.

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.

8.

Gramene Database: Navigating Plant Comparative Genomics Resources.

Gupta P, Naithani S, Tello-Ruiz MK, Chougule K, D'Eustachio P, Fabregat A, Jiao Y, Keays M, Lee YK, Kumari S, Mulvaney J, Olson A, Preece J, Stein J, Wei S, Weiser J, Huerta L, Petryszak R, Kersey P, Stein LD, Ware D, Jaiswal P.

Curr Plant Biol. 2016 Nov;7-8:10-15. doi: 10.1016/j.cpb.2016.12.005.

9.

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.

10.

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH.

Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. Epub 2016 Nov 28.

11.

Plant Reactome: a resource for plant pathways and comparative analysis.

Naithani S, Preece J, D'Eustachio P, Gupta P, Amarasinghe V, Dharmawardhana PD, Wu G, Fabregat A, Elser JL, Weiser J, Keays M, Fuentes AM, Petryszak R, Stein LD, Ware D, Jaiswal P.

Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039. doi: 10.1093/nar/gkw932. Epub 2016 Oct 30.

12.

Modeling biochemical pathways in the gene ontology.

Hill DP, D'Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA.

Database (Oxford). 2016 Sep 1;2016. pii: baw126. doi: 10.1093/database/baw126. Print 2016.

13.

Guidelines for the functional annotation of microRNAs using the Gene Ontology.

Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gillespie ME, Howe D, Kalea AZ, Maegdefessel L, Osumi-Sutherland D, Petri V, Smith JR, Van Auken K, Wood V, Zampetaki A, Mayr M, Lovering RC.

RNA. 2016 May;22(5):667-76. doi: 10.1261/rna.055301.115. Epub 2016 Feb 25.

14.

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.

15.

Gramene 2016: comparative plant genomics and pathway resources.

Tello-Ruiz MK, Stein J, Wei S, Preece J, Olson A, Naithani S, Amarasinghe V, Dharmawardhana P, Jiao Y, Mulvaney J, Kumari S, Chougule K, Elser J, Wang B, Thomason J, Bolser DM, Kerhornou A, Walts B, Fonseca NA, Huerta L, Keays M, Tang YA, Parkinson H, Fabregat A, McKay S, Weiser J, D'Eustachio P, Stein L, Petryszak R, Kersey PJ, Jaiswal P, Ware D.

Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40. doi: 10.1093/nar/gkv1179. Epub 2015 Nov 8.

16.

Correction: Toll-Like Receptor Signaling in Vertebrates: Testing the Integration of Protein, Complex, and Pathway Data in the Protein Ontology Framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Jun 18;10(6):e0131148. doi: 10.1371/journal.pone.0131148. eCollection 2015. No abstract available.

17.

Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Apr 20;10(3):e0122978. doi: 10.1371/journal.pone.0122978. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131148.

18.

Gene Ontology Consortium: going forward.

Gene Ontology Consortium.

Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56. doi: 10.1093/nar/gku1179. Epub 2014 Nov 26.

19.

Protein Ontology: a controlled structured network of protein entities.

Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

20.

The Reactome pathway knowledgebase.

Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D'Eustachio P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. doi: 10.1093/nar/gkt1102. Epub 2013 Nov 15.

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