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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. Tello-Ruiz MK, et al. Among authors: fabregat a. Nucleic Acids Res. 2018 Jan 4;46(D1):D1181-D1189. doi: 10.1093/nar/gkx1111. Nucleic Acids Res. 2018. PMID: 29165610 Free PMC article.
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. Naithani S, et al. Among authors: fabregat a. Nucleic Acids Res. 2017 Jan 4;45(D1):D1029-D1039. doi: 10.1093/nar/gkw932. Epub 2016 Oct 30. Nucleic Acids Res. 2017. PMID: 27799469 Free PMC article.
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. Gupta P, et al. Among authors: fabregat a. Curr Plant Biol. 2016 Nov;7-8:10-15. doi: 10.1016/j.cpb.2016.12.005. Curr Plant Biol. 2016. PMID: 28713666 Free PMC article.
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. Tello-Ruiz MK, et al. Among authors: fabregat a. Nucleic Acids Res. 2016 Jan 4;44(D1):D1133-40. doi: 10.1093/nar/gkv1179. Epub 2015 Nov 8. Nucleic Acids Res. 2016. PMID: 26553803 Free PMC article.
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. Fabregat A, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D481-7. doi: 10.1093/nar/gkv1351. Epub 2015 Dec 9. Nucleic Acids Res. 2016. PMID: 26656494 Free PMC article.
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. Fabregat A, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D649-D655. doi: 10.1093/nar/gkx1132. Nucleic Acids Res. 2018. PMID: 29145629 Free PMC article.
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. Fabregat A, et al. Bioinformatics. 2018 Apr 1;34(7):1208-1214. doi: 10.1093/bioinformatics/btx752. Bioinformatics. 2018. PMID: 29186351 Free PMC article.
MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. ...As graph-based visualization of complex data is a frequent challenge in bioinformatics, many of the individual strategies presented here are …
MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. ...As graph …
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. Fabregat A, et al. PLoS Comput Biol. 2018 Jan 29;14(1):e1005968. doi: 10.1371/journal.pcbi.1005968. eCollection 2018 Jan. PLoS Comput Biol. 2018. PMID: 29377902 Free PMC article.
The reactome pathway knowledgebase.
Jassal B, Matthews L, Viteri G, Gong C, Lorente P, Fabregat A, Sidiropoulos K, Cook J, Gillespie M, Haw R, Loney F, May B, Milacic M, Rothfels K, Sevilla C, Shamovsky V, Shorser S, Varusai T, Weiser J, Wu G, Stein L, Hermjakob H, D'Eustachio P. Jassal B, et al. Among authors: fabregat a. Nucleic Acids Res. 2020 Jan 8;48(D1):D498-D503. doi: 10.1093/nar/gkz1031. Nucleic Acids Res. 2020. PMID: 31691815 Free PMC article.
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. Koscielny G, et al. Among authors: fabregat a. Nucleic Acids Res. 2017 Jan 4;45(D1):D985-D994. doi: 10.1093/nar/gkw1055. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899665 Free PMC article.
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