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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. Sidiropoulos K, et al. Among authors: fabregat a. Bioinformatics. 2017 Nov 1;33(21):3461-3467. doi: 10.1093/bioinformatics/btx441. Bioinformatics. 2017. PMID: 29077811 Free PMC article.
MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. ...AVAILABILITY AND IMPLEMENTATION: http://reactome.org. CONTACT: fabregat@ebi.ac.uk or hhe@ebi.ac.uk....
MOTIVATION: Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. ...AVAILAB …
Expression data analysis with Reactome.
Jupe S, Fabregat A, Hermjakob H. Jupe S, et al. Among authors: fabregat a. Curr Protoc Bioinformatics. 2015 Mar 9;49:8.20.1-8.20.9. doi: 10.1002/0471250953.bi0820s49. Curr Protoc Bioinformatics. 2015. PMID: 25754994 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.
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. Fabregat A, et al. BMC Bioinformatics. 2017 Mar 2;18(1):142. doi: 10.1186/s12859-017-1559-2. BMC Bioinformatics. 2017. PMID: 28249561 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 2022.
Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P. Gillespie M, et al. Among authors: fabregat a. Nucleic Acids Res. 2022 Jan 7;50(D1):D687-D692. doi: 10.1093/nar/gkab1028. Nucleic Acids Res. 2022. PMID: 34788843 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.
Reactome and ORCID-fine-grained credit attribution for community curation.
Viteri G, Matthews L, Varusai T, Gillespie M, Milacic M, Cook J, Weiser J, Shorser S, Sidiropoulos K, Fabregat A, Haw R, Wu G, Stein L, D'Eustachio P, Hermjakob H. Viteri G, et al. Among authors: fabregat a. Database (Oxford). 2019 Jan 1;2019:baz123. doi: 10.1093/database/baz123. Database (Oxford). 2019. PMID: 31802127 Free PMC article.
73 results