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Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches.
Niarakis A, Ostaszewski M, Mazein A, Kuperstein I, Kutmon M, Gillespie ME, Funahashi A, Acencio ML, Hemedan A, Aichem M, Klein K, Czauderna T, Burtscher F, Yamada TG, Hiki Y, Hiroi NF, Hu F, Pham N, Ehrhart F, Willighagen EL, Valdeolivas A, Dugourd A, Messina F, Esteban-Medina M, Peña-Chilet M, Rian K, Soliman S, Aghamiri SS, Puniya BL, Naldi A, Helikar T, Singh V, Fernández MF, Bermudez V, Tsirvouli E, Montagud A, Noël V, Ponce-de-Leon M, Maier D, Bauch A, Gyori BM, Bachman JA, Luna A, Piñero J, Furlong LI, Balaur I, Rougny A, Jarosz Y, Overall RW, Phair R, Perfetto L, Matthews L, Rex DAB, Orlic-Milacic M, Gomez LCM, De Meulder B, Ravel JM, Jassal B, Satagopam V, Wu G, Golebiewski M, Gawron P, Calzone L, Beckmann JS, Evelo CT, D'Eustachio P, Schreiber F, Saez-Rodriguez J, Dopazo J, Kuiper M, Valencia A, Wolkenhauer O, Kitano H, Barillot E, Auffray C, Balling R, Schneider R; COVID-19 Disease Map Community. Niarakis A, et al. Among authors: gillespie me. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. eCollection 2023. Front Immunol. 2024. PMID: 38414974 Free PMC article.
Reactome: a knowledge base of biologic pathways and processes.
Vastrik I, D'Eustachio P, Schmidt E, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, Matthews L, Wu G, Birney E, Stein L. Vastrik I, et al. Genome Biol. 2007;8(3):R39. doi: 10.1186/gb-2007-8-3-r39. Genome Biol. 2007. PMID: 17367534 Free PMC article.
Reactome knowledgebase of human biological pathways and processes.
Matthews L, Gopinath G, Gillespie M, Caudy M, Croft D, de Bono B, Garapati P, Hemish J, Hermjakob H, Jassal B, Kanapin A, Lewis S, Mahajan S, May B, Schmidt E, Vastrik I, Wu G, Birney E, Stein L, D'Eustachio P. Matthews L, et al. Nucleic Acids Res. 2009 Jan;37(Database issue):D619-22. doi: 10.1093/nar/gkn863. Epub 2008 Nov 3. Nucleic Acids Res. 2009. PMID: 18981052 Free PMC article.
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. Croft D, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D472-7. doi: 10.1093/nar/gkt1102. Epub 2013 Nov 15. Nucleic Acids Res. 2014. PMID: 24243840 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.
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. 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. Database (Oxford). 2019 Jan 1;2019:baz123. doi: 10.1093/database/baz123. Database (Oxford). 2019. PMID: 31802127 Free PMC article.
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.
Ostaszewski M, Mazein A, Gillespie ME, Kuperstein I, Niarakis A, Hermjakob H, Pico AR, Willighagen EL, Evelo CT, Hasenauer J, Schreiber F, Dräger A, Demir E, Wolkenhauer O, Furlong LI, Barillot E, Dopazo J, Orta-Resendiz A, Messina F, Valencia A, Funahashi A, Kitano H, Auffray C, Balling R, Schneider R. Ostaszewski M, et al. Among authors: gillespie me. Sci Data. 2020 May 5;7(1):136. doi: 10.1038/s41597-020-0477-8. Sci Data. 2020. PMID: 32371892 Free PMC article.
Using Reactome to build an autophagy mechanism knowledgebase.
Varusai TM, Jupe S, Sevilla C, Matthews L, Gillespie M, Stein L, Wu G, D'Eustachio P, Metzakopian E, Hermjakob H. Varusai TM, et al. Autophagy. 2021 Jun;17(6):1543-1554. doi: 10.1080/15548627.2020.1761659. Epub 2020 Jun 2. Autophagy. 2021. PMID: 32486891 Free PMC article.
38 results