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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: d eustachio p. Front Immunol. 2024 Feb 13;14:1282859. doi: 10.3389/fimmu.2023.1282859. eCollection 2023. Front Immunol. 2024. PMID: 38414974 Free PMC article.
Using the Reactome Database.
Rothfels K, Milacic M, Matthews L, Haw R, Sevilla C, Gillespie M, Stephan R, Gong C, Ragueneau E, May B, Shamovsky V, Wright A, Weiser J, Beavers D, Conley P, Tiwari K, Jassal B, Griss J, Senff-Ribeiro A, Brunson T, Petryszak R, Hermjakob H, D'Eustachio P, Wu G, Stein L. Rothfels K, et al. Curr Protoc. 2023 Apr;3(4):e722. doi: 10.1002/cpz1.722. Curr Protoc. 2023. PMID: 37053306
Illuminating Dark Proteins using Reactome Pathways.
Brunson T, Sanati N, Matthews L, Haw R, Beavers D, Shorser S, Sevilla C, Viteri G, Conley P, Rothfels K, Hermjakob H, Stein L, D'Eustachio P, Wu G. Brunson T, et al. bioRxiv [Preprint]. 2023 Jun 5:2023.06.05.543335. doi: 10.1101/2023.06.05.543335. bioRxiv. 2023. PMID: 37333417 Free PMC article. Preprint.
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie M, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Orlic-Milacic M, et al. Among authors: d eustachio p. bioRxiv [Preprint]. 2023 Oct 21:2023.10.18.562964. doi: 10.1101/2023.10.18.562964. bioRxiv. 2023. PMID: 37904913 Free PMC article. Updated. Preprint.
Perspectives on tracking data reuse across biodata resources.
Ross KE, Bastian FB, Buys M, Cook CE, D'Eustachio P, Harrison M, Hermjakob H, Li D, Lord P, Natale DA, Peters B, Sternberg PW, Su AI, Thakur M, Thomas PD, Bateman A; and the UniProt Consortium. Ross KE, et al. Among authors: d eustachio p. Bioinform Adv. 2024 Apr 25;4(1):vbae057. doi: 10.1093/bioadv/vbae057. eCollection 2024. Bioinform Adv. 2024. PMID: 38721398 Free PMC article.
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes.
Orlic-Milacic M, Rothfels K, Matthews L, Wright A, Jassal B, Shamovsky V, Trinh Q, Gillespie ME, Sevilla C, Tiwari K, Ragueneau E, Gong C, Stephan R, May B, Haw R, Weiser J, Beavers D, Conley P, Hermjakob H, Stein LD, D'Eustachio P, Wu G. Orlic-Milacic M, et al. Among authors: d eustachio p. Database (Oxford). 2024 May 7;2024:baae031. doi: 10.1093/database/baae031. Database (Oxford). 2024. PMID: 38713862 Free article.
ChatGPT usage in the Reactome curation process.
Tiwari K, Matthews L, May B, Shamovsky V, Orlic-Milacic M, Rothfels K, Ragueneau E, Gong C, Stephan R, Li N, Wu G, Stein L, D'Eustachio P, Hermjakob H. Tiwari K, et al. Among authors: d eustachio p. bioRxiv [Preprint]. 2023 Nov 8:2023.11.08.566195. doi: 10.1101/2023.11.08.566195. bioRxiv. 2023. PMID: 37986970 Free PMC article. Preprint.
192 results