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Page 1
Analyzing causal relationships in proteomic profiles using CausalPath.
Luna A, Siper MC, Korkut A, Durupinar F, Dogrusoz U, Aslan JE, Sander C, Demir E, Babur O. Luna A, et al. Among authors: siper mc. STAR Protoc. 2021 Nov 23;2(4):100955. doi: 10.1016/j.xpro.2021.100955. eCollection 2021 Dec 17. STAR Protoc. 2021. PMID: 34877547 Free PMC article.
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.
Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C. Rodchenkov I, et al. Among authors: siper mc. Nucleic Acids Res. 2020 Jan 8;48(D1):D489-D497. doi: 10.1093/nar/gkz946. Nucleic Acids Res. 2020. PMID: 31647099 Free PMC article.
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.
Babur Ö, Luna A, Korkut A, Durupinar F, Siper MC, Dogrusoz U, Vaca Jacome AS, Peckner R, Christianson KE, Jaffe JD, Spellman PT, Aslan JE, Sander C, Demir E. Babur Ö, et al. Among authors: siper mc. Patterns (N Y). 2021 May 12;2(6):100257. doi: 10.1016/j.patter.2021.100257. eCollection 2021 Jun 11. Patterns (N Y). 2021. PMID: 34179843 Free PMC article.
Author-sourced capture of pathway knowledge in computable form using Biofactoid.
Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C. Wong JV, et al. Among authors: siper mc. Elife. 2021 Dec 3;10:e68292. doi: 10.7554/eLife.68292. Elife. 2021. PMID: 34860157 Free PMC article.
DORMAN: Database of Reconstructed MetAbolic Networks.
Ozden F, Siper MC, Acarsoy N, Elmas T, Marty B, Qi X, Cicek AE. Ozden F, et al. Among authors: siper mc. IEEE/ACM Trans Comput Biol Bioinform. 2021 Jul-Aug;18(4):1474-1480. doi: 10.1109/TCBB.2019.2944905. Epub 2021 Aug 6. IEEE/ACM Trans Comput Biol Bioinform. 2021. PMID: 31581093