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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: rodchenkov i. Elife. 2021 Dec 3;10:e68292. doi: 10.7554/eLife.68292. Elife. 2021. PMID: 34860157 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. Nucleic Acids Res. 2020 Jan 8;48(D1):D489-D497. doi: 10.1093/nar/gkz946. Nucleic Acids Res. 2020. PMID: 31647099 Free PMC article.
The BioPAX community standard for pathway data sharing.
Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Ruebenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Le Novère N, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD. Demir E, et al. Among authors: rodchenkov i. Nat Biotechnol. 2010 Sep;28(9):935-42. doi: 10.1038/nbt.1666. Epub 2010 Sep 9. Nat Biotechnol. 2010. PMID: 20829833 Free PMC article.
Pathway Commons, a web resource for biological pathway data.
Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C. Cerami EG, et al. Among authors: rodchenkov i. Nucleic Acids Res. 2011 Jan;39(Database issue):D685-90. doi: 10.1093/nar/gkq1039. Epub 2010 Nov 10. Nucleic Acids Res. 2011. PMID: 21071392 Free PMC article.
Using biological pathway data with paxtools.
Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. Demir E, et al. Among authors: rodchenkov i. PLoS Comput Biol. 2013;9(9):e1003194. doi: 10.1371/journal.pcbi.1003194. Epub 2013 Sep 19. PLoS Comput Biol. 2013. PMID: 24068901 Free PMC article.
The BioPAX Validator.
Rodchenkov I, Demir E, Sander C, Bader GD. Rodchenkov I, et al. Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5. Bioinformatics. 2013. PMID: 23918249 Free PMC article.
Pattern search in BioPAX models.
Babur Ö, Aksoy BA, Rodchenkov I, Sümer SO, Sander C, Demir E. Babur Ö, et al. Among authors: rodchenkov i. Bioinformatics. 2014 Jan 1;30(1):139-40. doi: 10.1093/bioinformatics/btt539. Epub 2013 Sep 16. Bioinformatics. 2014. PMID: 24045775 Free PMC article.
13 results