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The BioPAX Validator.
Rodchenkov I, Demir E, Sander C, Bader GD. Rodchenkov I, et al. Among authors: demir e. Bioinformatics. 2013 Oct 15;29(20):2659-60. doi: 10.1093/bioinformatics/btt452. Epub 2013 Aug 5. Bioinformatics. 2013. PMID: 23918249 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. 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: demir e. 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.
BioPAX support in CellDesigner.
Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD. Mi H, et al. Among authors: demir e. Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21. Bioinformatics. 2011. PMID: 22021903 Free PMC article.
Software support for SBGN maps: SBGN-ML and LibSBGN.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. van Iersel MP, et al. Among authors: demir e. Bioinformatics. 2012 Aug 1;28(15):2016-21. doi: 10.1093/bioinformatics/bts270. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581176 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: demir e. Bioinformatics. 2014 Jan 1;30(1):139-40. doi: 10.1093/bioinformatics/btt539. Epub 2013 Sep 16. Bioinformatics. 2014. PMID: 24045775 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. 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.
Integrating biological pathways and genomic profiles with ChiBE 2.
Babur Ö, Dogrusoz U, Çakır M, Aksoy BA, Schultz N, Sander C, Demir E. Babur Ö, et al. Among authors: demir e. BMC Genomics. 2014 Aug 3;15(1):642. doi: 10.1186/1471-2164-15-642. BMC Genomics. 2014. PMID: 25086704 Free PMC article.
586 results