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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.
Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A. Rougny A, et al. Among authors: sorokin a. J Integr Bioinform. 2019 Jun 13;16(2):20190022. doi: 10.1515/jib-2019-0022. J Integr Bioinform. 2019. PMID: 31199769 Free PMC article. Review.
A community-driven global reconstruction of human metabolism.
Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. Thiele I, et al. Among authors: sorokin a. Nat Biotechnol. 2013 May;31(5):419-25. doi: 10.1038/nbt.2488. Epub 2013 Mar 3. Nat Biotechnol. 2013. PMID: 23455439 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: sorokin a. Bioinformatics. 2012 Aug 1;28(15):2016-21. doi: 10.1093/bioinformatics/bts270. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581176 Free PMC article.
RKappa: Software for Analyzing Rule-Based Models.
Sorokin A, Sorokina O, Douglas Armstrong J. Sorokin A, et al. Methods Mol Biol. 2019;1945:363-390. doi: 10.1007/978-1-4939-9102-0_17. Methods Mol Biol. 2019. PMID: 30945256
ASAR: visual analysis of metagenomes in R.
Orakov AN, Sakenova NK, Sorokin A, Goryanin II. Orakov AN, et al. Among authors: sorokin a. Bioinformatics. 2018 Apr 15;34(8):1404-1405. doi: 10.1093/bioinformatics/btx775. Bioinformatics. 2018. PMID: 29211828 Free PMC article.
A simulator for spatially extended kappa models.
Sorokina O, Sorokin A, Douglas Armstrong J, Danos V. Sorokina O, et al. Among authors: sorokin a. Bioinformatics. 2013 Dec 1;29(23):3105-6. doi: 10.1093/bioinformatics/btt523. Epub 2013 Sep 9. Bioinformatics. 2013. PMID: 24021382 Free PMC article.
702 results