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Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2.
Zhang F, Smith LP, Blinov ML, Faeder J, Hlavacek WS, Juan Tapia J, Keating SM, Rodriguez N, Dräger A, Harris LA, Finney A, Hu B, Hucka M, Meier-Schellersheim M. Zhang F, et al. Among authors: harris la. J Integr Bioinform. 2020 Jul 6;17(2-3):20200015. doi: 10.1515/jib-2020-0015. J Integr Bioinform. 2020. PMID: 32628633 Free PMC article.
BioNetGen 2.2: advances in rule-based modeling.
Harris LA, Hogg JS, Tapia JJ, Sekar JA, Gupta S, Korsunsky I, Arora A, Barua D, Sheehan RP, Faeder JR. Harris LA, et al. Bioinformatics. 2016 Nov 1;32(21):3366-3368. doi: 10.1093/bioinformatics/btw469. Epub 2016 Jul 8. Bioinformatics. 2016. PMID: 27402907 Free PMC article.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
GPU-powered model analysis with PySB/cupSODA.
Harris LA, Nobile MS, Pino JC, Lubbock ALR, Besozzi D, Mauri G, Cazzaniga P, Lopez CF. Harris LA, et al. Bioinformatics. 2017 Nov 1;33(21):3492-3494. doi: 10.1093/bioinformatics/btx420. Bioinformatics. 2017. PMID: 28666314 Free PMC article.
An unbiased metric of antiproliferative drug effect in vitro.
Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR. Harris LA, et al. Nat Methods. 2016 Jun;13(6):497-500. doi: 10.1038/nmeth.3852. Epub 2016 May 2. Nat Methods. 2016. PMID: 27135974 Free PMC article.
152 results