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PyBioNetFit and the Biological Property Specification Language.
Mitra ED, Suderman R, Colvin J, Ionkov A, Hu A, Sauro HM, Posner RG, Hlavacek WS. Mitra ED, et al. Among authors: sauro hm. iScience. 2019 Sep 27;19:1012-1036. doi: 10.1016/j.isci.2019.08.045. Epub 2019 Aug 28. iScience. 2019. PMID: 31522114 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. Among authors: sauro hm. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Antimony: a modular model definition language.
Smith LP, Bergmann FT, Chandran D, Sauro HM. Smith LP, et al. Among authors: sauro hm. Bioinformatics. 2009 Sep 15;25(18):2452-4. doi: 10.1093/bioinformatics/btp401. Epub 2009 Jul 3. Bioinformatics. 2009. PMID: 19578039 Free PMC article.
phraSED-ML: A paraphrased, human-readable adaptation of SED-ML.
Choi K, Smith LP, Medley JK, Sauro HM. Choi K, et al. Among authors: sauro hm. J Bioinform Comput Biol. 2016 Dec;14(6):1650035. doi: 10.1142/S0219720016500359. Epub 2016 Sep 30. J Bioinform Comput Biol. 2016. PMID: 27774871 Free PMC article.
Editorial Reproducibility of Computational Models.
Sauro HM, Choi K, Medley K, Smith L. Sauro HM, et al. IEEE Trans Biomed Eng. 2016 Oct;63(10):1995-1996. doi: 10.1109/TBME.2016.2594702. Epub 2016 Sep 22. IEEE Trans Biomed Eng. 2016. PMID: 32636531 Free PMC article.
Design patterns of biological cells.
Andrews SS, Wiley HS, Sauro HM. Andrews SS, et al. Among authors: sauro hm. Bioessays. 2024 Mar;46(3):e2300188. doi: 10.1002/bies.202300188. Epub 2024 Jan 21. Bioessays. 2024. PMID: 38247191 Review.
SBML2TikZ: supporting the SBML render extension in LaTeX.
Shen SY, Bergmann F, Sauro HM. Shen SY, et al. Among authors: sauro hm. Bioinformatics. 2010 Nov 1;26(21):2794-5. doi: 10.1093/bioinformatics/btq512. Epub 2010 Sep 9. Bioinformatics. 2010. PMID: 20829443 Free PMC article.
Publishing reproducible dynamic kinetic models.
Porubsky V, Smith L, Sauro HM. Porubsky V, et al. Among authors: sauro hm. Brief Bioinform. 2021 May 20;22(3):bbaa152. doi: 10.1093/bib/bbaa152. Brief Bioinform. 2021. PMID: 32793969 Free PMC article.
135 results