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BioSimulators: a central registry of simulation engines and services for recommending specific tools.
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Sheriff RSM, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep J, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk D, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR. Shaikh B, et al. Among authors: choi k. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
Controlling E. coli Gene Expression Noise.
Kim KH, Choi K, Bartley B, Sauro HM. Kim KH, et al. Among authors: choi k. IEEE Trans Biomed Circuits Syst. 2015 Aug;9(4):497-504. doi: 10.1109/TBCAS.2015.2461135. Epub 2015 Sep 10. IEEE Trans Biomed Circuits Syst. 2015. PMID: 26372647
Synthetic Biology Open Language (SBOL) Version 2.2.0.
Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A. Cox RS, et al. Among authors: choi k. J Integr Bioinform. 2018 Apr 2;15(1):20180001. doi: 10.1515/jib-2018-0001. J Integr Bioinform. 2018. PMID: 29605823 Free PMC article.
A portable structural analysis library for reaction networks.
Bedaso Y, Bergmann FT, Choi K, Medley K, Sauro HM. Bedaso Y, et al. Among authors: choi k. Biosystems. 2018 Jul;169-170:20-25. doi: 10.1016/j.biosystems.2018.05.008. Epub 2018 May 30. Biosystems. 2018. PMID: 29857031 Free PMC article.
Editorial Reproducibility of Computational Models.
Sauro HM, Choi K, Medley K, Smith L. Sauro HM, et al. Among authors: choi k. 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.
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