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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: hellerstein jl. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
libsbmljs-Enabling web-based SBML tools.
Medley JK, Hellerstein J, Sauro HM. Medley JK, et al. Biosystems. 2020 Jul;195:104150. doi: 10.1016/j.biosystems.2020.104150. Epub 2020 Apr 24. Biosystems. 2020. PMID: 32339626 Free PMC article.
A compiler for biological networks on silicon chips.
Medley JK, Teo J, Woo SS, Hellerstein J, Sarpeshkar R, Sauro HM. Medley JK, et al. PLoS Comput Biol. 2020 Sep 23;16(9):e1008063. doi: 10.1371/journal.pcbi.1008063. eCollection 2020 Sep. PLoS Comput Biol. 2020. PMID: 32966274 Free PMC article.
Cesium: A public database of evolved oscillatory reaction networks.
Tatka LT, Luk W, Elston TC, Hellerstein JL, Sauro HM. Tatka LT, et al. Among authors: hellerstein jl. Biosystems. 2023 Feb;224:104836. doi: 10.1016/j.biosystems.2023.104836. Epub 2023 Jan 11. Biosystems. 2023. PMID: 36640942 Free PMC article.
An Automated Model Annotation System (AMAS) for SBML Models.
Shin W, Gennari JH, Hellerstein JL, Sauro HM. Shin W, et al. Among authors: hellerstein jl. bioRxiv [Preprint]. 2023 Jul 21:2023.07.19.549722. doi: 10.1101/2023.07.19.549722. bioRxiv. 2023. PMID: 37503075 Free PMC article. Updated. Preprint.
Sensitivity and Frequency Response of Biochemical Cascades.
Kochen MA, Hellerstein JL, Sauro HM. Kochen MA, et al. Among authors: hellerstein jl. bioRxiv [Preprint]. 2023 Sep 23:2023.09.14.557821. doi: 10.1101/2023.09.14.557821. bioRxiv. 2023. PMID: 37781602 Free PMC article. Preprint.
An automated model annotation system (AMAS) for SBML models.
Shin W, Gennari JH, Hellerstein JL, Sauro HM. Shin W, et al. Among authors: hellerstein jl. Bioinformatics. 2023 Nov 1;39(11):btad658. doi: 10.1093/bioinformatics/btad658. Bioinformatics. 2023. PMID: 37882737 Free PMC article.
16 results