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Page 1
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: faeder jr. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
Depicting signaling cascades.
Blinov ML, Yang J, Faeder JR, Hlavacek WS. Blinov ML, et al. Among authors: faeder jr. Nat Biotechnol. 2006 Feb;24(2):137-8; author reply 138. doi: 10.1038/nbt0206-137. Nat Biotechnol. 2006. PMID: 16465147 No abstract available.
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: faeder jr. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Combination treatment optimization using a pan-cancer pathway model.
Schmucker R, Farina G, Faeder J, Fröhlich F, Saglam AS, Sandholm T. Schmucker R, et al. PLoS Comput Biol. 2021 Dec 28;17(12):e1009689. doi: 10.1371/journal.pcbi.1009689. eCollection 2021 Dec. PLoS Comput Biol. 2021. PMID: 34962919 Free PMC article.
Modeling the early signaling events mediated by FcepsilonRI.
Goldstein B, Faeder JR, Hlavacek WS, Blinov ML, Redondo A, Wofsy C. Goldstein B, et al. Among authors: faeder jr. Mol Immunol. 2002 Sep;38(16-18):1213-9. doi: 10.1016/s0161-5890(02)00066-4. Mol Immunol. 2002. PMID: 12217386 Review.
The complexity of complexes in signal transduction.
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B. Hlavacek WS, et al. Among authors: faeder jr. Biotechnol Bioeng. 2003 Dec 30;84(7):783-94. doi: 10.1002/bit.10842. Biotechnol Bioeng. 2003. PMID: 14708119 Review.
83 results