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Predicting gene level sensitivity to JAK-STAT signaling perturbation using a mechanistic-to-machine learning framework.
Cheemalavagu N, Shoger KE, Cao YM, Michalides BA, Botta SA, Faeder JR, Gottschalk RA. Cheemalavagu N, et al. Among authors: faeder jr. bioRxiv [Preprint]. 2023 May 20:2023.05.19.541151. doi: 10.1101/2023.05.19.541151. bioRxiv. 2023. Update in: Cell Syst. 2024 Jan 17;15(1):37-48.e4. doi: 10.1016/j.cels.2023.12.006 PMID: 37292918 Free PMC article. Updated. Preprint.
A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Faeder JR, Andricioaei I, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, Chong LT. Bogetti AT, et al. Among authors: faeder jr. Living J Comput Mol Sci. 2023;5(1):1655. doi: 10.33011/livecoms.5.1.1655. Living J Comput Mol Sci. 2023. PMID: 37200895 Free PMC article.
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.
Model Integration in Computational Biology: The Role of Reproducibility, Credibility and Utility.
Karr J, Malik-Sheriff RS, Osborne J, Gonzalez-Parra G, Forgoston E, Bowness R, Liu Y, Thompson R, Garira W, Barhak J, Rice J, Torres M, Dobrovolny HM, Tang T, Waites W, Glazier JA, Faeder JR, Kulesza A. Karr J, et al. Among authors: faeder jr. Front Syst Biol. 2022;2:822606. doi: 10.3389/fsysb.2022.822606. Epub 2022 Mar 7. Front Syst Biol. 2022. PMID: 36909847 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: 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.
Iterative community-driven development of a SARS-CoV-2 tissue simulator.
Getz M, Wang Y, An G, Asthana M, Becker A, Cockrell C, Collier N, Craig M, Davis CL, Faeder JR, Ford Versypt AN, Mapder T, Gianlupi JF, Glazier JA, Hamis S, Heiland R, Hillen T, Hou D, Islam MA, Jenner AL, Kurtoglu F, Larkin CI, Liu B, Macfarlane F, Maygrundter P, Morel PA, Narayanan A, Ozik J, Pienaar E, Rangamani P, Saglam AS, Shoemaker JE, Smith AM, Weaver JJA, Macklin P. Getz M, et al. Among authors: faeder jr. bioRxiv [Preprint]. 2021 Nov 10:2020.04.02.019075. doi: 10.1101/2020.04.02.019075. bioRxiv. 2021. PMID: 32511322 Free PMC article. Preprint.
78 results