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Year Number of Results
2016 2
2017 2
2018 2
2020 4
2021 5
2022 2
2024 0

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14 results

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Organizing genome engineering for the gigabase scale.
Bartley BA, Beal J, Karr JR, Strychalski EA. Bartley BA, et al. Nat Commun. 2020 Feb 4;11(1):689. doi: 10.1038/s41467-020-14314-z. Nat Commun. 2020. PMID: 32019919 Free PMC article. Review.
Emerging whole-cell modeling principles and methods.
Goldberg AP, Szigeti B, Chew YH, Sekar JA, Roth YD, Karr JR. Goldberg AP, et al. Curr Opin Biotechnol. 2018 Jun;51:97-102. doi: 10.1016/j.copbio.2017.12.013. Epub 2017 Dec 21. Curr Opin Biotechnol. 2018. PMID: 29275251 Free PMC article. Review.
Building Structural Models of a Whole Mycoplasma Cell.
Maritan M, Autin L, Karr J, Covert MW, Olson AJ, Goodsell DS. Maritan M, et al. J Mol Biol. 2022 Jan 30;434(2):167351. doi: 10.1016/j.jmb.2021.167351. Epub 2021 Nov 10. J Mol Biol. 2022. PMID: 34774566 Free PMC article.
A blueprint for human whole-cell modeling.
Szigeti B, Roth YD, Sekar JAP, Goldberg AP, Pochiraju SC, Karr JR. Szigeti B, et al. Curr Opin Syst Biol. 2018 Feb;7:8-15. doi: 10.1016/j.coisb.2017.10.005. Epub 2017 Nov 9. Curr Opin Syst Biol. 2018. PMID: 29806041 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. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 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. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Toward Community Standards and Software for Whole-Cell Modeling.
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PE, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DF, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knupfer C, Konig M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song JH, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F. Waltemath D, et al. IEEE Trans Biomed Eng. 2016 Oct;63(10):2007-14. doi: 10.1109/TBME.2016.2560762. Epub 2016 Jun 10. IEEE Trans Biomed Eng. 2016. PMID: 27305665 Free PMC article.
14 results