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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: calzone l. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
Qualitative dynamics semantics for SBGN process description.
Rougny A, Froidevaux C, Calzone L, Paulevé L. Rougny A, et al. Among authors: calzone l. BMC Syst Biol. 2016 Jun 16;10(1):42. doi: 10.1186/s12918-016-0285-0. BMC Syst Biol. 2016. PMID: 27306057 Free PMC article.
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology.
Niarakis A, Waltemath D, Glazier J, Schreiber F, Keating SM, Nickerson D, Chaouiya C, Siegel A, Noël V, Hermjakob H, Helikar T, Soliman S, Calzone L. Niarakis A, et al. Among authors: calzone l. Brief Bioinform. 2022 Jul 18;23(4):bbac212. doi: 10.1093/bib/bbac212. Brief Bioinform. 2022. PMID: 35671510 Free PMC article.
The Systems Biology Graphical Notation.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. Le Novère N, et al. Among authors: calzone l. Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Nat Biotechnol. 2009. PMID: 19668183 Free article.
MaBoSS 2.0: an environment for stochastic Boolean modeling.
Stoll G, Caron B, Viara E, Dugourd A, Zinovyev A, Naldi A, Kroemer G, Barillot E, Calzone L. Stoll G, et al. Among authors: calzone l. Bioinformatics. 2017 Jul 15;33(14):2226-2228. doi: 10.1093/bioinformatics/btx123. Bioinformatics. 2017. PMID: 28881959
Dynamical Boolean Modeling of Immunogenic Cell Death.
Checcoli A, Pol JG, Naldi A, Noel V, Barillot E, Kroemer G, Thieffry D, Calzone L, Stoll G. Checcoli A, et al. Among authors: calzone l. Front Physiol. 2020 Nov 12;11:590479. doi: 10.3389/fphys.2020.590479. eCollection 2020. Front Physiol. 2020. PMID: 33281620 Free PMC article.
UPMaBoSS: A Novel Framework for Dynamic Cell Population Modeling.
Stoll G, Naldi A, Noël V, Viara E, Barillot E, Kroemer G, Thieffry D, Calzone L. Stoll G, et al. Among authors: calzone l. Front Mol Biosci. 2022 Mar 2;9:800152. doi: 10.3389/fmolb.2022.800152. eCollection 2022. Front Mol Biosci. 2022. PMID: 35309516 Free PMC article. Review.
67 results