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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: gennari jh. Nucleic Acids Res. 2022 Jul 5;50(W1):W108-W114. doi: 10.1093/nar/gkac331. Nucleic Acids Res. 2022. PMID: 35524558 Free PMC article.
Standard biological parts knowledgebase.
Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Galdzicki M, et al. Among authors: gennari jh. PLoS One. 2011 Feb 24;6(2):e17005. doi: 10.1371/journal.pone.0017005. PLoS One. 2011. PMID: 21390321 Free PMC article.
A reappraisal of how to build modular, reusable models of biological systems.
Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. Neal ML, et al. Among authors: gennari jh. PLoS Comput Biol. 2014 Oct 2;10(10):e1003849. doi: 10.1371/journal.pcbi.1003849. eCollection 2014 Oct. PLoS Comput Biol. 2014. PMID: 25275523 Free PMC article. No abstract available.
Harmonizing semantic annotations for computational models in biology.
Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D. Neal ML, et al. Among authors: gennari jh. Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Brief Bioinform. 2019. PMID: 30462164 Free PMC article. Review.
Model annotation and discovery with the Physiome Model Repository.
Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, Bono B, Atalag K, Hunter PJ, Nickerson DP. Sarwar DM, et al. Among authors: gennari jh. BMC Bioinformatics. 2019 Sep 6;20(1):457. doi: 10.1186/s12859-019-2987-y. BMC Bioinformatics. 2019. PMID: 31492098 Free PMC article.
OMEX metadata specification (version 1.2).
Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. Gennari JH, et al. J Integr Bioinform. 2021 Oct 20;18(3):20210020. doi: 10.1515/jib-2021-0020. J Integr Bioinform. 2021. PMID: 34668356 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: gennari jh. Bioinformatics. 2023 Nov 1;39(11):btad658. doi: 10.1093/bioinformatics/btad658. Bioinformatics. 2023. PMID: 37882737 Free PMC article.
73 results