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The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.
Galdzicki M, Clancy KP, Oberortner E, Pocock M, Quinn JY, Rodriguez CA, Roehner N, Wilson ML, Adam L, Anderson JC, Bartley BA, Beal J, Chandran D, Chen J, Densmore D, Endy D, Grünberg R, Hallinan J, Hillson NJ, Johnson JD, Kuchinsky A, Lux M, Misirli G, Peccoud J, Plahar HA, Sirin E, Stan GB, Villalobos A, Wipat A, Gennari JH, Myers CJ, Sauro HM. Galdzicki M, et al. Among authors: gennari jh. Nat Biotechnol. 2014 Jun;32(6):545-50. doi: 10.1038/nbt.2891. Epub 2014 Jun 6. Nat Biotechnol. 2014. PMID: 24911500
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.
Synthetic Biology Open Language (SBOL) Version 2.0.0.
Bartley B, Beal J, Clancy K, Misirli G, Roehner N, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang Z, Gennari JH, Myers C, Wipat A, Sauro H. Bartley B, et al. Among authors: gennari jh. J Integr Bioinform. 2015 Sep 4;12(2):272. doi: 10.2390/biecoll-jib-2015-272. J Integr Bioinform. 2015. PMID: 26528570
Sharing Structure and Function in Biological Design with SBOL 2.0.
Roehner N, Beal J, Clancy K, Bartley B, Misirli G, Grünberg R, Oberortner E, Pocock M, Bissell M, Madsen C, Nguyen T, Zhang M, Zhang Z, Zundel Z, Densmore D, Gennari JH, Wipat A, Sauro HM, Myers CJ. Roehner N, et al. Among authors: gennari jh. ACS Synth Biol. 2016 Jun 17;5(6):498-506. doi: 10.1021/acssynbio.5b00215. Epub 2016 May 4. ACS Synth Biol. 2016. PMID: 27111421
Synthetic Biology Open Language (SBOL) Version 2.1.0.
Beal J, Cox RS, Grünberg R, McLaughlin J, Nguyen T, Bartley B, Bissell M, Choi K, Clancy K, Macklin C, Madsen C, Misirli G, Oberortner E, Pocock M, Roehner N, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari J, Myers C, Sauro H, Wipat A. Beal J, et al. J Integr Bioinform. 2016 Dec 18;13(3):291. doi: 10.2390/biecoll-jib-2016-291. J Integr Bioinform. 2016. PMID: 28187407
Synthetic Biology Open Language (SBOL) Version 2.2.0.
Cox RS, Madsen C, McLaughlin JA, Nguyen T, Roehner N, Bartley B, Beal J, Bissell M, Choi K, Clancy K, Grünberg R, Macklin C, Misirli G, Oberortner E, Pocock M, Samineni M, Zhang M, Zhang Z, Zundel Z, Gennari JH, Myers C, Sauro H, Wipat A. Cox RS, et al. Among authors: gennari jh. J Integr Bioinform. 2018 Apr 2;15(1):20180001. doi: 10.1515/jib-2018-0001. J Integr Bioinform. 2018. PMID: 29605823 Free PMC article.
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.
73 results