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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: zhang m, zhang z. J Integr Bioinform. 2018 Apr 2;15(1):20180001. doi: 10.1515/jib-2018-0001. J Integr Bioinform. 2018. PMID: 29605823 Free PMC article.
Efficient analysis methods in synthetic biology.
Madsen C, Myers C, Roehner N, Winstead C, Zhang Z. Madsen C, et al. Among authors: zhang z. Methods Mol Biol. 2015;1244:217-57. doi: 10.1007/978-1-4939-1878-2_11. Methods Mol Biol. 2015. PMID: 25487100
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: zhang z. 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: zhang m, zhang z. 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. Among authors: zhang m, zhang z. 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 2.3.
Madsen C, Goñi Moreno A, P U, Palchick Z, Roehner N, Atallah C, Bartley B, Choi K, Cox RS, Gorochowski T, Grünberg R, Macklin C, McLaughlin J, Meng X, Nguyen T, Pocock M, Samineni M, Scott-Brown J, Tarter Y, Zhang M, Zhang Z, Zundel Z, Beal J, Bissell M, Clancy K, Gennari JH, Misirli G, Myers C, Oberortner E, Sauro H, Wipat A. Madsen C, et al. Among authors: zhang m, zhang z. J Integr Bioinform. 2019 Jun 13;16(2):20190025. doi: 10.1515/jib-2019-0025. J Integr Bioinform. 2019. PMID: 31199770 Free PMC article.
iBioSim 3: A Tool for Model-Based Genetic Circuit Design.
Watanabe L, Nguyen T, Zhang M, Zundel Z, Zhang Z, Madsen C, Roehner N, Myers C. Watanabe L, et al. Among authors: zhang m, zhang z. ACS Synth Biol. 2019 Jul 19;8(7):1560-1563. doi: 10.1021/acssynbio.8b00078. Epub 2018 Jul 11. ACS Synth Biol. 2019. PMID: 29944839
Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA.
Buecherl L, Roberts R, Fontanarrosa P, Thomas PJ, Mante J, Zhang Z, Myers CJ. Buecherl L, et al. Among authors: zhang z. ACS Synth Biol. 2021 Oct 15;10(10):2532-2540. doi: 10.1021/acssynbio.1c00159. Epub 2021 Oct 4. ACS Synth Biol. 2021. PMID: 34606710
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