Zhen Zhang

Publications | Abstracts

• Zhang, Z., A computational model of the effect of VEGF production in wet age-related macular degeneration on neovascularization. Annual Meeting of the Association for Research in Vision and Ophthalmology (ARVO), 2020

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | Book Chapters

• Neupane, T., Zhang, Z., (2019). Approximation Techniques for Stochastic Analysis of Biological Systems: Automated Reasoning for Systems Biology and Medicine. Automated Reasoning for Systems Biology and Medicine, Springer, 2019
• Zhang, Z., (2015). Efficient Analysis Methods in Synthetic Biology: Computational Methods in Synthetic Biology. Springer New York

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | Journal Articles

Academic Journal

• Buecherl, L., Roberts, R., Fontanarrosa, P., Mante, J., Zhang, Z., Myers, C.J, (2021). Stochastic Hazard Analysis of Genetic Circuits in iBioSim and STAMINA. ACS Synthetic Biology, 10:10, 2532-2540. doi: 10.1021/acssynbio.1c00159
• Cotner, M., Zhan, J., Zhang, Z., (2021). A Computational Metabolic Model for Engineered Production of Resveratrol in Escherichia coli. ACS Synthetic Biology, 10:8, 1992–2001. doi: 10.1021/acssynbio.1c00163
• Watanabe, L., Nguyen, T., Zhang, M., Zundel, Z., Zhang, Z., Madsen, C., Roehner, N., Myers, C., (2019). iBioSim 3: A Tool for Model-Based Genetic Circuit Design. ACS Synthetic Biology, 8:7, 1560-1563. doi: 10.1021/acssynbio.8b00078
• Sidney, C.R, Curtis, M., Alastair, M.J, Tramy, N., Nicholas, R., Bryan, B., Jacob, B., Michael, B., Kiri, C., Kevin, C., Raik, Gr\"unberg, , Chris, M., Goksel, M., Ernst, O., Matthew, P., Meher, S., Michael, Z., Zhang, Z., Zach, Z., H., G.J, Chris, M., Herbert, S., Anil, W., (2018). Synthetic Biology Open Language (SBOL) Version 2.2.0. Journal of Integrative Bioinformatics, De Gruyter, 15:1, doi: 10.1515/jib-2018-0001
• Zundel, Z., Samineni, M., Zhang, Z., Myers, C.J, (2017). A Validator and Converter for the Synthetic Biology Open Language. ACS Synthetic Biology, 6:7, 1161-1168.
• Zhang, Z., Serwe, W., Wu, J., Yoneda, T., Zheng, H., Myers, C., (2016). An improved fault-tolerant routing algorithm for a Network-on-Chip derived with formal analysis. Science of Computer Programming, 118, 24 - 39.
• Roehner, N., Beal, J., Clancy, K., Bartley, B., Misirli, G., Gr\"unberg, Raik, , Oberortner, E., Pocock, M., Bissell, M., Madsen, C., Nguyen, T., Zhang, M., Zhang, Z., Zundel, Z., Densmore, D., Gennari, J.H, Wipat, A., Sauro, H.M, Myers, C.J, (2016). Sharing Structure and Function in Biological Design with SBOL 2.0. ACS Synthetic Biology, 5:6, 498-506.
• Zhang, Z., Nguyen, T., Roehner, N., Misirli, G., Pocock, M., Oberortner, E., Samineni, M., Zundel, Z., Beal, J., Clancy, K., Wipat, A., Myers, C.J, (2015). libSBOLj 2.0: A Java Library to Support SBOL 2.0. IEEE Life Sciences Letters, 1:4, 34-37.
• Bryan, B., Jacob, B., Kevin, C., Goksel, M., Nicholas, R., Ernst, O., Matthew, P., Michael, B., Curtis, M., Tramy, N., Zhang, Z., H., G.J, Chris, M., Anil, W., Herbert, S., (2015). Synthetic Biology Open Language (SBOL) Version 2.0.0. Journal of Integrative Bioinformatics, 12, 902.
• Roehner, N., Zhang, Z., Nguyen, T., Myers, C.J, (2015). Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language. ACS Synthetic Biology, 4:8, 873-879.
• Zheng, H., Zhang, Z., Myers, C.J, Rodriguez, E., Zhang, Y., (2015). Compositional Model Checking of Concurrent Systems. IEEE Transactions on Computers, 64:6, 1607-1621.
• Madsen, C., Zhang, Z., Roehner, N., Winstead, C.J, Myers, C., (2014). Stochastic Model Checking of Genetic Circuits. J. Emerg. Technol. Comput. Syst., 11:3, 23:1--23:21.

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | MultiMedia

Software

• Zhang, Z., (2023). VERAPAK software tool: Refutation-based Deep Neural Network verification tool. *
• Israelsen, B., Taylor, L., Zhang, Z., (2023). RAGTIMER software tool: a rare-event formal verification tool for Chemical Reaction Networks. 29th International Symposium on Model Checking of Software (SPIN 2023) *
• Taylor, L., Zhang, Z., (2023). Cycle and Commute expansion for the RAGTIMER software tool for drastic improvement of formal analysis of Chemical Reaction Networks. 23rd Conference on Formal Methods in Computer-Aided Design – FMCAD 2023
• Jeppson, J., Zhang, Z., (2023). STAMINA C++ 2.0 software tool. 20th International Conference on Quantitative Evaluation of Systems (QEST 2023)

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.

Publications | Other

Other

• Zhang, Z., (2011). A Fault-Tolerant Routing Algorithm for a Network-on-Chip Using a Link Fault Model.

An asterisk (*) at the end of a publication indicates that it has not been peer-reviewed.