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English Information

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Authors
# Name
1 Luis H. Costa Neto(lneto@inf.puc-rio.br)
2 Sérgio Lifschitz(sergio@inf.puc-rio.br)
3 Marcos Catanho(mcatanho@fiocruz.br)
4 Antônio B. de Miranda(amiranda@fiocruz.br)
5 Edward Haeusler(hermann@inf.puc-rio.br)

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Reference
# Reference
1 Consortium, T. U. (2024). Uniprot: the universal protein knowledgebase in 2025. Nucleic Acids Research, 53(D1):D609–D617
2 Dworzanski, L. W. and Lomazova, I. A. (2016). Structural place invariants for analyzing the behavioral properties of nested petri nets. In Kordon, F. and Moldt, D., editors, Application and Theory of Petri Nets and Concurrency, pages 325–344, Cham. Springer International Publishing
3 Haeusler, E. H., Cuconato, B., Glatzl, L. A., Guateque, M. L., Vieira, D. M., de Armas, E. M., Baião, F., Catanho, M., de Miranda, A. B., and Lifschitz, S. (2023). Intentional semantics for molecular biology. In Proceedings of the 16th Brazilian Symposium on Bioinformatics (BSB 2023), page 94–105. Springer-Verlag
4 Irina, A. L. and Vera, E. (2016). Verification of nested petri nets using an unfolding approach. In Lawrence Cabac, Lars Michael Kristensen, H. R., editor, Petri Nets and Software Engineering, pages 93–112. CEUR-WS
5 Jia, X., He, X., Huang, C., Li, J., Dong, Z., and Liu, K. (2024). Protein translation: biological processes and therapeutic strategies for human diseases. Signal Transduct. Target. Ther., 9(1):44
6 Murata, T. (1989). Petri nets: Properties, analysis and applications. Proceedings of the IEEE, 77(4):541–580
7 Neto, L. C., Lifschitz, S., Catanho, M., Miranda, A., and Haeusler, E. (2024a). Towards a simpler semantics for systems biology. In Proceedings of the Brazilian Symposium on Bioinformatics (BSB), pages 95–106. SBC
8 Neto, L. H. C. (2025). mrna petrinet. https://github.com/lhcnetop/mrna petrinet/commit/cbab7a06c9cdd7e4b3d033cfe11b80db42f09e3d. GitHub repository, accessed July 20, 2025, commit cbab7a06c9cdd7e4b3d033cfe11b80db42f09e3d.
9 Neto, L. H. C., Lifschitz, S., Bai˜ ao, F., Catanho, M., de Miranda, A. B., and Haeusler, E. H. (2024b). On the expressiveness of petri nets for modeling biological processes: The case for mRNA translation and protein synthesis. In Procs Advances in Conceptual Modeling ER CMLS Workshop, LNCS 14932, pages 137–147.
10 Noller, H. F. (2024). The ribosome comes to life. Cell, 187(23):6486–6500.
11 Petri, C. A. (1962). Kommunikation mit automaten (communication with automata). Schriften des Rheinisch-Westf¨ alischen Instituts f¨ ur Instrumentelle Mathematik, Bonn, Germany.
12 Object Petri Nets, pages 819–848. Springer, Berlin, Heidelberg.
13 Venero, M. L. F. and da Silva, F. S. C. (2014). A general translation from nested petri nets into promela.