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Tuyéras, R. (2018). Category theory for genetics I: mutations and sequence alignments. ArXiv:1805.07002 [Math]. Retrieved from http://arxiv.org/abs/1805.07002
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Tuyéras, R. (2018). Category theory for genetics II: genotype, phenotype and haplotype. ArXiv:1805.07004 [Math]. Retrieved from http://arxiv.org/abs/1805.07004
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Boutillier, P., Maasha, M., Li, X., Medina-Abarca, H. F., Krivine, J., Feret, J., … Fontana, W. (2018). The Kappa platform for rule-based modeling. Bioinformatics, 34(13), i583–i592. https://doi.org/10/gdrhw6
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Fages, F., Martinez, T., Rosenblueth, D. A., & Soliman, S. (2018). Influence Networks Compared with Reaction Networks: Semantics, Expressivity and Attractors. IEEE/ACM Trans. Comput. Biol. Bioinformatics, 15(4), 1138–1151. https://doi.org/10/ggdf94
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Tuyéras, R. (2018). Category Theory for Genetics. ArXiv:1708.05255 [Math]. Retrieved from http://arxiv.org/abs/1708.05255
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Ehresmann, A. C. (2018). Applications of Categories to Biology and Cognition. https://doi.org/10/ggdf93
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Mascari, J.-F., Giacchero, D., & Sfakianakis, N. (2017). Symetries and asymetries of the immune system response: A categorification approach. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 1451–1454). https://doi.org/10/ggdnd3
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Ehresmann, A. C., & Gomez-Ramirez, J. (2015). Conciliating neuroscience and phenomenology via category theory. Progress in Biophysics and Molecular Biology, 119(3), 347–359. https://doi.org/10/f75jzr
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Baez, J. C., & Otter, N. (2015). Operads and Phylogenetic Trees.
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Fages, F. (2014). Cells as Machines: Towards Deciphering Biochemical Programs in the Cell. In R. Natarajan (Ed.), Distributed Computing and Internet Technology (pp. 50–67). Cham: Springer International Publishing. https://doi.org/10/ggdf96
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Danos, V., Feret, J., Fontana, W., Harmer, R., & Krivine, J. (2008). Rule-Based Modelling, Symmetries, Refinements. In J. Fisher (Ed.), Formal Methods in Systems Biology (pp. 103–122). Berlin, Heidelberg: Springer. https://doi.org/10/dc5k68
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Fages, F., Calzone, L., & Soliman, S. (2006). BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics, 22(14), 1805–1807. https://doi.org/10/dfv
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Wilkinson, D. J. (2006). Stochastic Modelling for Systems Biology. CRC Press.
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Fages, F., Calzone, L., Chabrier-Rivier, N., & Soliman, S. (2006). Machine Learning Biochemical Networks from Temporal Logic Properties. In C. Priami & G. Plotkin (Eds.), Transactions on Computational Systems Biology VI (pp. 68–94). Berlin, Heidelberg: Springer. https://doi.org/10/dd8
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Baas, N. A., & Emmeche, C. (1997). On Emergence and Explanation. Intellectica. Revue de l’Association Pour La Recherche Cognitive, 25(2), 67–83. https://doi.org/10/ggdf9z
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Rosen, R. (1958). The representation of biological systems from the standpoint of the theory of categories. The Bulletin of Mathematical Biophysics, 20(4), 317–341. https://doi.org/10/fdgzxz
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Gromov, M. (n.d.). Structures, Learning and Ergosystems: Chapters, 159.
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Boutillier, P., Feret, J., Krivine, J., & Fontana, W. (n.d.). The Kappa Language and Kappa Tools, 52.
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