Related publications#
Publications related to BoNesis methodology#
BoNesis: a Python-Based Declarative Environment for the Verification, Reprogramming, and Synthesis of Most Permissive Boolean Networks (Chevalier, S., Boyenval, D., Magaña-López, G., Roncalli, T., Vaginay, A., Paulevé, L.). In: Computational Methods in Systems Biology. CMSB 2024. Lecture Notes in Computer Science, vol 14971, 2024. Springer, Cham. doi:10.1007/978-3-031-71671-3_6
Synthesis/Inference#
Synthesis of Boolean Networks from Biological Dynamical Constraints using Answer-Set Programming (S Chevalier, C Froidevaux, L Paulevé, A Zinovyev). In 2019 IEEE 31st International Conference on Tools with Artificial Intelligence (ICTAI), 34–41. Portland, Oregon, United States, 2019. IEEE. doi:10.1109/ICTAI.2019.00014
Synthesis and Simulation of Ensembles of Boolean Networks for Cell Fate Decision (S Chevalier, V Noël, L Calzone, A Zinovyev, L Paulevé) In 18th International Conference on Computational Methods in Systems Biology (CMSB). Online, Germany, 2020. Preprint at https://hal.archives-ouvertes.fr/hal-02898849/file/cmsb2020.pdf
Control/Reprogramming#
Tackling universal properties of minimal trap spaces of Boolean networks (S Riva, J-M Lagniez, G Magaña López, L Paulevé), CMSB, 2023 doi:10.1007/978-3-031-42697-1_11 arXiv:2305.02442
Marker and source-marker reprogramming of Most Permissive Boolean networks and ensembles with BoNesis (L Paulevé), Peer Community Journal, 2023 doi:10.24072/pcjournal.255
Publications using BoNesis#
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Chevalier, S., Becker, J., Gui, Y. et al. (2025). Data-driven inference of Boolean networks from transcriptomes to predict cellular differentiation and reprogramming. npj Systems Biology and Applications 11, 105. doi:10.1038/s41540-025-00569-z
Paulevé, L., & Gaucherel, C. (2025). Inference of ecological networks and possibilistic dynamics based on Boolean networks from observations and prior knowledge. Methods in Ecology and Evolution, 16, 1851–1867. doi:10.1111/2041-210X.70090
Hérault, L., Poplineau, M., Duprez, E., & Remy, É. (2023). A novel boolean network inference strategy to model early hematopoiesis aging. Computational and Structural Biotechnology Journal, 21 , 21–3. doi:10.1016/j.csbj.2022.10.040
Réda, C., & Delahaye-Duriez, A. (2022). Prioritization of candidate genes through boolean networks. In Computational methods in systems biology (pp. 89–121). Springer International Publishing. doi:10.1007/978-3-031-15034-0_5