Publications

[Journal article] Representing Catalytic Mechanisms with Rule Composition
Jakob Lykke Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, J.K., Christophe V.F.P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022, Journal of Chemical Information and Modeling 62, 5513–5524
DOI: https://doi.org/10.1021/acs.jcim.2c00426

[Technical report] Efficient Modular Graph Transformation Rule Application
Jakob Lykke Andersen, Rolf Fagerberg, J.K., Christophe V.F.P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022, arXiv
DOI: https://doi.org/10.48550/arXiv.2201.04360

[Conference article] Graph transformation for enzymatic mechanisms
Jakob Lykke Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, J.K., Christophe V.F.P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2021, Bioinformatics 37 (Supplement_1), i392–i400 (ISMB/ECCB 2021 Proceedings)
DOI: https://doi.org/10.1093/bioinformatics/btab296

[Journal article] Reconciling qualitative, abstract, and scalable modeling of biological networks
Loïc Paulevé, J.K., Thomas Chatain, Stefan Haar
2020, Nature communications 11 (1), 4256
DOI: https://doi.org/10.1038/s41467-020-18112-5

[Conference article] Relational differential dynamic logic
J.K., Jérémy Dubut, Ichiro Hasuo, Shin-ya Katsumata, David Sprunger, Akihisa Yamada
2020, International Conference on Tools and Algorithms for the Construction and Analysis of Systems, 191–208
DOI: https://doi.org/10.1007/978-3-030-45190-5_11

[Journal article] Concurrency in Boolean networks
Thomas Chatain, Stefan Haar, J.K., Loïc Paulevé, Aalok Thakkar
2020, Natural Computing 19, 91–109
DOI: https://doi.org/10.1007/s11047-019-09748-4

[Journal article] Parameter space abstraction and unfolding semantics of discrete regulatory networks
J.K., David Šafránek, Stefan Haar, Loïc Paulevé
2019, Theoretical Computer Science 765, 120–144
DOI: https://doi.org/10.1016/j.tcs.2018.03.009

[Poster abstract] Relational differential dynamic logic
J.K., Ichiro Hasuo, Jérémy Dubut, Shin-ya Katsumata, David Sprunger, Akihisa Yamada
2019, Proceedings of the 22nd ACM International Conference on Hybrid Systems: Computation and Control, 284–285
DOI: https://doi.org/10.1145/3302504.3313362

[Conference article] Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics
Stefan Haar, J.K., Loïc Paulevé
2019, Verification, Model Checking, and Abstract Interpretation, 555–576
DOI: https://doi.org/10.1007/978-3-030-11245-5_26

[Workshop article] Unfolding of Parametric Boolean Networks
J.K., David Šafránek, Stefan Haar, Loïc Paulevé
2018, Electronic Notes in Computer Science 335, 67–90 (Proceedings of SASB 2016)
DOI: https://doi.org/10.1016/j.entcs.2018.03.009

[Conference article] Parameter identification and model ranking of thomas networks
Hannes Klarner, Adam Streck, David Šafránek, J.K., Heike Siebert
2012, International Conference on Computational Methods in Systems Biology, 207–226
DOI: https://doi.org/10.1007/978-3-642-33636-2_13