14. References

[AFMS-MØD]
A Software Package for Chemically Inspired Graph Transformation
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
Graph Transformation - 9th International Conference, ICGT 2016, 73-88, 2016 [ DOI | TR ]

14.1. Rule Application and Reaction Network (Derivation Graph) Generation

[AFMS-Strat]
Generic Strategies for Chemical Space Exploration
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
International Journal of Computational Biology and Drug Design, 7(2/3):225-258, 2014. [ DOI | TR ]
[AFMS-Stereo]
Chemical Graph Transformation with Stereo-Information
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Graph Transformation - 10th International Conference, ICGT 2017, 54-69, 2017 [ DOI ]
[AM-Canon]
Conference version: A Generic Framework for Engineering Graph Canonization Algorithms
Jakob L. Andersen, Daniel Merkle
2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX), 2018 [ DOI | TR ]
Extended journal version: A Generic Framework for Engineering Graph Canonization Algorithms
Jakob L. Andersen, Daniel Merkle
Journal of Experimental Algorithms, 25(1), 2020 [ DOI ]

14.2. Rule Composition

[AFMS-RC]
Rule Composition in Graph Transformation Models of Chemical Reactions
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
MATCH, Communications in Mathematical and in Computer Chemistry, 80(3), 661-704, 2018 [ HTTP ]
[AFMS-RC-AtomMap]
50 Shades of Rule Composition — From Chemical Reactions to Higher Levels of Abstraction
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
Formal Methods in Macro-Biology, 8738:117-135, 2014. [ DOI ]
[AFMS-RC-Matrix]
Inferring chemical reaction patterns using rule composition in graph grammars.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
Journal of Systems Chemistry, 4(1):4, 2013. [ DOI | http ]

14.3. Hyperflows

[AFMS-NPFlow]
Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
Journal of Systems Chemistry, 3(1):1, 2012. [ DOI | http ]
[AFMS-Hyperflows]
Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16(2), 510-523, 2019 [ DOI | TR ] (date of preprint publication: December 2017)
[AFMS-Autocata]
Defining Autocatalysis in Chemical Reaction Networks
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Journal of Systems Chemistry, 8, 2020 [ HTTP | TR ]

14.4. Other

[AFMS-Levels]
An Intermediate Level of Abstraction for Computational Systems Chemistry
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences, 375(2109), 2017 [ DOI | TR ]
[AHMNP-EpiM]
A Graph-Based Tool to Embed the $\pi$-Calculus into a Computational DPO Framework
Jakob L. Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Marco Peressotti
In Proceedings of the SOFSEM 2020 Doctoral Student Research Forum, CEUR Workshop Proceedings, 121-132, 2020 [ HTTP | PDF ]