Algorithmic Cheminformatics

My main research area is Algorithmic Cheminformatics, see for more details. See for an online version of our cheminformatics software MØD, which heavily relies on the double pushout approach for graph rewriting.

Double Pushout Approach

Selected References

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 ]

Finding the K best synthesis plans Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle and Peter F. Stadler, J Cheminform (2018) 10:19, [ DOI |PDF ]

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]

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, 2017 [ DOI | TR ]

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 ]