Research¶
I work on formal methods for modelling and analysing chemical systems (algorithmic cheminformatics) and combines it with algorithm engineering to obtain implementations that are useful in practice. I am in general interested in algorithmics (in particular graph algorithms) and generic programming.
See also
The Algorithms Group homepage.
The Cheminformatics Group homepage.
Software¶
The development of new methods in algorithmic cheminformatics has resultet in multiple software packages, libraries, and incidental open source contributions. See also my GitHub page.
MØD: a package for graph-based cheminformatics.
GraphCanon: a C++ library with an algorithm framework for graph canonicalization, graph isomorphism, and computation of automorphism groups of graphs.
GraphCanon Visualizer: a visualizer for the GraphCanon library, showing and animaing how a canonicalization run proceeded. Try it here.
PermGroup: a C++ library working efficiently with permutation groups.
Sphinx: Sphinx is a documentation tool that supports multiple programming languages (domains). I am the author and maintainer of the C and C++ domains.
Breathe: A Sphinx extension for rendering Doxygen documentation. I have made several large contributions to the project.
List of Publications¶
Most of the publications use the tradition of ordering authors by name. The exceptions, marked with (\(\tau\)) before the authors, use the traditions, e.g., from life-science to order names.
- An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions(\(\tau\)) Aayush Arya, Jessica Ray, Siddhant Sharma, Romulo Cruz Simbron, Alejandro Lozano, Harrison B. Smith, Jakob L. Andersen, Huan Chen, Markus Meringer, Henderson James CleavesChemical Sciemce, 13(17), 4838-4853, 2022 [ DOI ]
- Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases(\(\tau\)) Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emilia Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph FlammIn Advances in Bioinformatics and Computational Biology - 13th Brazilian Symposium on Bioinformatics, BSB, 247-258, 2020 [ DOI ]
- Conference version: A Generic Framework for Engineering Graph Canonization AlgorithmsJakob L. Andersen, Daniel Merkle2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX), 2018 [ DOI | TR ]Extended journal version: A Generic Framework for Engineering Graph Canonization AlgorithmsJakob L. Andersen, Daniel MerkleJournal of Experimental Algorithms, 25(1), 2020 [ DOI ]
- Information Processing in Chemical SystemsJakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. StadlerIn The Energetics of Computing in Life and Machines, SFI Press, 2019 [ ISBN ]
- Conference version: Graph Transformations, Semigroups, and Isotopic LabelingJakob L. Andersen, Daniel Merkle, Peter S. RasmussenBioinformatics Research and Applications - 15th International Symposium, ISBRA, 196-207, 2019 [ DOI ]Journal version: Combining Graph Transformations and Semigroups for Isotopic Labeling DesignJakob L. Andersen, Daniel Merkle, Peter S. RasmussenJournal of Computational Biology, 27(2), 269-287, 2020 [ DOI ]
- Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks(\(\tau\)) Waldeyr M. C. da Silva, Jakob L. Andersen, Maristela T. Holanda, Maria Emília M. T. Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph FlammProcesses, 7(4), 240, 2019 [ DOI ]
- Rule Composition in Graph Transformation Models of Chemical ReactionsJakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. StadlerMATCH, Communications in Mathematical and in Computer Chemistry, 80(3), 661-704, 2018 [ HTTP ]
- Towards Mechanistic Prediction of Mass Spectra Using Graph TransformationJakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. StadlerMATCH, Communications in Mathematical and in Computer Chemistry, 80(3), 705-731, 2018 [ HTTP ]
- Chemical Graph Transformation with Stereo-InformationJakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. StadlerGraph Transformation - 10th International Conference, ICGT 2017, 54-69, 2017 [ DOI ]
- 50 Shades of Rule Composition — From Chemical Reactions to Higher Levels of AbstractionJakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. StadlerFormal Methods in Macro-Biology, 8738:117-135, 2014. [ DOI ]
- Conference version: Towards an Optimal DNA-Templated Molecular AssemblerJakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel MerkleALIFE 14: The Fourteenth Conference on the Synthesis and Simulation of Living Systems, 14:557-564, 2014. [ DOI | http ]Journal version: Towards Optimal DNA-Templated ComputingJakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel MerkleInternational Journal of Unconventional Computing, 11(3-4):185-203, 2015. [ http ]