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

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.

  • MedØlDatschgerl (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 uses the tradition of ordering authors by name. The exceptions, marked with (\(\tau\)) before the authors, uses the traditions, e.g., from life-science to order names.

  • Graph transformation for enzymatic mechanisms
    Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, and Nikolai Nøjgaard},
    Bioinformatics, 37(Supplement_1), 2021 [ DOI, TR ]
  • Rewriting theory for the life Sciences: A unifying theory of CTMC semantics
    (\(\tau\)) Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
    Theoretical Computer Science, 884, 68-115, 2021 [ DOI, TR ]
  • Defining Autocatalysis in Chemical Reaction Networks
    Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
    Journal of Systems Chemistry, 8, 2020 [ HTTP | TR ]
  • 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 Flamm
    In 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 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 ]
  • 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 ]
  • Information Processing in Chemical Systems
    Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
    In The Energetics of Computing in Life and Machines, SFI Press, 2019 [ ISBN ]
  • Conference version: Graph Transformations, Semigroups, and Isotopic Labeling
    Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
    Bioinformatics Research and Applications - 15th International Symposium, ISBRA, 196-207, 2019 [ DOI ]
    Journal version: Combining Graph Transformations and Semigroups for Isotopic Labeling Design
    Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
    Journal of Computational Biology, 27(2), 269-287, 2020 [ DOI ]
  • 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)
  • 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 Flamm
    Processes, 7(4), 240, 2019 [ DOI ]
  • 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 ]
  • Towards Mechanistic Prediction of Mass Spectra Using Graph Transformation
    Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler
    MATCH, Communications in Mathematical and in Computer Chemistry, 80(3), 705-731, 2018 [ HTTP ]
  • 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 ]
  • 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 ]
  • 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 ]
  • In silico Support for Eschenmoser’s Glyoxylate Scenario
    Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F. Stadler
    Israel Journal of Chemistry, 55(8):919-933, 2015. [ DOI | TR ]
  • 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 ]
  • Conference version: Towards an Optimal DNA-Templated Molecular Assembler
    Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel Merkle
    ALIFE 14: The Fourteenth Conference on the Synthesis and Simulation of Living Systems, 14:557-564, 2014. [ DOI | http ]
    Journal version: Towards Optimal DNA-Templated Computing
    Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, and Daniel Merkle
    International Journal of Unconventional Computing, 11(3-4):185-203, 2015. [ http ]
  • 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 ]
  • Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
    Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, and Peter F. Stadler
    Entropy, 15(10):4066-4083, 2013. [ DOI | http ]
  • 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 ]
  • 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 ]