Research

Overview

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

List of Publications

ORCID: 0000-0002-4165-3732

(BibTeX)

  • 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]
  • 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 ]
  • 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 ]
  • 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 ]

Software

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). For version 1.3 I rewrote the C++ domain and has since maintained it.