:tocdepth: 2


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 <http://algorithms.sdu.dk>`__ homepage.
- The `Cheminformatics Group <http://cheminf.imada.sdu.dk/>`__ homepage.
- My `official SDU researcher profile page <https://portal.findresearcher.sdu.dk/en/persons/jlandersen>`__.


.. _software:

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 <https://github.com/jakobandersen>`__ page.

* `MØD <http://mod.imada.sdu.dk>`__:
  a package for graph-based cheminformatics.
* `GraphCanon <https://github.com/jakobandersen/graph_canon>`__:
  a C++ library with an algorithm framework for graph canonicalization, graph isomorphism, and computation of automorphism groups of graphs.
* `GraphCanon Visualizer <https://github.com/jakobandersen/graph_canon_vis>`__:
  a visualizer for the GraphCanon library, showing and animaing how a canonicalization run proceeded.
  Try it `here <https://jakobandersen.github.io/graph_canon_vis>`__.
* `PermGroup <https://github.com/jakobandersen/perm_group>`__:
  a C++ library working efficiently with permutation groups. 
* `Sphinx <http://www.sphinx-doc.org/>`__:
  Sphinx is a documentation tool that supports multiple programming languages (domains).
  I am the author and maintainer of the C and C++ domains.
* `Breathe <https://breathe.readthedocs.io>`__:
  A Sphinx extension for rendering Doxygen documentation.
  I have made several large contributions to the project.


.. _publications:

List of Publications
--------------------

| ORCID: `0000-0002-4165-3732 <http://orcid.org/0000-0002-4165-3732>`__
| `BibTeX <../_static/papers.bib>`__

Most of the publications use the tradition of ordering authors by name.
The exceptions, marked with (:math:`\tau`) before the authors, use the traditions, e.g., from life-science to order names.

* | **Reconciling Inconsistent Molecular Structures from Biochemical Databases**
  | (:math:`\tau`) Casper Asbj{\o}rn Eriksen, Jakob L. Andersen, Rolf Fagerberg, Daniel Merkle
  | *International Symposium on Bioinformatics Research and Applications, ISBRA*, 58-71, 2023
    [ `DOI <https://doi.org/10.1007/978-981-99-7074-2_5>`__,
      `TR <https://arxiv.org/abs/2308.12735>`__ ]

* | **On the Realisability of Chemical Pathways**
  | Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
  | *International Symposium on Bioinformatics Research and Applications, ISBRA*, 409-419, 2023
	[ `DOI <https://doi.org/10.1007/978-981-99-7074-2_32>`__,
      `TR <https://arxiv.org/abs/2309.10629>`__ ]

* | **Representing Catalytic Mechanisms with Rule Composition**
  | Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juri Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, and Nikolai Nøjgaard
  | *Journal of Chemical Information and Modeling*, 62(22), 5513-5524, 2022
    [ `DOI <https://doi.org/10.1021/acs.jcim.2c00426>`__,
      `TR <https://arxiv.org/abs/2201.04515>`__ ]

* | **An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions**
  | (:math:`\tau`) Aayush Arya, Jessica Ray, Siddhant Sharma, Romulo Cruz Simbron, Alejandro Lozano, Harrison B. Smith, Jakob L. Andersen, Huan Chen, Markus Meringer, Henderson James Cleaves
  | *Chemical Sciemce*, 13(17), 4838-4853, 2022
    [ `DOI <https://doi.org/10.1039/D2SC00256F>`__ ]

* | **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 <https://doi.org/10.1093/bioinformatics/btab296>`__,
      `TR <https://arxiv.org/abs/2102.03292>`__ ]

* | **Rewriting theory for the life Sciences: A unifying theory of CTMC semantics**
  | (:math:`\tau`) Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
  | *Theoretical Computer Science*, 884, 68-115, 2021
    [ `DOI <https://doi.org/10.1016/j.tcs.2021.07.026>`__,
      `TR <https://arxiv.org/abs/2106.02573>`__ ]

* | **Defining Autocatalysis in Chemical Reaction Networks**
  | Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
  | *Journal of Systems Chemistry*, 8, 2020
    [ `HTTP <http://www.nls-publishers.com/shop/journal/journal+of+systems+chemistry+2020%2c+volume+8>`__ |
      `TR <https://arxiv.org/abs/2107.03086>`__ ]

* | **Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases**
  | (:math:`\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 <http://doi.org/10.1007/978-3-030-65775-8_23>`__ ]

* | 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 <http://doi.org/10.1137/1.9781611975055.13>`__ |
    `TR <http://arxiv.org/abs/1711.08289>`__ ]
  | Extended journal version: **A Generic Framework for Engineering Graph Canonization Algorithms**
  | Jakob L. Andersen, Daniel Merkle
  | *Journal of Experimental Algorithms*, 25(1), 2020
    [ `DOI <http://doi.org/10.1145/3356020>`__ ]

* | **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 <http://ceur-ws.org/Vol-2568/>`__ |
      `PDF <http://ceur-ws.org/Vol-2568/paper11.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 <https://isbnsearch.org/isbn/1947864076>`__ ]

* | 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 <http://doi.org/10.1007/978-3-030-20242-2_17>`__ ]
  | 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 <http://doi.org/10.1089/cmb.2019.0291>`__ ]

* | **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 <http://doi.org/10.1109/TCBB.2017.2781724>`__ |
    `TR <https://arxiv.org/abs/1712.02594>`__ ]
    (date of preprint publication: December 2017)

* | **Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks**
  | (:math:`\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 <https://doi.org/10.3390/pr7040240>`__ ]

* | **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 <http://match.pmf.kg.ac.rs/content80n3.htm>`__ ]

* | **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 <http://match.pmf.kg.ac.rs/content80n3.htm>`__ ]

* | **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 <http://doi.org/10.1098/rsta.2016.0354>`__ |
    `TR <http://arxiv.org/abs/1701.09097>`__ ]

* | **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 <http://doi.org/10.1007/978-3-319-61470-0_4>`__ ]

* | **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 <http://doi.org/10.1007/978-3-319-40530-8_5>`__ |
    `TR <http://arxiv.org/abs/1603.02481>`__ ]

* | **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 <http://doi.org/10.1002/ijch.201400187>`__ |
    `TR <http://arxiv.org/abs/1502.07555>`__ ]

* | **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 <http://doi.org/10.1007/978-3-319-10398-3_9>`__ ]

* | 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://doi.org/10.7551/978-0-262-32621-6-ch090>`__ |
    `http <http://mitpress.mit.edu/sites/default/files/titles/content/alife14/ch090.html>`__ ]
  | 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 <http://www.oldcitypublishing.com/journals/ijuc-home/ijuc-issue-contents/ijuc-volume-11-number-3-4-2015/ijuc-11-3-4-p-185-203>`__ ]

* | **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 <http://doi.org/10.1504/IJCBDD.2014.061649>`__ |
    `TR <http://arxiv.org/abs/1302.4006>`__ ]

* | **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://doi.org/10.3390/e15104066>`__ |
    `http <http://www.mdpi.com/1099-4300/15/10/4066>`__ ]

* | **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://doi.org/10.1186/1759-2208-4-4>`__ |
    `http <http://www.jsystchem.com/content/4/1/4>`__ ]

* | **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://doi.org/10.1186/1759-2208-3-1>`__ |
    `http <http://www.jsystchem.com/content/3/1/1>`__ ]