Jakob L. Andersen

Publication Activity (10 Years)

Years Active: 2011-2024
Publications (10 Years): 24

Top Topics

Graph Transformation

Computational Systems

Chemical Reactions

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler
Reaction rebalancing: a novel approach to curating reaction databases. J. Cheminformatics 16 (1) (2024)
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Automated Inference of Graph Transformation Rules. CoRR (2024)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. ISBRA (2023)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. CoRR (2023)
Jakob L. Andersen, Rolf Fagerberg, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Efficient Modular Graph Transformation Rule Application. CoRR (2022)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Characterizing Catalytic Mechanisms with Overlay Graphs. CoRR (2022)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Representing Catalytic Mechanisms with Rule Composition. J. Chem. Inf. Model. 62 (22) (2022)
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
Rewriting theory for the life sciences: A unifying theory of CTMC semantics. Theor. Comput. Sci. 884 (2021)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Graph Transformation for Enzymatic Mechanisms. CoRR (2021)
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version). CoRR (2021)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Defining Autocatalysis in Chemical Reaction Networks. CoRR (2021)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Graph transformation for enzymatic mechanisms. Bioinform. 37 (Supplement) (2021)
Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. BSB (2020)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. ACM J. Exp. Algorithmics 25 (2020)
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
Combining Graph Transformations and Semigroups for Isotopic Labeling Design. J. Comput. Biol. 27 (2) (2020)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
Graph Transformations, Semigroups, and Isotopic Labeling. ISBRA (2019)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. ALENEX (2018)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports 7 (11) (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. ICGT (2016)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. CoRR (2016)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards Optimal DNA-Templated Computing. Int. J. Unconv. Comput. 11 (3-4) (2015)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Support for Eschenmoser's Glyoxylate Scenario. CoRR (2015)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des. 7 (2/3) (2014)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards an Optimal DNA-Templated Molecular Assembler. ALIFE (2014)
Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy 15 (10) (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Generic Strategies for Chemical Space Exploration CoRR (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars CoRR (2012)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete CoRR (2011)