Jakob L. Andersen

According to our database, Jakob L. Andersen authored at least 31 papers between 2011 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Reaction rebalancing: a novel approach to curating reaction databases.

Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler

J. Cheminformatics, December, 2024

Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases.

Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

J. Comput. Biol., 2024

Automated Inference of Graph Transformation Rules.

Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

CoRR, 2024

2023

Reconciling Inconsistent Molecular Structures from Biochemical Databases.

Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

On the Realisability of Chemical Pathways.

Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022

Representing Catalytic Mechanisms with Rule Composition.

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

J. Chem. Inf. Model., 2022

Characterizing Catalytic Mechanisms with Overlay Graphs.

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

CoRR, 2022

Efficient Modular Graph Transformation Rule Application.

Jakob L. Andersen, Rolf Fagerberg, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

CoRR, 2022

2021

Rewriting theory for the life sciences: A unifying theory of CTMC semantics.

Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle

Theor. Comput. Sci., 2021

Defining Autocatalysis in Chemical Reaction Networks.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

CoRR, 2021

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version).

Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle

CoRR, 2021

Graph transformation for enzymatic mechanisms.

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

Bioinform., 2021

2020

A Generic Framework for Engineering Graph Canonization Algorithms.

Jakob L. Andersen, Daniel Merkle

ACM J. Exp. Algorithmics, 2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design.

Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen

J. Comput. Biol., 2020

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.

Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm

Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework.

Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Marco Peressotti

Proceedings of the SOFSEM 2020 Doctoral Student Research Forum co-located with the 46th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2020), 2020

2019

Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Graph Transformations, Semigroups, and Isotopic Labeling.

Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

2017

Algorithmic Cheminformatics (Dagstuhl Seminar 17452).

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Dagstuhl Reports, 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

CoRR, 2017

Chemical Graph Transformation with Stereo-Information.

Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Proceedings of the Graph Transformation - 10th International Conference, 2017

2016

Analysis of Generative Chemistries

Jakob Lykke Andersen

PhD thesis, 2016

A Software Package for Chemically Inspired Graph Transformation.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Proceedings of the Graph Transformation - 9th International Conference, 2016

2015

Towards Optimal DNA-Templated Computing.

Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle

Int. J. Unconv. Comput., 2015

Support for Eschenmoser's Glyoxylate Scenario.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

CoRR, 2015

2014

Generic strategies for chemical space exploration.

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Int. J. Comput. Biol. Drug Des., 2014

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction.

Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

Towards an Optimal DNA-Templated Molecular Assembler.

Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle

Proceedings of the Fourteenth International Conference on the Simulation and Synthesis of Living Systems, 2014

2013

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, Peter F. Stadler

Entropy, 2013

2012

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

CoRR, 2012

2011

Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

CoRR, 2011