Jakob L. Andersen

Orcid: 0000-0002-4165-3732

According to our database1, Jakob L. Andersen authored at least 31 papers between 2011 and 2024.

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Bibliography

2024
Reaction rebalancing: a novel approach to curating reaction databases.
J. Cheminformatics, December, 2024

Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases.
J. Comput. Biol., 2024

Automated Inference of Graph Transformation Rules.
CoRR, 2024

2023
Reconciling Inconsistent Molecular Structures from Biochemical Databases.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

On the Realisability of Chemical Pathways.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022
Representing Catalytic Mechanisms with Rule Composition.
J. Chem. Inf. Model., 2022

Characterizing Catalytic Mechanisms with Overlay Graphs.
CoRR, 2022

Efficient Modular Graph Transformation Rule Application.
CoRR, 2022

2021
Rewriting theory for the life sciences: A unifying theory of CTMC semantics.
Theor. Comput. Sci., 2021

Defining Autocatalysis in Chemical Reaction Networks.
CoRR, 2021

Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version).
CoRR, 2021

Graph transformation for enzymatic mechanisms.
Bioinform., 2021

2020
A Generic Framework for Engineering Graph Canonization Algorithms.
ACM J. Exp. Algorithmics, 2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design.
J. Comput. Biol., 2020

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework.
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.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Graph Transformations, Semigroups, and Isotopic Labeling.
Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

2017
Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
Dagstuhl Reports, 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry.
CoRR, 2017

Chemical Graph Transformation with Stereo-Information.
Proceedings of the Graph Transformation - 10th International Conference, 2017

2016
Analysis of Generative Chemistries
PhD thesis, 2016

A Software Package for Chemically Inspired Graph Transformation.
Proceedings of the Graph Transformation - 9th International Conference, 2016

2015
Towards Optimal DNA-Templated Computing.
Int. J. Unconv. Comput., 2015

Support for Eschenmoser's Glyoxylate Scenario.
CoRR, 2015

2014
Generic strategies for chemical space exploration.
Int. J. Comput. Biol. Drug Des., 2014

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction.
Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

Towards an Optimal DNA-Templated Molecular Assembler.
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.
Entropy, 2013

2012
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
CoRR, 2012

2011
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR, 2011


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