Jakob L. Andersen

35 papers A 1B 1C 1Journal 29Unranked 3
YearRankTypeTitle / Venue / Authors
2026 J jnl
A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems.
J. Chem. Inf. Model.
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg, Daniel Merkle
2026 J jnl
Computing double-pushout graph transformation rules and atom-to-atom maps from KEGG RCLASS data.
Algorithms Mol. Biol.
Nora Beier, Thomas Gatter, Jakob L. Andersen, Peter F. Stadler
2025 J jnl
Pathway Realizability in Chemical Networks.
J. Comput. Biol.
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2024 J jnl
Automated Inference of Graph Transformation Rules.
CoRR
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2024 J jnl
Reaction rebalancing: a novel approach to curating reaction databases.
J. Cheminformatics
Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler
2023 — conf
On the Realisability of Chemical Pathways.
ISBRA
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2023 J jnl
On the Realisability of Chemical Pathways.
CoRR
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2022 J jnl
Characterizing Catalytic Mechanisms with Overlay Graphs.
CoRR
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022 J jnl
Efficient Modular Graph Transformation Rule Application.
CoRR
Jakob L. Andersen, Rolf Fagerberg, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022 J jnl
Representing Catalytic Mechanisms with Rule Composition.
J. Chem. Inf. Model.
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2021 J jnl
Defining Autocatalysis in Chemical Reaction Networks.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2021 J jnl
Graph Transformation for Enzymatic Mechanisms.
CoRR
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2021 J jnl
Graph transformation for enzymatic mechanisms.
Bioinform.
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2021 J jnl
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version).
CoRR
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
2021 J jnl
Rewriting theory for the life sciences: A unifying theory of CTMC semantics.
Theor. Comput. Sci.
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
2020 J jnl
A Generic Framework for Engineering Graph Canonization Algorithms.
ACM J. Exp. Algorithmics
Jakob L. Andersen, Daniel Merkle
2020 J jnl
Combining Graph Transformations and Semigroups for Isotopic Labeling Design.
J. Comput. Biol.
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
2020 — conf
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
BSB
Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm
2019 J jnl
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2019 — conf
Graph Transformations, Semigroups, and Isotopic Labeling.
ISBRA
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
2018 A conf
A Generic Framework for Engineering Graph Canonization Algorithms.
ALENEX
Jakob L. Andersen, Daniel Merkle
2017 J jnl
A Generic Framework for Engineering Graph Canonization Algorithms.
CoRR
Jakob L. Andersen, Daniel Merkle
2017 J jnl
Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
Dagstuhl Reports
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 J jnl
An Intermediate Level of Abstraction for Computational Systems Chemistry.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 J jnl
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016 B conf
A Software Package for Chemically Inspired Graph Transformation.
ICGT
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016 J jnl
A Software Package for Chemically Inspired Graph Transformation.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2015 J jnl
Support for Eschenmoser's Glyoxylate Scenario.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2015 J jnl
Towards Optimal DNA-Templated Computing.
Int. J. Unconv. Comput.
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
2014 J jnl
Generic strategies for chemical space exploration.
Int. J. Comput. Biol. Drug Des.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014 C conf
Towards an Optimal DNA-Templated Molecular Assembler.
ALIFE
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
2013 J jnl
Generic Strategies for Chemical Space Exploration
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2013 J jnl
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
Entropy
Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler
2012 J jnl
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2011 J jnl
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler