Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2011)

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2012)

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)

Towards an Optimal DNA-Templated Molecular Assembler. - Jakob L. Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle (ALIFE, 2014)

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (FMMB, 2014)

Generic strategies for chemical space exploration. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Int. J. Comput. Biol. Drug Des., 2014)

Support for Eschenmoser's Glyoxylate Scenario. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2015)

Towards Optimal DNA-Templated Computing. - Jakob L. Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle (Int. J. Unconv. Comput., 2015)

A Software Package for Chemically Inspired Graph Transformation. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2016)

Analysis of Generative Chemistries - Jakob Lykke Andersen (2016)

Chemical Graph Transformation with Stereo-Information. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2017)

An Intermediate Level of Abstraction for Computational Systems Chemistry. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2017)

Algorithmic Cheminformatics (Dagstuhl Seminar 17452). - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 2017)

Graph Transformations, Semigroups, and Isotopic Labeling. - Jakob L. Andersen; Daniel Merkle; Peter S. Rasmussen (ISBRA, 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)

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 (SOFSEM (Doctoral Student Research Forum), 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 (BSB, 2020)

Combining Graph Transformations and Semigroups for Isotopic Labeling Design. - Jakob L. Andersen; Daniel Merkle; Peter S. Rasmussen (J. Comput. Biol., 2020)

A Generic Framework for Engineering Graph Canonization Algorithms. - Jakob L. Andersen; Daniel Merkle (ACM J. Exp. Algorithmics, 2020)

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)

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)

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. - Nicolas Behr; Jean Krivine; Jakob L. Andersen; Daniel Merkle (Theor. Comput. Sci., 2021)

Efficient Modular Graph Transformation Rule Application. - Jakob L. Andersen; Rolf Fagerberg; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 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)

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)

On the Realisability of Chemical Pathways. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ISBRA, 2023)

Reconciling Inconsistent Molecular Structures from Biochemical Databases. - Casper Asbjørn Eriksen; Jakob Lykke Andersen; Rolf Fagerberg; Daniel Merkle (ISBRA, 2023)

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)

Finding Thermodynamically Favorable Pathways in Reaction Networks using Flows in Hypergraphs and Mixed Integer Linear Programming. - Adittya Pal; Rolf Fagerberg; Jakob Lykke Andersen; Christoph Flamm; Peter Dittrich; Daniel Merkle (CoRR, 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)

Reaction rebalancing: a novel approach to curating reaction databases. - Tieu-Long Phan; Klaus Weinbauer; Thomas Gärtner 001; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Peter F. Stadler (J. Cheminformatics, 2024)

Pathway Realizability in Chemical Networks. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (J. Comput. Biol., 2025)

Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming. - Adittya Pal; Rolf Fagerberg; Jakob Lykke Andersen; Christoph Flamm; Peter Dittrich; Daniel Merkle (J. Chem. Inf. Model., 2025)

SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. - Tieu-Long Phan; Klaus Weinbauer; Marcos E. González Laffitte; Yingjie Pan; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Peter F. Stadler (J. Chem. Inf. Model., 2025)

Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming. - Adittya Pal; Rolf Fagerberg; Jakob Lykke Andersen; Peter Dittrich; Daniel Merkle (CoRR, 2025)

ChemReservoir - An Open-Source Framework for Chemically-Inspired Reservoir Computing. - Mehmet Aziz Yirik; Jakob Lykke Andersen; Rolf Fagerberg; Daniel Merkle (CoRR, 2025)