An Ant Algorithm with a New Pheromone Evaluation Rule for Total Tardiness Problems. - Daniel Merkle; Martin Middendorf (EvoWorkshops, 2000)

Ant Colony Optimization for Resource-Constrained Projet Scheduling. - Daniel Merkle; Martin Middendorf; Hartmut Schmeck (GECCO, 2000)

Bi-Criterion Optimization with Multi Colony Ant Algorithms. - Steffen Iredi; Daniel Merkle; Martin Middendorf (EMO, 2001)

A New Approach to Solve Permutation Scheduling Problems with Ant Colony Optimization. - Daniel Merkle; Martin Middendorf (EvoWorkshops, 2001)

Fast ant colony optimization on reconfigurable processor arrays. - Daniel Merkle; Martin Middendorf (IPDPS, 2001)

Coevolutionary Ant Algorithms Playing Games. - Jürgen Branke; Michael Decker; Daniel Merkle; Hartmut Schmeck (Ant Algorithms, 2002)

Modelling ACO: Composed Permutation Problems. - Daniel Merkle; Martin Middendorf (Ant Algorithms, 2002)

Ant Colony Optimization with the Relative Pheromone Evaluation Method. - Daniel Merkle; Martin Middendorf (EvoWorkshops, 2002)

Studies On The Dynamics Of Ant Colony Optimization Algorithms. - Daniel Merkle; Martin Middendorf (GECCO, 2002)

Modeling the Dynamics of Ant Colony Optimization. - Daniel Merkle; Martin Middendorf (Evol. Comput., 2002)

Formal language recognition by stochastic cellular automata. - Daniel Merkle; Thomas Worsch (Fundam. Informaticae, 2002)

Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays. - Daniel Merkle; Martin Middendorf (Genet. Program. Evolvable Mach., 2002)

Ant colony optimization for resource-constrained project scheduling. - Daniel Merkle; Martin Middendorf; Hartmut Schmeck (IEEE Trans. Evol. Comput., 2002)

Ameisenalgorithmen: Optimierung und Modellierung. - Daniel Merkle (2002)

Ant Colony Optimization with Global Pheromone Evaluation for Scheduling a Single Machine. - Daniel Merkle; Martin Middendorf (Appl. Intell., 2003)

On Enforced Convergence of ACO and its Implementation on the Reconfigurable Mesh Architecture Using Size Reduction Tasks. - Stefan Janson; Daniel Merkle; Martin Middendorf; Hossam A. ElGindy; Hartmut Schmeck (J. Supercomput., 2003)

Competition Controlled Pheromone Update for Ant Colony Optimization. - Daniel Merkle; Martin Middendorf (ANTS Workshop, 2004)

Decentralized Packet Clustering in Networks. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (IPDPS, 2004)

Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects. - Daniel Merkle; Martin Middendorf (Adapt. Behav., 2004)

Dynamic Decentralized Packet Clustering in Networks. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (EvoWorkshops, 2005)

A New Multi-objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking. - Stefan Janson; Daniel Merkle (Hybrid Metaheuristics, 2005)

Modelling Ant Brood Tending Behavior with Cellular Automata. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (International Conference on Computational Science (2), 2005)

A Parallel Algorithm for Solving the Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (PPAM, 2005)

Decentralized packet clustering in router-based networks. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (Int. J. Found. Comput. Sci., 2005)

On solving permutation scheduling problems with ant colony optimization. - Daniel Merkle; Martin Middendorf (Int. J. Syst. Sci., 2005)

Swarm Intelligence - An Optimization-Based Introduction. - Daniel Merkle; Christian Blum 001 (Künstliche Intell., 2005)

Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. - Daniel Merkle; Martin Middendorf (Theory Biosci., 2005)

The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. - Matthias Bernt; Daniel Merkle; Martin Middendorf (CompLife, 2006)

Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (IWSOS/EuroNGI, 2006)

Self-organized task allocation for computing systems with reconfigurable components. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (IPDPS, 2006)

Marco Dorigo and Thomas Stützle, Ant Colony Optimization, MIT Press (2004) ISBN 0-262-04219-3. - Daniel Merkle; Martin Middendorf (Eur. J. Oper. Res., 2006)

Modeling Ant Brood ending Patterns with Cellular Automata. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (J. Cell. Autom., 2006)

Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. - Matthias Bernt; Daniel Merkle; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

A Fast and Exact Algorithm for the Perfect Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (ISBRA, 2007)

Swarm Controlled Emergence - Designing an Anti-Clustering Ant System. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (SIS, 2007)

Using median sets for inferring phylogenetic trees. - Matthias Bernt; Daniel Merkle; Martin Middendorf (Bioinform., 2007)

CREx: inferring genomic rearrangements based on common intervals. - Matthias Bernt; Daniel Merkle; Kai Ramsch; Guido Fritzsch; Marleen Perseke; Detlef Bernhard; Martin Schlegel; Peter F. Stadler; Martin Middendorf (Bioinform., 2007)

Self-adaptive Worker-Helper Systems with Self-Organized Task Allocation. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (Organic Computing, 2008)

Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems. - Arne Brutschy; Alexander Scheidler; Daniel Merkle; Martin Middendorf (ANTS Conference, 2008)

Emergent Sorting in Networks of Router Agents. - Alexander Scheidler; Christian Blum 001; Daniel Merkle; Martin Middendorf (ANTS Conference, 2008)

Congestion Control in Ant Like Moving Agent Systems. - Alexander Scheidler; Daniel Merkle; Martin Middendorf (BICC, 2008)

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. - Matthias Bernt; Daniel Merkle; Martin Middendorf (RECOMB-CG, 2008)

Molecular docking with multi-objective Particle Swarm Optimization. - Stefan Janson; Daniel Merkle; Martin Middendorf (Appl. Soft Comput., 2008)

A decentralization approach for swarm intelligence algorithms in networks applied to multi swarm PSO. - Stefan Janson; Daniel Merkle; Martin Middendorf (Int. J. Intell. Comput. Cybern., 2008)

Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (J. Math. Model. Algorithms, 2008)

Swarm intelligence and signal processing [DSP Exploratory]. - Daniel Merkle; Martin Middendorf (IEEE Signal Process. Mag., 2008)

Solving the Preserving Reversal Median Problem. - Matthias Bernt; Daniel Merkle; Martin Middendorf (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Stability and performance of ant queue inspired task partitioning methods. - Alexander Scheidler; Daniel Merkle; Martin Middendorf (Theory Biosci., 2008)

Organic Computing and Swarm Intelligence. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (Swarm Intelligence, 2008)

Finding All Sorting Tandem Duplication Random Loss Operations. - Matthias Bernt; Ming-Chiang Chen; Daniel Merkle; Hung-Lung Wang; Kun-Mao Chao; Martin Middendorf (CPM, 2009)

On the Design of RNA Sequences for Realizing Extended Shapes. - Marc Hellmuth; Daniel Merkle; Martin Middendorf (IJCBS, 2009)

Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects. - Konrad Diwold; Daniel Merkle; Martin Middendorf (Adv. Complex Syst., 2009)

Editorial: Artificial Life. - Konstantin Klemm; Daniel Merkle; Eckehard Olbrich (Adv. Complex Syst., 2009)

Extended shapes for the combinatorial design of RNA sequences. - Marc Hellmuth; Daniel Merkle; Martin Middendorf (Int. J. Comput. Biol. Drug Des., 2009)

Special issue on ant colony optimization. - Karl F. Doerner; Daniel Merkle; Thomas Stützle (Swarm Intell., 2009)

Barrier Trees for Continuous Fitness Landscapes. - Jacob Midtgaard-Olesen; Carsten Baldauf; Daniel Merkle (ALIFE, 2010)

A parameter-adaptive dynamic programming approach for inferring cophylogenies. - Daniel Merkle; Martin Middendorf; Nicolas Wieseke (BMC Bioinform., 2010)

Ant Inspired Methods for Organic Computing. - Alexander Scheidler; Arne Brutschy; Konrad Diwold; Daniel Merkle; Martin Middendorf (Organic Computing, 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)

Finding all sorting tandem duplication random loss operations. - Matthias Bernt; Kuan-Yu Chen 002; Ming-Chiang Chen; An-Chiang Chu; Daniel Merkle; Hung-Lung Wang; Kun-Mao Chao; Martin Middendorf (J. Discrete Algorithms, 2011)

Exploring Chemistry Using SMT. - Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Philipp Peters (CP, 2012)

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

Barrier Trees for Metabolic Adjustment Landscapes. - Christoph Flamm; Chris Hemmingsen; Daniel Merkle (ECAL, 2013)

FooPar: A Functional Object Oriented Parallel Framework in Scala. - Felix Palludan Hargreaves; Daniel Merkle (PPAM (2), 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)

Swarm controlled emergence for ant clustering. - Alexander Scheidler; Daniel Merkle; Martin Middendorf (Int. J. Intell. Comput. Cybern., 2013)

On the Complexity of Reconstructing Chemical Reaction Networks. - Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Philipp Peters; Peter F. Stadler (Math. Comput. Sci., 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)

Group communication patterns for high performance computing in scala. - Felix Palludan Hargreaves; Daniel Merkle; Peter Schneider-Kamp (FHPC@ICFP, 2014)

Algorithmic Cheminformatics (Dagstuhl Seminar 14452). - Wolfgang Banzhaf; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 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)

Task allocation in organic computing systems: networks with reconfigurable helper units. - Daniel Merkle; Martin Middendorf; Alexander Scheidler (Int. J. Auton. Adapt. Commun. Syst., 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)

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. - Christoph Flamm; Daniel Merkle; Peter F. Stadler; Uffe Thorsen (ICGT, 2016)

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

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (WABI, 2017)

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

Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (CoRR, 2017)

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

Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings. - Marc Hellmuth; Anders S. Knudsen; Michal Kotrbcík; Daniel Merkle; Nikolai Nøjgaard (ALENEX, 2018)

Partial Homology Relations - Satisfiability in Terms of Di-Cographs. - Nikolai Nøjgaard; Nadia El-Mabrouk; Daniel Merkle; Nicolas Wieseke; Marc Hellmuth (COCOON, 2018)

Time-consistent reconciliation maps and forbidden time travel. - Nikolai Nøjgaard; Manuela Geiß; Daniel Merkle; Peter F. Stadler; Nicolas Wieseke; Marc Hellmuth (Algorithms Mol. Biol., 2018)

Finding the K best synthesis plans. - Rolf Fagerberg; Christoph Flamm; Rojin Kianian; Daniel Merkle; Peter F. Stadler (J. Cheminformatics, 2018)

DNA-templated synthesis optimization. - Bjarke N. Hansen; Kim S. Larsen; Daniel Merkle; Alexei Mihalchuk (Nat. Comput., 2018)

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)

Atom Tracking Using Cayley Graphs. - Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard (ISBRA, 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 (SOFSEM (Doctoral Student Research Forum), 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)

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. - Nikolai Nøjgaard; Walter Fontana; Marc Hellmuth; Daniel Merkle (J. Comput. Biol., 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)

Generic Context-Aware Group Contributions. - Christoph Flamm; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 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)

Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions. - Marcos E. González Laffitte; Klaus Weinbauer; Tieu-Long Phan; Nora Beier; Nico Domschke; Christoph Flamm; Thomas Gatter; Daniel Merkle; Peter F. Stadler (Symmetry, 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)

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

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)

On Finding All Connected Maximum-Sized Common Subgraphs in Multiple Labeled Graphs. - Johannes B. S. Petersen; Akbar Davoodi; Thomas Gärtner 001; Marc Hellmuth; Daniel Merkle (CoRR, 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)

Assembly in Directed Hypergraphs. - Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2025)