Daniel Merkle

ORCID

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 47

Top Venues

Karlsruhe Institute of Technology, Germany (PHD)

Education History

Karlsruhe Institute of Technology, Germany

PHD

Publications

Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler
Reaction rebalancing: a novel approach to curating reaction databases. J. Cheminformatics 16 (1) (2024)
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Automated Inference of Graph Transformation Rules. CoRR (2024)
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle
Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases. J. Comput. Biol. 31 (6) (2024)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. ISBRA (2023)
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle
Reconciling Inconsistent Molecular Structures from Biochemical Databases. ISBRA (2023)
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle
Reconciling Inconsistent Molecular Structures from Biochemical Databases. CoRR (2023)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. CoRR (2023)
Jakob L. Andersen, Rolf Fagerberg, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Efficient Modular Graph Transformation Rule Application. CoRR (2022)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Characterizing Catalytic Mechanisms with Overlay Graphs. CoRR (2022)
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler
Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Representing Catalytic Mechanisms with Rule Composition. J. Chem. Inf. Model. 62 (22) (2022)
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
Rewriting theory for the life sciences: A unifying theory of CTMC semantics. Theor. Comput. Sci. 884 (2021)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Graph Transformation for Enzymatic Mechanisms. CoRR (2021)
Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle
Rewriting Theory for the Life Sciences: A Unifying Theory of CTMC Semantics (Long version). CoRR (2021)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Defining Autocatalysis in Chemical Reaction Networks. CoRR (2021)
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
Graph transformation for enzymatic mechanisms. Bioinform. 37 (Supplement) (2021)
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth, Daniel Merkle
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. CoRR (2021)
Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth, Daniel Merkle
Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry. J. Comput. Biol. 28 (7) (2021)
Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Marco Peressotti
A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework. SOFSEM (Doctoral Student Research Forum) (2020)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. ACM J. Exp. Algorithmics 25 (2020)
Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard
Atom Tracking Using Cayley Graphs. ISBRA (2020)
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
Combining Graph Transformations and Semigroups for Isotopic Labeling Design. J. Comput. Biol. 27 (2) (2020)
Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Marco Peressotti
A Graph-Based Tool to Embed the π-Calculus into a Computational DPO Framework. CoRR (2019)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. IEEE ACM Trans. Comput. Biol. Bioinform. 16 (2) (2019)
Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen
Graph Transformations, Semigroups, and Isotopic Labeling. ISBRA (2019)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. ALENEX (2018)
Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk
DNA-templated synthesis optimization. Nat. Comput. 17 (4) (2018)
Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth
Partial Homology Relations - Satisfiability in Terms of Di-Cographs. COCOON (2018)
Marc Hellmuth, Anders S. Knudsen, Michal Kotrbcík, Daniel Merkle, Nikolai Nøjgaard
Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings. ALENEX (2018)
Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Time-consistent reconciliation maps and forbidden time travel. Algorithms Mol. Biol. 13 (1) (2018)
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler
Finding the K best synthesis plans. J. Cheminformatics 10 (1) (2018)
Jakob L. Andersen, Daniel Merkle
A Generic Framework for Engineering Graph Canonization Algorithms. CoRR (2017)
Nikolai Nøjgaard, Manuela Geiß, Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, Marc Hellmuth
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. WABI (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports 7 (11) (2017)
Nikolai Nøjgaard, Manuela Geiß, Peter F. Stadler, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth
Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR (2017)
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Graph Transformation with Stereo-Information. ICGT (2017)
Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth
Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs. CoRR (2017)
Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk
DNA-Templated Synthesis Optimization. DNA (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. ICGT (2016)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. CoRR (2016)
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. CoRR (2016)
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. ICGT (2016)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Task allocation in organic computing systems: networks with reconfigurable helper units. Int. J. Auton. Adapt. Commun. Syst. 8 (1) (2015)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards Optimal DNA-Templated Computing. Int. J. Unconv. Comput. 11 (3-4) (2015)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Support for Eschenmoser's Glyoxylate Scenario. CoRR (2015)
Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 14452). Dagstuhl Reports 4 (11) (2014)
Felix Palludan Hargreaves, Daniel Merkle, Peter Schneider-Kamp
Group communication patterns for high performance computing in scala. FHPC@ICFP (2014)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des. 7 (2/3) (2014)
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. FMMB (2014)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards an Optimal DNA-Templated Molecular Assembler. ALIFE (2014)
Felix Palludan Hargreaves, Daniel Merkle, Peter Schneider-Kamp
Group Communication Patterns for High Performance Computing in Scala. CoRR (2014)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
On the Complexity of Reconstructing Chemical Reaction Networks. Math. Comput. Sci. 7 (3) (2013)
Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. Entropy 15 (10) (2013)
Felix Palludan Hargreaves, Daniel Merkle
FooPar: A Functional Object Oriented Parallel Framework in Scala CoRR (2013)
Christoph Flamm, Chris Hemmingsen, Daniel Merkle
Barrier Trees for Metabolic Adjustment Landscapes. ECAL (2013)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
On the Complexity of Reconstructing Chemical Reaction Networks. CoRR (2013)
Felix Palludan Hargreaves, Daniel Merkle
FooPar: A Functional Object Oriented Parallel Framework in Scala. PPAM (2) (2013)
Alexander Scheidler, Daniel Merkle, Martin Middendorf
Swarm controlled emergence for ant clustering. Int. J. Intell. Comput. Cybern. 6 (1) (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Generic Strategies for Chemical Space Exploration CoRR (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars CoRR (2012)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters
Exploring Chemistry Using SMT. CP (2012)
Matthias Bernt, Kuan-Yu Chen, Ming-Chiang Chen, An-Chiang Chu, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
Finding all sorting tandem duplication random loss operations. J. Discrete Algorithms 9 (1) (2011)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete CoRR (2011)
Daniel Merkle, Martin Middendorf, Nicolas Wieseke
A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinform. 11 (S-1) (2010)
Jacob Midtgaard-Olesen, Carsten Baldauf, Daniel Merkle
Barrier Trees for Continuous Fitness Landscapes. ALIFE (2010)
Konrad Diwold, Daniel Merkle, Martin Middendorf
Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects. Adv. Complex Syst. 12 (3) (2009)
Marc Hellmuth, Daniel Merkle, Martin Middendorf
Extended shapes for the combinatorial design of RNA sequences. Int. J. Comput. Biol. Drug Des. 2 (4) (2009)
Matthias Bernt, Ming-Chiang Chen, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations. CPM (2009)
Konstantin Klemm, Daniel Merkle, Eckehard Olbrich
Editorial: Artificial Life. Adv. Complex Syst. 12 (3) (2009)
Marc Hellmuth, Daniel Merkle, Martin Middendorf
On the Design of RNA Sequences for Realizing Extended Shapes. IJCBS (2009)
Karl F. Doerner, Daniel Merkle, Thomas Stützle
Special issue on ant colony optimization. Swarm Intell. 3 (1) (2009)
Alexander Scheidler, Daniel Merkle, Martin Middendorf
Stability and performance of ant queue inspired task partitioning methods. Theory Biosci. 127 (2) (2008)
Alexander Scheidler, Christian Blum, Daniel Merkle, Martin Middendorf
Emergent Sorting in Networks of Router Agents. ANTS Conference (2008)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Solving the Preserving Reversal Median Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 5 (3) (2008)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components. J. Math. Model. Algorithms 7 (2) (2008)
Stefan Janson, Daniel Merkle, Martin Middendorf
A decentralization approach for swarm intelligence algorithms in networks applied to multi swarm PSO. Int. J. Intell. Comput. Cybern. 1 (1) (2008)
Arne Brutschy, Alexander Scheidler, Daniel Merkle, Martin Middendorf
Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems. ANTS Conference (2008)
Matthias Bernt, Daniel Merkle, Martin Middendorf
An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree. RECOMB-CG (2008)
Alexander Scheidler, Daniel Merkle, Martin Middendorf
Congestion Control in Ant Like Moving Agent Systems. BICC (2008)
Daniel Merkle, Martin Middendorf
Swarm intelligence and signal processing [DSP Exploratory]. IEEE Signal Process. Mag. 25 (6) (2008)
Stefan Janson, Daniel Merkle, Martin Middendorf
Molecular docking with multi-objective Particle Swarm Optimization. Appl. Soft Comput. 8 (1) (2008)
Matthias Bernt, Daniel Merkle, Martin Middendorf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem. ISBRA (2007)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Using median sets for inferring phylogenetic trees. Bioinform. 23 (2) (2007)
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter F. Stadler, Martin Middendorf
CREx: inferring genomic rearrangements based on common intervals. Bioinform. 23 (21) (2007)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Swarm Controlled Emergence - Designing an Anti-Clustering Ant System. SIS (2007)
Daniel Merkle, Martin Middendorf
Marco Dorigo and Thomas Stützle, Ant Colony Optimization, MIT Press (2004) ISBN 0-262-04219-3. Eur. J. Oper. Res. 168 (1) (2006)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Modeling Ant Brood ending Patterns with Cellular Automata. J. Cell. Autom. 1 (2) (2006)
Matthias Bernt, Daniel Merkle, Martin Middendorf
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals. IEEE ACM Trans. Comput. Biol. Bioinform. 3 (3) (2006)
Matthias Bernt, Daniel Merkle, Martin Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders. CompLife (2006)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Self-organized task allocation for computing systems with reconfigurable components. IPDPS (2006)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units. IWSOS/EuroNGI (2006)
Matthias Bernt, Daniel Merkle, Martin Middendorf
A Parallel Algorithm for Solving the Reversal Median Problem. PPAM (2005)
Daniel Merkle, Martin Middendorf
On solving permutation scheduling problems with ant colony optimization. Int. J. Syst. Sci. 36 (5) (2005)
Daniel Merkle, Martin Middendorf
Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information. Theory Biosci. 123 (4) (2005)
Stefan Janson, Daniel Merkle
A New Multi-objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking. Hybrid Metaheuristics (2005)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Dynamic Decentralized Packet Clustering in Networks. EvoWorkshops (2005)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Decentralized packet clustering in router-based networks. Int. J. Found. Comput. Sci. 16 (2) (2005)
Daniel Merkle, Martin Middendorf, Alexander Scheidler
Modelling Ant Brood Tending Behavior with Cellular Automata. International Conference on Computational Science (2) (2005)

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Publication Activity (10 Years)

Top Topics

Top Venues

Daniel Merkle