Publications

SynCat: molecule-level attention graph neural network for precise reaction classification

Phuoc-Chung Van Nguyen, Van-Thinh To, Ngoc-Vi Nguyen Tran, Tieu-Long Phan, Tuyen Ngoc Truong, Thomas Gärtner, Daniel Merkle, Peter F. Stadler

Digital Discovery 5, 241-253 · 2026

ProQSAR: A modular and reproducible framework for small-data QSAR modeling with fit-and-use models

Tuyet-Minh Phan, Tieu-Long Phan, Phuoc-Chung van Nguyen, Hoang-Son Lai Le, Van-Thinh To, Tuyen Ngoc Truong, Daniel Merkle, Peter F. Stadler

J. Cheminformatics 18, 52 · 2026

Half-edge graphs, Lewis Formulas, and Electron Pushing

Rebecca Holzschuh, Christoph Flamm, Daniel Merkle, Peter F. Stadler

ChemRxiv · 2026

Finding Pathways in Reaction Networks Guided by Energy Barriers Using Integer Linear Programing

Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Peter Dittrich, Daniel Merkle

Molecular Informatics 45 · 2026

Exact Enumeration of All Connected Maximum Common Subgraphs in Multiple Labeled Graphs: Application to Cheminformatics

Johannes B. S. Petersen, Akbar Davoodi, Thomas Gärtner, Marc Hellmuth, Daniel Merkle

Match Communications in Mathematical and in Computer Chemistry 97 (2027), 821 · 2026

Computational approaches in chemical space exploration for carbon fixation pathways

Anne-Susann Abel, Nino Lauber, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle, Christoph Flamm

npj Systems Biology and Applications 12 · 2026

CombOL: a Library for Practical Enumeration and Boltzmann Sampling of Combinatorial Classes

Casper Asbjørn Eriksen, Daniel Merkle

arXiv · 2026

Automated Inference of Graph Transformation Rules

Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

Fundam. Informaticae 196 · 2026

A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems

Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg, Daniel Merkle

J. Chem. Inf. Model. 66, 1637-1651 · 2026

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. 65, 2882-2896 · 2025

SynKit : A Graph-Based Python Framework for Rule-Based Reaction Modeling and Analysis

Tieu-Long Phan, Marcos E. González Laffitte, Klaus Weinbauer, Daniel Merkle, Jakob Lykke Andersen, Rolf Fagerberg, Thomas Gatter, Peter F. Stadler

J. Chem. Inf. Model. 65, 13012-13019 · 2025

Saturation-Based Atom Provenance Tracing in Chemical Reaction Networks

Marcel Friedrichs, Daniel Merkle

arXiv · 2025

Petri net modeling and simulation of post-transcriptional regulatory networks of human embryonic stem cell (hESC) differentiation to cardiomyocytes

Aruana F. F. Hansel-Fröse, Christoph Brinkrolf, Marcel Friedrichs, Bruno Dallagiovanna, Lucía Spangenberg

J. Integr. Bioinform. 22 · 2025

Pathway Realizability in Chemical Networks

Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler

J. Comput. Biol. 32, 164-187 · 2025

On Finding All Connected Maximum-Sized Common Subgraphs in Multiple Labeled Graphs

Johannes B. S. Petersen, Akbar Davoodi, Thomas Gärtner, Marc Hellmuth, Daniel Merkle

arXiv · 2025

NAR db status Version 2 and miRNAverse: Over Two Years of Manual Meta-Registry Curation and Updates

Marcel Friedrichs, Cassandra Königs

arXiv · 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. 65, 6772-6787 · 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

arXiv · 2025

Continuous Petri Nets for Fast Yield Computation: Polynomial-Time and MILP Approaches

Addie Jordon, Juraj Kolčák, Daniel Merkle

arXiv · 2025

Continuous Petri Nets Faithfully Fluidify Most Permissive Boolean Networks

Stefan Haar, Juraj Kolčák

CMSB, 89-105 · 2025

Computation in chemical graph rewriting networks

Christoph Flamm, Daniel Merkle, Peter F Stadler

Journal of Physics: Complexity 6, 015014 · 2025

ChemReservoir - An Open-Source Framework for Chemically-Inspired Reservoir Computing

Mehmet Aziz Yirik, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

IEEE Access 13, 149197-149202 · 2025

Automated Graph-Based Data Integration and Information Fusion: An Open-Source Ecosystem of Tools With a Focus on Maintainability and Usability

Marcel Friedrichs

2025

Assembly in Directed Hypergraphs

Christoph Flamm, Daniel Merkle, Peter F. Stadler

Proceedings of the Royal Society A 481, 20250331 · 2025

Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases

Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

J. Comput. Biol. 31, 498-512 · 2024

Reaction rebalancing: a novel approach to curating reaction databases

Tieu-Long Phan, Klaus Weinbauer, Thomas Gärtner, Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, Peter F. Stadler

J. Cheminformatics 16, 82 · 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 16, 1217 · 2024

MicroRNA Databases

Aruana F. F. Hansel Fröse, Marcel Friedrichs, Jens Allmer

Epigenetics and Human Health, 21-40 · 2024

International symposium on integrative bioinformatics 2024 - editorial

Can Türker, Christian Panse, Björn Sommer, Marcel Friedrichs, Ralf Hofestädt

J. Integr. Bioinform. 21 · 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

arXiv · 2024

Alternative polyadenylation and dynamic 3′ UTR length is associated with polysome recruitment throughout the cardiomyogenic differentiation of hESCs

Aruana F. F. Hansel-Frose, Jens Allmer, Marcel Friedrichs, Hellen Geremias dos Santos, Bruno Dallagiovanna, Lucía Spangenberg

Frontiers in Molecular Biosciences 11 · 2024

Reconciling Inconsistent Molecular Structures from Biochemical Databases

Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle

ISBRA, 58-71 · 2023

On the Realisability of Chemical Pathways

Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler

ISBRA, 409-419 · 2023

A web-based platform for the annotation and analysis of NAR-published databases

Marcel Friedrichs, Cassandra Königs

PLOS ONE 18, e0293134 · 2023

A web-based annotation tool for clinical trial failure reasons

Marcel Friedrichs

German Medical Science GMS Publishing House · 2023

QWalkVis: Quantum Walks Visualization Application

Addie Jordon, Austin Hawkins-Seagram, Samantha Norrie, José Ossorio, Ulrike Stege

IEEE International Conference on Quantum Computing and Engineering (QCE), 87-93 · 2023

The heterogeneous pharmacological medical biochemical network PharMeBINet

Cassandra Königs, Marcel Friedrichs, Theresa Dietrich

Scientific Data 9 · 2022

Representing Catalytic Mechanisms with Rule Composition

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

J. Chem. Inf. Model. 62, 5513-5524 · 2022

Generic Context-Aware Group Contributions

Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler

IEEE ACM Trans. Comput. Biol. Bioinform. 19, 429-442 · 2022

Efficient Modular Graph Transformation Rule Application

Jakob L. Andersen, Rolf Fagerberg, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

arXiv · 2022

Data Integration Applications in Medical Information Systems

Marcel Friedrichs

Integrative Bioinformatics, 223-234 · 2022

Characterizing Catalytic Mechanisms with Overlay Graphs

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

arXiv · 2022

Automation in Graph-Based Data Integration and Mapping

Marcel Friedrichs

Integrative Bioinformatics, 97-110 · 2022

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

Nicolas Behr, Jean Krivine, Jakob L. Andersen, Daniel Merkle

arXiv · 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. 884, 68-115 · 2021

Graph transformation for enzymatic mechanisms

Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

Bioinform. 37, 392-400 · 2021

Dépliages et interprétation abstraite pour réseaux de régulation biologiques paramétrés. (Unfoldings and Abstract Interpretation for Parametric Biological Regulatory Networks)

Juraj Kolčák

2021

Defining Autocatalysis in Chemical Reaction Networks

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

arXiv · 2021

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry

Nikolai Nøjgaard, Walter Fontana, Marc Hellmuth, Daniel Merkle

J. Comput. Biol. 28, 701-715 · 2021

BioDWH2: an automated graph-based data warehouse and mapping tool

Marcel Friedrichs

J. Integr. Bioinform. 18, 167-176 · 2021

A Modular Approach to Non-deterministic Dynamic Fault Trees

Sascha Müller, Addie Jordon, Andreas Gerndt, Thomas Noll

Computer Safety, Reliability, and Security, 243-257 · 2021

Relational Differential Dynamic Logic

Juraj Kolčák, Jérémy Dubut, Ichiro Hasuo, Shin-ya Katsumata, David Sprunger, Akihisa Yamada

TACAS (1), 191-208 · 2020

Reconciling qualitative, abstract, and scalable modeling of biological networks

Loïc Paulevé, Juri Kolčák, Thomas Chatain, Stefan Haar

Nature Communications 11 · 2020

Concurrency in Boolean networks

Thomas Chatain, Stefan Haar, Juraj Kolčák, Loïc Paulevé, Aalok Thakkar

Nat. Comput. 19, 91-109 · 2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design

Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen

J. Comput. Biol. 27, 269-287 · 2020

Atom Tracking Using Cayley Graphs

Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard

ISBRA, 406-415 · 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), 121-132 · 2020

A Generic Framework for Engineering Graph Canonization Algorithms

Jakob L. Andersen, Daniel Merkle

ACM J. Exp. Algorithmics 25, 1-26 · 2020

Relational differential dynamic logic: poster abstract

Juraj Kolčák, Ichiro Hasuo, Jérémy Dubut, Shin-ya Katsumata, David Sprunger, Akihisa Yamada

HSCC, 284-285 · 2019

Parameter space abstraction and unfolding semantics of discrete regulatory networks

Juraj Kolčák, David Safránek, Stefan Haar, Loïc Paulevé

Theor. Comput. Sci. 765, 120-144 · 2019

JIB.tools 2.0 - A Bioinformatics Registry for Journal Published Tools with Interoperability to bio.tools

Marcel Friedrichs, Alban Shoshi, Piotr Chmura, Jon C. Ison, Veit Schwämmle, Falk Schreiber, Ralf Hofestädt, Björn Sommer

J. Integr. Bioinform. 16 · 2019

Information Processing in Chemical Systems

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Energetics of Computing in Life and Machines, 83-102 · 2019

History and Future of KALIS: Towards Computer-assisted Decision Making in Prescriptive Medicine

Marcel Friedrichs, Alban Shoshi

J. Integr. Bioinform. 16 · 2019

Graph Transformations, Semigroups, and Isotopic Labeling

Jakob L. Andersen, Daniel Merkle, Peter S. Rasmussen

ISBRA, 196-207 · 2019

Combining Refinement of Parametric Models with Goal-Oriented Reduction of Dynamics

Stefan Haar, Juraj Kolčák, Loïc Paulevé

VMCAI, 555-576 · 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. 16, 510-523 · 2019

A Graph-Based Tool to Embed the pi-Calculus into a Computational DPO Framework

Jakob Lykke Andersen, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Marco Peressotti

arXiv · 2019

Unfolding of Parametric Boolean Networks

Juraj Kolčák, David Safránek, Stefan Haar, Loïc Paulevé

SASB 335, 67-90 · 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. 13, 2:1-2:17 · 2018

Partial Homology Relations - Satisfiability in Terms of Di-Cographs

Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth

COCOON, 403-415 · 2018

Linear Time Canonicalization and Enumeration of Non-Isomorphic 1-Face Embeddings

Marc Hellmuth, Anders S. Knudsen, Michal Kotrbcík, Daniel Merkle, Nikolai Nøjgaard

ALENEX, 154-168 · 2018

GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks

Alban Shoshi, Ralf Hofestädt, Olga I. Zolotareva, Marcel Friedrichs, Alex Maier, Vladimir A. Ivanisenko, Victor E. Dosenko, Elena Yu. Bragina

J. Integr. Bioinform. 15 · 2018

Finding the K best synthesis plans

Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler

J. Cheminformatics 10, 19:1-19:21 · 2018

DNA-templated synthesis optimization

Bjarke N. Hansen, Kim S. Larsen, Daniel Merkle, Alexei Mihalchuk

Nat. Comput. 17, 693-707 · 2018

Data-Driven Assessment of Potentially Inappropriate Medication in the Elderly

Marcel Friedrichs, Alban Shoshi, Maren Kleine

GMDS, 125-129 · 2018

Partial Orthology, Paralogy and Xenology Relations - Satisfiability in terms of Di-Cographs

Nikolai Nøjgaard, Nadia El-Mabrouk, Daniel Merkle, Nicolas Wieseke, Marc Hellmuth

arXiv · 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, 17:1-17:12 · 2017

Chemical Graph Transformation with Stereo-Information

Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

ICGT, 54-69 · 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Philosophical Transactions of the Royal Society A 375, 20160354 · 2017

Algorithmic Cheminformatics (Dagstuhl Seminar 17452)

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Dagstuhl Reports 7, 28-45 · 2017

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions

Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen

ICGT, 206-222 · 2016

A Software Package for Chemically Inspired Graph Transformation

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

ICGT, 73-88 · 2016

Towards Optimal DNA-Templated Computing

Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle

Int. J. Unconv. Comput. 11, 185-203 · 2015

Task allocation in organic computing systems: networks with reconfigurable helper units

Daniel Merkle, Martin Middendorf, Alexander Scheidler

Int. J. Auton. Adapt. Commun. Syst. 8, 60-80 · 2015

Support for Eschenmoser's Glyoxylate Scenario

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

arXiv · 2015

In silico support for Eschenmoser’s glyoxylate scenario

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Israel Journal of Chemistry 55, 919-933 · 2015

Towards an Optimal DNA-Templated Molecular Assembler

Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle

ALIFE, 557-564 · 2014

Group communication patterns for high performance computing in scala

Felix Palludan Hargreaves, Daniel Merkle, Peter Schneider-Kamp

FHPC@ICFP, 75-85 · 2014

Generic strategies for chemical space exploration

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Int. J. Comput. Biol. Drug Des. 7, 225-258 · 2014

Computational methods for the analysis of mitochondrial genome rearrangements

Matthias Bernt, Daniel Merkle, Martin Middendorf, Bernd Schierwater, Martin Schlegel, Peter F. Stadler

Deep Metazoan Phylogeny: The Backbone of the Tree of Life, 515-530 · 2014

Algorithmic Cheminformatics (Dagstuhl Seminar 14452)

Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Dagstuhl Reports 4, 22-39 · 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, 117-135 · 2014

Swarm controlled emergence for ant clustering

Alexander Scheidler, Daniel Merkle, Martin Middendorf

Int. J. Intell. Comput. Cybern. 6, 62-82 · 2013

On the Complexity of Reconstructing Chemical Reaction Networks

Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler

Math. Comput. Sci. 7, 275-292 · 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 15, 4066-4083 · 2013

FooPar: A Functional Object Oriented Parallel Framework in Scala

Felix Palludan Hargreaves, Daniel Merkle

PPAM (2), 118-129 · 2013

Barrier Trees for Metabolic Adjustment Landscapes

Christoph Flamm, Chris Hemmingsen, Daniel Merkle

ECAL, 1151-1158 · 2013

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Journal of Systems Chemistry 4, 4 · 2013

Parameter Identification and Model Ranking of Thomas Networks

Hannes Klarner, Adam Streck, David Safránek, Juraj Kolčák, Heike Siebert

CMSB, 207-226 · 2012

Exploring Chemistry Using SMT

Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters

CP, 900-915 · 2012

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

Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler

Journal of Systems Chemistry 3, 1 · 2012

Finding all sorting tandem duplication random loss operations

Matthias Bernt, Kuan-Yu Chen, Ming-Chiang Chen, An-Chiang Chu, Daniel Merkle, Hung-Lung Wang, Kun-Mao Chao, Martin Middendorf

J. Discrete Algorithms 9, 32-48 · 2011

Ant Inspired Methods for Organic Computing

Alexander Scheidler, Arne Brutschy, Konrad Diwold, Daniel Merkle, Martin Middendorf

Organic Computing, 95-109 · 2011

Barrier Trees for Continuous Fitness Landscapes

Jacob Midtgaard-Olesen, Carsten Baldauf, Daniel Merkle

ALIFE, 368-369 · 2010

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Daniel Merkle, Martin Middendorf, Nicolas Wieseke

BMC Bioinform. 11, 60 · 2010

Special issue on ant colony optimization

Karl F. Doerner, Daniel Merkle, Thomas Stützle

Swarm Intell. 3, 1-2 · 2009

On the Design of RNA Sequences for Realizing Extended Shapes

Marc Hellmuth, Daniel Merkle, Martin Middendorf

IJCBS, 167-173 · 2009

Extended shapes for the combinatorial design of RNA sequences

Marc Hellmuth, Daniel Merkle, Martin Middendorf

Int. J. Comput. Biol. Drug Des. 2, 371-384 · 2009

Editorial: Artificial Life

Konstantin Klemm, Daniel Merkle, Eckehard Olbrich

Adv. Complex Syst. 12 · 2009

Adapting to Dynamic Environments: Polyethism in Response Threshold Models for Social Insects

Konrad Diwold, Daniel Merkle, Martin Middendorf

Adv. Complex Syst. 12, 327-346 · 2009

Swarm Intelligence: Introduction and Applications

Swarm Intelligence · 2008

Swarm intelligence and signal processing [DSP Exploratory]

Daniel Merkle, Martin Middendorf

IEEE Signal Process. Mag. 25, 152-158 · 2008

Stability and performance of ant queue inspired task partitioning methods

Alexander Scheidler, Daniel Merkle, Martin Middendorf

Theory Biosci. 127, 149-161 · 2008

Solving the Preserving Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf

IEEE ACM Trans. Comput. Biol. Bioinform. 5, 332-347 · 2008

Self-Organized Task Allocation for Service Tasks in Computing Systems with Reconfigurable Components

Daniel Merkle, Martin Middendorf, Alexander Scheidler

J. Math. Model. Algorithms 7, 237-254 · 2008

Self-adaptive Worker-Helper Systems with Self-Organized Task Allocation

Daniel Merkle, Martin Middendorf, Alexander Scheidler

Organic Computing, 221-239 · 2008

Organic Computing and Swarm Intelligence

Daniel Merkle, Martin Middendorf, Alexander Scheidler

Swarm Intelligence, 253-281 · 2008

Molecular docking with multi-objective Particle Swarm Optimization

Stefan Janson, Daniel Merkle, Martin Middendorf

Appl. Soft Comput. 8, 666-675 · 2008

Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems

Arne Brutschy, Alexander Scheidler, Daniel Merkle, Martin Middendorf

ANTS Conference, 96-107 · 2008

Evolution of mitochondrial gene orders in echinoderms

Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, Martin Schlegel

Molecular phylogenetics and evolution 47, 855-864 · 2008

Emergent Sorting in Networks of Router Agents

Alexander Scheidler, Christian Blum, Daniel Merkle, Martin Middendorf

ANTS Conference, 299-306 · 2008

Congestion Control in Ant Like Moving Agent Systems

Alexander Scheidler, Daniel Merkle, Martin Middendorf

BICC, 33-43 · 2008

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree

Matthias Bernt, Daniel Merkle, Martin Middendorf

RECOMB-CG, 143-157 · 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. 1, 25-45 · 2008

Using median sets for inferring phylogenetic trees

Matthias Bernt, Daniel Merkle, Martin Middendorf

Bioinform. 23, 129-135 · 2007

Swarm Controlled Emergence - Designing an Anti-Clustering Ant System

Daniel Merkle, Martin Middendorf, Alexander Scheidler

SIS, 242-249 · 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. 23, 2957-2958 · 2007

A Fast and Exact Algorithm for the Perfect Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf

ISBRA, 305-316 · 2007

Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units

Daniel Merkle, Martin Middendorf, Alexander Scheidler

IWSOS/EuroNGI, 137-147 · 2006

The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders

Matthias Bernt, Daniel Merkle, Martin Middendorf

CompLife, 52-63 · 2006

Self-organized task allocation for computing systems with reconfigurable components

Daniel Merkle, Martin Middendorf, Alexander Scheidler

IPDPS · 2006

Phylogenetic parameter estimation on COWs

Ekkehard Petzold, Daniel Merkle, Martin Middendorf, Arndt von Haeseler, Heiko A. Schmidt

Parallel Computing for Bioinformatics and Computational Biology. Wiley Interscience, 347-368 · 2006

Modeling Ant Brood ending Patterns with Cellular Automata

Daniel Merkle, Martin Middendorf, Alexander Scheidler

J. Cell. Autom. 1, 183-194 · 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. 168, 269-271 · 2006

Genome Rearrangement Based on Reversals that Preserve Conserved Intervals

Matthias Bernt, Daniel Merkle, Martin Middendorf

IEEE ACM Trans. Comput. Biol. Bioinform. 3, 275-288 · 2006

Swarm Intelligence - An Optimization-Based Introduction

Daniel Merkle, Christian Blum

Künstliche Intell. 19, 5-10 · 2005

Swarm intelligence

Daniel Merkle, Martin Middendorf

Search methodologies, 401-435 · 2005

Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information

Daniel Merkle, Martin Middendorf

Theory Biosci. 123, 277-299 · 2005

Parallel ant colony algorithms

Stefan Janson, Daniel Merkle, Martin Middendorf

Parallel Metaheuristics: A New Class of Metaheuristics, 171-201 · 2005

On solving permutation scheduling problems with ant colony optimization

Daniel Merkle, Martin Middendorf

Int. J. Syst. Sci. 36, 255-266 · 2005

Modelling Ant Brood Tending Behavior with Cellular Automata

Daniel Merkle, Martin Middendorf, Alexander Scheidler

International Conference on Computational Science (2), 412-419 · 2005

Dynamic Decentralized Packet Clustering in Networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler

EvoWorkshops, 574-583 · 2005

Decentralized packet clustering in router-based networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler

Int. J. Found. Comput. Sci. 16, 321-341 · 2005

A Parallel Algorithm for Solving the Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf

PPAM, 1089-1096 · 2005

A New Multi-objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking

Stefan Janson, Daniel Merkle

Hybrid Metaheuristics, 128-141 · 2005

Dynamic Polyethism and Competition for Tasks in Threshold Reinforcement Models of Social Insects

Daniel Merkle, Martin Middendorf

Adapt. Behav. 12, 251-262 · 2004

Decentralized Packet Clustering in Networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler

IPDPS · 2004

Competition Controlled Pheromone Update for Ant Colony Optimization

Daniel Merkle, Martin Middendorf

ANTS Workshop, 95-105 · 2004

On the behavior of ACO algorithms: Studies on simple problems

Daniel Merkle, Martin Middendorf

Metaheuristics: computer decision-making, 465-480 · 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. 26, 221-238 · 2003

Ant Colony Optimization with Global Pheromone Evaluation for Scheduling a Single Machine

Daniel Merkle, Martin Middendorf

Appl. Intell. 18, 105-111 · 2003

Studies On The Dynamics Of Ant Colony Optimization Algorithms

Daniel Merkle, Martin Middendorf

GECCO, 105-112 · 2002

Modelling ACO: Composed Permutation Problems

Daniel Merkle, Martin Middendorf

Ant Algorithms, 149-162 · 2002

Modeling the Dynamics of Ant Colony Optimization

Daniel Merkle, Martin Middendorf

Evol. Comput. 10, 235-262 · 2002

Formal language recognition by stochastic cellular automata

Daniel Merkle, Thomas Worsch

Fundam. Informaticae 52, 183-201 · 2002

Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays

Daniel Merkle, Martin Middendorf

Genet. Program. Evolvable Mach. 3, 345-361 · 2002

Coevolutionary Ant Algorithms Playing Games

Jürgen Branke, Michael Decker, Daniel Merkle, Hartmut Schmeck

Ant Algorithms, 298-299 · 2002

Ant Colony Optimization with the Relative Pheromone Evaluation Method

Daniel Merkle, Martin Middendorf

EvoWorkshops, 325-333 · 2002

Ant colony optimization for resource-constrained project scheduling

Daniel Merkle, Martin Middendorf, Hartmut Schmeck

IEEE Trans. Evol. Comput. 6, 333-346 · 2002

Ameisenalgorithmen: Optimierung und Modellierung

Daniel Merkle

, 1-2122002

Fast ant colony optimization on reconfigurable processor arrays

Daniel Merkle, Martin Middendorf

IPDPS, 144 · 2001

Bi-Criterion Optimization with Multi Colony Ant Algorithms

Steffen Iredi, Daniel Merkle, Martin Middendorf

EMO, 359-372 · 2001

A New Approach to Solve Permutation Scheduling Problems with Ant Colony Optimization

Daniel Merkle, Martin Middendorf

EvoWorkshops, 484-494 · 2001

Pheromone evaluation in ant colony optimization

D. Merkle, M. Middendorf, H. Schmeck

2000 26th Annual Conference of the IEEE Industrial Electronics Society. IECON 2000. 2000 IEEE International Conference on Industrial Electronics, Control and Instrumentation. 21st Century Technologies 4, 2726-2731 · 2000

Ant Colony Optimization for Resource-Constrained Projet Scheduling

Daniel Merkle, Martin Middendorf, Hartmut Schmeck

GECCO, 893- · 2000

An Ant Algorithm with a New Pheromone Evaluation Rule for Total Tardiness Problems

Daniel Merkle, Martin Middendorf

EvoWorkshops, 287-296 · 2000