Daniel Merkle

发表

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

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2006, CompLife.

Swarm controlled emergence for ant clustering

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2013, Int. J. Intell. Comput. Cybern..

Combining Graph Transformations and Semigroups for Isotopic Labeling Design.

Daniel Merkle, Jakob L Andersen, Peter S Rasmussen, 2019, Journal of computational biology : a journal of computational molecular cell biology.

An intermediate level of abstraction for computational systems chemistry

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2017, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

Rule composition in graph transformation models of chemical reactions

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2018 .

Group communication patterns for high performance computing in scala

Daniel Merkle, Peter Schneider-Kamp, Felix Palludan Hargreaves, 2014, FHPC '14.

Generic Strategies for Chemical Space Exploration

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2013, Int. J. Comput. Biol. Drug Des..

Artificial Life XII Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems

Kasper Stoy, Daniel Merkle, Steen Rasmussen, 2010 .

Swarm Intelligence and Signal Processing

Daniel Merkle, Martin Middendorf, 2008 .

Partial Homology Relations - Satisfiability in Terms of Di-Cographs

Daniel Merkle, Nadia El-Mabrouk, Nicolas Wieseke, 2017, COCOON.

Towards Optimal DNA-Templated Computing

Daniel Merkle, Christoph Flamm, Jakob L. Andersen, 2015, Int. J. Unconv. Comput..

On the Design of RNA Sequences for Realizing Extended Shapes

Daniel Merkle, Martin Middendorf, Marc Hellmuth, 2009, 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing.

Bi-Criterion Optimization with Multi Colony Ant Algorithms

Daniel Merkle, Martin Middendorf, Steffen Iredi, 2001, EMO.

Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2011, ArXiv.

Pheromone evaluation in Ant Colony Optimization

Hartmut Schmeck, Daniel Merkle, Martin Middendorf, 2000, 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.

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

Daniel Merkle, Nadia El-Mabrouk, Nicolas Wieseke, 2017, ArXiv.

Towards an Optimal DNA-Templated Molecular Assembler

Daniel Merkle, Christoph Flamm, Jakob L. Andersen, 2014, ALIFE.

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Daniel Merkle, Martin Middendorf, Nicolas Wieseke, 2010, BMC Bioinformatics.

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

Daniel Merkle, Martin Middendorf, M. Middendorf, 2004, Adapt. Behav..

Barrier Trees for Continuous Fitness Landscapes

Daniel Merkle, Jacob Midtgaard-Olesen, Carsten Baldauf, 2010, ALIFE.

Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps

Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, 2017, WABI.

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2013, Entropy.

On Enforced Convergence of ACO and its Implementation on the Reconfigurable Mesh Architecture Using Size Reduction Tasks

Hartmut Schmeck, Daniel Merkle, Martin Middendorf, 2004, The Journal of Supercomputing.

Ant Colony Optimization with the Relative Pheromone Evaluation Method

Daniel Merkle, Martin Middendorf, M. Middendorf, 2002, EvoWorkshops.

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

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, J. Math. Model. Algorithms.

DNA-Templated Synthesis Optimization

Daniel Merkle, Kim S. Larsen, Bjarke N. Hansen, 2017, DNA.

A Fast and Exact Algorithm for the Perfect Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2007, ISBRA.

Genome Rearrangement Based on Reversals that Preserve Conserved Intervals

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2006, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Artificial Life 14

Daniel Merkle, Christoph Flamm, Jakob L. Andersen, 2014 .

Ameisenalgorithmen: Optimierung und Modellierung

Daniel Merkle, 2002 .

DNA-templated synthesis optimization

Daniel Merkle, Kim S. Larsen, Bjarke N. Hansen, 2018, Natural Computing.

Coevolutionary Ant Algorithms Playing Games

Jürgen Branke, Hartmut Schmeck, Daniel Merkle, 2002, Ant Algorithms.

Solving the Preserving Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2008, IEEE ACM Trans. Comput. Biol. Bioinform..

Swarm Intelligence - An Optimization-Based Introduction

Christian Blum, Daniel Merkle, 2005, Künstliche Intell..

Time-consistent reconciliation maps and forbidden time travel

Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, 2017, Algorithms for Molecular Biology.

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

Daniel Merkle, Stefan Janson, S. Janson, 2005, Hybrid Metaheuristics.

Finding all sorting tandem duplication random loss operations

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2009, J. Discrete Algorithms.

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2008, RECOMB-CG.

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

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2006, IWSOS/EuroNGI.

A Software Package for Chemically Inspired Graph Transformation

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2016, ICGT.

Swarm Intelligence: Introduction and Applications

Christian Blum, Daniel Merkle, C. Blum, 2008, Swarm Intelligence.

On the Behaviour of ACO Algorithms : Studies on Simple Problems

Daniel Merkle, Martin Middendorf, M. Middendorf, 2001 .

Stability and performance of ant queue inspired task partitioning methods

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, Theory in Biosciences.

CREx: inferring genomic rearrangements based on common intervals

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2007, Bioinform..

Parallel Ant Colony Algorithms

Daniel Merkle, Martin Middendorf, Stefan Janson, 2005 .

Atom Tracking Using Cayley Graphs

Daniel Merkle, Marc Hellmuth, Nikolai Nøjgaard, 2020, ISBRA.

Algorithmic Cheminformatics (Dagstuhl Seminar 14452)

Daniel Merkle, Wolfgang Banzhaf, Peter F. Stadler, 2014, Dagstuhl Reports.

International Journal of Intelligent Computing and Cybernetics A decentralization approach for swarm intelligence algorithms in networks applied to multi swarm PSO

Daniel Merkle, Martin Middendorf, Stefan Janson, 2016 .

The Influence of Dynamic Environments on Polyethism in Response Threshold Models for Social Insects

Daniel Merkle, Martin Middendorf, Konrad Diwold, 2009 .

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

Daniel Merkle, Martin Middendorf, M. Middendorf, 2004, Applied Intelligence.

Decentralized packet clustering in router-based networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2005, Int. J. Found. Comput. Sci..

Using median sets for inferring phylogenetic trees

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2007, Bioinform..

8th German Workshop on Artificial Life - Proceedings of the GWAL-8, Leipzig, Germany

Daniel Merkle, Eckehard Olbrich, Konstantin Klemm, 2009 .

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

Daniel Merkle, Martin Middendorf, M. Middendorf, 2005, Theory in Biosciences.

A Parallel Algorithm for Solving the Reversal Median Problem

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2005, PPAM.

Generic Context-Aware Group Contributions.

Daniel Merkle, Christoph Flamm, Marc Hellmuth, 2020, IEEE/ACM transactions on computational biology and bioinformatics.

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

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2016, ICGT.

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

Daniel Merkle, Martin Middendorf, 2001, EvoWorkshops.

FooPar: A Functional Object Oriented Parallel Framework in Scala

Daniel Merkle, Felix Palludan Hargreaves, 2013, PPAM.

Support for Eschenmoser's Glyoxylate Scenario pdf

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2015, ArXiv.

Fast ant colony optimization on reconfigurable processor arrays

Daniel Merkle, Martin Middendorf, 2001, Proceedings 15th International Parallel and Distributed Processing Symposium. IPDPS 2001.

Inferring chemical reaction patterns using rule composition in graph grammars

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2012, ArXiv.

Swarm Controlled Emergence - Designing an Anti-Clustering Ant System

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2007, 2007 IEEE Swarm Intelligence Symposium.

Modelling ACO: Composed Permutation Problems

Daniel Merkle, Martin Middendorf, M. Middendorf, 2002, Ant Algorithms.

Formal language recognition by stochastic cellular automata

Daniel Merkle, Thomas Worsch, 2002, Fundam. Informaticae.

Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays

Daniel Merkle, Martin Middendorf, M. Middendorf, 2002, Genetic Programming and Evolvable Machines.

Algorithmic Cheminformatics (Dagstuhl Seminar 17452)

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2017, Dagstuhl Reports.

Time-Consistent Reconciliation Maps and Forbidden Time Travel

Daniel Merkle, Peter F. Stadler, Nicolas Wieseke, 2017 .

Ant Inspired Methods for Organic Computing

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2011, Organic Computing.

Organic Computing and Swarm Intelligence

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, Swarm Intelligence.

Ant colony optimization for resource-constrained project scheduling

Hartmut Schmeck, Daniel Merkle, Martin Middendorf, 2000, IEEE Trans. Evol. Comput..

A Generic Framework for Engineering Graph Canonization Algorithms pdf

Daniel Merkle, Jakob L. Andersen, 2018, ALENEX.

Information Processing in Chemical Systems

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2019, The Energetics of Computing in Life and Machines.

Extended shapes for the combinatorial design of RNA sequences

Daniel Merkle, Martin Middendorf, Marc Hellmuth, 2009, Int. J. Comput. Biol. Drug Des..

Finding all sorting tandem duplication random loss operations

Kuan-Yu Chen, Matthias Bernt, Daniel Merkle, 2011, J. Discrete Algorithms.

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2014, FMMB.

On the Complexity of Reconstructing Chemical Reaction Networks

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2013, Math. Comput. Sci..

Dynamic Decentralized Packet Clustering in Networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2005, EvoWorkshops.

Special issue on ant colony optimization

Thomas Stützle, Daniel Merkle, Karl F. Doerner, 2009, Swarm Intelligence.

Chemical Transformation Motifs—Modelling Pathways as Integer Hyperflows

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2017, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Self-organized task allocation for computing systems with reconfigurable components

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2006, Proceedings 20th IEEE International Parallel & Distributed Processing Symposium.

Marco Dorigo and Thomas Stützle, Ant Colony Optimization, MIT Press (2004) ISBN 0-262-04219-3

Daniel Merkle, Martin Middendorf, 2006, Eur. J. Oper. Res..

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

Daniel Merkle, Martin Middendorf, M. Middendorf, 2000, EvoWorkshops.

Ant colony optimization and its application to adaptive routing in telecommunication networks

Daniel Merkle, Martin Middendorf, F. C. Santos, 2004 .

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

Daniel Merkle, Martin Middendorf, Konrad Diwold, 2009, Adv. Complex Syst..

An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree

Matthias Bernt, Daniel Merkle, Martin Middendorf, 2008, RECOMB 2008.

Barrier Trees for Metabolic Adjustment Landscapes

Daniel Merkle, Christoph Flamm, Chris Hemmingsen, 2013, ECAL.

Congestion Control in Ant Like Moving Agent Systems

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, BICC.

Exploring Chemistry Using SMT

Daniel Merkle, Christoph Flamm, Rolf Fagerberg, 2012, CP.

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

Daniel Merkle, Marc Hellmuth, Nikolai Nøjgaard, 2018, ALENEX.

Graph Transformations, Semigroups, and Isotopic Labeling

Daniel Merkle, Jakob L. Andersen, Peter S. Rasmussen, 2019, ISBRA.

Ant Colony Optimization for Resource-Constrained Projet Scheduling

Hartmut Schmeck, Daniel Merkle, Martin Middendorf, 2000, GECCO.

Emergent Sorting in Networks of Router Agents

Christian Blum, Daniel Merkle, Martin Middendorf, 2008, ANTS Conference.

A Generic Framework for Engineering Graph Canonization Algorithms

Daniel Merkle, Jakob L. Andersen, 2020 .

Finding the K best synthesis plans

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2018, Journal of Cheminformatics.

Chemical Graph Transformation with Stereo-Information

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2017, ICGT.

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

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, Organic Computing.

Competition Controlled Pheromone Update for Ant Colony Optimization

Daniel Merkle, Martin Middendorf, 2004, ANTS Workshop.

Decentralized packet clustering in networks

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2004, 18th International Parallel and Distributed Processing Symposium, 2004. Proceedings..

Modeling Ant Brood ending Patterns with Cellular Automata

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2006, J. Cell. Autom..

On solving permutation scheduling problems with ant colony optimization

Daniel Merkle, Martin Middendorf, 2005, Int. J. Syst. Sci..

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

Daniel Merkle, Marco Peressotti, Marc Hellmuth, 2020, SOFSEM.

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

Daniel Merkle, Martin Middendorf, Alexander Scheidler, 2008, ANTS Conference.

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry

Daniel Merkle, Walter Fontana, Marc Hellmuth, 2021, J. Comput. Biol..

Efficient Modular Graph Transformation Rule Application

Daniel Merkle, Jakob L. Andersen, Rolf Fagerberg, 2022 .

Characterizing Catalytic Mechanisms with Overlay Graphs pdf

Daniel Merkle, Walter Fontana, Christoph Flamm, 2022, ArXiv.

Rewriting theory for the life sciences: A unifying theory of CTMC semantics

Daniel Merkle, Jean Krivine, Jakob L. Andersen, 2021, Theor. Comput. Sci..

Graph transformation for enzymatic mechanisms

Daniel Merkle, Walter Fontana, Christoph Flamm, 2021, Bioinform..

Defining Autocatalysis in Chemical Reaction Networks pdf

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2021, ArXiv.

Towards mechanistic prediction of mass spectra using graph transformation

Daniel Merkle, Peter F. Stadler, Christoph Flamm, 2018 .

A Hybrid Population based ACO Algorithm for Protein Folding

Daniel Merkle, Martin Middendorf, Torsten Thalheim, 2008 .

Protein Folding in the HP-Model Solved With a Hybrid Population Based ACO Algorithm

Daniel Merkle, Martin Middendorf, Torsten Thalheim, 2008 .

Phylogenetic Parameter Estimation on COWs

Daniel Merkle, Martin Middendorf, Arndt von Haeseler, 2005 .

Chapter 14 SWARM INTELLIGENCE

Daniel Merkle, Martin Middendorf, M. Middendorf, 2005 .