Daniel Merkle

J. Comput. Biol., 2024

Automated Inference of Graph Transformation Rules.

[BibT_eX]

[DOI]

CoRR, 2024

2023

Reconciling Inconsistent Molecular Structures from Biochemical Databases.

[BibT_eX]

[DOI]

Casper Asbjørn Eriksen

Jakob Lykke Andersen

Rolf Fagerberg

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

On the Realisability of Chemical Pathways.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022

Generic Context-Aware Group Contributions.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Representing Catalytic Mechanisms with Rule Composition.

[BibT_eX]

[DOI]

J. Chem. Inf. Model., 2022

Characterizing Catalytic Mechanisms with Overlay Graphs.

[BibT_eX]

[DOI]

CoRR, 2022

Efficient Modular Graph Transformation Rule Application.

[BibT_eX]

[DOI]

Rolf Fagerberg

Juraj Kolcák

CoRR, 2022

2021

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

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2021

Cayley Graphs of Semigroups Applied to Atom Tracking in Chemistry.

[BibT_eX]

[DOI]

J. Comput. Biol., 2021

Defining Autocatalysis in Chemical Reaction Networks.

[BibT_eX]

[DOI]

CoRR, 2021

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

[BibT_eX]

[DOI]

CoRR, 2021

Graph transformation for enzymatic mechanisms.

[BibT_eX]

[DOI]

Bioinform., 2021

2020

A Generic Framework for Engineering Graph Canonization Algorithms.

[BibT_eX]

[DOI]

ACM J. Exp. Algorithmics, 2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design.

[BibT_eX]

[DOI]

Peter S. Rasmussen

J. Comput. Biol., 2020

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

[BibT_eX]

[DOI]

Proceedings of the SOFSEM 2020 Doctoral Student Research Forum co-located with the 46th International Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM 2020), 2020

Atom Tracking Using Cayley Graphs.

[BibT_eX]

[DOI]

Marc Hellmuth

Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

2019

Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Graph Transformations, Semigroups, and Isotopic Labeling.

[BibT_eX]

[DOI]

Peter S. Rasmussen

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

2018

DNA-templated synthesis optimization.

[BibT_eX]

[DOI]

Nat. Comput., 2018

Finding the K best synthesis plans.

[BibT_eX]

[DOI]

J. Cheminformatics, 2018

Time-consistent reconciliation maps and forbidden time travel.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2018

Partial Homology Relations - Satisfiability in Terms of Di-Cographs.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

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

[BibT_eX]

[DOI]

Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments, 2018

2017

Algorithmic Cheminformatics (Dagstuhl Seminar 17452).

[BibT_eX]

[DOI]

Dagstuhl Reports, 2017

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

[BibT_eX]

[DOI]

CoRR, 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry.

[BibT_eX]

[DOI]

CoRR, 2017

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

[BibT_eX]

[DOI]

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Chemical Graph Transformation with Stereo-Information.

[BibT_eX]

[DOI]

Proceedings of the Graph Transformation - 10th International Conference, 2017

2016

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

[BibT_eX]

[DOI]

Proceedings of the Graph Transformation - 9th International Conference, 2016

A Software Package for Chemically Inspired Graph Transformation.

[BibT_eX]

[DOI]

Proceedings of the Graph Transformation - 9th International Conference, 2016

2015

Towards Optimal DNA-Templated Computing.

[BibT_eX]

[DOI]

Int. J. Unconv. Comput., 2015

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

[BibT_eX]

[DOI]

Felix Palludan Hargreaves

Int. J. Auton. Adapt. Commun. Syst., 2015

Support for Eschenmoser's Glyoxylate Scenario.

[BibT_eX]

[DOI]

CoRR, 2015

2014

Generic strategies for chemical space exploration.

[BibT_eX]

[DOI]

Int. J. Comput. Biol. Drug Des., 2014

Algorithmic Cheminformatics (Dagstuhl Seminar 14452).

[BibT_eX]

[DOI]

Dagstuhl Reports, 2014

Group communication patterns for high performance computing in scala.

[BibT_eX]

[DOI]

Peter Schneider-Kamp

Proceedings of the 3rd ACM SIGPLAN workshop on Functional high-performance computing, 2014

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

[BibT_eX]

[DOI]

Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

Towards an Optimal DNA-Templated Molecular Assembler.

[BibT_eX]

[DOI]

Proceedings of the Fourteenth International Conference on the Simulation and Synthesis of Living Systems, 2014

2013

On the Complexity of Reconstructing Chemical Reaction Networks.

[BibT_eX]

[DOI]

Math. Comput. Sci., 2013

Swarm controlled emergence for ant clustering.

[BibT_eX]

[DOI]

Felix Palludan Hargreaves

Int. J. Intell. Comput. Cybern., 2013

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

[BibT_eX]

[DOI]

Entropy, 2013

FooPar: A Functional Object Oriented Parallel Framework in Scala.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2013

Barrier Trees for Metabolic Adjustment Landscapes.

[BibT_eX]

[DOI]

Christoph Flamm

Chris Hemmingsen

Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life, 2013

2012

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars

[BibT_eX]

[DOI]

CoRR, 2012

Exploring Chemistry Using SMT.

[BibT_eX]

[DOI]

Proceedings of the Principles and Practice of Constraint Programming, 2012

2011

Finding all sorting tandem duplication random loss operations.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2011

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

[BibT_eX]

[DOI]

CoRR, 2011

Ant Inspired Methods for Organic Computing.

[BibT_eX]

[DOI]

Proceedings of the Organic Computing - A Paradigm Shift for Complex Systems, 2011

2010

A parameter-adaptive dynamic programming approach for inferring cophylogenies.

[BibT_eX]

[DOI]

Nicolas Wieseke

BMC Bioinform., 2010

Barrier Trees for Continuous Fitness Landscapes.

[BibT_eX]

[DOI]

Jacob Midtgaard-Olesen

Carsten Baldauf

Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, 2010

2009

Special issue on ant colony optimization.

[BibT_eX]

[DOI]

Karl F. Doerner

Thomas Stützle

Swarm Intell., 2009

Extended shapes for the combinatorial design of RNA sequences.

[BibT_eX]

[DOI]

Marc Hellmuth

Int. J. Comput. Biol. Drug Des., 2009

Editorial: Artificial Life.

[BibT_eX]

[DOI]

Konstantin Klemm

Eckehard Olbrich

Adv. Complex Syst., 2009

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

[BibT_eX]

[DOI]

Konrad Diwold

Adv. Complex Syst., 2009

On the Design of RNA Sequences for Realizing Extended Shapes.

[BibT_eX]

[DOI]

Marc Hellmuth

Proceedings of the International Joint Conferences on Bioinformatics, 2009

Finding All Sorting Tandem Duplication Random Loss Operations.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Pattern Matching, 20th Annual Symposium, 2009

2008

Organic Computing and Swarm Intelligence.

[BibT_eX]

[DOI]

Proceedings of the Swarm Intelligence: Introduction and Applications, 2008

Stability and performance of ant queue inspired task partitioning methods.

[BibT_eX]

[DOI]

Theory Biosci., 2008

Solving the Preserving Reversal Median Problem.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

Swarm intelligence and signal processing [DSP Exploratory].

[BibT_eX]

[DOI]

IEEE Signal Process. Mag., 2008

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

[BibT_eX]

[DOI]

J. Math. Model. Algorithms, 2008

A decentralization approach for swarm intelligence algorithms in networks applied to multi swarm PSO.

[BibT_eX]

[DOI]

Stefan Janson

Int. J. Intell. Comput. Cybern., 2008

Molecular docking with multi-objective Particle Swarm Optimization.

[BibT_eX]

[DOI]

Stefan Janson

Appl. Soft Comput., 2008

An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics, International Workshop, 2008

Congestion Control in Ant Like Moving Agent Systems.

[BibT_eX]

[DOI]

Proceedings of the Biologically-Inspired Collaborative Computing, 2008

Emergent Sorting in Networks of Router Agents.

[BibT_eX]

[DOI]

Proceedings of the Ant Colony Optimization and Swarm Intelligence, 2008

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

[BibT_eX]

[DOI]

Proceedings of the Ant Colony Optimization and Swarm Intelligence, 2008

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

[BibT_eX]

[DOI]

Proceedings of the Organic Computing, 2008

2007

CREx: inferring genomic rearrangements based on common intervals.

[BibT_eX]

[DOI]

Bioinform., 2007

Using median sets for inferring phylogenetic trees.

[BibT_eX]

[DOI]

Bioinform., 2007

Swarm Controlled Emergence - Designing an Anti-Clustering Ant System.

[BibT_eX]

[DOI]

Proceedings of the 2007 IEEE Swarm Intelligence Symposium, 2007

A Fast and Exact Algorithm for the Perfect Reversal Median Problem.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

2006

Genome Rearrangement Based on Reversals that Preserve Conserved Intervals.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

Modeling Ant Brood ending Patterns with Cellular Automata.

[BibT_eX]

[DOI]

J. Cell. Autom., 2006

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

[BibT_eX]

[DOI]

Eur. J. Oper. Res., 2006

Self-organized task allocation for computing systems with reconfigurable components.

[BibT_eX]

[DOI]

Proceedings of the 20th International Parallel and Distributed Processing Symposium (IPDPS 2006), 2006

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

[BibT_eX]

[DOI]

Proceedings of the Self-Organizing Systems, First International Workshop, 2006

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

[BibT_eX]

[DOI]

Proceedings of the Computational Life Sciences II, 2006

2005

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

[BibT_eX]

[DOI]

Theory Biosci., 2005

Swarm Intelligence - An Optimization-Based Introduction.

[BibT_eX]

[DOI]

Christian Blum

Künstliche Intell., 2005

On solving permutation scheduling problems with ant colony optimization.

[BibT_eX]

[DOI]

Int. J. Syst. Sci., 2005

Decentralized packet clustering in router-based networks.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 2005

A Parallel Algorithm for Solving the Reversal Median Problem.

[BibT_eX]

[DOI]

Proceedings of the Parallel Processing and Applied Mathematics, 2005

Modelling Ant Brood Tending Behavior with Cellular Automata.

[BibT_eX]

[DOI]

Proceedings of the Computational Science, 2005

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

[BibT_eX]

[DOI]

Stefan Janson

Proceedings of the Hybrid Metaheuristics, Second International Workshop, 2005

Dynamic Decentralized Packet Clustering in Networks.

[BibT_eX]

[DOI]

Proceedings of the Applications of Evolutionary Computing, 2005

2004

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

[BibT_eX]

[DOI]

Adapt. Behav., 2004

Decentralized Packet Clustering in Networks.

[BibT_eX]

[DOI]

Proceedings of the 18th International Parallel and Distributed Processing Symposium (IPDPS 2004), 2004

Competition Controlled Pheromone Update for Ant Colony Optimization.

[BibT_eX]

[DOI]

Proceedings of the Ant Colony Optimization and Swarm Intelligence, 2004

2003

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

[BibT_eX]

[DOI]

J. Supercomput., 2003

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

[BibT_eX]

[DOI]

Appl. Intell., 2003

2002

Ameisenalgorithmen: Optimierung und Modellierung.

[BibT_eX]

[DOI]

PhD thesis, 2002

Ant colony optimization for resource-constrained project scheduling.

[BibT_eX]

[DOI]

Hartmut Schmeck

IEEE Trans. Evol. Comput., 2002

Fast Ant Colony Optimization on Runtime Reconfigurable Processor Arrays.

[BibT_eX]

[DOI]

Genet. Program. Evolvable Mach., 2002

Formal language recognition by stochastic cellular automata.

[BibT_eX]

[DOI]

Thomas Worsch

Fundam. Informaticae, 2002

Modeling the Dynamics of Ant Colony Optimization.

[BibT_eX]

[DOI]

Evol. Comput., 2002

Studies On The Dynamics Of Ant Colony Optimization Algorithms.

[BibT_eX]

Proceedings of the GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference, 2002

Ant Colony Optimization with the Relative Pheromone Evaluation Method.

[BibT_eX]

[DOI]

Proceedings of the Applications of Evolutionary Computing, 2002

Modelling ACO: Composed Permutation Problems.

[BibT_eX]

[DOI]

Proceedings of the Ant Algorithms, Third International Workshop, 2002

Coevolutionary Ant Algorithms Playing Games.

[BibT_eX]

[DOI]

Proceedings of the Ant Algorithms, Third International Workshop, 2002

2001

Fast ant colony optimization on reconfigurable processor arrays.

[BibT_eX]

[DOI]

Proceedings of the 15th International Parallel & Distributed Processing Symposium (IPDPS-01), 2001

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

[BibT_eX]

[DOI]

Proceedings of the Applications of Evolutionary Computing, 2001

Bi-Criterion Optimization with Multi Colony Ant Algorithms.

[BibT_eX]

[DOI]

Steffen Iredi

Proceedings of the Evolutionary Multi-Criterion Optimization, 2001

2000

Ant Colony Optimization for Resource-Constrained Projet Scheduling.

[BibT_eX]

Hartmut Schmeck

Proceedings of the Genetic and Evolutionary Computation Conference (GECCO '00), 2000

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

[BibT_eX]

[DOI]