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Research Output 2008 2020

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Journal article
2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design

Andersen, J. L., Merkle, D. & Rasmussen, P. S., 2020, In : Journal of Computational Biology. 27, 2, p. 269-287 19 p.

Research output: Contribution to journalJournal articleResearchpeer-review

2019
118 Downloads (Pure)

Chemical transformation motifs: modelling pathways as integer hyperflows

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 1. Mar 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 2, p. 510-523

Research output: Contribution to journalJournal articleResearchpeer-review

File
Glycolysis
Metabolic Networks and Pathways
Pathway
Integer
Electric network analysis
2018
58 Downloads (Pure)

DNA-templated synthesis optimization

Hansen, B. N., Larsen, K. S., Merkle, D. & Mihalchuk, A., 2018, In : Natural Computing. 17, 4, p. 693-707

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
DNA
DNA sequences
Linear programming
Costs
141 Downloads (Pure)

Finding the K best synthesis plans

Fagerberg, R., Flamm, C., Kianian, R., Merkle, D. & Stadler, P. F., 5. Apr 2018, In : Journal of Cheminformatics. 10, 21 p., 19.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
planning
synthesis
Planning
costs
planning process
46 Downloads (Pure)

Rule composition in graph transformation models of chemical reactions

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 1. Jan 2018, In : Match. 80, 3, p. 661-704 44 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Chemical reactions
Atoms
Chemical analysis
Isotopes
Labeling
111 Downloads (Pure)

Time-consistent reconciliation maps and forbidden time travel

Nøjgaard, N., Geiß, M., Merkle, D., Stadler, P. F., Wieseke, N. & Hellmuth, M., 2018, In : Algorithms for Molecular Biology. 13, 1, 17 p., 2.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Reconciliation
Travel Time
Travel time
Genes
Time Consistency
49 Downloads (Pure)

Towards mechanistic prediction of mass spectra using graph transformation

Andersen, J. L., Fagerberg, R., Flamm, C., Kianian, R., Merkle, D. & Stadler, P. F., 1. Jan 2018, In : MATCH Communications in Mathematical and in Computer Chemistry. 80, 3, p. 705-731

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
Computational methods
Reaction rates
Mass spectrometry
Dynamical systems
2017
112 Downloads (Pure)

An intermediate level of abstraction for computational systems chemistry

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2017, In : Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 375, 2109, 20160354.

Research output: Contribution to journalJournal articleResearchpeer-review

File
Chemistry
Chemical reactions
Reaction Network
chemistry
Origin of Life
2015

Algorithmic Cheminformatics (Dagstuhl Seminar 14452)

Banzhaf, W., Flamm, C., Merkle, D. & Stadler, P. F., 2015, In : Dagstuhl Reports. 4, 11, p. 22-39 18 p.

Research output: Contribution to journalJournal articleResearchpeer-review

computer science
chemistry

In silico Support for Eschenmoser’s Glyoxylate Scenario

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2015, In : Israel Journal of Chemistry. 55, 8, p. 919–933

Research output: Contribution to journalJournal articleResearchpeer-review

Prebiotics
Complex networks
Metabolism
Sugars
Nucleotides

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

Merkle, D., Middendorf, M. & Scheidler, A., 2015, In : International Journal of Autonomous and Adaptive Communications Systems. 8, 1, p. 60-80

Research output: Contribution to journalJournal articleResearchpeer-review

Clustering algorithms
Reconfigurable hardware
Costs

Towards Optimal DNA-Templated Computing

Andersen, J. L., Flamm, C., Hanczyc, M. M. & Merkle, D., 2015, In : International Journal of Unconventional Computing. 11, 3-4, p. 185-203

Research output: Contribution to journalJournal articleResearchpeer-review

DNA
Program assemblers
2014

Generic Strategies for Chemical Space Exploration

Andersen, J. L., Merkle, D., Flamm, C. & Stadler, P., 28. May 2014, In : International Journal of Computational Biology and Drug Design. 7, 2/3, p. 225-258

Research output: Contribution to journalJournal articleResearchpeer-review

Functional programming
Molecules
Carbohydrates
Chemical reactions
Specifications
2013

Inferring chemical reaction patterns using rule composition in graph grammars

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 6. Jun 2013, In : Journal of Systems Chemistry. 4, 4

Research output: Contribution to journalJournal articleResearchpeer-review

Chemical reactions
Chemical analysis
Polymerization
Carbon
Terpenes

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

Andersen, J. L., Andersen, T., Flamm, C., Hanczyc, M., Merkle, D. & Stadler, P. F., 2013, In : Entropy. 15, 10, p. 4066-4083

Research output: Contribution to journalJournal articleResearchpeer-review

grammars
hydrolysis
mass spectroscopy
polymerization
hydrocyanic acid

On the Complexity of Reconstructing Chemical Reaction Networks

Fagerberg, R., Flamm, C., Merkle, D., Peters, P. & Stadler, P. F., Sep 2013, In : Mathematics in Computer Science. 7, 3, p. 275-292

Research output: Contribution to journalJournal articleResearchpeer-review

Chemical Reaction Networks
Hypergraph
Chemical reactions
Graph in graph theory
NP-completeness

Swarm controlled emergence for ant clustering

Scheidler, A., Merkle, D. & Middendorf, M., 2013, In : International Journal of Intelligent Computing and Cybernetics. 6, 1, p. 62-82 21 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Clustering algorithms
Robots
Experiments
2012

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

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2012, In : Journal of Systems Chemistry. 3, 1

Research output: Contribution to journalJournal articleResearchpeer-review

Chemical reactions
Cones
Metabolic Networks and Pathways
Fluxes
Polynomials
2011

Finding all sorting tandem duplication random loss operations

Bernt, M., Chen, K. Y., Chen, M. C., Chu, A. C., Merkle, D., Wang, H. L., Chao, K. M. & Middendorf, M., Mar 2011, In : Journal of Discrete Algorithms. 9, 1, p. 32-48

Research output: Contribution to journalJournal articleResearchpeer-review

Duplication
Sorting
Genes
Gene
Permutation
2010

A parameter-adaptive dynamic programming approach for inferring cophylogenies

Merkle, D., Middendorf, M. & Wieseke, N., 18. Jan 2010, In : BMC Bioinformatics. 11, SUPPLL.1, S60.

Research output: Contribution to journalJournal articleResearchpeer-review

Adaptive Dynamics
Dynamic programming
Dynamic Programming
Costs
History
2009

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

Diwold, K., Merkle, D. & Middendorf, M., 2009, In : Advances in Complex Systems. 12, 3, p. 327-346

Research output: Contribution to journalJournal articleResearchpeer-review

Personnel

Extended shapes for the combinatorial design of RNA sequences

Hellmuth, M., Merkle, D. & Middendorf, M., 2009, In : International Journal of Computational Biology and Drug Design. 2, 4, p. 371-384

Research output: Contribution to journalJournal articleResearchpeer-review

RNA
Base Pairing
Polynomials
2008

A Decentralization Approach for Swarm Intelligence Algorithms in Networks Applied to Multi Swarm PSO

Janson, S., Merkle, D. & Middendorf, M., 2008, In : International Journal of Intelligent Computing and Cybernetics. 1, 1, p. 24-45

Research output: Contribution to journalJournal articleResearchpeer-review

Particle swarm optimization (PSO)
Function evaluation
Swarm intelligence
Set theory
Routers

Evolution of Mitochondrial Gene Orders in Echinoderms

Perseke, M., Fritzsch, G., Ramsch, K., Bernt, M., Merkle, D., Middendorf, M., Bernhard, D., Stadler, P. & Schlegel, M., 2008, In : Molecular Phylogenetics and Evolution. 47, p. 855–864

Research output: Contribution to journalJournal articleResearchpeer-review

Mitochondrial Genes
echinoderm
Echinodermata
Transfer RNA
genome

Molecular Docking with Multi-Objective Particle Swarm Optimization

Janson, S., Merkle, D. & Middendorf, M., 2008, In : Applied Soft Computing. 8, 1, p. 666-675

Research output: Contribution to journalJournal articleResearchpeer-review

Particle swarm optimization (PSO)
Ligands
Molecules
Simulated annealing
Electron energy levels

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

Merkle, D., Middendorf, M. & Scheidler, A., 2008, In : Understanding Complex Systems. p. 221-240 20 p.

Research output: Contribution to journalJournal articleResearchpeer-review

Reconfigurable hardware
Clustering algorithms
Costs

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

Merkle, D., Middendorf, M. & Scheidler, A., 2008, In : Journal of Mathematical Modelling and Algorithms. 7, 2, p. 237-254

Research output: Contribution to journalJournal articleResearchpeer-review

Reconfigurable hardware
Task Allocation
Computing
Reconfigurable Hardware
Social Insects

Solving the Preserving Reversal Median Problem

Bernt, M., Merkle, D. & Middendorf, M., 1. Jan 2008, In : IEEE ACM Transactions on Computational Biology and Bioinformatics. 5, 3, p. 332-347

Research output: Contribution to journalJournal articleResearchpeer-review

Stability and Performance of Ant Queue Inspired Task Partitioning Methods

Scheidler, A., Merkle, D. & Middendorf, M., 2008, In : Theory in Biosciences. 127, 2, p. 149-161

Research output: Contribution to journalJournal articleResearchpeer-review

ant
Queue
Partitioning
Formicidae
partitioning

Swarm Intelligence and Signal Processing

Merkle, D. & Middendorf, M., 1. Jan 2008, In : IEEE Signal Processing Magazine. 25, 6, p. 152-158

Research output: Contribution to journalJournal articleResearchpeer-review