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Research Output 2008 2020

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

Graph Transformations, Semigroups, and Isotopic Labeling

Andersen, J. L., Merkle, D. & Rasmussen, P. S., 2019, Bioinformatics Research and Applications. ISBRA 2019. Cai, Z., Skums, P. & Li, M. (eds.). Springer, p. 196-207 (Lecture Notes in Computer Science, Vol. 11490).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Labeling
Chemical reactions
Atoms
Chemical compounds
Pyruvic Acid

Information Processing in Chemical Systems

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2019, The Energetics of Computing in Life and Machines. Wolpert, D. H., Kempes, C., Stadler, P. F. & Grochow, J. A. (eds.). SFI Press

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

2018
133 Downloads (Pure)

A generic framework for engineering graph canonization algorithms

Andersen, J. L. & Merkle, D., Jan 2018, 2018 Proceedings of the 20th Workshop on Algorithm Engineering and Experiments, ALENEX 2018. Venkatasubramanian, S. & Pagh, R. (eds.). Society for Industrial and Applied Mathematics Publications, p. 139-153

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

File
Visualization
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

Linear time canonicalization and enumeration of non-Isomorphic 1-Face embeddings

Hellmuth, M., Knudsen, A. S., Kotrbík, M., Merkle, D. & Nøjgaard, N., 2018, 2018 Proceedings of the 20th Workshop on Algorithm Engineering and Experiments, ALENEX 2018. Venkatasubramanian, S. & Pagh, R. (eds.). Society for Industrial and Applied Mathematics Publications, p. 154-168

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Antiparallel
Enumeration
Linear Time
Trace
Face
90 Downloads (Pure)

Partial homology relations - satisfiability in terms of di-cographs

Nøjgaard, N., El-Mabrouk, N., Merkle, D., Wieseke, N. & Hellmuth, M., 2018, Computing and Combinatorics: 24th International Conference, COCOON 2018, Proceedings. Zhu, D. & Wang, L. (eds.). Springer, Vol. 10976. p. 403-415 (Lecture Notes in Computer Science, Vol. 10976).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

File
genes
methodology
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

Chemical Graph Transformation with Stereo-Information

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2017, Graph Transformation: 10th International Conference, ICGT 2017, Held as Part of STAF 2017, Marburg, Germany, July 18-19, 2017, Proceedings: Proceedings of the 10th International Conference on Graph Transformation. de Lara, J. & Plump, D. (eds.). Cham: Springer, p. 54-69 (Lecture Notes in Computer Science, Vol. 10373).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Stereoisomerism
Chemical reactions
Aconitate Hydratase
Equivalence classes
Chemical compounds

DNA-Templated Synthesis Optimization

Hansen, B. N., Larsen, K. S., Merkle, D. & Mihalchuk, A., 2017, 23rd International Conference on DNA Computing and Molecular Programming. Springer, p. 17-32 (Lecture Notes in Computer Science, Vol. 10467).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

DNA
DNA sequences
Costs
29 Downloads (Pure)

Forbidden time travel: Characterization of time-consistent tree reconciliation maps

Nøjgaard, N., Geiß, M., Merkle, D., Stadler, P. F., Wieseke, N. & Hellmuth, M., 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Schwartz, R. & Reinert, K. (eds.). Dagstuhl: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 17. (Leibniz International Proceedings in Informatics, Vol. 88).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Open Access
File
travel time
gene
gene transfer
history
2016

A Software Package for Chemically Inspired Graph Transformation

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2016, Graph Transformation: Proceedings of the 9th International Conference on Graph Transformation. Echahed, R. & Minas, M. (eds.). Springer, p. 73-88 (Lecture Notes in Computer Science, Vol. 9761).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Software packages
Molecules
Chemical reactions
Chemical analysis

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

Flamm, C., Merkle, D., Stadler, P. F. & Thorsen, U., 2016, Graph Transformation: Proceedings of the 9th International Conference on Graph Transformation. Echahed, R. & Minas, M. (eds.). Springer, p. 206-222 (Lecture Notes in Computer Science, Vol. 9761).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Chemical reactions
Atoms
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

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

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2014, Formal Methods in Macro-Biology: Proceedings of the First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Fages, F. & Piazza, C. (eds.). Springer, p. 117-135 (Lecture Notes in Computer Science, Vol. 8738).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Chemical reactions
Atoms
Biological systems
Chemical analysis
Isotopes

Computational methods for the analysis of mitochondrial genome rearrangements

Bernt, M., Merkle, D., Middendorf, M., Schierwater, B., Schlegel, M. & Stadler, P., 2014, Deep Metazoan Phylogeny: The backbone of the Tree of Life: New insights from analyses of molecules, morphology, and theory of data analysis. Wägele, J. W. & Bartolomaeus, T. (eds.). De Gruyter, p. 515-529

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

genes
phylogeny
methodology
genome
mitochondrial genome

FooPar: A Functional Object Oriented Parallel Framework in Scala

Hargreaves, F. P. & Merkle, D., 2014, Parallel Processing and Applied Mathematics : 10th International Conference, PPAM 2013, Warsaw, Poland, September 8-11, 2013, Revised Selected Papers, Part II. Wyrzykowski, R., Dongarra, J., Karczewski, K. & Waśniewski, J. (eds.). Springer, p. 118-129 (Lecture Notes in Computer Science, Vol. 8385).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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

Group Communication Patterns for High Performance Computing in Scala

Hargreaves, F. P., Merkle, D. & Schneider-Kamp, P., 2014, Proceedings of the 3rd ACM SIGPLAN Workshop on Functional High-Performance Computing. Association for Computing Machinery, p. 75-85

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Communication
Object oriented programming
Data structures
Specifications
Data storage equipment

Towards an Optimal DNA-Templated Molecular Assembler

Andersen, J. L., Flamm, C., Hanczyc, M. M. & Merkle, D., 30. Jul 2014, Artificial Life 14: Proceedings of the Fourteenth Conference on the Synthesis and Simulation of Living Systems. Sayama, H., Rieffel, J., Risi, S., Doursat, R. & Lipson, H. (eds.). MIT Press, p. 557-564

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

DNA
Program assemblers
Complementary DNA
High level synthesis
2013

Barrier Trees for Metabolic Adjustment Landscapes

Flamm, C., Hemmingsen, C. & Merkle, D., 2013, Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life. p. 1151-1158

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

Open Access
cost
fitness
metabolism
gene
carbon

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

Exploring Chemistry Using SMT

Fagerberg, R., Flamm, C., Merkle, D. & Peters, P., 2012, In : Lecture Notes in Computer Science. 7514

Research output: Contribution to journalConference articleResearchpeer-review

Chemistry
Modulo
Planning
Chemical Synthesis
Chemical compounds

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

Ant Inspired Methods for Organic Computing

Scheidler, A., Brutschy, A., Diwold, K., Merkle, D. & Middendorf, M., 2011, Organic Computing - A Paradigm Shift for Complex Systems. Müller-Schloer, C., Scmeck, H. & Ungerer, T. (eds.). Springer, p. 95-109

Research output: Chapter in Book/Report/Conference proceedingBook chapterResearchpeer-review

ant
social insect
labor division
pheromone
sorting

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

群智能 (Swarm intelligence introduction and applications)

Translated title of the contribution: Swarm intelligence introduction and applications (translation of Springer version)Blum, C. & Merkle, D., 2011, National Defence Industry Press. 286 p.

Research output: Book/anthology/thesis/reportBookResearchpeer-review

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

Artificial Life XII: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, Odense, Denmark, August 19-23, 2010

Fellermann, H. (ed.), Dörr, M. (ed.), Hanczyc, M. M. (ed.), Laursen, L. L. (ed.), Maurer, S. E. (ed.), Merkle, D. (ed.), Monnard, P-A. (ed.), Støy, K. (ed.) & Rasmussen, S. (ed.), 2010, MIT Press.

Research output: Book/anthology/thesis/reportBookResearchpeer-review

2009

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

Klemm, K., Merkle, D. & Olbrich, E., 2009, IOS Press. 160 p.

Research output: Book/anthology/thesis/reportBookResearch

cognition
metapopulation
robotics
stochasticity
population dynamics

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

Editorial: Artificial Life

Klemm, K., Merkle, D. & Olbrich, E., 2009, In : Advances in Complex Systems. 12, 3, p. vii-viii

Research output: Contribution to journalEditorialResearch

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

Finding All Sorting Tandem Duplication Random Loss Operations

Bernt, M., Chen, M-C., Merkle, D., Wang, H-L., Chao, K-M. & Middendorf, M., 2009, Combinatorial Pattern Matching (LNCS). Springer, p. 301-313 (Lecture Notes in Computer Science; No. 5577).

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

sorting
genes
genome
ingredients
history

On the Design of RNA Sequences for Realizing Extended Shapes

Hellmuth, M., Merkle, D. & Middndorf, M., 2009, Proceedings of the 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE Press, p. 167-173

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

RNA
Polynomials

Special issue on ant colony optimization

Doerner, K., Merkle, D. & Stützle, T., 2009, In : Swarm Intelligence. 3, 1, p. 1-2

Research output: Contribution to journalEditorialResearch

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

Diwold, K., Merkle, D. & Middendorf, M., 2009, Proceedings of the 8th German Workshop on Artificial Life (GWAL). IOS Press, p. 37-48

Research output: Chapter in Book/Report/Conference proceedingArticle in proceedingsResearchpeer-review

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

A Hybrid Population based ACO Algorithm for Protein Folding

Thalheim, T., Merkle, D. & Middendorf, M., 2008. 6 p.

Research output: Contribution to conference without publisher/journalPaperResearchpeer-review

Protein folding
Ant colony optimization
Bioinformatics