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  • 2020
  • 2018
  • 2017
  • 2016

Author

  • Daniel Merkle
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

2018

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

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
128 Downloads (Pure)
2020

Combining Graph Transformations and Semigroups for Isotopic Labeling Design

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

Research output: Contribution to journalJournal articleResearchpeer-review

2017

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
137 Downloads (Pure)
2020

A Generic Framework for Engineering Graph Canonization Algorithms

Andersen, J. L. & Merkle, D., Apr 2020, In : A C M Journal of Experimental Algorithmics. 25, 1, 1.2.

Research output: Contribution to journalJournal articleResearchpeer-review

A graph-based tool to embed the π-calculus into a computational DPO framework

Andersen, J. L., Hellmuth, M., Merkle, D., Nøjgaard, N. & Peressotti, M., 8. Mar 2020, In : CEUR Workshop Proceedings. 2568, p. 121-132

Research output: Contribution to journalConference articleResearchpeer-review

Open Access
File
2017

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
32 Downloads (Pure)
2018

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
134 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
182 Downloads (Pure)
2017

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

2018

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
185 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
57 Downloads (Pure)
2016

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

2017

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

2018

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
78 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
56 Downloads (Pure)