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  • Daniel Merkle
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. (red.). Cham: Springer, s. 54-69 (Lecture Notes in Computer Science, Bind 10373).

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review

2019

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. (red.). SFI Press

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingBidrag til bog/antologiForskningpeer 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, s. 17-32 (Lecture Notes in Computer Science, Bind 10467).

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer 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. (red.). Society for Industrial and Applied Mathematics Publications, s. 154-168

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review

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. (red.). Springer, s. 73-88 (Lecture Notes in Computer Science, Bind 9761).

Publikation: Bidrag til bog/antologi/rapport/konference-proceedingKonferencebidrag i proceedingsForskningpeer review

2018

Rule composition in graph transformation models of chemical reactions

Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 1. jan. 2018, I : Match. 80, 3, s. 661-704 44 s.

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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, I : MATCH Communications in Mathematical and in Computer Chemistry. 80, 3, s. 705-731

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52 Downloads (Pure)

Time-consistent reconciliation maps and forbidden time travel

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

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127 Downloads (Pure)

DNA-templated synthesis optimization

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

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73 Downloads (Pure)
2017

An intermediate level of abstraction for computational systems chemistry

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

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128 Downloads (Pure)
2018

Finding the K best synthesis plans

Fagerberg, R., Flamm, C., Kianian, R., Merkle, D. & Stadler, P. F., 5. apr. 2018, I : Journal of Cheminformatics. 10, 21 s., 19.

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174 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. (red.). Springer, Bind 10976. s. 403-415 (Lecture Notes in Computer Science, Bind 10976).

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121 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. (red.). Springer, s. 206-222 (Lecture Notes in Computer Science, Bind 9761).

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2019

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. (red.). Springer, s. 196-207 (Lecture Notes in Computer Science, Bind 11490).

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Chemical transformation motifs: modelling pathways as integer hyperflows

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

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149 Downloads (Pure)
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. (red.). Dagstuhl: Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing, 17. (Leibniz International Proceedings in Informatics, Bind 88).

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31 Downloads (Pure)
2018

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. (red.). Society for Industrial and Applied Mathematics Publications, s. 139-153

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169 Downloads (Pure)