If you made any changes in Pure these will be visible here soon.

Research Output 2008 2020

Filter
Article in proceedings
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. (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
2018
136 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

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
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

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
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

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

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
2009

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

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