20122020

Research output per year

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Research Output

  • 12 Journal article
  • 7 Article in proceedings
  • 1 Ph.D. thesis
  • 1 Book chapter
2020

A Graph-Based Tool to Embed the pi-Calculus into a Computational DPO Framework

Andersen, J. L., Hellmuth, M., Merkle, D., Nøjgaard, N. & Peressotti, M., 2020, Proceedings of the SOFSEM 2020 Doctoral Student Research. ceur workshop proceedings, Vol. 2568. p. 121-132 12 p. (CEUR Workshop Proceedings).

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

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

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
144 Downloads (Pure)

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

Silva, W. M. C. D., Andersen, J. L., Holanda, M. T., Walter, M. E. M. T., Brigido, M. M., Stadler, P. F. & Flamm, C., 2019, In : Processes. 7, 4, 18 p., 240.

Research output: Contribution to journalJournal articleResearchpeer-review

Open Access
File
71 Downloads (Pure)

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

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

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
162 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
54 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
51 Downloads (Pure)
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
122 Downloads (Pure)

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

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

2015

Analysis of Generative Chemistries

Andersen, J. L., 2015, Odense: Syddansk Universitet. Det Naturvidenskabelige Fakultet.

Research output: Book/anthology/thesis/reportPh.D. thesisResearch

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

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

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

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

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

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

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

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