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Collaborations and top research areas from the last five years
Research output
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A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems
Herrera Machado, E. M., Andersen, J. L., Fagerberg, R. & Merkle, D., 9. Feb 2026, In: Journal of Chemical Information and Modeling. 66, 3, p. 1637-1651Research output: Contribution to journal › Journal article › Research › peer-review
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Computational approaches in chemical space exploration for carbon fixation pathways
Abel, A. S., Lauber, N., Andersen, J. L., Fagerberg, R., Merkle, D. & Flamm, C., Dec 2026, In: npj Systems Biology and Applications. 12, 1, 17.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile8 Downloads (Pure) -
SynCat: molecule-level attention graph neural network for precise reaction classification
Van Nguyen, P. C., To, V. T., Nguyen Tran, N. V., Phan, T. L., Truong, T. N., Gärtner, T., Merkle, D. & Stadler, P. F., Jan 2026, In: Digital Discovery. 5, 1, p. 241-253 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile -
Assembly in Directed Hypergraphs
Flamm, C., Merkle, D. & Stadler, P. F., Oct 2025, In: Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 481, 2324, 21 p., 20250331.Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile4 Downloads (Pure) -
ChemReservoir—An Open-Source Framework for Chemically-Inspired Reservoir Computing
Yirik, M. A., Andersen, J. L., Fagerberg, R. & Merkle, D., 2025, In: IEEE Access. 13, p. 149197-149202Research output: Contribution to journal › Journal article › Research › peer-review
Open AccessFile31 Downloads (Pure)
Activities
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Teaching Committee, IMADA (External organisation)
Merkle, D. (Member)
2015 → …Activity: Membership › Membership of commitees, commissions, boards, councils, associations, organisations, or similar
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University of Southern Denmark (External organisation)
Merkle, D. (Member)
2015 → …Activity: Membership › Membership of commitees, commissions, boards, councils, associations, organisations, or similar
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Dagstuhl Seminar - Algorithmic Cheminformatics
Merkle, D. (Organizer)
2. Nov 2014 → 7. Nov 2014Activity: Attending an event › Conference organisation or participation
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COST Action CM1304 "Emergence and Evolution of Complex Chemical Systems" (External organisation)
Merkle, D. (Member)
3. Dec 2013 → 2. Dec 2017Activity: Membership › Board duties in companies, associations, or public organisations
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COST Action TD1308: Origins and evolution of life on Earth and in the Universe (ORIGINS) (External organisation)
Merkle, D. (Member)
2013 → 2017Activity: Membership › Board duties in companies, associations, or public organisations
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Novo Nordisk Fonden - MATOMIC - Mathematical Modelling for Microbial Community Induced Metabolic Diseases
Merkle, D. (Project participant)
01/01/2022 → 31/12/2027
Project: Research
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EU - Horizon Europe - TACsy - (Drift) Training Alliance for Computational Systems chemistry
Merkle, D. (Project participant)
01/03/2021 → 01/03/2027
Project: EU
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EU - Horizon Europe - TACsy - (PhD) Training Alliance for Computational Systems chemistry
Merkle, D. (Project participant)
01/03/2023 → 28/02/2027
Project: EU
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Challenge Programme Symposium 2024 - Novo Nordisk Fonden
Merkle, D. (PI)
01/05/2024 → 31/12/2024
Project: Private Foundations
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Novo Nordisk Fonden - From Category Theory to Enzyme Design: Unleashing the Potential of Computational Systems Chemistry
Merkle, D. (Approving authority)
01/07/2020 → 30/06/2022
Project: Private Foundations
Press/Media
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Med 366 mio. kr. i ryggen får syv ambitiøse forskningsprojekter luft under vingerne med Novo Nordisk Fondens Challenge Programme 2021
21/08/2025
1 Media contribution
Press/Media: Press / Media
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Matematisk sygdomsmodellering løftes med to store bevillinger
21/08/2025
1 Media contribution
Press/Media: Press / Media
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PRM / Matematik skal afsløre, hvad der foregår i overvægtiges tarmsystem
28/07/2022
1 Media contribution
Press/Media: Press / Media
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PRM / Matematik skal afsløre, hvad der foregår i overvægtiges tarmsystem
28/07/2022
1 Media contribution
Press/Media: Press / Media
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Matematik skal afsløre, hvad der foregår i overvægtiges tarmsystem
28/07/2022
1 Media contribution
Press/Media: Press / Media
Impacts
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PRM / Matematik skal afsløre, hvad der foregår i overvægtiges tarmsystem
Merkle, D. (Participant)
Impact: Quality of life impact