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| Phan TL, Weinbauer K, Laffitte MEG, et al. (2025) SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. Journal of Chemical Information and Modeling |
| Andersen JL, Banke S, Fagerberg R, et al. (2025) Pathway Realizability in Chemical Networks. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 32: 164-187 |
| Müller S, Flamm C, Stadler PF. (2022) What makes a reaction network "chemical"? Journal of Cheminformatics. 14: 63 |
| Flamm C, Hellmuth M, Merkle D, et al. (2020) Generic Context-Aware Group Contributions. Ieee/Acm Transactions On Computational Biology and Bioinformatics |
| Silva WMCd, Andersen JL, Holanda MT, et al. (2019) Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks Processes. 7: 240 |
| Wolfinger MT, Flamm C, Hofacker IL. (2018) Efficient computation of co-transcriptional RNA-ligand interaction dynamics. Methods (San Diego, Calif.) |
| Findeiß S, Hammer S, Wolfinger MT, et al. (2018) In silico design of ligand triggered RNA switches. Methods (San Diego, Calif.) |
| Fagerberg R, Flamm C, Kianian R, et al. (2018) Finding the K best synthesis plans. Journal of Cheminformatics. 10: 19 |
| Andersen JL, Flamm C, Merkle D, et al. (2017) Chemical Transformation Motifs --- Modelling Pathways as Integer Hyperflows. Ieee/Acm Transactions On Computational Biology and Bioinformatics |
| Andersen JL, Flamm C, Merkle D, et al. (2017) An intermediate level of abstraction for computational systems chemistry. Philosophical Transactions. Series a, Mathematical, Physical, and Engineering Sciences. 375 |