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Page 1
Representing Catalytic Mechanisms with Rule Composition.
J Chem Inf Model. 2022 Nov 28;62(22):5513-5524. doi: 10.1021/acs.jcim.2c00426. Epub 2022 Nov 3.
J Chem Inf Model. 2022.
PMID: 36326605
Graph transformation for enzymatic mechanisms.
Andersen JL, Fagerberg R, Flamm C, Fontana W, Kolčák J, Laurent CVFP, Merkle D, Nøjgaard N.
Andersen JL, et al.
Bioinformatics. 2021 Jul 12;37(Suppl_1):i392-i400. doi: 10.1093/bioinformatics/btab296.
Bioinformatics. 2021.
PMID: 34252947
Free PMC article.
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Chemical Transformation Motifs-Modelling Pathways as Integer Hyperflows.
Andersen JL, Flamm C, Merkle D, Stadler PF.
Andersen JL, et al.
IEEE/ACM Trans Comput Biol Bioinform. 2019 Mar-Apr;16(2):510-523. doi: 10.1109/TCBB.2017.2781724. Epub 2017 Dec 11.
IEEE/ACM Trans Comput Biol Bioinform. 2019.
PMID: 29990045
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Generic strategies for chemical space exploration.
Andersen JL, Flamm C, Merkle D, Stadler PF.
Andersen JL, et al.
Int J Comput Biol Drug Des. 2014;7(2-3):225-58. doi: 10.1504/IJCBDD.2014.061649. Epub 2014 May 28.
Int J Comput Biol Drug Des. 2014.
PMID: 24878732
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Combining Graph Transformations and Semigroups for Isotopic Labeling Design.
Andersen JL, Merkle D, Rasmussen PS.
Andersen JL, et al.
J Comput Biol. 2020 Feb;27(2):269-287. doi: 10.1089/cmb.2019.0291. Epub 2019 Nov 22.
J Comput Biol. 2020.
PMID: 31750739
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An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions.
Arya A, Ray J, Sharma S, Cruz Simbron R, Lozano A, Smith HB, Andersen JL, Chen H, Meringer M, Cleaves HJ 2nd.
Arya A, et al.
Chem Sci. 2022 Mar 23;13(17):4838-4853. doi: 10.1039/d2sc00256f. eCollection 2022 May 4.
Chem Sci. 2022.
PMID: 35655880
Free PMC article.
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An intermediate level of abstraction for computational systems chemistry.
Andersen JL, Flamm C, Merkle D, Stadler PF.
Andersen JL, et al.
Philos Trans A Math Phys Eng Sci. 2017 Dec 28;375(2109):20160354. doi: 10.1098/rsta.2016.0354.
Philos Trans A Math Phys Eng Sci. 2017.
PMID: 29133452
Free PMC article.
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