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Database and Resource Publications

Submitted publications:

"Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism", Preciat, G., Wegrzyn, A.B., Lucumi Moreno, E., Willacey, C. C.W., Modamio, J., Monteiro, F.L., El Assal, D., Schurink, A., Oliveira, M.A.P., Zhang, Z., Cousins,B., Haraldsdóttir, H.S., Hachi, S., Zach, S., Leparc, G., Lee, Y.T.,  Hengerer,  B., Vempala, S., Saunders,  M.A., Harms, A., Glaab, E.,  Schwamborn, J.C.,  Thiele, I.,  Hankemeier, T., Fleming, R.M.T., (submitted)

Peer-reviewed publications:

2023
2022
2021
2020
2019
2017
2022
2023
2020
2021
2017
2019
"APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", Heinken et al., (submitted). 
"Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.", Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., Thiele, I., Nat Biotechnol (2023). https://doi.org/10.1038/s41587-022-01628-0
"Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication.", Thiele, I., Fleming, R. M. T., Computational and Structural Biotechnology, 4098-4109 (2022).
"DEMETER: Efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations", Heinken, A., Magnusdottir, S., Fleming, R.M.T., Thiele, I., Bioinformatics, btab622 (2021).
"Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine", Heinken, A., Basile, A., Hertel. J., Thinnes, C., Thiele, I., Annual Review of Microbiology, 75 (2021).
"Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism.", Zhu, L., Pei, W., Thiele, I., Mahadevan, R., PLoS Computational Biology, 17(8): e1009110 (2021).
"Personalized whole-body models integrate metabolism, physiology, and the gut microbiome", Thiele, I., Sahoo, S., Heinken, A., Hertel, J., Heirendt, L., Aurich, M.K., Fleming, R.M.T., , Molecular Systems Biology, 16:e8982 (2020).
"The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease", Noronha, A., Modamio, J., Jarosz, Y., Sompairac, N., Gonzalez, G., DanÃielsdottir, A.D., Krecke, M., Merten, D., Haraldsdottir, H.S., , A., Heirendt, L., Magnusdottir, S., Ravcheev, D.A., Sahoo, S., Gawron, P., Guerard, E., Friscioni, L., Garcia, B., Prendergast, M., Rodrigues, M., Roy, A., Rouquaya, M., Wiltgen, L., Zagare, A., John, E., Krueger, M., Kuperstein, I., Zinovyev, A., Schneider, R., Fleming, R.M.T.,  Thiele, I., Nucleic Acids Research, 47(D1): D614-D624 (2019).  Breakthrough Article.
"Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota", Magnusdottir, S., Heinken, A., Kutt, L., Ravcheev, D.A., Bauer, E., Noronha, A., Greenhalgh, K., Jaeger, C., Baginska, J., Wilmes, P., Fleming, R.M.T., Thiele, I., Nature Biotechnology, 35(1):81-89 (2017). 

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