Parkinson's Disease Publications
Thiele & Fleming labs
Submitted publications:
26. Heinken et al., "APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites", (submitted).
25. Luo, X., Liu, Y., Balck, A., Klein, C., Fleming, R.M.T., "Identification of metabolites reproducibly associated with Parkinson’sDisease via meta-analysis and computational modelling", (submitted).
24. Preciat, G., Wegrzyn, A. B., Thiele, I., Hankemeier, T., Fleming, R.M.T.,” XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models”, submitted.
23. 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., “Mechanistic model-driven exometabolomic characterisation of human dopaminergic neuronal metabolism”, (submitted).
22. Moreno, E.L., Hachi, S., Nickels, S.L., Kane, K.I.W. , Moein, M., Schwamborn, J.C., Skupin, A., Vanden Berghe, P., Fleming, R.M.T., “Neuronal hyperactivity in a LRRK2-G2019S cellular model of Parkinson’s Disease” (submitted)..
Peer-reviewed publications:
21. 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., "Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine." Nat Biotechnol (2023). https://doi.org/10.1038/s41587-022-01628-0
20. Zagare, A., Preciat, G., Nickels, S.L., Luo, X., Monzel, A.S., Gomez-Giro, G., Robertson, G., Jaeger, C., Sharif, J., Koseki, H., Diederich, N.J., Glaab, E. , Fleming, R.M.T., Schwamborn, J.C., "Omics data integration suggests a potential idiopathic Parkinson’s disease signature." Communications Biology, 6(1), p.1179 (2023).
19.Huang, L., Drouin, N., Causon, J., Wegrzyn, A., Castro-Perez, J., Fleming, R.M.T., Harms, A., Hankemeier, T., “Reconstruction of Glutathione Metabolism in the Neuronal Model of Rotenone-Induced Neurodegeneration Using Mass Isotopologue Analysis with Hydrophilic Interaction Liquid Chromatography-Zeno High-Resolution Multiple Reaction Monitoring”, Analytical Chemistry, 95 (6), 3255-3266 (2023).
18. Heinken, A., Basile, A., Hertel. J., Thinnes, C., Thiele, I., "Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine", Annual Review of Microbiology, 75 (2021).
17. Heinken, A., Basile, A., Thiele, I., "Advances in constraint-based modelling of microbial communities." Current Opinion in Systems Biology, 27: 100346 (2021).
16. Baldini, F., Hertel, J., Sandt, E., Thinnes, C.C., Neuberger-Castillo, L., Pavelka, L., Betsou, F., Krüger, R., Thiele, I., "Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes", BMC Biology, 18(60) (2020).
15. Sturchio, A., Marsili, L., Vizcarra, J.A., Dwivedi, A.K., Kauffman, M.A., Duker, A.P., Lu, P., Pauciulo, M.W., Wissel, B.D., Hill, E.J., Stecher, B., Keeling, E.G., Vagal, A.S., Wang, L., Haslam, D.B., Robson, M.J., Tanner, C.M., Hagey, D.W., El Andaloussi, S., Ezzat, K., Fleming, R.M.T., Lu, L.J., Little, M.A., Espay, A.J., “Phenotype-Agnostic Molecular Subtyping of Neurodegenerative Disorders: The Cincinnati Cohort Biomarker Program (CCBP)”, Front. Aging Neurosci., Volume 12 (2020).
14. Kane, K.I.W., Jarazo, J., Moreno, E.L., Fleming, R.M.T., Schwamborn, J.C., “Passive controlled flow for Parkinson's disease neuronal cell culture in 3D microfluidic devices”, Organs-on-a-Chip, Volume 2 (2020).
13. Hertel, J., Harms, A.C., Heinken, A., Baldini, F., Thinnes. C.C., Glaab, E., Vasco, D.A., Pietzner, M., Stewart, I.D., Wareham, N.J., Langenberg, C., Trenkwalder, C., Krüger, R., Hankemeier, T., Fleming, R.M.T., Mollenhauer, B., Thiele, I., "Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease", Cell Reports (2019).
12. 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., "The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease". Nucleic Acids Research, 47(D1): D614-D624 (2019). Breakthrough Article.
11. Kane, K.I.W., Moreno, E.L., Hachi, S., Walter, M., Jarazo, J., Oliveira, M.A.P., Hankemeier, T., Vulto, P., Schwamborn, J.C., Thoma, M., Fleming, R.M.T., “Automated microfluidic cell culture of stem cell derived dopaminergic neurons”, Scientific Reports, 9: 1796 (2019).
10. Willacey, C.C.W, Naaktgeboren, M., Moreno, E.L., Wegrzyn, A.B., van der Es, D., Karu, N., Fleming, R.M.T., Harms, A.C., Hankemeier, T., “LC–MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide”, Journal of Chromatography A, Volume 1608 (2019).
9. Chen-Plotkin, A.S., Albin, R., Alcalay, R., Babcock, D., Bajaj, V., Bowman, D., Buko, A., Cedarbaum, J., Chelsky, D., Cookson, M.R., Dawson, T.M., Dewey, R., Foroud, T., Frasier, M., German, D., Gwinn, K., Huang, X., Kopil, C., Kremer, T., Lasch, S., Marek, K., Marto, J.A., Merchant, K., Mollenhauer, B., Naito, A., Potashkin, J., Reimer, A., Rosenthal, L.S., Saunders-Pullman, R., Scherzer, C.R., Sherer, T., Singleton, A., Sutherland, M., Thiele, I., van der Brug, M. Van Keuren-Jensen, K., Vaillancourt, D., Walt, D., West, A., Zhang, J., "Finding useful biomarkers for Parkinson's disease", Science Translational Medicine, 10(454): eaam6003 (2018).
8. Bolognin, S., Fossépré, M., Qing, X., Jarazo, J., Ščančar, J., Lucumi Moreno, E.L., Nickels, S.L., Wasner, K., Ouzren, N., Walter, J., Grünewald, A., Glaab, E., Salamanca, L., Fleming, R.M.T., Antony, P.M.A., Schwamborn, J.C., “3D Cultures of Parkinson's Disease-Specific Dopaminergic Neurons for High Content Phenotyping and Drug Testing”, Adv Sci (Weinh), 6(1):1800927 (2018).
7. Thiele, I., Clancy, C.M., Heinken, A., Fleming, R.M.T., ''Quantitative systems pharmacology and the personalized drug-microbiota-diet axis'', Current Opinion in Systems Biology, 4: 43-52 (2017).
6. Oliveira, M.A.P., Smidt, M.P., Fleming, R.M.T., ”Embryonic development of selectively vulnerable neurons in Parkinson’s disease”, npj Parkinson's Disease 3, 21 (2017).
5. Monzel, A.S., Smits, L.M., Hemmer, K., Hachi, S., Moreno, E.L., van Wuellen, T., Jarazo, J., Walter, J., Bruggemann, I., Boussaad, I., Berger, E., Fleming, R.M.T., Bolognin, S., Schwamborn, J.C., “Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells“, Stem Cell Reports, 8: 5, P1144-1154 (2017).
4. Noronha, A., Danielsdottir, A.D., Gawron, P., Johannsson, F., Jonsdottir, S., Jarlsson, S., Gunnarsson, J.P., Brynjolfsson, S., Schneider, R., Thiele, I., Fleming, R.M.T., ''ReconMap: an interactive visualization of human metabolism'', Bioinformatics, 33(4):605-607 (2016).
3. Ben Guebila, M., Thiele, I., ''Model-based dietary optimization for late-stage, levodopa-treated Parkinson's disease patients'', Systems Biology and Applications (2016).
2. Moreno, E.L., Hachi, S., Hemmer, K., Trietsch, S.J., Baumuratov, A.S., Hankemeier, T., Vulto, P., Schwamborn, J.C., Fleming, R.M.T., “Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture”, Lab on a chip, 11 (2015).
1. Mao, L., Nicolae, A., Oliveira, M.A.P., He, F., Hachi, S., Fleming, R.M.T., “A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease”, Computational and Structural Biotechnology Journal 13, 484–491(2015).