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Parkinson's disease publications

Submitted publications:

"Identification of metabolites reproducibly associated with Parkinson’s Disease via meta-analysis and computational modelling", Luo, X., Liu, Y., Balck, A., Klein, C., Fleming, R.M.T., (submitted).
"XomicsToModel: Omics data integration and generation of thermodynamically consistent metabolic models", Preciat, G., Wegrzyn, A. B., Thiele, I., Hankemeier, T., Fleming, R.M.T., (submitted).
"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)
"Neuronal hyperactivity in a LRRK2-G2019S cellular model of Parkinson’s Disease", 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., (submitted).

Peer-reviewed publications:

2023
"Omics data integration suggests a potential idiopathic Parkinson’s disease signature.", 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., Communications Biology, 6(1), p.1179 (2023).
"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", Huang, L., Drouin, N., Causon, J., Wegrzyn, A., Castro-Perez, J., Fleming, R.M.T., Harms, A., Hankemeier, T., Analytical Chemistry, 95 (6), 3255-3266 (2023).
"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
2021
2020
"Passive controlled flow for Parkinson"s disease neuronal cell culture in 3D microfluidic devices", Kane, K.I.W., Jarazo, J., Moreno, E.L., Fleming, R.M.T., Schwamborn, J.C., Organs-on-a-Chip, Volume 2 (2020)
"Phenotype-Agnostic Molecular Subtyping of Neurodegenerative Disorders: The Cincinnati Cohort Biomarker Program (CCBP)", 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., Front. Aging Neurosci., Volume 12 (2020)
2019
"Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease", 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., Ines Thiele, I., Cell Reports (2019).
"LC–MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide", C.C.W. Willacey, M. Naaktgeboren, E.L. Moreno, A.B. Wegrzyn, D. Van der Es, et. al., Journal of Chromatography a 1608, 460413, (2019)
"3D cultures of Parkinson"s disease‐specific dopaminergic neurons for high content phenotyping and drug testing", S. Bolognin, M. Fossépré, X. Qing, J. Jarazo, J. Ščančar, E.L. Moreno, et. al, Advanced Science 6 (1), 1800927, (2019)
"Automated microfluidic cell culture of stem cell derived dopaminergic neurons", K.I.W. Kane, E.L. Moreno, S. Hachi, M. Walter, J. Jarazo, M.A.P. Oliveira, et. al., Scientific reports 9 (1), 1-12, (2019)
"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.
2018
2023
2021
2020
2019
2025
"Finding useful biomarkers for Parkinson"s disease", 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., Science Translational Medicine, 10(454): eaam6003 (2018).
"Parkinson’s disease-associated alterations of the gut microbiome can invoke disease-relevant metabolic changes", Baldini, F., Hertel, J., Sandt, E., Thinnes, C.C., Neuberger-Castillo, L., Pavelka, L., Betsou, F., Krüger, R., Thiele, I., BMC Biology, 18(60) (2020).
"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).
"Advances in constraint-based modelling of microbial communities.", Heinken, A., Basile, A., Thiele, I., Current Opinion in Systems Biology, 27: 100346 (2021).
2017
"Quantitative systems pharmacology and the personalized drug-microbiota-diet axis", Thiele, I., Clancy, C.M., Heinken, A., Fleming, R.M.T., Current Opinion in Systems Biology, 4: 43-52 (2017).
"Embryonic development of selectively vulnerable neurons in Parkinson’s disease", M.A.P. Oliveira, R. Balling, M.P. Smidt, R.M.T. Fleming, npj Parkinson's Disease 3 (1), 1-13, (2017)
2018
2017
"Derivation of human midbrain-specific organoids from neuroepithelial stem cells", A.S. Monzel, L.M. Smits, K. Hemmer, S. Hachi, E.L. Moreno, T. van Wuellen, et. al., Stem cell reports 8 (5), 1144-1154, (2017)
2016
"ReconMap: an interactive visualization of human metabolism", 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., Bioinformatics, 33(4):605-607 (2016). 
"Model-based dietary optimization for late-stage, levodopa-treated Parkinson"s disease patients", Ben Guebila, M., Thiele, I., Systems Biology and Applications (2016).
2015
"A constraint-based modelling approach to metabolic dysfunction in Parkinson"s disease", L Mao, A Nicolae, MAP Oliveira, F He, S Hachi, RMT Fleming Computational and structural biotechnology journal 13, 484-491, (2015)
"Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture", EL Moreno, S Hachi, K Hemmer, SJ Trietsch, AS Baumuratov, T Hankemeier, P Vulto, JC Schwamborn, RMT Fleming, Lab on a Chip 15 (11), 2419-2428, (2015)
2016
2015
2025
"Metabolic modeling links gut microbiota to metabolic markers of Parkinson’s disease", Hensen, T., Thiele, I., Gut Microbes 17(1), (2025).

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