Ronan Fleming
Assistant Professor
- Name
- Dr. R.M. Fleming
- Telephone
- +31 71 527 2727
- r.m.fleming@lacdr.leidenuniv.nl
- ORCID iD
- 0000-0001-5346-9812
After studying anatomy, physiology, biochemistry, pathology and clinical veterinary medicine, Dr. Fleming began preparing for a systems biology Ph.D. by studying computer science and mathematics. His Ph.D. concerned the analysis of transcriptomic data in E. coli using empirical mode decomposition, and laterly, a mathematical exploration of the physico-chemical basis of constraint-based modeling. Dr. Fleming leads the Systems Biochemistry Group, an interdiscipinary research group of mathematical, computational and experimental biologists. The fundamental interest is to develop scalable mathematical and numerical analysis techniques that increase the predictive fidelity of biomolecular network models, by incorporating physico-chemical constraints, motivated by optimality principles. Their applied interest is in the aetiopathogenesis and amelioration of Parkinson’s disease. Model predictions are used for optimal experimental design and compared with quantitative experimental data, including that obtained from their microfluidic cell cultures of dopaminergic neurons, derived from normal and Parkinsonian human subjects using stem cell biology techniques.
PhD/Postdocs
Assistant Professor
- Science
- Leiden Academic Centre for Drug Research
- LACDR/Analytical Biosciences
- Fleming R.M.T., Haraldsdottir H.S., Minh L.H., Vuong P.T., HankemeierT. & Thiele I. (2023), Cardinality optimization in constraint-based modelling: application to human metabolism, Bioinformatics 39(9): btad450.
- Huang L., Drouin N.F.P., Causon J., Wegrzyn A.B., Castro-Perez J., Fleming R.M., Harms A.C. & Hankemeier T. (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, Analytical Chemistry 95(6): 3255-3266.
- Thiele I., Preciat G. & Fleming R.M. (2022), MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions, Bioinformatics 38(20): 4831-4832.
- Thiele I. & Fleming R.M. (2022), Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication, Computational and Structural Biotechnology Journal 20: 4098-4109.
- Lieven C., Beber M.E., Olivier B.G., Bergmann F.T., Ataman M., Babaei. P., Bartell J.A., Blank L.M., Chauhan S., Correia K., Diener C., Drager A., Ebert B.E., Edirisinghe J.N., Faria J.P., Feist A.M., Fengos G., Fleming R.M.T., Garcia-Jimenez B., Hatzimanikatis V., Helvoirt W. van, Henry C.S., Hermjakob H., Herrgard M.J., Kaafarani A., Kim H.U., King Z, Klamt S., Klipp E., Koehorst J.J., Konig M., Lakshmanan M., Lee D.Y., Lee S.Y., Lee S.J., Lewis N.E., Liu F., Ma H.W., Machado D., Mahadevan R., Maia P., Mardinoglu A., Medlock G.L., Monk J.M., Nielsen J., Nielsen L.K., Nogales J., Nookaew I., Palsson B.O., Papin J.A., Patil K.R., Poolman M, Price N.D., Resendis-Antonio O., Richelle A., Rocha I., Sanchez B.J., Schaap P.J., Sheriff R.S.M., Shoaie S., Sonnenschein N., Teusink B., Vilaca P., Vik J.O., Wodke J.A.H., Xavier J.C., Yuan QQ, Zakhartsev M. & Zhang C. (2020), Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing, Nature Biotechnology 38: 504.
- Thiele I., Sahoo S., Heinken A., Hertel J., Heirendt L., Aurich M.K. & Fleming R.M. (2020), Personalized whole-body models integrate metabolism, physiology, and the gut microbiome, Molecular Systems Biology 16(5): e8982.
- Sturchio A., Marsili L., Vizcarra J.A., Dwivedi A.K., Kauffman M.A., Duker A.P., Lu P.X., Pauciulo M.W., Wissel B.D., Hill E.J., Stecher B., Keeling E.G., Vagal A.S., Wang L.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. (2020), Phenotype-agnostic molecular subtyping of neurodegenerative disorders: the Cincinnati Cohort Biomarker Program (CCBP), Frontiers in Aging Neuroscience 12: 553635.
- Ghaderi S., Haraldsdottir H.S., Ahookhosh M., Arreckx S. & Fleming R.M.T. (2020), Structural conserved moiety splitting of a stoichiometric matrix, Journal of Theoretical Biology 499: 110276.
- Kane K.I.W., Lucumi Moreno E., Hachi S., Walter M., Jarazo J., Oliveira Miguel A.P., Hankemeier T., Vulto P., Schwamborn J.C., Thoma M. & Fleming R.M.T. (2019), Automated microfluidic cell culture of stem cell derived dopaminergic neurons, Scientific Reports 9: 1796.
- 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., Kruger R., Hankemeier T., Fleming R.M.T., Mollenhauer B. & Thiele I. (2019), Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease, Cell Reports 29(7): 1767-1777.
- Willacey C.C.W., Naaktgeboren M., Moreno E.L., Wegrzyn A.B., Es D. van der, Karu N., Fleming R.M.T., Harms A.C. & Hankemeier T. (2019), LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide, Journal of Chromatography A 1608: 460413.
- Masoud Ahookhosh M., Arag F.J., Aragon Artacho F.J., Fleming R.M. & Vuong P.T. (2019), Local convergence of the Levenberg-Marquardt method under Hölder metric subregularity, Advances in Computational Mathematics : 1-36.
- Haraldsdottir H.S., Cousins B., Thiele I., Fleming R.M. & Vempala S. (2017), CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models, Bioinformatics 33(11): 1741-1743.
- Preciat Gonzalez G.A., El Assal L., Noronhan A., Thiele I., Haraldsdóttir H. & Fleming R.M. (2017), Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D, Journal of Cheminformatics 9(1): 39.
- Monzel A.S., Smits L.M., Hemmer K., Hachi S., Moreno E.L., Wuellen T. van, Jarazo J., Walter J., Brüggemann I., Boussaad I., Berger E., Fleming R.M., Bolognin S. & Schwamborn J.C. (2017), Derivation of human midbrain-specific organoids from neuroepithelial Stem Cells, Stem Cell Reports 8(5): 1144-1154.
- Heirendt L., Thiele I. & Fleming R.M. (2017), DistributedFBA. jl: high-level, high-performance flux balance analysis in Julia, Bioinformatics 33(9): 1421-1423.
- Magnúsdóttir S., Heinken A., Kutt L., Ravcheev D.A., Bauer E., Noronha A., Greenhalgh K., Jäger C., Baginska J., Wilmes P., Fleming R.M. & Thiele I. (2017), Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota, Nature Biotechnology 35: 81-89.
- Thiele I., Clancy C.M., Heinken A. & Fleming R.M. (2017), Quantitative systems pharmacology and the personalized drug-microbiota-diet axis, Current Opinion in Systems Biology 4: 43-52.
- Ma D., Yang L., Fleming R.M., Thiele I., Palsson B.O. & Saunders M.A. (2017), Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression, Scientific Reports 7: 40863.
- Fleming R.M., Vlassis N., Thiele I. & Saunders M.A. (2016), Conditions for duality between fluxes and concentrations in biochemical networks, Journal of Theoretical Biology 409: 1-10.
- Haraldsdoattir H.S. & Fleming R.M. (2016), Identification of conserved moieties in metabolic networks by graph theoretical analysis of atom transition networks, PLoS Computational Biology 12(11): e1004999.
- Moreno E.L., Hachi S., Hemmer K., Trietsch S.J., Baumuratov A.S., Hankemeier T., Vulto P., Schwamborn J.C. & Fleming R.M.T. (2015), Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture, Lab on a Chip 15(11): 2419-2428.