Ronan Fleming
Universitair docent
- Naam
- Dr. R.M. Fleming
- Telefoon
- +31 71 527 2727
- r.m.fleming@lacdr.leidenuniv.nl
- ORCID iD
- 0000-0001-5346-9812
Meer informatie over Ronan Fleming op zijn Engelstalige profielpagina.
Universitair docent
- Wiskunde en Natuurwetenschappen
- 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. & Fleming R.M. (2022), Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication, Computational and Structural Biotechnology Journal 20: 4098-4109.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
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