Publications by authors named "Ronan Fleming"

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XomicsToModel: omics data integration and generation of thermodynamically consistent metabolic models.
German Preciat, Agnieszka B Wegrzyn, Xi Luo, Ines Thiele, Thomas Hankemeier, Ronan M T Fleming

Nat Protoc· December 2025

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GBA1 Gene-Associated Transcriptomic Signatures Reveal Risk Genes in Parkinson's Disease.
Yanjun Liu, Xi Luo, Ronan M T Fleming

Biomedicines· November 2025

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mzQuality: An Open-Source Software Tool for Quality Monitoring and Reporting of Targeted Mass Spectrometry Measurements.
Marielle van der Peet, Pascal Maas, Agnieszka Wegrzyn, Lieke Lamont, Ronan Fleming

J Am Soc Mass Spectrom· August 2025

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Constraint-based modeling of bioenergetic differences between synaptic and non-synaptic components of dopaminergic neurons in Parkinson's disease.
Xi Luo, Diana C El Assal, Yanjun Liu, Samira Ranjbar, Ronan M T Fleming

Front Comput Neurosci· June 2025

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The role of dopaminergic medication and specific pathway alterations in idiopathic and -mediated Parkinson's disease.
Alexander Balck, Max Borsche, Philip Campbell, Xi Luo, John Harvey, Ronan Fleming

Sci Adv· May 2025

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A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
Almut Heinken, Timothy Otto Hulshof, Bram Nap, Filippo Martinelli, Arianna Basile, Ronan M T Fleming

Cell Syst· February 2025

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Integration of proteomic data with genome-scale metabolic models: A methodological overview.
Farid Zare, Ronan M T Fleming

Protein Sci· October 2024

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Identification of metabolites reproducibly associated with Parkinson's Disease via meta-analysis and computational modelling.
Xi Luo, Yanjun Liu, Alexander Balck, Christine Klein, Ronan M T Fleming

NPJ Parkinsons Dis· June 2024

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Omics data integration suggests a potential idiopathic Parkinson's disease signature.
Alise Zagare, German Preciat, Sarah L Nickels, Xi Luo, Anna S Monzel, Ronan M T Fleming

Commun Biol· November 2023

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APOLLO: A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
Almut Heinken, Timothy Otto Hulshof, Bram Nap, Filippo Martinelli, Arianna Basile, Ronan M T Fleming

bioRxiv· October 2023

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Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine.
Almut Heinken, Johannes Hertel, Geeta Acharya, Dmitry A Ravcheev, Malgorzata Nyga, Ronan M T Fleming

Nat Biotechnol· September 2023

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Cardinality optimization in constraint-based modelling: application to human metabolism.
Ronan M T Fleming, Hulda S Haraldsdottir, Le Hoai Minh, Phan Tu Vuong, Thomas Hankemeier

Bioinformatics· September 2023

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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.
Luojiao Huang, Nicolas Drouin, Jason Causon, Agnieszka Wegrzyn, Jose Castro-Perez, Ronan Fleming

Anal Chem· February 2023

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MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructions.
Ines Thiele, German Preciat, Ronan M T Fleming

Bioinformatics· October 2022

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Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication.
Ines Thiele, Ronan M T Fleming

Comput Struct Biotechnol J· July 2022

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DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations.
Almut Heinken, Stefanía Magnúsdóttir, Ronan M T Fleming, Ines Thiele

Bioinformatics· November 2021

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Phenotype-Agnostic Molecular Subtyping of Neurodegenerative Disorders: The Cincinnati Cohort Biomarker Program (CCBP).
Andrea Sturchio, Luca Marsili, Joaquin A Vizcarra, Alok K Dwivedi, Marcelo A Kauffman, Ronan M T Fleming

Front Aging Neurosci· October 2020

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Structural conserved moiety splitting of a stoichiometric matrix.
Susan Ghaderi, Hulda S Haraldsdóttir, Masoud Ahookhosh, Sylvain Arreckx, Ronan M T Fleming

J Theor Biol· August 2020

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Personalized whole-body models integrate metabolism, physiology, and the gut microbiome.
Ines Thiele, Swagatika Sahoo, Almut Heinken, Johannes Hertel, Laurent Heirendt, Ronan Mt Fleming

Mol Syst Biol· May 2020

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Publisher Correction: MEMOTE for standardized genome-scale metabolic model testing.
Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Ronan M T Fleming

Nat Biotechnol· April 2020

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MEMOTE for standardized genome-scale metabolic model testing.
Christian Lieven, Moritz E Beber, Brett G Olivier, Frank T Bergmann, Meric Ataman, Ronan M T Fleming

Nat Biotechnol· March 2020

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LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide.
Cornelius C W Willacey, Martijn Naaktgeboren, Edinson Lucumi Moreno, Agnieszka B Wegrzyn, Daan van der Es, Ronan M T Fleming

J Chromatogr A· December 2019

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Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson's Disease.
Johannes Hertel, Amy C Harms, Almut Heinken, Federico Baldini, Cyrille C Thinnes, Ronan M T Fleming

Cell Rep· November 2019

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Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.
Almut Heinken, Dmitry A Ravcheev, Federico Baldini, Laurent Heirendt, Ronan M T Fleming

Microbiome· May 2019

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Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.
Nicolas Sompairac, Jennifer Modamio, Emmanuel Barillot, Ronan M T Fleming, Andrei Zinovyev

BMC Bioinformatics· April 2019

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