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Ronan MT Fleming

Ronan MT  Fleming

Senior Research Associate

Faculty or Centre Luxembourg Centre for Systems Biomedicine
Postal Address Université du Luxembourg
6, avenue du Swing
L-4367 Belvaux
Campus Office BioTech II, 2.16
Telephone (+352) 46 66 44 5528
Video Dr. Ronan Fleming (LCSB)
Dr. Ronan Fleming (LCSB)
Associate Prof. Dr. Ronan Fleming (LCSB)

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.

Dr. Ronan Fleming is also an Adjunct Assistant Professor in the Division of Analytical Biosciences, Leiden Academic Centre for Drug Research at the University of Leiden, The Netherlands.


Students interested in pursuing a master's degree at the interface of experimental biology and computer science may want to consider our programme Master in Integrated Systems Biology.

Last updated on: Thursday July 27 2017

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2015 -

Technical and Quality Manager, European Commission, Research and Innovation action, "Systems Medicine of Mitochondrial Parkinson’s Disease".

2015 -

Assistant Professor (Adjunct), Analytical Biosciences Division, Leiden Academic Centre for Drug Research, University of Leiden

2013 -     

Senior Research Associate & Principal Investigator, Systems Biochemistry Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg

2012 - 2013            

Assistant Professor, Department of Biochemistry & Molecular Biology, University of Iceland

2010 - 2013      

Principal Investigator, Centre for Systems Biology, University of Iceland


2004 - 2008    

Doctoral Student, School of Natural Sciences, National University of Ireland, Galway

1995 - 2001     

Bachelor of Veterinary Medicine & Surgery (B.V.M.S.), University of Glasgow Veterinary School, Glasgow, Scotland.


2004 - 2008     

Veterinary Surgeon, Oughterard Veterinary Surgery, Galway, Ireland                                                               

2002 - 2003

Resident in Anatomic Pathology, Royal Veterinary College, Herts., England


2012 - 2013    

Metabolism and Nutrition, Medical, Physiology and Biology Undergraduate Courses, University of Iceland.          

2009 - 2012     

Systems Biology Short Course, University of Iceland.

Honors and Achievements

European Molecular Biology Organisation, 2012 Short Term Fellowship to visit the Netherlands Metabolomic Center.

Statistical and Applied Mathematical Sciences Institute, 2008 Algebraic Methods in Systems Biology and Statistics scholarship.

Research Institute for Symbolic Computation, 2007 Algebraic Biology summer school scholarship.

University of California-National University of Ireland 2005-2006 exchange program visiting scholarship.

Sante Fe Institute, 2006 Complex systems summer school scholarship

Last updated on: 23 Nov 2016

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Full Text
See detailA systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines
Aurich, Maike Kathrin; Thiele, Ines; Fleming, Ronan MT

in PLoS Computational Biology (2017)

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See detailCHRR: Coordi- nate hit-and-run with rounding for uniform sampling of constraint-based models
Haraldsdottir, Hulda; Cousin, B; Thiele, Ines; Fleming, Ronan MT; Vempala, S

in Bioinformatics (2017)

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See detailDistributedFBA.jl: High-level, high-performance flux balance analysis in Julia.
Heirendt, Laurent; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2017)

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See detailAutomated micro uidic cell culture of stem cell derived dopaminergic neurons in Parkinson's disease
Kane, Khalid; Lucumi Moreno, Edinson; Hachi, Siham; Walter, Moriz; Jarazo, Javier; Hankemeier, Thomas; Vulto, Paul; Schwamborn, Jens Christian; Thoma, Martin; Fleming, Ronan MT

in bioRxiv (2017)

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See detailReliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ma, Ding; Yang, Laurence; Fleming, Ronan MT; Thiele, Ines; Palsson, Bernhard; Saunders, Michael

in Scientific Reports (2017)

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See detailDerivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells
Monzel, Anna Sophia; Smits, Lisa; Hemmer, Kathrin; Hachi, Siham; Lucumi Moreno, Edinson; Van Wüllen, Thea Maria; Jarazo, Javier; Walter, Jonas; Werthschulte, Inga; Boussaad, Ibrahim; Berger, Emanuel; Fleming, Ronan MT; Bolognin, Silvia; Schwamborn, Jens Christian

in Stem Cell Reports (2017)

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See detailEmbryonic development of selectively vulnerable neurons in Parkinson’s disease
Oliveira, Miguel; Balling, Rudi; Smidt, Marten; Fleming, Ronan MT

in NPJ Parkinson's Disease (2017), 3

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See detailComparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
Preciat Gonzalez, German Andres; El Assal, Lemmer; Noronha, Alberto; Thiele, Ines; Haraldsdottir, Hulda; Fleming, Ronan MT

in Journal of Cheminformatics (2017)

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See detailQuantitative systems pharmacology and the personalized drug–microbiota–diet axis
Thiele, Ines; Clancy, Catherine; Heinken, Almut Katrin; Fleming, Ronan MT

in Current Opinion in Systems Biology (2017), 4

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See detailMetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models
Aurich, Maike Kathrin; Fleming, Ronan MT; Thiele, Ines

in Frontiers in Physiology (2016)

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See detailConditions for duality between fluxes and concentrations in biochemical networks
Fleming, Ronan MT; Vlassis, Nikos; Thiele, Ines; Saunders, Michael

in Journal of Theoretical Biology (2016), 409(21), 1-10

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See detailGeneration of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Magnusdottir, Stefania; Heinken, Almut Katrin; Kutt, Laura; Ravcheev, Dmitry; Bauer, Eugen; Noronha, Alberto; Greenhalgh, Kacy; Jäger, Christian; Baginska, Joanna; Wilmes, Paul; Fleming, Ronan MT; Thiele, Ines

in Nature Biotechnology (2016)

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See detailReconMap: An interactive visualisation of human metabolism
Noronha, Alberto; Danielsdóttir, Anna Dröfn; Jóhannsson, Freyr; Jónsdóttir, Soffia; Jarlsson, Sindri; Gunnarsson, Jón Pétur; Brynjólfsson, Sigurður; Gawron, Piotr; Schneider, Reinhard; Thiele, Ines; Fleming, Ronan MT

in Bioinformatics (2016)

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See detailGlobally convergent algorithms for finding zeros of duplomonotone mappings
Aragón Artacho, Francisco Javier; Fleming, Ronan MT

in Optimization Letters (2015), 3(3), 569584

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See detailAccelerating the DC algorithm for smooth functions
Aragón Artacho, Francisco Javier; Fleming, Ronan MT; Phan, Vuong

E-print/Working paper (2015)

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See detailPrediction of intracellular metabolic states from extracellular metabolomic data
Aurich, Maike Kathrin; Paglia, Guiseppe; Rolfsson, Ottar; Hrafnsdottir, Sigrun; Magnusdottir, Manuela; Stefaniak, Madgalena K.; Palsson, Bernhard O.; Fleming, Ronan MT; Thiele, Ines

in Metabolomics : Official journal of the Metabolomic Society (2015), 11(3), 603-619

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See detailDo Genome-scale Models Need Exact Solvers or Clearer Standards?
Ebrahim, Ali; Almaas, Eivind; Bauer, Eugen; Bordbar, Aarash; Burgard, Anthony P.; Chang, Roger L.; Dräger, Andreas; Famili, Iman; Feist, Adam M.; Fleming, Ronan MT; Fong, Stephen S.; Hatzimanikatis, Vassily; Herrgård, Markus J.; Holder, Allen; Hucka, Michael; Hyduke, Daniel; Jamshidi, Neema; Lee, Sang Yup; Le Novère, Nicolas; Lerman, Joshua A.; Lewis, Nathan E.; Ma, Ding; Mahadevan, Radhakrishnan; Maranas, Costas; Nagarajan, Harish; Navid, Ali; Nielsen, Jens; Nielsen, Lars K.; Nogales, Juan; Noronha, Alberto; Pal, Csaba; Palsson, Bernhard O.; Papin, Jason A.; Patil, Kiran R.; Price, Nathan D.; Reed, Jennifer L.; Saunders, Michael; Senger, Ryan S.; Sonnenschein, Nikolaus; Sun, Yuekai; Thiele, Ines

in Molecular Systems Biology (2015), 11(10), 1

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See detailAdvantages and challenges of microfluidic cell culture in polydimethylsiloxane devices
Halldórsson, Skarphédinn; Lucumi Moreno, Edinson; Gómez-Sjöberg, Rafael; Fleming, Ronan MT

in Biosensors and Bioelectronics (2015), 63

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See detailDifferentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture
Lucumi Moreno, Edinson; Hachi, Siham; Hemmer, Kathrin; Trietsch, Sebastian; Baumuratov, Aidos; Hankemeier, Thomas; Vulto, Paul; Schwamborn, Jens Christian; Fleming, Ronan MT

in Lab on a Chip - Miniaturisation for Chemistry & Biology (2015), 15

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See detailA constraint-based modelling approach to metabolic dysfunction in Parkinson's disease
Mao, Longfei; Nicolae, Averina; Oliveira, Miguel; He, Feng; Hachi, Siham; Fleming, Ronan MT

in Computational and Structural Biotechnology Journal (2015), 13

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See detailModeling the effects of commonly used drugs on human metabolism
Sahoo, Swagatika; Haraldsdottir, Hulda; Fleming, Ronan MT; Thiele, Ines

in FEBS Journal (2014)

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See detailFASTGAPFILL: Efficient gap filling in metabolic networks
Thiele, Ines; Vlassis, Nikos; Fleming, Ronan MT

in Bioinformatics (2014), 30(17), 2529-2531

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See detailExistence of Positive Steady States for Mass Conserving and Mass-Action Chemical Reaction Networks with a Single Terminal-Linkage Class
Fleming, Ronan MT; Akle, Santiago; Dalal, Onkar; Saunders, Michael; Taheri, Nicole; Ye, Yinyu

in arXiv preprint arXiv:1105.2359 (2013)

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See detailSystems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut.
Heinken, Almut Katrin; Sahoo, Swagatika; Fleming, Ronan MT; Thiele, Ines

in Gut microbes (2013), 4(1), 28-40

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See detailReal-time optical pH measurement in a standard microfluidic cell culture system
Magnusson, E. B.; Halldorsson, S.; Fleming, Ronan MT; Leosson, K.

in Biomedical Optics Express (2013), 4(9), 1749-1758

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See detailConsistent Estimation of Gibbs Energy Using Component Contributions
Noor, Elad; Haraldsdottir, Hulda; Milo, Ron; Fleming, Ronan MT

in PLoS Computational Biology (2013), 9(7), 1003098

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See detailRobust flux balance analysis of multi- scale biochemical reaction networks
Sun, Y; Fleming, Ronan MT; Thiele, Ines; Saunders, MA

in BMC Bioinformatics (2013), 1(14), 240

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See detailA systems biology approach to studying the role of microbes in human health.
Thiele, Ines; Heinken, Almut Katrin; Fleming, Ronan MT

in Current Opinion in Biotechnology (2013), 24(1), 4-12

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See detailA community-driven global reconstruction of human metabolism.
Thiele, Ines; Swainston, N.; Fleming, Ronan MT; Hoppe, A.; Sahoo, Swagatika; Aurich, Maike Kathrin; Haraldsdottir, Hulda; Mo, M. L.; Rolfsson, O.; Stobbe, M. D.; Thorleifsson, S. G.; Agren, R.; Bölling, C.; Bordel, S.; Chavali, A. K.; Dobson, P.; Dunn, W. B.; Endler, L.; Hala, D.; Hucka, M.; Hull, D.; Jameson, D.; Jamshidi, N.; Jonsson, J. J.; Juty, N.; Keating, S.; Nookaew, I.; Le Novère, N.; Malys, N.; Mazein, A.; Papin, J. A.; Price, N. D.; Selkov, E. Sr; Sigurdsson, M. I.; Simeonidis, Evangelos; Sonnenschein, N.; Smallbone, K.; Sorokin, A.; van Beek, J. H.; Weichart, D.; Goryanin, I.; Nielsen, J.; Westerhoff, H. V.; Kell, D. B.; Mendes, P.; Palsson, B. O.

in Nature Biotechnology (2013), 31

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See detailA variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks
Fleming, Ronan MT; Maes, C. M.; Saunders, M. A.; Ye, Y.; Palsson, B. O.

in Journal of Theoretical Biology (2012), 292

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See detailQuantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction
Haraldsdottir, Hulda; Thiele, Ines; Fleming, Ronan MT

in Biophysical Journal (2012), 102(8), 17031711

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See detailMonitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).
Paglia, Giuseppe; Hrafnsdottir, Sigrun; Magnusdottir, Manuela; Fleming, Ronan MT; Thorlacius, Steinunn; Palsson, Bernhard O.; Thiele, Ines

in Analytical and Bioanalytical Chemistry (2012), 402(3), 1183-98

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See detailA systems biology approach to drug targets in Pseudomonas aeruginosa biofilm.
Sigurdsson, Gunnar; Fleming, Ronan MT; Heinken, Almut Katrin; Thiele, Ines

in PLoS ONE (2012), 7(4), 34337

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See detailMultiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.
Thiele, Ines; Fleming, Ronan MT; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard O.

in PLoS ONE (2012), 7(9), 45635

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See detailvon Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.
Fleming, Ronan MT; Thiele, Ines

in Bioinformatics (Oxford, England) (2011), 27(1), 142-3

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See detailQuantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Schellenberger, Jan; Que, Richard; Fleming, Ronan MT; Thiele, Ines; Orth, Jeffrey D.; Feist, Adam M.; Zielinski, Daniel C.; Bordbar, Aarash; Lewis, Nathan E.; Rahmanian, Sorena; Kang, Joseph; Hyduke, Daniel R.; Palsson, Bernhard O.

in Nature Protocols (2011), 6(9), 1290-1307

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See detailA community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.
Thiele, Ines; Hyduke, Daniel R.; Steeb, Benjamin; Fankam, Guy; Allen, Douglas K.; Bazzani, Susanna; Charusanti, Pep; Chen, Feng-Chi; Fleming, Ronan MT; Hsiung, Chao A.; De Keersmaecker, Sigrid C. J.; Liao, Yu-Chieh; Marchal, Kathleen; Mo, Monica L.; Ozdemir, Emre; Raghunathan, Anu; Reed, Jennifer L.; Shin, Sook-Il; Sigurbjornsdottir, Sara; Steinmann, Jonas; Sudarsan, Suresh; Swainston, Neil; Thijs, Inge M.; Zengler, Karsten; Palsson, Bernhard O.; Adkins, Joshua N.; Bumann, Dirk

in BMC Systems Biology (2011), 5

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See detailIntegrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, Ronan MT; Thiele, Ines; Provan, G.; Nasheuer, H. P.

in Journal of Theoretical Biology (2010), 264(3), 683-92

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See detailFunctional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
Thiele, Ines; Fleming, Ronan MT; Bordbar, Aarash; Schellenberger, Jan; Palsson, Bernhard O.

in Biophysical Journal (2010), 98(10), 2072-81

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See detailQuantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli.
Fleming, Ronan MT; Thiele, Ines; Nasheuer, H. P.

in Biophysical Chemistry (2009), 145(2-3), 47-56

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See detailGenome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
Thiele, Ines; Jamshidi, Neema; Fleming, Ronan MT; Palsson, Bernhard O.

in PLoS Computational Biology (2009), 5(3), 1000312

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