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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
162 A, avenue de la Faïencerie
L-1511 Luxembourg
Telephone (+352) 46 66 44 5528
Video Dr. Ronan Fleming (LCSB)
Dr. Ronan Fleming (LCSB)
Joined the University in 2013
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.

Last updated on: Wednesday, 06 August 2014

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2013 to present

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: 06 Aug 2014

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In press

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

in Optimization Letters (in press)

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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 (in press)

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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)

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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)

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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)

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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), 1290-307

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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 detailReconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide
Orth, J. D.; Fleming, Ronan MT; Palsson, B. O.

in Chapter 10.2.1 in Escherichia coli and Salmonella: Cellular and Molecular Biology, Washington, DC. (2010)

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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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