Profil

FLEMING Ronan MT

Main Referenced Co-authors
THIELE, Ines  (34)
HARALDSDOTTIR, Hulda  (9)
Palsson, Bernhard O. (9)
HEINKEN, Almut Katrin  (8)
NORONHA, Alberto  (6)
Main Referenced Keywords
Models, Biological (9); Humans (5); Thermodynamics (5); Computer Simulation (4); Metabolic Networks and Pathways (4);
Main Referenced Unit & Research Centers
Luxembourg Centre for Systems Biomedicine (LCSB): Systems Biochemistry (Fleming Group) (14)
Luxembourg Centre for Systems Biomedicine (LCSB): Molecular Systems Physiology (Thiele Group) (8)
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group) (3)
Luxembourg Centre for Systems Biomedicine (LCSB) (1)
Luxembourg Centre for Systems Biomedicine (LCSB): Developmental and Cellular Biology (Schwamborn Group) (1)
Main Referenced Disciplines
Life sciences: Multidisciplinary, general & others (32)
Biochemistry, biophysics & molecular biology (13)
Engineering, computing & technology: Multidisciplinary, general & others (3)
Biotechnology (3)
Mathematics (2)

Publications (total 50)

The most downloaded
2618 downloads
Orth, J. D., Fleming, R. M., & Palsson, B. O. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal Plus. doi:10.1128/ecosalplus.10.2.1 https://hdl.handle.net/10993/16532

The most cited

1081 citations (OpenCitations)

Schellenberger, J., Que, R., Fleming, R. M., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R., & Palsson, B. O. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols, 6 (9), 1290-1307. doi:10.1038/nprot.2011.308 https://hdl.handle.net/10993/16514

ZAGARE, A., Preciat, G., NICKELS, S. L., Luo, X., MONZEL, A. S., Gomez-Giro, G., ROBERTSON, G., Jaeger, C., Sharif, J., Koseki, H., DIEDERICH, N., GLAAB, E., FLEMING, R. M., & SCHWAMBORN, J. C. (20 November 2023). Omics data integration suggests a potential idiopathic Parkinson's disease signature. Communications Biology, 6 (1), 1179. doi:10.1038/s42003-023-05548-w
Peer Reviewed verified by ORBi

Heinken, A. K., Ravcheev, D., Baldini, F., Heirendt, L., Fleming, R. M., & Thiele, I. (2019). Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. Microbiome. doi:10.1186/s40168-019-0689-3
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Noronha, A., Modamio Chamarro, J., Jarosz, Y., Guerard, E., Sompairac, N., Preciat Gonzalez, G. A., Danielsdottir, A. D., Krecke, M., Merten, D., Haraldsdottir, H., Heinken, A. K., Heirendt, L., Magnusdottir, S., Ravcheev, D., Sahoo, S., Gawron, P., Friscioni, L., Garcia Santa Cruz, B., Prendergast, M., ... Thiele, I. (2018). The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Research. doi:10.1093/nar/gky992
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Brunk, E., Sahoo, S., Zielinski, D. C., Altunkaya, A., Drager, A., Mih, N., Gatto, F., Nilsson, A., Preciat Gonzalez, G. A., Aurich, M. K., Prlic, A., Sastry, A., Danielsdottir, A. D., Heinken, A. K., Noronha, A., Rose, P. W., Burley, S. K., Fleming, R. M., Nielsen, J., ... Palsson, B. O. (2018). Recon3D enables a three-dimensional view of gene variation in human metabolism. Nature Biotechnology, 36 (3), 272-281. doi:10.1038/nbt.4072
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Ostaszewski, M., Gebel, S., Kuperstein, I., Mazein, A., Zinovyev, A., Dogrusoz, U., Hasenauer, J., Fleming, R. M., Le Novere, N., Gawron, P., Ligon, T., Niarakis, A., Nickerson, D., Weindl, D., Balling, R., Barillot, E., Auffray, C., & Schneider, R. (2018). Community-driven roadmap for integrated disease maps. Briefings in Bioinformatics. doi:10.1093/bib/bby024
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Thiele, I., Clancy, C., Heinken, A. K., & Fleming, R. M. (August 2017). Quantitative systems pharmacology and the personalized drug–microbiota–diet axis. Current Opinion in Systems Biology, 4, 43-52. doi:10.1016/j.coisb.2017.06.001
Peer reviewed

Aurich, M. K., Thiele, I., & Fleming, R. M. (2017). A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines. PLoS Computational Biology. doi:10.1371/journal.pcbi.1005698
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Oliveira, M., Balling, R., Smidt, M., & Fleming, R. M. (26 June 2017). Embryonic development of selectively vulnerable neurons in Parkinson’s disease. NPJ Parkinson's Disease, 3. doi:10.1038/s41531-017-0022-4
Peer reviewed

Preciat Gonzalez, G. A., El Assal, L., Noronha, A., Thiele, I., Haraldsdottir, H., & Fleming, R. M. (2017). Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. Journal of Cheminformatics. doi:10.1186/s13321-017-0223-1
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Heirendt, L., Thiele, I., & Fleming, R. M. (2017). DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia. Bioinformatics. doi:10.1093/bioinformatics/btw838
Peer reviewed

Kane, K., Lucumi Moreno, E., Hachi, S., Walter, M., Jarazo, J., Hankemeier, T., Vulto, P., Schwamborn, J. C., Thoma, M., & Fleming, R. M. (2017). Automated micro uidic cell culture of stem cell derived dopaminergic neurons in Parkinson's disease. bioRxiv. doi:10.1038/s41598-018-34828-3

Monzel, A. S., Smits, L., Hemmer, K., Hachi, S., Lucumi Moreno, E., Van Wüllen, T. M., Jarazo, J., Walter, J., Werthschulte, 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. doi:10.1016/j.stemcr.2017.03.010
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Haraldsdottir, H., Cousin, B., Thiele, I., Fleming, R. M., & Vempala, S. (2017). CHRR: Coordi- nate hit-and-run with rounding for uniform sampling of constraint-based models. Bioinformatics. doi:10.1093/bioinformatics/btx052
Peer reviewed

Ma, D., Yang, L., Fleming, R. M., Thiele, I., Palsson, B., & Saunders, M. (2017). Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression. Scientific Reports. doi:10.1038/srep40863
Peer Reviewed verified by ORBi

Fleming, R. M., Vlassis, N., Thiele, I., & Saunders, M. (November 2016). Conditions for duality between fluxes and concentrations in biochemical networks. Journal of Theoretical Biology, 409 (21), 1-10. doi:10.1016/j.jtbi.2016.06.033
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Magnusdottir, S., Heinken, A. K., Kutt, L., Ravcheev, D., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., Fleming, R. M., & Thiele, I. (2016). Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nature Biotechnology. doi:10.1038/nbt.3703
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Aurich, M. K., Fleming, R. M., & Thiele, I. (2016). MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models. Frontiers in Physiology. doi:10.3389/fphys.2016.00327
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Haraldsdottir, H., & Fleming, R. M. (2016). Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PLoS Computational Biology. doi:10.1371/journal.pcbi.1004999
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Noronha, A., Danielsdóttir, A. D., Jóhannsson, F., Jónsdóttir, S., Jarlsson, S., Gunnarsson, J. P., Brynjólfsson, S., Gawron, P., Schneider, R., Thiele, I., & Fleming, R. M. (2016). ReconMap: An interactive visualisation of human metabolism. Bioinformatics. doi:10.1093/bioinformatics/btw667
Peer reviewed

Halldórsson, S.* , Lucumi Moreno, E.* , Gómez-Sjöberg, R., & Fleming, R. M. (15 January 2015). Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices. Biosensors and Bioelectronics, 63, 218-231. doi:10.1016/j.bios.2014.07.029
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* These authors have contributed equally to this work.

Aragón Artacho, F. J., & Fleming, R. M. (2015). Globally convergent algorithms for finding zeros of duplomonotone mappings. Optimization Letters, 3 (3), 569–584. doi:10.1007/s11590-014-0769-z
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Aurich, M. K., Paglia, G., Rolfsson, O., Hrafnsdottir, S., Magnusdottir, M., Stefaniak, M. K., Palsson, B. O., Fleming, R. M., & Thiele, I. (2015). Prediction of intracellular metabolic states from extracellular metabolomic data. Metabolomics : Official journal of the Metabolomic Society, 11 (3), 603-619. doi:10.1007/s11306-014-0721-3
Peer reviewed

Mao, L., Nicolae, A., Oliveira, M., He, F., Hachi, S., & Fleming, R. M. (2015). A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease. Computational and Structural Biotechnology Journal, 13, 484 - 491. doi:10.1016/j.csbj.2015.08.002
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Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., Fong, S. S., Hatzimanikatis, V., Herrgård, M. J., Holder, A., Hucka, M., Hyduke, D., Jamshidi, N., Lee, S. Y., Le Novère, N., ... Thiele, I. (2015). Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11 (10), 1. doi:10.15252/msb.20156157
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Aragón Artacho, F. J., Fleming, R. M., & Phan, V. (2015). Accelerating the DC algorithm for smooth functions. ORBilu-University of Luxembourg. https://orbilu.uni.lu/handle/10993/26848.

Lucumi Moreno, E., Hachi, S., Hemmer, K., Trietsch, S., Baumuratov, A., Hankemeier, T., Vulto, P., Schwamborn, J. C., & Fleming, R. M. (2015). Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture. Lab on a Chip - Miniaturisation for Chemistry and Biology, 15, 2419-2428. doi:10.1039/C5LC00180C
Peer reviewed

Haraldsdottir, H., Thiele, I., & Fleming, R. M. (2014). Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. Journal of Cheminformatics, 6, 2. doi:10.1186/1758-2946-6-2
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Thiele, I., Vlassis, N., & Fleming, R. M. (2014). FASTGAPFILL: Efficient gap filling in metabolic networks. Bioinformatics, 30 (17), 2529-2531. doi:10.1093/bioinformatics/btu321
Peer reviewed

Sahoo, S., Haraldsdottir, H., Fleming, R. M., & Thiele, I. (2014). Modeling the effects of commonly used drugs on human metabolism. FEBS Journal. doi:10.1111/febs.13128
Peer reviewed

Fleming, R. M., Akle, S., Dalal, O., Saunders, M., Taheri, N., & Ye, Y. (2013). Existence of Positive Steady States for Mass Conserving and Mass-Action Chemical Reaction Networks with a Single Terminal-Linkage Class. arXiv preprint arXiv:1105.2359.
Peer reviewed

Noor, E., Haraldsdottir, H., Milo, R., & Fleming, R. M. (11 July 2013). Consistent Estimation of Gibbs Energy Using Component Contributions. PLoS Computational Biology, 9 (7), 1003098. doi:10.1371/journal.pcbi.1003098
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Thiele, I., Heinken, A. K., & Fleming, R. M. (2013). A systems biology approach to studying the role of microbes in human health. Current Opinion in Biotechnology, 24 (1), 4-12. doi:10.1016/j.copbio.2012.10.001
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Magnusson, E. B., Halldorsson, S., Fleming, R. M., & Leosson, K. (2013). Real-time optical pH measurement in a standard microfluidic cell culture system. Biomedical Optics Express, 4 (9), 1749-1758. doi:10.1364/BOE.4.001749
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Thiele, I.* , Swainston, N.* , Fleming, R. M., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., 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., ... Palsson, B. O. (2013). A community-driven global reconstruction of human metabolism. Nature Biotechnology, 31, 419-425. doi:10.1038/nbt.2488
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* These authors have contributed equally to this work.

Sun, Y., Fleming, R. M., Thiele, I., & Saunders, M. (2013). Robust flux balance analysis of multi- scale biochemical reaction networks. BMC Bioinformatics, 1 (14), 240. doi:10.1186/1471-2105-14-240
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Heinken, A. K., Sahoo, S., Fleming, R. M., & Thiele, I. (2013). Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut. Gut Microbes, 4 (1), 28-40. doi:10.4161/GMIC.22370
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Sigurdsson, G., Fleming, R. M., Heinken, A. K., & Thiele, I. (2012). A systems biology approach to drug targets in Pseudomonas aeruginosa biofilm. PLoS ONE, 7 (4), 34337. doi:10.1371/journal.pone.0034337
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Paglia, G., Hrafnsdottir, S., Magnusdottir, M., Fleming, R. M., Thorlacius, S., Palsson, B. O., & Thiele, I. (2012). Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS). Analytical and Bioanalytical Chemistry, 402 (3), 1183-98. doi:10.1007/s00216-011-5556-4
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Thiele, I., Fleming, R. M., Que, R., Bordbar, A., Diep, D., & Palsson, B. O. (2012). Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage. PLoS ONE, 7 (9), 45635. doi:10.1371/journal.pone.0045635
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Fleming, R. M., & Thiele, I. (2012). Mass conserved elementary kinetics is sufficient for the existence of a non-equilibrium steady state concentration. Journal of Theoretical Biology, 314, 173-181. doi:10.1016/j.jtbi.2012.08.021
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Haraldsdottir, H., Thiele, I., & Fleming, R. M. (2012). Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction. Biophysical Journal, 102 (8), 1703–1711. doi:10.1016/j.bpj.2012.02.032
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Fleming, R. M., Maes, C. M., Saunders, M. A., Ye, Y., & Palsson, B. O. (2012). A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks. Journal of Theoretical Biology, 292, 71-77. doi:10.1016/j.jtbi.2011.09.029
Peer reviewed

Thiele, I., Hyduke, D. R., Steeb, B., Fankam, G., Allen, D. K., Bazzani, S., Charusanti, P., Chen, F.-C., Fleming, R. M., Hsiung, C. A., De Keersmaecker, S. C. J., Liao, Y.-C., Marchal, K., Mo, M. L., Ozdemir, E., Raghunathan, A., Reed, J. L., Shin, S.-I., Sigurbjornsdottir, S., ... Bumann, D. (2011). A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2. BMC Systems Biology, 5, 8. doi:10.1186/1752-0509-5-8
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Schellenberger, J., Que, R., Fleming, R. M., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R., & Palsson, B. O. (2011). Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nature Protocols, 6 (9), 1290-1307. doi:10.1038/nprot.2011.308
Peer Reviewed verified by ORBi

Fleming, R. M., & Thiele, I. (2011). von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models. Bioinformatics, 27 (1), 142-3. doi:10.1093/bioinformatics/btq607
Peer reviewed

Orth, J. D., Fleming, R. M., & Palsson, B. O. (2010). Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal Plus. doi:10.1128/ecosalplus.10.2.1
Peer Reviewed verified by ORBi

Fleming, R. M., Thiele, I., Provan, G., & Nasheuer, H. P. (2010). Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism. Journal of Theoretical Biology, 264 (3), 683-92. doi:10.1016/j.jtbi.2010.02.044
Peer Reviewed verified by ORBi

Thiele, I., Fleming, R. M., Bordbar, A., Schellenberger, J., & Palsson, B. O. (2010). Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery. Biophysical Journal, 98 (10), 2072-81. doi:10.1016/j.bpj.2010.01.060
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Thiele, I., Jamshidi, N., Fleming, R. M., & Palsson, B. O. (2009). Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Computational Biology, 5 (3), 1000312. doi:10.1371/journal.pcbi.1000312
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Fleming, R. M., Thiele, I., & Nasheuer, H. P. (2009). Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. Biophysical Chemistry, 145 (2-3), 47-56. doi:10.1016/j.bpc.2009.08.007
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