  | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
  | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 |
 | 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 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi* 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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. |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi* 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |
 | 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 |
 | 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 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 |
 | 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 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 |
 | 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., & 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 Peer Reviewed verified by ORBi |
 | 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 Peer Reviewed verified by ORBi |