![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() * 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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. ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() * 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |
![]() ![]() | 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 ![]() |