Fleming, Ronan M T

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., et al. (2011) · Nature Protocols

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 1,835

Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices

Halldorsson, S., Lucumi, E., Gómez-Sjöberg, R., & Fleming, R. M. T. (2015) · Biosensors and Bioelectronics

Microfluidic and Capillary Electrophoresis Applications3D Printing in Biomedical Research

Cited by 1,027

A community-driven global reconstruction of human metabolism

Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionBioinformatics and Genomic Networks

Cited by 1,019

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

Magnúsdóttir, S., Heinken, A., Kutt, L., Ravcheev, D. A., Bauer, E., Noronha, A., Greenhalgh, K., Jäger, C., Baginska, J., Wilmes, P., et al. (2017) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGut microbiota and health

Cited by 798

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 509

Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells

Monzel, A. S., Smits, L. M., Hemmer, K., Hachi, S., Moreno, E. L., van Wuellen, T., Jarazo, J., Walter, J., Brüggemann, I., Boussaad, I., et al. (2017) · Stem Cell Reports

Pluripotent Stem Cells ResearchNeurogenesis and neuroplasticity mechanisms

Cited by 435

Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization

Thiele, I., Jamshidi, N., Fleming, R. M. T., & Palsson, B. Ø. (2009) · PLoS Computational Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 182

Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease

Hertel, J., Harms, A. C., Heinken, A., Baldini, F., Thinnes, C. C., Glaab, E., Vasco, D. A., Pietzner, M., Stewart, I. D., Wareham, N. J., et al. (2019) · Cell Reports

Gut microbiota and healthParkinson's Disease Mechanisms and Treatments

Cited by 162

A systems biology approach to studying the role of microbes in human health

Thiele, I., Heinken, A., & Fleming, R. M. (2013) · Current Opinion in Biotechnology

Microbial Metabolic Engineering and BioproductionGut microbiota and health

Cited by 114

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A., Almaas, E., Bauer, E., Bordbar, A., Burgard, A. P., Chang, R. L., Dräger, A., Famili, I., Feist, A. M., Fleming, R. M., et al. (2015) · Molecular Systems Biology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 57