Ronan M.T. Fleming
Ronan M.T. Fleming
Assistant Professor, Systems Biochemistry Group, Division of Systems Biomedicine and Pharmacology
Verified email at lacdr.leidenuniv.nl - Homepage
TitleCited byYear
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2. 0
J Schellenberger, R Que, RMT Fleming, I Thiele, JD Orth, AM Feist, ...
Nature protocols 6 (9), 1290, 2011
12442011
A community-driven global reconstruction of human metabolism
I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ...
Nature biotechnology 31 (5), 419, 2013
8432013
Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices
S Halldorsson, E Lucumi, R Gómez-Sjöberg, RMT Fleming
Biosensors and Bioelectronics 63, 218–231, 2015
4402015
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
S Magnúsdóttir, A Heinken, L Kutt, DA Ravcheev, E Bauer, A Noronha, ...
Nature biotechnology 35 (1), 81, 2017
2242017
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization
I Thiele, N Jamshidi, RMT Fleming, BØ Palsson
PLoS computational biology 5 (3), e1000312, 2009
1892009
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
A Heinken, S Sahoo, RMT Fleming, I Thiele
Gut microbes 4 (1), 28-40, 2013
1632013
Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide
JD Orth, RMT Fleming, BO Palsson
EcoSal plus, 2010
1572010
Consistent estimation of Gibbs energy using component contributions
E Noor, HS Haraldsdóttir, R Milo, RMT Fleming
PLoS computational biology 9 (7), e1003098, 2013
1542013
A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2
I Thiele, DR Hyduke, B Steeb, G Fankam, DK Allen, S Bazzani, ...
BMC systems biology 5 (1), 8, 2011
1222011
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
L Heirendt, S Arreckx, T Pfau, SN Mendoza, A Richelle, A Heinken, ...
Nature protocols 14 (3), 639, 2019
107*2019
Recon3D enables a three-dimensional view of gene variation in human metabolism
E Brunk, S Sahoo, DC Zielinski, A Altunkaya, A Dräger, N Mih, F Gatto, ...
Nature biotechnology 36 (3), 272, 2018
992018
Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli
RMT Fleming, I Thiele, HP Nasheuer
Biophysical chemistry 145 (2-3), 47-56, 2009
942009
Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage
I Thiele, RMT Fleming, R Que, A Bordbar, D Diep, BO Palsson
PloS one 7 (9), e45635, 2012
932012
Derivation of human midbrain-specific organoids from neuroepithelial stem cells
AS Monzel, LM Smits, K Hemmer, S Hachi, EL Moreno, T van Wuellen, ...
Stem Cell Reports 8 (5), 1144-1154, 2017
882017
A systems biology approach to studying the role of microbes in human health
I Thiele, A Heinken, RMT Fleming
Current opinion in biotechnology 24 (1), 4-12, 2013
802013
Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture
EL Moreno, S Hachi, K Hemmer, SJ Trietsch, AS Baumuratov, ...
Lab on a Chip 15 (11), 2419-2428, 2015
722015
Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole–time of flight mass spectrometry (UPLC–Q–ToF-MS)
G Paglia, S Hrafnsdóttir, M Magnúsdóttir, RMT Fleming, S Thorlacius, ...
Analytical and bioanalytical chemistry 402 (3), 1183-1198, 2012
682012
fastGapFill: efficient gap filling in metabolic networks
I Thiele, N Vlassis, RMT Fleming
Bioinformatics 30 (17), 2529-2531, 2014
652014
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery
I Thiele, RMT Fleming, A Bordbar, J Schellenberger, BØ Palsson
Biophysical journal 98 (10), 2072-2081, 2010
602010
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
RMT Fleming, I Thiele, G Provan, HP Nasheuer
Journal of theoretical biology 264 (3), 683-692, 2010
562010
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Articles 1–20