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Ronan M.T. Fleming
Ronan M.T. Fleming
Assoc. Prof., School of Medicine, University of Galway.
Verified email at universityofgalway.ie - Homepage
Title
Cited by
Cited by
Year
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), 1290-1307, 2011
16602011
A community-driven global reconstruction of human metabolism
I Thiele, N Swainston, RMT Fleming, A Hoppe, S Sahoo, MK Aurich, ...
Nature biotechnology 31 (5), 419-425, 2013
11842013
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
11192015
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), 639-702, 2019
10192019
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), 81-89, 2017
7152017
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), 272-281, 2018
6252018
MEMOTE for standardized genome-scale metabolic model testing
C Lieven, ME Beber, BG Olivier, FT Bergmann, M Ataman, P Babaei, ...
Nature biotechnology 38 (3), 272-276, 2020
400*2020
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
3822017
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
A Noronha, J Modamio, Y Jarosz, E Guerard, N Sompairac, G Preciat, ...
Nucleic acids research 47 (D1), D614-D624, 2019
3162019
Consistent estimation of Gibbs energy using component contributions
E Noor, HS Haraldsdóttir, R Milo, RMT Fleming
PLoS computational biology 9 (7), e1003098, 2013
2972013
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide
JD Orth, RMT Fleming, BØ Palsson
EcoSal plus 4 (1), 10.1128/ecosalplus. 10.2. 1, 2010
2942010
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
2512013
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
A Heinken, DA Ravcheev, F Baldini, L Heirendt, RMT Fleming, I Thiele
Microbiome 7, 1-18, 2019
2452019
Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its …
I Thiele, N Jamshidi, RMT Fleming, BØ Palsson
PLoS computational biology 5 (3), e1000312, 2009
2422009
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
2112020
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
I Thiele, S Sahoo, A Heinken, J Hertel, L Heirendt, MK Aurich, ...
Molecular systems biology 16 (5), e8982, 2020
180*2020
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, 1-9, 2011
1692011
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
1662015
fastGapFill: efficient gap filling in metabolic networks
I Thiele, N Vlassis, RMT Fleming
Bioinformatics 30 (17), 2529-2531, 2014
1292014
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
F Baldini, A Heinken, L Heirendt, S Magnusdottir, RMT Fleming, I Thiele
Bioinformatics 35 (13), 2332-2334, 2019
1272019
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Articles 1–20