Ronan M.T. Fleming
Ronan M.T. Fleming
Assoc. Prof., National University of Ireland, Galway, & Asst. Prof., Leiden University
Verified email at lacdr.leidenuniv.nl - 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
14682011
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
10062013
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
7122015
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
4372019
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
4172017
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
2972018
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
2232017
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
2212009
Consistent estimation of Gibbs energy using component contributions
E Noor, HS Haraldsdóttir, R Milo, RMT Fleming
PLoS computational biology 9 (7), e1003098, 2013
2172013
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), 2010
2082010
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
2042013
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
151*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), 1-9, 2011
1442011
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
1392019
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
1262015
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
Public Library of Science 7 (9), e45635, 2012
1132012
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
1052009
fastGapFill: efficient gap filling in metabolic networks
I Thiele, N Vlassis, RMT Fleming
Bioinformatics 30 (17), 2529-2531, 2014
962014
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
962013
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), 1-18, 2019
882019
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Articles 1–20