Ronan M.T. Fleming

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Ines ThieleNational University of Ireland, GalwayVerified email at nuigalway.ie
Bernhard PalssonUCSDVerified email at eng.ucsd.edu
Almut HeinkenNational University of Ireland, GalwayVerified email at nuigalway.ie
Aarash BordbarSinopia BiosciencesVerified email at sinopiabio.com
Alberto NoronhaNium SàrlVerified email at nium.io
Richard QueUniversity of California, San DiegoVerified email at ucsd.edu
Jens SchwambornUniversity of Luxembourg, Luxembourg Centre for Systems BiomedicineVerified email at uni.lu
Jan SchellenbergerGrail Bio, LinkedIn, UC San DiegoVerified email at grailbio.com
Swagatika SahooIndian Institute of Technology MadrasVerified email at iitm.ac.in
Jeff OrthComputational Biologist, X, the moonshot factoryVerified email at x.team
Laurent HeirendtUniversity of Luxembourg, Luxembourg Centre for Systems BiomedicineVerified email at uni.lu
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Hulda S. HaraldsdóttirPostdoc in the Systems Biochemistry Group, Luxembourg Centre for Systems Biomedicine, University of LuxembourgVerified email at uni.lu
Dmitry RavcheevNational University of Ireland GalwayVerified email at nuigalway.ie
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
Javier JarazoUniversity of Luxembourg - Luxembourg Centre for Systems Biomedicine (LCSB)Verified email at uni.lu
Thomas HankemeierProfessor of Analytical Biosciences, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Skarphéðinn HalldórssonPost Doc investigator, Surgical Research Institute, Oslo University HospitalVerified email at rr-research.no
Adam FeistUCSD / DTUVerified email at ucsd.edu
Kathrin HemmerPhD, University of LuxembourgVerified email at uni.lu

Ronan M.T. Fleming

Senior Lecturer, National University of Ireland, Galway, & Asst. Professor, Leiden University

Verified email at lacdr.leidenuniv.nl - Homepage

Biological optimality principles Parkinson's disease Constraint-based modeling Non-equilibrium thermodynamics Optimization


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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	1446	2011
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	984	2013
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	671	2015
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	374	2017
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	373	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	257	2018
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 Comput Biol 5 (3), e1000312, 2009	214	2009
Consistent estimation of Gibbs energy using component contributions E Noor, HS Haraldsdóttir, R Milo, RMT Fleming PLoS Comput Biol 9 (7), e1003098, 2013	211	2013
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	198	2013
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	198	2010
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	188	2017
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	139	2011
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	124*	2020
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	117	2019
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	117	2015
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	109	2012
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	102	2009
fastGapFill: efficient gap filling in metabolic networks I Thiele, N Vlassis, RMT Fleming Bioinformatics 30 (17), 2529-2531, 2014	93	2014
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	90	2013
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	82	2012

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