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 HeinkenUniversity of LorraineVerified email at univ-lorraine.fr
Jens SchwambornUniversity of Luxembourg, Luxembourg Centre for Systems BiomedicineVerified email at uni.lu
Alberto NoronhaNium SàrlVerified email at nium.io
Aarash BordbarSinopia BiosciencesVerified email at sinopiabio.com
Jeff OrthComputational Biologist, X, the moonshot factoryVerified email at x.team
Richard QueUniversity of California, San DiegoVerified email at ucsd.edu
Swagatika SahooIndian Institute of Technology MadrasVerified email at iitm.ac.in
Jan SchellenbergerGrail Bio, LinkedIn, UC San DiegoVerified email at grailbio.com
Laurent HeirendtUniversity of Luxembourg, Luxembourg Centre for Systems BiomedicineVerified email at uni.lu
Stefania MagnusdottirPhD Student, University of LuxembourgVerified email at uni.lu
German PreciatLeiden Academic Centre for Drug ResearchVerified email at lacdr.leidenuniv.nl
Thomas HankemeierProfessor of Analytical Biosciences, Leiden UniversityVerified email at lacdr.leidenuniv.nl
Dmitry RavcheevNational University of Ireland GalwayVerified email at nuigalway.ie
Javier JarazoUniversity of Luxembourg - Luxembourg Centre for Systems Biomedicine (LCSB)Verified email at uni.lu
Hulda S. HaraldsdóttirPostdoc in the Systems Biochemistry Group, Luxembourg Centre for Systems Biomedicine, University of LuxembourgVerified email at uni.lu
Nathan E LewisAssociate Professor, University of California, San DiegoVerified email at ucsd.edu
Skarphéðinn HalldórssonPost Doc investigator, Surgical Research Institute, Oslo University HospitalVerified email at rr-research.no
Michael SaundersProfessor of Operations Research, Stanford UniversityVerified email at stanford.edu

Ronan M.T. Fleming

Assoc. Prof., National University of Ireland, Galway, & Asst. Prof., 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), 1290-1307, 2011	1517	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	1052	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	811	2015
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	602	2019
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	486	2017
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	379	2018
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	264	2017
Consistent estimation of Gibbs energy using component contributions E Noor, HS Haraldsdóttir, R Milo, RMT Fleming PLoS computational biology 9 (7), e1003098, 2013	246	2013
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	230	2009
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	223	2010
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	218*	2020
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	214	2013
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	184	2019
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	152	2011
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	140	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	137	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 Public Library of Science 7 (9), e45635, 2012	114	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	107	2009
fastGapFill: efficient gap filling in metabolic networks I Thiele, N Vlassis, RMT Fleming Bioinformatics 30 (17), 2529-2531, 2014	102	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	101	2013

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