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R. Fleming · SciRah

Researcher profile · Semantic Scholar

R. Fleming

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R. Fleming — researcher profile on SciRah

h-index: 45
Works: 124
Citations: 13K

Most-cited papers

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0
Laurent Heirendt, Sylvain Arreckx, T. Pfau, Sebastián N. Mendoza +51 more
2019Nature Protocols1,072 citations Open access
Semantic Scholar
Advantages and challenges of microfluidic cell culture in polydimethylsiloxane devices.
S. Halldorsson, E. Lucumi, R. Gómez-Sjöberg, R. Fleming
2015Biosensors & bioelectronics942 citations Open access
Semantic Scholar
Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
Stefanía Magnúsdóttir, A. Heinken, Laura Kütt, D. Ravcheev +8 more
2016Nature Biotechnology735 citations Open access
Semantic Scholar
Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism
Elizabeth Brunk, Swagatika Sahoo, D. Zielinski, Ali Altunkaya +17 more
2018Nature Biotechnology513 citations Open access
Semantic Scholar
MEMOTE for standardized genome-scale metabolic model testing
Christian Lieven, M. Beber, Brett G. Olivier, Frank T. Bergmann +65 more
2020Nature Biotechnology464 citations Open access
Semantic Scholar
Derivation of Human Midbrain-Specific Organoids from Neuroepithelial Stem Cells
A. Monzel, Lisa M. Smits, Kathrin Hemmer, Siham Hachi +10 more
2017Stem Cell Reports400 citations Open access
Semantic Scholar
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease
Alberto Noronha, J. Modamio, Y. Jarosz, Elisabeth Guerard +28 more
2018bioRxiv374 citations Open access
Semantic Scholar
Consistent Estimation of Gibbs Energy Using Component Contributions
Elad Noor, Hulda S. Haraldsdóttir, R. Milo, R. Fleming
2013PLoS Comput. Biol.305 citations Open access
Semantic Scholar
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease
A. Heinken, D. Ravcheev, Federico Baldini, Laurent Heirendt +2 more
2019Microbiome299 citations Open access
Semantic Scholar
SBML Level 3: an extensible format for the exchange and reuse of biological models
Sarah M. Keating, D. Waltemath, Matthias König, Feng-Kai Zhang +137 more
2020Molecular Systems Biology269 citations Open access
Semantic Scholar
Genome-scale metabolic reconstruction of 7,302 human microbes for personalised medicine
A. Heinken, J. Hertel, Geeta Acharya, D. Ravcheev +11 more
2023Nature Biotechnology230 citations Open access
Semantic Scholar
Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
A. Heinken, Swagatika Sahoo, R. Fleming, I. Thiele
2013Gut microbes217 citations Open access
Semantic Scholar
Parkinson’s disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions
Federico Baldini, Johannes Hertel, E. Sandt, C. Thinnes +110 more
2020BMC Biology207 citations Open access
Semantic Scholar
Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome
I. Thiele, Swagatika Sahoo, A. Heinken, Johannes Hertel +3 more
2020Molecular Systems Biology197 citations Open access
Semantic Scholar
Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0.
Laurent Heirendt, Sylvain Arreckx, T. Pfau, Sebastián N. Mendoza +47 more
2017168 citations
Semantic Scholar
Integrated Analyses of Microbiome and Longitudinal Metabolome Data Reveal Microbial-Host Interactions on Sulfur Metabolism in Parkinson’s Disease
Johannes Hertel, A. Harms, A. Heinken, Federico Baldini +13 more
2019Cell Reports154 citations Open access
Semantic Scholar
Differentiation of neuroepithelial stem cells into functional dopaminergic neurons in 3D microfluidic cell culture.
E. L. Moreno, Siham Hachi, Kathrin Hemmer, S. Trietsch +5 more
2015Lab on a Chip146 citations Open access
Semantic Scholar
The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities
Federico Baldini, A. Heinken, Laurent Heirendt, Stefanía Magnúsdóttir +2 more
2018bioRxiv137 citations Open access
Semantic Scholar
3D Cultures of Parkinson's Disease‐Specific Dopaminergic Neurons for High Content Phenotyping and Drug Testing
S. Bolognin, Marie Fossépré, Xiaobing Qing, J. Jarazo +12 more
2018Advancement of science128 citations Open access
Semantic Scholar
Accelerating the DC algorithm for smooth functions
F. J. Aragón Artacho, R. Fleming, P. T. Vuong
2015Mathematical programming123 citations Open access
Semantic Scholar
fastGapFill: efficient gap filling in metabolic networks
I. Thiele, N. Vlassis, R. Fleming
2014Bioinform.118 citations Open access
Semantic Scholar
A systems biology approach to studying the role of microbes in human health.
I. Thiele, A. Heinken, R. Fleming
2013Current Opinion in Biotechnology113 citations Open access
Semantic Scholar
CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models
Hulda S. Haraldsdóttir, Benjamin Cousins, I. Thiele, R. Fleming +1 more
2017Bioinform.107 citations Open access
Semantic Scholar
Automated microfluidic cell culture of stem cell derived dopaminergic neurons
Khalid I. W. Kane, E. L. Moreno, Siham Hachi, Moriz Walter +7 more
2019Scientific Reports90 citations Open access
Semantic Scholar
Community-driven roadmap for integrated disease maps
M. Ostaszewski, S. Gebel, I. Kuperstein, A. Mazein +14 more
2018Briefings Bioinform.69 citations Open access
Semantic Scholar
Prediction of intracellular metabolic states from extracellular metabolomic data
M. Aurich, G. Paglia, Ó. Rolfsson, Sigrún Hrafnsdóttir +5 more
2014Metabolomics67 citations Open access
Semantic Scholar
Do genome-scale models need exact solvers or clearer standards?
A. Ebrahim, E. Almaas, Eugen Bauer, A. Bordbar +37 more
2015Molecular Systems Biology66 citations Open access
Semantic Scholar
ReconMap: an interactive visualization of human metabolism
Alberto Noronha, A. D. Daníelsdóttir, P. Gawron, F. Jóhannsson +7 more
2016Bioinform.64 citations Open access
Semantic Scholar
Memote: A community driven effort towards a standardized genome-scale metabolic model test suite
Christian Lieven, M. Beber, Brett G. Olivier, Frank T. Bergmann +63 more
2018bioRxiv53 citations Open access
Semantic Scholar
Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression
Ding Ma, Laurence Yang, R. Fleming, I. Thiele +2 more
2016Scientific Reports51 citations Open access
Semantic Scholar
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models
M. Aurich, R. Fleming, I. Thiele
2016Frontiers in Physiology51 citations Open access
Semantic Scholar
Quantitative systems pharmacology and the personalized drug–microbiota–diet axis
I. Thiele, Catherine M. Clancy, A. Heinken, R. Fleming
2017Current Opinion in Systems Biology45 citations Open access
Semantic Scholar
Local convergence of the Levenberg–Marquardt method under Hölder metric subregularity
Masoud Ahookhosh, F. J. Aragón Artacho, R. Fleming, P. T. Vuong
2017Advances in Computational Mathematics37 citations Open access
Semantic Scholar
AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities
A. Heinken, Geeta Acharya, D. Ravcheev, Johannes Hertel +10 more
2020bioRxiv35 citations Open access
Semantic Scholar
LC-MS/MS analysis of the central energy and carbon metabolites in biological samples following derivatization by dimethylaminophenacyl bromide.
C. Willacey, M. Naaktgeboren, Edinson Lucumi Moreno, A. Wegrzyn +5 more
2019Journal of Chromatography A35 citations Open access
Semantic Scholar
Determination of the rheological properties of Matrigel for optimum seeding conditions in microfluidic cell cultures
Khalid I. W. Kane, E. L. Moreno, C. Lehr, Siham Hachi +5 more
2018AIP Advances35 citations Open access
Semantic Scholar
Real-time optical pH measurement in a standard microfluidic cell culture system.
E. B. Magnusson, S. Halldorsson, R. Fleming, K. Leosson
2013Biomedical Optics Express35 citations Open access
Semantic Scholar
Personalized modeling of the human gut microbiome reveals distinct bile acid deconjugation and biotransformation potential in healthy and IBD individuals
A. Heinken, D. Ravcheev, Federico Baldini, Laurent Heirendt +2 more
2017bioRxiv32 citations Open access
Semantic Scholar
Modeling the effects of commonly used drugs on human metabolism
Swagatika Sahoo, Hulda S. Haraldsdóttir, R. Fleming, I. Thiele
2015The FEBS Journal31 citations Open access
Semantic Scholar
Phenotype-Agnostic Molecular Subtyping of Neurodegenerative Disorders: The Cincinnati Cohort Biomarker Program (CCBP)
Andrea Sturchio, L. Marsili, J. A. Vizcarra, A. Dwivedi +20 more
2020Frontiers in Aging Neuroscience30 citations Open access
Semantic Scholar
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks
Hulda S. Haraldsdóttir, R. Fleming
2016PLoS Comput. Biol.30 citations Open access
Semantic Scholar
DistributedFBA.jl: high-level, high-performance flux balance analysis in Julia
Laurent Heirendt, I. Thiele, R. Fleming
2016Bioinform.30 citations Open access
Semantic Scholar
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
A. Heinken, Stefanía Magnúsdóttir, R. Fleming, I. Thiele
2021Bioinform.29 citations Open access
Semantic Scholar
Robust flux balance analysis of multiscale biochemical reaction networks
Yuekai Sun, R. Fleming, I. Thiele, M. Saunders
2013BMC Bioinformatics29 citations Open access
Semantic Scholar
When metabolism meets physiology: Harvey and Harvetta
I. Thiele, Swagatika Sahoo, A. Heinken, Laurent Heirendt +3 more
2018bioRxiv28 citations Open access
Semantic Scholar
Identification of metabolites reproducibly associated with Parkinson’s Disease via meta-analysis and computational modelling
Xi Luo, Yanjun Liu, Alexander Balck, C. Klein +1 more
2024npj Parkinson's Disease27 citations Open access
Semantic Scholar
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D
German A. Preciat Gonzalez, Lemmer R. P. El Assal, Alberto Noronha, I. Thiele +2 more
2017Journal of Cheminformatics24 citations Open access
Semantic Scholar
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2
Hulda S. Haraldsdóttir, I. Thiele, R. Fleming
2014Journal of Cheminformatics24 citations Open access
Semantic Scholar
A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
A. Heinken, T. Hulshof, B. Nap, Filippo Martinelli +18 more
2025Cell Systems23 citations Open access
Semantic Scholar
Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication
I. Thiele, R. Fleming
2022bioRxiv22 citations Open access
Semantic Scholar

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