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I. Thiele · SciRah

Researcher profile · Semantic Scholar

I. Thiele

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I. Thiele — researcher profile on SciRah

h-index: 61
Works: 149
Citations: 24K

Most-cited papers

Gut microbiota functions: metabolism of nutrients and other food components
I. Rowland, G. Gibson, A. Heinken, K. Scott +3 more
2017European Journal of Nutrition2,422 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 +51 more
2019Nature Protocols1,072 citations Open access
Semantic Scholar
Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes
Stefanía Magnúsdóttir, D. Ravcheev, V. de Crécy-Lagard, I. Thiele
2015Frontiers in Genetics801 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
Metabolomics enables precision medicine: “A White Paper, Community Perspective”
R. Beger, W. Dunn, Michael A. Schmidt, S. Gross +14 more
2016Metabolomics533 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
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
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
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Eugen Bauer, J. Zimmermann, Federico Baldini, I. Thiele +1 more
2017PLoS Comput. Biol.273 citations Open access
Semantic Scholar
Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe
A. Heinken, M. T. Khan, G. Paglia, D. Rodionov +2 more
2014Journal of Bacteriology221 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
The contribution of gut bacterial metabolites in the human immune signaling pathway of non-communicable diseases
F. Hosseinkhani, A. Heinken, I. Thiele, P. Lindenburg +2 more
2021Gut microbes212 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
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
Finding Useful Biomarkers for Parkinson’s Disease
A. Chen-Plotkin, R. Albin, R. Alcalay, D. Babcock +36 more
2018Science Translational Medicine132 citations Open access
Semantic Scholar
Modeling metabolism of the human gut microbiome.
Stefanía Magnúsdóttir, I. Thiele
2018Current Opinion in Biotechnology126 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
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
Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico
A. Heinken, I. Thiele
2015Applied and Environmental Microbiology107 citations Open access
Semantic Scholar
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework
A. Heinken, I. Thiele
2015Gut microbes106 citations Open access
Semantic Scholar
Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides
D. Ravcheev, I. Thiele
2017Frontiers in Genetics102 citations Open access
Semantic Scholar
Systems biology of host–microbe metabolomics
A. Heinken, I. Thiele
2015Wiley Interdisciplinary Reviews: Systems Biology and Medicine93 citations Open access
Semantic Scholar
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota
Eugen Bauer, I. Thiele
2018mSystems84 citations Open access
Semantic Scholar
Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells.
Kacy Greenhalgh, J. Ramiro‐Garcia, A. Heinken, P. Ullmann +12 more
2019Cell Reports78 citations Open access
Semantic Scholar
Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease
Swagatika Sahoo, M. Aurich, J. Jonsson, I. Thiele
2014Frontiers in Physiology75 citations Open access
Semantic Scholar
Leigh map: A novel computational diagnostic resource for mitochondrial disease
Joyeeta Rahman, Alberto Noronha, I. Thiele, S. Rahman
2017Annals of Neurology74 citations Open access
Semantic Scholar
From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease
Eugen Bauer, I. Thiele
2018npj Systems Biology and Applications73 citations Open access
Semantic Scholar
Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells
Swagatika Sahoo, I. Thiele
2013Human Molecular Genetics71 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
Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine.
A. Heinken, Arianna Basile, Johannes Hertel, C. Thinnes +1 more
2021Annual Review of Microbiology65 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
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis
D. Ravcheev, I. Thiele
2016Frontiers in Microbiology54 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
Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota
D. Ravcheev, I. Thiele
2014Frontiers in Microbiology47 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
Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires
Eugen Bauer, C. Laczny, Stefanía Magnúsdóttir, P. Wilmes +1 more
2015Microbiome44 citations Open access
Semantic Scholar
Model-based dietary optimization for late-stage, levodopa-treated, Parkinson’s disease patients
M. Ben Guebila, I. Thiele
2016npj Systems Biology and Applications40 citations Open access
Semantic Scholar
Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production
Johannes Hertel, A. Heinken, Filippo Martinelli, I. Thiele
2021Gut microbes39 citations Open access
Semantic Scholar
Rare genetic variants affecting urine metabolite levels link population variation to inborn errors of metabolism
Yu-Rong Cheng, P. Schlosser, Johannes Hertel, P. Sekula +10 more
2021Nature Communications38 citations Open access
Semantic Scholar
Computational Modeling of Human Metabolism and Its Application to Systems Biomedicine.
M. Aurich, I. Thiele
2016Methods in molecular biology36 citations
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
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
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

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