Search Results - "Thiele, Ines"

Computationally efficient flux variability analysis by Gudmundsson, Steinn, Thiele, Ines

“…Flux variability analysis is often used to determine robustness of metabolic models in various simulation conditions. However, its use has been somehow limited…”
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Gut microbiota functions: metabolism of nutrients and other food components by Rowland, Ian, Gibson, Glenn, Heinken, Almut, Scott, Karen, Swann, Jonathan, Thiele, Ines, Tuohy, Kieran

“…The diverse microbial community that inhabits the human gut has an extensive metabolic repertoire that is distinct from, but complements the activity of…”
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From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota by Bauer, Eugen, Thiele, Ines

“…An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity…”
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BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities by Bauer, Eugen, Zimmermann, Johannes, Baldini, Federico, Thiele, Ines, Kaleta, Christoph

“…Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for…”
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Leigh map: A novel computational diagnostic resource for mitochondrial disease by Rahman, Joyeeta, Noronha, Alberto, Thiele, Ines, Rahman, Shamima

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Metabolic modelling reveals broad changes in gut microbial metabolism in inflammatory bowel disease patients with dysbiosis by Heinken, Almut, Hertel, Johannes, Thiele, Ines

“…Inflammatory bowel diseases, such as Crohn’s Disease, are characterised by an altered blood and faecal metabolome, and changes in gut microbiome composition…”
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A protocol for generating a high-quality genome-scale metabolic reconstruction by Palsson, Bernhard Ø, Thiele, Ines

“…Network reconstructions are a common denominator in systems biology. Bottom–up metabolic network reconstructions have been developed over the last 10 years…”
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Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota by Magnúsdóttir, Stefanía, Heinken, Almut, Kutt, Laura, Ravcheev, Dmitry A, Bauer, Eugen, Noronha, Alberto, Greenhalgh, Kacy, Jäger, Christian, Baginska, Joanna, Wilmes, Paul, Fleming, Ronan M T, Thiele, Ines

“…A large set of microbial metabolic models (AGORA) could be applied to better understand the functions of the human gut microbiome. Genome-scale metabolic…”
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Microbial metabolism marvels: a comprehensive review of microbial drug transformation capabilities by Martinelli, Filippo, Thiele, Ines

“…This comprehensive review elucidates the pivotal role of microbes in drug metabolism, synthesizing insights from an exhaustive analysis of over two hundred…”
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Personalized whole‐body models integrate metabolism, physiology, and the gut microbiome by Thiele, Ines, Sahoo, Swagatika, Heinken, Almut, Hertel, Johannes, Heirendt, Laurent, Aurich, Maike K, Fleming, Ronan MT

“…Comprehensive molecular‐level models of human metabolism have been generated on a cellular level. However, models of whole‐body metabolism have not been…”
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Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework by Heinken, Almut, Thiele, Ines

“…The gut microbiota is well known to affect host metabolic phenotypes. The systemic effects of the gut microbiota on host metabolism are generally evaluated via…”
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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 by Ravcheev, Dmitry A, Thiele, Ines

“…The colonic mucus layer is a dynamic and complex structure formed by secreted and transmembrane mucins, which are high-molecular-weight and heavily…”
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Integration of a physiologically-based pharmacokinetic model with a whole-body, organ-resolved genome-scale model for characterization of ethanol and acetaldehyde metabolism by Zhu, Leo, Pei, William, Thiele, Ines, Mahadevan, Radhakrishnan

“…Ethanol is one of the most widely used recreational substances in the world and due to its ubiquitous use, ethanol abuse has been the cause of over 3.3 million…”
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From metagenomic data to personalized in silico microbiotas: predicting dietary supplements for Crohn’s disease by Bauer, Eugen, Thiele, Ines

“…Crohn’s disease (CD) is associated with an ecological imbalance of the intestinal microbiota, consisting of hundreds of species. The underlying complexity as…”
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Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease by Heinken, Almut, Ravcheev, Dmitry A, Baldini, Federico, Heirendt, Laurent, Fleming, Ronan M T, Thiele, Ines

“…The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis…”
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Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis by Nogales, Juan, Gudmundsson, Steinn, Knight, Eric M, Palsson, Bernhard O, Thiele, Ines

“…Photosynthesis has recently gained considerable attention for its potential role in the development of renewable energy sources. Optimizing photosynthetic…”
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Predicting gastrointestinal drug effects using contextualized metabolic models by Ben Guebila, Marouen, Thiele, Ines

“…Gastrointestinal side effects are among the most common classes of adverse reactions associated with orally absorbed drugs. These effects decrease patient…”
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Integration of constraint-based modeling with fecal metabolomics reveals large deleterious effects of Fusobacterium spp. on community butyrate production by Hertel, Johannes, Heinken, Almut, Martinelli, Filippo, Thiele, Ines

“…Characterizing the metabolic functions of the gut microbiome in health and disease is pivotal for translating alterations in microbial composition into…”
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Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe by Heinken, Almut, Khan, M. Tanweer, Paglia, Giuseppe, Rodionov, Dmitry A, Harmsen, Hermie J. M, Thiele, Ines

“…The human gut microbiota plays a central role in human well-being and disease. In this study, we present an integrated, iterative approach of computational…”
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Reconstruction of biochemical networks in microorganisms by Palsson, Bernhard Ø, Feist, Adam M, Herrgård, Markus J, Thiele, Ines, Reed, Jennie L

“…Key Points Our ability to reconstruct genome-scale metabolic networks in microbial cells from genomic and high-throughput data has grown substantially in…”
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