ArticleMetabolites2024
MIGRENE: The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling.
Article in Metabolites, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 11 citations in OpenAlex.
- Gut microbiome and metabolic health: mechanisms and precision interventions.Gut microbes · 2026Review
- Systems engineering of engineered live biotherapeutics: A discovery-to-translation framework for streamlining microbiome therapeutic development.Journal of controlled release : official journal of the Controlled Release Society · 2026Review
- Article
- Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.Briefings in bioinformatics · 2026Review
- Microbiome signatures of virulence in the oral-gut-brain axis influence Parkinson's disease and cognitive decline pathophysiology.Gut microbes · 2025Article
- Systems biology and microbiome innovations for personalized diabetic retinopathy management.NPJ systems biology and applications · 2025Review
- Leveraging chemical synthesis to discover metabolites from the gut microbiome.Annals of the New York Academy of Sciences · 2025Review
- Toward the Next Generation of In Silico Modeling of Dynamic Host-Microbiota Interactions in the Skin.JID innovations : skin science from molecules to population health · 2025Review
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes.Genome biology · 2024Article
- Transient colonizing microbes promote gut dysbiosis and functional impairment.NPJ biofilms and microbiomes · 2024Article
- Global compositional and functional states of the human gut microbiome in health and disease.Genome research · 2024Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 2 countries.
Funding
Abstract
Understanding microbial metabolism is crucial for evaluating shifts in human host-microbiome interactions during periods of health and disease. However, the primary hurdle in the realm of constraint-based modeling and genome-scale metabolic models (GEMs) pertaining to host-microbiome interactions lays in the efficient utilization of metagenomic data for constructing GEMs that encompass unexplored and uncharacterized genomes. Challenges persist in effectively employing metagenomic data to address individualized microbial metabolisms to investigate host-microbiome interactions. To tackle this issue, we have created a computational framework designed for personalized microbiome metabolisms. This framework takes into account factors such as microbiome composition, metagenomic species profiles and microbial gene catalogues. Subsequently, it generates GEMs at the microbial level and individualized microbiome metabolisms, including reaction richness, reaction abundance, reactobiome, individualized reaction set enrichment (iRSE), and community models. Using the toolbox, our findings revealed a significant reduction in both reaction richness and GEM richness in individuals with liver cirrhosis. The study highlighted a potential link between the gut microbiota and liver cirrhosis, i.e., increased level of LPS, ammonia production and tyrosine metabolism on liver cirrhosis, emphasizing the importance of microbiome-related factors in liver health.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.