ArticleScientific reports2023
Identifying metabolic shifts in Crohn's disease using' omics-driven contextualized computational metabolic network models.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 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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Who cites it
11 citing papers in PubMed, 20 citations in OpenAlex.
- Constraint-based modelling of metabolic dysregulation in Gaucher disease: mitochondrial dysfunction and disrupted cholesterol homeostasis.Orphanet journal of rare diseases · 2026Article
- Metabolic network analysis of Crohn's disease reveals sex- and age-specific cellular phenotypes.Cell systems · 2025Article
- Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.NPJ systems biology and applications · 2025Review
- Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.Briefings in bioinformatics · 2025Review
- Metabolic modeling reveals a multi-level deregulation of host-microbiome metabolic networks in IBD.Nature communications · 2025Article
- How Artificial Intelligence Will Transform Clinical Care, Research, and Trials for Inflammatory Bowel Disease.Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association · 2025Review
- Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.Journal of microbiology (Seoul, Korea) · 2025Review
- Deciphering and designing microbial communities by genome-scale metabolic modelling.Computational and structural biotechnology journal · 2024Review
- A novel computational approach for the mining of signature pathways using species co-occurrence networks in gut microbiomes.BMC microbiology · 2024Article
- Article
- Bridging systems biology and tissue engineering: Unleashing the full potential of complex 3DBiophysics reviews · 2024Review
Corrections and comments
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Authors and funding
16 authors at 3 institutions in 1 country.
Funding
Abstract
Crohn's disease (CD) is a chronic inflammatory disease of the gastrointestinal tract. A clear gap in our existing CD diagnostics and current disease management approaches is the lack of highly specific biomarkers that can be used to streamline or personalize disease management. Comprehensive profiling of metabolites holds promise; however, these high-dimensional profiles need to be reduced to have relevance in the context of CD. Machine learning approaches are optimally suited to bridge this gap in knowledge by contextualizing the metabolic alterations in CD using genome-scale metabolic network reconstructions. Our work presents a framework for studying altered metabolic reactions between patients with CD and controls using publicly available transcriptomic data and existing gene-driven metabolic network reconstructions. Additionally, we apply the same methods to patient-derived ileal enteroids to explore the utility of using this experimental in vitro platform for studying CD. Furthermore, we have piloted an untargeted metabolomics approach as a proof-of-concept validation strategy in human ileal mucosal tissue. These findings suggest that in silico metabolic modeling can potentially identify pathways of clinical relevance in CD, paving the way for the future discovery of novel diagnostic biomarkers and therapeutic targets.
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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.