ArticleCell host & microbe2021
Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.
Article in Cell host & microbe, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed, 25 citations in OpenAlex.
- Mechanisms by which proline reductase ofmBio · 2026Article
- Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.Nature communications · 2026Article
- Clostridioides difficile pathogenesis and control.Nature reviews. Microbiology · 2026Review
- Systematic evaluation of metatranscriptomic differential gene expressionbioRxiv : the preprint server for biology · 2025Article
- Personalized Clostridioides difficile colonization risk prediction and probiotic therapy assessment in the human gut.Cell systems · 2025Article
- Moving from genome-scale to community-scale metabolic models for the human gut microbiome.Nature microbiology · 2025Review
- Impacts ofJournal of bacteriology · 2025Article
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- Approaching pathogenicbioRxiv : the preprint server for biology · 2024Article
- Reconsidering the in vivo functions of Clostridial Stickland amino acid fermentations.Anaerobe · 2022Review
- Mathematical models to study the biology of pathogens and the infectious diseases they cause.iScience · 2022Review
- Computational approaches to understanding Clostridioides difficile metabolism and virulence.Current opinion in microbiology · 2022Review
- In vivo commensal control of Clostridioides difficile virulence.Cell host & microbe · 2021Article
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12 authors at 1 institution in 1 country.
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Abstract
We present predictive models for comprehensive systems analysis of Clostridioides difficile, the etiology of pseudomembranous colitis. By leveraging 151 published transcriptomes, we generated an EGRIN model that organizes 90% of C. difficile genes into a transcriptional regulatory network of 297 co-regulated modules, implicating genes in sporulation, carbohydrate transport, and metabolism. By advancing a metabolic model through addition and curation of metabolic reactions including nutrient uptake, we discovered 14 amino acids, diverse carbohydrates, and 10 metabolic genes as essential for C. difficile growth in the intestinal environment. Finally, we developed a PRIME model to uncover how EGRIN-inferred combinatorial gene regulation by transcription factors, such as CcpA and CodY, modulates essential metabolic processes to enable C. difficile growth relative to commensal colonization. The C. difficile interactive web portal provides access to these model resources to support collaborative systems-level studies of context-specific virulence mechanisms in C. difficile.
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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.