ArticleInternational journal of molecular sciences2024
Machine Learning Analysis of RNA-Seq Data Identifies Key Gene Signatures and Pathways in Mpox Virus-Induced Gastrointestinal Complications Using Colon Organoid Models.
Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Monkeypox virus replication and host response in vaginal and ectocervical epithelial cells.Virulence · 2026Article
- Stem cell-based tactics in the remodeling and treatment of intestinal diseases.Stem cell research & therapy · 2026Review
- Integrative Transcriptomic Analysis Reveals Distinct and Shared Host Responses in Dengue and Chikungunya Infections.International journal of molecular sciences · 2026Article
- Exploring Ebola virus-associated gene expression through comparative analysis.Frontiers in genetics · 2026Article
- Tool choice matters: Evaluating edgeR vs. DESeq2 for sensitivity, robustness, and cross-study performance.PloS one · 2026Article
- Transcriptional signatures of respiratory syncytial virus (RSV) infection using relaxed magnitude altitude score with hub-centric network analysis (RMAS-HCNA).Frontiers in genetics · 2026Article
- Artificial Intelligence in Bulk RNA-Seq: Challenges and Potential Solutions.Computational and structural biotechnology journal · 2026Review
- Opposite regulation of immune genes in blood and skin highlights tissue-specific dynamics of mpox virus.Scientific reports · 2025Article
- Organoids: physiologically relevantJournal of virology · 2025Review
- Transcriptional Consequences of MeCP2 Knockdown and Overexpression in Mouse Primary Cortical Neurons.International journal of molecular sciences · 2025Article
- Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis.Scientific reports · 2025Article
- Assessing concordance between RNA-Seq and NanoString technologies in Ebola-infected nonhuman primates using machine learning.BMC genomics · 2025Article
- Transcriptomic profiling of human endothelial cells infected with venezuelan equine encephalitis virus reveals NRF2 driven host reprogramming mediated by omaveloxolone treatment.Frontiers in genetics · 2025Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Mpox, caused by the Mpox virus (MPXV), emerged globally in 2022 with the Clade IIb strain, presenting a critical public health challenge. While MPXV is primarily characterized by fever and rash, gastrointestinal (GI) complications, such as diarrhea and proctitis, have also been observed. This study is a reanalysis of GSE219036 without own data and focuses on the impact of MPXV infection on the colon, using human-induced pluripotent stem cell-derived colon organoids as a model. We applied a tailored statistical framework for RNA-seq data, Generalized Linear Models with Quasi-Likelihood F-tests and Relaxed Magnitude-Altitude Scoring (GLMQL-RMAS), to identify differentially expressed genes (DEGs) across MPXV clades: MPXV I (Zr-599 Congo Basin), MPXV IIa (Liberia), and MPXV IIb (2022 MPXV). Through a novel methodology called Cross-RMAS, we ranked genes by integrating statistical significance and biological relevance across all clades. Machine learning analysis using the genes identified by Cross-RMAS, demonstrated 100% accuracy in differentiating between the different MPXV strains and mock samples. Furthermore, our findings reveal that MPXV Clade I induces the most extensive alterations in gene expression, with significant upregulation of stress response genes, such as
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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 Socratic graph.