Publications by authors named "T S Furey"
Genome-wide association studies (GWAS) have identified over 300 loci associated with the inflammatory bowel diseases (IBD), but putative causal genes for most are unknown. We conducted the largest disease-focused expression quantitative trait loci (eQTL) analysis using colon tissue from 252 IBD patients to determine genetic effects on gene expression and potential contribution to IBD. Combined with two non-IBD colon eQTL studies, we identified 194 potential target genes for 108 GWAS loci.
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- Crohn's disease (CD) is a long-lasting GI disorder that leads to complications requiring surgery, with many patients facing post-operative issues and disease recurrence despite medical advances.
- This study analyzed gene expression data from 45 CD patients to explore common genes and pathways linked to post-operative complications and disease recurrence, using techniques like gene set enrichment analysis and logistic regression.
- Results showed certain inflammatory pathways were raised in recurrent cases and septic complications, while a decrease in myogenesis in colon tissue linked both outcomes, highlighting potential biomarkers for improving patient management.
Polymerized β-actin may provide a structural basis for chromatin accessibility and actin transport into the nucleus can guide mesenchymal stem cell (MSC) differentiation. Using MSC, we show that using CK666 to inhibit Arp2/3 directed secondary actin branching results in decreased nuclear actin structure, and significantly alters chromatin access measured with ATACseq at 24 h. The ATAC-seq results due to CK666 are distinct from those caused by cytochalasin D (CytoD), which enhances nuclear actin structure.
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- Network inference models biological interactions among genes, proteins, and metabolites, playing a key role in understanding diseases.
- CoVar is a new machine learning framework that goes beyond traditional differential expression analysis by identifying variational genes, which reflect changes in gene expression interactions rather than just individual gene changes.
- The framework has demonstrated its effectiveness in recognizing crucial driver genes and capturing complex regulatory dynamics through analyses of synthetic and real biological data, such as yeast expression affected by mitochondrial genome deletion.
Crohn's disease (CD) is a chronic inflammatory gut disorder. Molecular mechanisms underlying the clinical heterogeneity of CD remain poorly understood. MicroRNAs (miRNAs) are important regulators of gut physiology, and several have been implicated in the pathogenesis of adult CD.
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