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Articles 1 - 5 of 5
Full-Text Articles in Biomedical Informatics
Recurrence And Co-Occurrence Of Enhancer-Promoter Interactions Across Human Samples, Satvik Gunjala
Recurrence And Co-Occurrence Of Enhancer-Promoter Interactions Across Human Samples, Satvik Gunjala
Honors Undergraduate Theses
Experimental mapping of enhancer-promoter interactions (EPIs) is resource-intensive, and current computational prediction methods struggle with intrinsic genomic complexity and reliance on limited training data. To address this bottleneck and provide insights for improved computational methods, this study systematically analyzed chromatin contact datasets to investigate the recurrence and co-occurrence of enhancer-promoter interactions across human samples. Putative interactions were evaluated across two HiChIP datasets comprising 218 total samples and one Hi-C dataset comprising 266 samples to assess recurrence across samples and assess sequencing depth related to unique EPIs. Additionally, a preliminary item-based collaborative filtering recommender model was developed to assess co-occurrence patterns …
Mechanistic Insights Into The Antimicrobial Action Of Fungus-Derived Xanthoquinodins Against Clostridioides Difficile, Erika A. Serravalle
Mechanistic Insights Into The Antimicrobial Action Of Fungus-Derived Xanthoquinodins Against Clostridioides Difficile, Erika A. Serravalle
Graduate Thesis and Dissertation post-2024
The bacterial pathogen Clostridioides difficile is the leading cause of antibiotic- and healthcare-associated diarrhea, imposing significant clinical and economic impacts. The emergence of hypervirulent strains, such as PCR ribotype 027 (RT027), has exacerbated disease severity, recurrence rates, antibiotic resistance, and epidemiological spread. Expanding resistance profiles among C. difficile strains continue to limit the effectiveness of current IDSA-SHEA recommended therapies, which are already compromised by high recurrence rates due to antibiotic-induced disruption of the gut microbiota. These challenges highlight the urgent clinical need to identify and characterize antimicrobial compounds targeting alternative pathways in C. difficile physiology. We report the discovery and …
Synthesis And Evaluation Of Chalcones As Treatment For Negative Sense Single Stranded Rna Viruses And Applications As Broad-Spectrum Antivirals, Lorael Kirton
Graduate Thesis and Dissertation post-2024
Chalcones are a class of compounds naturally found in plants and are predicated upon a 1,3-diphenylprop-2-en-1-one scaffold. Chalcones possess many biological activities ranging from anticancer to antiviral activities. This thesis investigates the broad-spectrum antiviral properties of chalcones. Some chalcones have been reported to affect host cell mechanisms such as mammalian target of rapamycin (mTOR) signaling cascade or the cell cycle to reduce viral replication. Previously, a series of chalcones 8 were synthesized and investigated in human cytomegalovirus virus (HCMV) and human immunodeficiency virus (HIV). In this study, ten new chalcones predicated upon the design of 8 were synthesized and a …
Fgf19 Facilitates Metastatic Phenotypes In Colorectal Cancer, Joseph W. Nolff
Fgf19 Facilitates Metastatic Phenotypes In Colorectal Cancer, Joseph W. Nolff
Graduate Thesis and Dissertation post-2024
Colorectal cancer (CRC) is the second leading cause of cancer-related deaths in the United States. With 154,000 new cases estimated in 2025, there is an increased need for early screening to detect CRC prior to metastasis. Our laboratory has focused on enteroendocrine hormone Fibroblast Growth Factor-19 (FGF19) as it is overexpressed in a subset of CRC tumors. FGF19 is an intestinal-derived hormone involved with lipid homeostasis when bound to its receptor, Fibroblast Growth Factor Receptor-4 (FGFR4). Our objective focuses on FGF19 contribution towards an epithelial-to-mesenchymal transition (EMT) and overall metastatic properties including rapid proliferation and/or increased cell motility. Immunofluorescence was …
Tim/Tam Receptors: A Potential Biomarker For Predicting Sensitivity To Zika Virus-Induced Oncolysis In Non-Small Cell Lung Cancers, Shankari Somasekar
Tim/Tam Receptors: A Potential Biomarker For Predicting Sensitivity To Zika Virus-Induced Oncolysis In Non-Small Cell Lung Cancers, Shankari Somasekar
Honors Undergraduate Theses
Non-small cell lung cancers (NSCLC) constitute 80-85% of lung cancers and are the leading cause of cancer-related deaths globally. The most common cause is prolonged smoking. Current treatment options for NSCLC include surgery, radiation, chemotherapy, targeted drug therapy, and immunotherapy. Although these medications are effective in the short term, patients often face issues of drug resistance and debilitating side effects with prolonged use. Currently, the use of Zika virus (ZIKV) is being researched as a possible alternative treatment for cancer, which minimizes side effects and the risk of drug resistance. TIM/TAM proteins are identified as the putative ZIKV receptors on …