Genomics Commons^™

Sox18 Unleashed Exploring The Transcriptomic Landscape - Differential Gene Expression Analysis Via Rna Seq In Overexpressed Sox18, Van Nguyen, Kahlie Hernandez, Monabelle Elbayeh

Posters - 2026

Cancer remains a leading cause of death worldwide, and childhood sarcomas such as Rhabdomyosarcoma (RMS) and Ewing Sarcoma (ES) are particularly aggressive with limited targeted treatment options. Despite advancements in cancer therapies, metastatic sarcomas still have a survival rate below 30%, emphasizing the need for new therapeutic targets. SOX18, a transcription factor has played a role in vascular development and endothelial differentiation, functioning as a key driver of angiogenesis. In cancer, increased SOX18 expression has been linked to dysregulated cell migration, invasion, and therapy resistance mechanisms. However, the extent to which SOX18 influences RMS and ES at the transcriptional level …

Lab-Made 100 Bp Dna Ladder Using Polymerase Chain Reaction And Human Dna, Muhammad Ilmam Bariqi, Zulham Yamamoto, Putri Chalya Firjatu, Luthfi Umam Hakim Nasution, Oryza Sativa Lubis

Makara Journal of Science

Polymerase chain reaction (PCR) is a rapid, molecular biology technique widely used in disease diagnosis and genetic engineering. Conventional PCR products require agarose gel electrophoresis, which employs a DNA ladder as a size reference. Most commercial ladders are plasmid-based and reliable but require additional culture time. We suggest a more efficient method for producing a DNA ladder using DNA derived from human blood. DNA was isolated using a commercial kit. Primer sets generating 100–1000 base pair (bp)-long fragments bearing target regions p12, p13, and p14 were designed using Primer-BLAST. DNA was amplified by routine PCR, visualized on a 1% (w/v) …

Supplemental Data For Gulf Coast Walleye Edna Survey, Kevin W. Jones

Research Data

This file contains the full eDNA collection and amplification dataset for:

Jones, K.W. (2026). Development and application of an eDNA protocol for the detection of Gulf Coast Walleye (Sander vitreus) in Mississippi [Thesis submitted for publication]. Department of Wildlife, Fisheries, and Aquaculture, Mississippi State University.

Metagenomic Profiling Of Gut Microbiome Signatures Across Liver Disease Stages And Hcv-Related Hepatocellular Carcinoma In Egyptian Patients, Marwa A. Zahra

Theses and Dissertations

Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study profiles the gut microbiome in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt. Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients. Healthy and treated HCV patients exhibited distinct microbial profiles characterized by …

Computational Tools For Tandem Repeat Detection Using Long-Read Sequencing, Qian Liu, Jincheng Li

Life Sciences Faculty Research

Tandem repeats (TRs) play essential roles in a variety of biological functions, and their abnormal expansions are significantly implicated in phenotypic variation and cause >60 human diseases. However, long TR regions cannot be reliably detected using short-read sequencing, and long-read sequencing enables accurate genome-wide detection of TRs. In recent years, various computational tools have been developed to detect and genotype TRs from long-read data. In this survey, we systematically categorize and review 39 computational tools designed for TR detection, visualization and functional interpretation. We discuss their strengths and limitations for TR detection from long-read sequencing data, highlighting current challenges and …

Characterization And Advancement Of Molluscan Venom Gland Cell Model Systems, James V. Parziale

Dissertations, Theses, and Capstone Projects

Venomous mollusks, including cone snails and coleoid cephalopods, produce rich repertoires of bioactive peptides with profound effects on cellular physiology, yet there are few tractable experimental systems that exist to study their development, maintenance, and venom secretion. Although therapeutics such as the cone snail peptide Ziconotide demonstrate the biomedical potential of molluscan venoms, progress in understanding how venom glands form, function, and evolve has been hindered by the lack of reliable husbandry and the complete absence of in vitro cell models. Modern comparative genomics has revealed widespread convergent evolution across venomous lineages, but molluscan datasets remain underrepresented, limiting insights into …

Computational Comparative Genome Analysis Reveals The Characteristics Of Acinetobacter Baumannii C123 Strains, Jennilyn Nicole G. Mendoza

The Lasallian Journal of Health

Acinetobacter baumannii is a Gram-negative, aerobic and multi-drug resistant bacterial pathogen commonly associated with nosocomial infections. This species has several strains and is known to cause pneumonia, septi cemia, meningitis, urinary tract infection and wound infection which are associated with high mortality rates. This study focused on a genome-wide compari son among target C123 strain and 15 other reference strains to predict the overall properties, and resistance mechanisms of the C123 strain. A total of 16 whole genome sequence strains were retrieved from NCBI database for analysis. The selected strains were assem bled and annotated using computational tools. Further more, …

Varying Dna Methylation Patterns In The Florida Sand Skink (Plestiodon Reynoldsi) In Relation To Fire Histories, Victoire Hj Litre

College of Graduate Studies: Theses & Dissertations

Epigenetics is the study of changes in phenotype not caused by changes in DNA sequence. DNA methylation is the most well-studied epigenetic mechanism in an ecological context. Reptiles use DNA methylation to respond to environmental stressors and differences among habitats. The Florida Sand Skink (Plastidome reynoldsi) is federally listed as a threatened species. They are endemic to the threatened, fire-dependent Florida scrub habitat. As they persist in burned habitats, the Florida Sand Skink must be able to rapidly respond to wildfires. To better understand how the Florida Sand Skink adjusts to fire-driven habitat changes, it is important to …

From Molecules To Minds: Integrative Multi-Omics In Psychiatry, Hossein Abbasi, Sage E. Hawn, Arash Javanbakht, Soraya Seedat, Kyle Bourassa, Sinead M. Sinnott, Antonia V. Seligowski, Sian Hemmings, Nathan A. Kimbrel, Alicia K. Smith, Leslie Brick, Divya Mehta

Psychology Faculty Publications

Psychiatric disorders are biologically complex conditions arising from interactions across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. Single-omics approaches rarely capture more than a fraction of the variance in complex conditions, underscoring the importance of integrative multi-omics frameworks. This mini-review summarizes key methodologies and their application in psychiatric research, with a focus on systems-level integration of genomic risk scores, transcriptomic networks, and neuroimaging data to advance biological understanding of disorders such as depression, schizophrenia, and Alzheimer’s disease. We also outline the infrastructural requirements for effective multi-omics research, including standardized biobanking, Laboratory Information Management Systems, adherence to FAIR data principles, …

Nutrient-Driven Transcription Factor-Dna Interactions And Their Signaling Mechanisms In Metabolic Disease, Evelyn A. Bates

Theses and Dissertations--Nutritional Sciences

Metabolic homeostasis is maintained through tightly coordinated signaling networks that integrate diverse physiological inputs. Central to this regulation are transcription factors, which sense nutrient, hormonal, and vitamin-derived signals and translate them into coordinated gene expression programs. Transcription factor activity is governed by DNA binding, recruitment of coregulatory proteins, and interactions with specific response elements in gene promoters, which allows them to selectively modulate diverse metabolic pathways. Owing to their multifactorial and tunable nature, transcription factors have emerged as promising targets for the treatment and diagnosis of metabolic diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). This dissertation explores the molecular …

Toward Interpretable Multi-Omics Multimodal Biomedical Artificial Intelligence, Yanjun Lyu

Computer Science and Engineering Dissertations

The complexity of human disease arises from biological processes that unfold across multiple scales, from molecular variation through cellular function, tissue organisation, brain phenotypes, each of which is associated with distinct measurement modalities, regularities, and characteristic. Contemporary biomedical artificial intelligence has brought the opportunity to reveal the complexity with in; however, its methodological default, in which models are trained on most readily available modality, does not adequately engage with the multi-scale connected structure by which biological meaning is constituted. The research area of multi-omics and multi-modal AI for biomedicine remains at an early exploratory stage, and the work presented in …

A Framework For Characterizing The Peripheral Immune Isonome Using Long-Read Single-Cell Rna Sequencing And Its Relevance To Neurological Disease, Patricia Hayes Doyle

Theses and Dissertations--Neuroscience

Long-read single-cell RNA sequencing provides an opportunity to understand human health and disease at isoform resolution, revealing cellular diversity and disease mechanisms difficult to resolve with bulk or short-read methodologies.

Using a modified PIPseq workflow and computational pipeline adapted for Oxford Nanopore (ONT) sequencing, we profiled isoform usage across immune cells, integrating marker expression and isoform discovery, generating the largest long-read single-cell dataset of human immune cells from a single individual to date. We identified non-canonical protein-coding variants of GZMB and CD3G enriched in unexpected cell types. We also discovered novel transcripts from CMC1 and LYAR with cell-type-specific signatures that …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

Microbial Community Structure In Global Soils, Matthew Jabro

CMC Senior Theses

Soil harbors the most diverse microbial communities on Earth, yet whether predictable community types exist across biomes and whether taxonomic composition encodes habitat of origin remain open questions at global scale. This thesis addresses both questions by applying unsupervised clustering and supervised classification to transformed 16S ribosomal RNA (rRNA) amplicon profiles from two independent datasets: the global topsoil survey of Bahram et al. (193 samples) and the Earth Microbiome Project (EMP) soil subset of Thompson et al. (2,209 samples). Application of a sample clustering method based on a mixture of Gaussian Graphical Models (MixGGM) identified 19 clusters in the topsoil …

Phylogeography, Fungal Host Specificity, And Fitness In The Corallorhiza Maculata Species Complex, Hana Thixton-Nolan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Mycoheterotrophic plants exploit fungi for most or all nutritional needs, providing a compelling system to address the evolutionary consequences of genome reduction, population-level variation, and germination requirements. I am using the widespread Corallorhiza maculata species complex to address questions of genomic variation, fungal host specificity, morphological variation, and germination requirements across the broad geographic range from Mexico to northern North America. This complex contains C. bulbosa, C. macrantha, and C. mertensiana, the latter with three varieties (maculata, occidentalis, and mexicana). These taxa vary in flowering time, floral morphology, and fungal associations. However, the degree …

An Ensemble Classifier For Ordinal Outcomes In High-Dimensional Genomics Data, Heranga K. Rathnasekara, Sinjini Sikdar

Mathematics & Statistics Faculty Publications

Analysis of genomics data for predicting disease outcomes is a fast-growing field in medical research. There often exist categorical, specifically, ordinal outcomes that need to be predicted based on genomic profiles. This has led to recent development of some high-dimensional ordinal classification methods that can address the large dimensionality of the genomic covariate set. These high-dimensional ordinal models tend to vary widely in their performance depending on the data they are applied to and the evaluation criteria used. In this article, we outline an ensemble ordinal classifier that integrates different ordinal modeling approaches through bootstrap-based model evaluation, multi-metric performance assessment, …

Systematics Of Disk-Winged Bats (Thyroptera), Courtney L. Klumpp

Capstone Showcase

This thesis investigates the evolutionary relationships among disk-winged bats in the genus Thyroptera, a small group of Neotropical bats known for the adhesive suction disks on their wings and feet that allow them to roost inside tightly rolled leaves. The distinctive morphology and behavior of these bats have not been extensively documented, and their phylogenetic relationships remain only partially resolved. The goal of this research is to better understand how these species are related to one another and to determine whether the five recognized species of Thyroptera form a single monophyletic group. To address this question, morphological and genetic …

Dosage Sensitivity And The Evolution Of Dosage Compensation: Tests Of The Insensitive Sex Chromosome Hypothesis In Flour Beetles, Shana Pau

Biology Dissertations

Sex chromosome evolution generates imbalances in gene dosage that can disrupt gene expression and organismal function. These imbalances are often resolved through dosage compensation mechanisms, yet the factors that drive the emergence and diversity of these systems remain poorly understood. This dissertation addresses a central question in evolutionary genomics: what governs the evolution of dosage compensation?

Focusing on dosage sensitivity as a potential driver, I evaluate the Insensitive Sex Chromosome Hypothesis (ISCH), which predicts that chromosome-wide compensation is more likely to evolve in genomic contexts that are not depleted of dosage-sensitive genes. Using flour beetles (Tribolium spp.) as a …

Genomic Determinants Of Appetite Regulation And Their Role In Obesity Risk, Timothy J. Renier

Dartmouth College Ph.D Dissertations

Over 40% of US adults and 20% of children live with obesity. It is related to increased risks of diseases including type II diabetes and cancer, is a source of harmful stigma, and impairs child development. Appetitive traits describing patterns of food approach and avoidance behaviors may serve as windows into the underlying pathophysiology of obesity. As both obesity and appetitive traits are heritable, common genetic drivers of obesity may lead to phenotypic obesity through appetitive traits as a disease mechanism. Additionally, GLP-1 receptor agonists (GLP-1RAs) have been shown to exert their profound clinical effects in part by modulating appetite. …

Characterization Of Microrna Expression In Neuron-Enriched Extracellular Vesicles During Early Life, Allison Molen

Theses and Dissertations

Extracellular vesicles (EVs) are membrane-bound sacs released by cells that carry molecular cargo reflective of their cell of origin. EVs enriched using L1 cell adhesion molecule (L1CAM) as a marker of putative neuronal origin can cross the blood–brain barrier and provide a minimally invasive window into brain-related processes. Exosomal microRNA (miRNA) regulate gene expression and have been implicated in psychiatric disorders, including major depressive disorder (MDD). However, measuring and analyzing miRNA from L1CAM-positive EVs presents substantial analytical challenges due to low abundance and sparse detection across samples.

Plasma samples from participants recruited through the Mid-Atlantic Twin Registry (MATR) were used …