Genomics Commons^™

The Hitchhiker's Guide To The Host: Fleas And The History Of Pikas In North America, Josh Pletcher

All NMU Master's Theses

Parasite phylogenetics can offer windows into the cryptic evolutionary history of hosts, often highlighting events that are not recorded by the phylogenetics of the host. Pikas (small lagomorphs) host a diverse parasite community comprising endoparasites (e.g., coccidians, nematodes, and cestodes) and ectoparasites (e.g., fleas and mites). Phylogenetic analysis of pika endoparasites has revealed pikas evolved in Asia and colonized North America in two waves, and that contact between these two pika lineages allowed parasites to be transferred from one lineage to another and to survive the extinction of their original host. To uncover these cryptic histories, understanding the biogeography of …

Population Structure And Connectivity Of Atlantic Nurse Sharks (Ginglymostoma Cirratum) In The Bahamas And Outlying Areas, Baylie A. Fadool

School of Natural Resources: Dissertations, Theses, and Student Research

Understanding animal ecosystem dynamics and behavior at the individual and population levels is essential for identifying life-history patterns and important areas for management and conservation. Marine fish species often face minimal geographic barriers to movement, but environmental (temperature, salinity, current) or intrinsic barriers (philopatry, site fidelity) can dictate gene flow. Atlantic nurse sharks (Ginglymostoma cirratum) are an International Union for Conservation of Nature (IUCN) listed ‘vulnerable’ species and present a unique opportunity to investigate patterns of population structure and connectivity in large-bodied sharks. They are benthic and display reproductive philopatry, with recent work suggesting they have the capacity …

Effects Of M6a Dna Methylation By Bacterial Methyltransferase In Colorectal Cancer, Fabian Alejandro Mendoza Galvan

Dissertations and Theses (Open Access)

Effects of m6A DNA methylation by bacterial methyltransferase in colorectal cancer Fabian Alejandro Mendoza Galvan Advisory Professor: Angela H. Ting, Ph.D. Fusobacterium nucleatum animalis (Fna) is found in the human oral cavity and gut. A distinct clade of Fna is primarily enriched in the tumor microenvironment (TME) and within colorectal cancer (CRC) cells. This clade DNA methylation pattern is primarily catalyzed by a cell-cycle regulated methyltransferase (CcrM) ortholog, M.FnI, that targets the GANTC sequence motif through methyl-6-Adenine (m6A) DNA methylation. We hypothesized that M.FnI enzyme can induce m6A methylation abnormalities in CRC cells to promote cancer progression. Evidence for endogenous …

Understanding Epigenomic Landscapes In Cancer Progression And Immunotherapy Response, Jonathan Schulz

Dissertations and Theses (Open Access)

Nonmutational epigenomic reprogramming has emerged as a key hallmark of cancer that plays crucial roles in tumor evolution during its progression and response to therapy. However, the extent and nature of epigenomic reprogramming remains poorly understood. This dissertation examines how epigenetic regulation shapes cancer progression and response to immunotherapy. Working at the intersection of cancer biology and computational genomics, it develops analytical frameworks for characterizing chromatin structure and DNA methylation across diverse tumor contexts and uses these frameworks to address two complementary biological questions: how promoter-associated chromatin organization varies across cancer types, and how epigenetic perturbation modulates tumor immunogenicity in …

Denisovan Introgression And Selection At Cntnap2 In Ancient And Modern American Populations, Matthew Barker

All Theses

The peopling of the Americas created new opportunities for genetic adaptation as ancient populations encountered novel environments across North and South America. Previous research has shown that segments of Indigenous American ancestry contain elevated proportions of Denisovan alleles. The gene CNTNAP2, which is involved in brain development and neuronal function, contains a Denisovan-derived haplotype that represents a candidate locus for adaptive introgression in admixed American populations. A Denisovan-derived core haplotype approximately 55 kb in length was identified within intron 13 of CNTNAP2. This haplotype is primarily found in admixed American populations and occurs rarely outside the Americas, and …

Discovering The Genetics Underlying Speciation Traits In Heuchera (Coral Bells), Tajinder Singh

Honors Theses

Hybridization is a key evolutionary mechanism for generating biological diversity, ultimately shaping diversification and adaptation of plant lineages in natural and agroecosystems.  Our understanding of the frequency, distribution, and significance of hybridization is rapidly increasing, but the external driving forces that dictate why certain species hybridize, and others do not remain obscure. The physical traits that shape gene flow and trait sharing among species are likely to be among the key factors that directly control hybridization. Gene flow in most plants is mediated by pollinating insects and thus by pollination syndromes, which are suites of floral traits that have evolved …

Cleft Palate And The Coordination Of Wnt Signaling And Pax9 In Murine Palatogenesis, Landon Wyatt

Honors Theses

Cleft palate is a common craniofacial birth defect that arises when the molecular and morphogenetic events guiding secondary palate formation lose coordination during a narrow developmental window. In mice, successful palatogenesis requires the paired palatal shelves to grow vertically, elevate above the tongue, and fuse at the midline; disruption of any of these steps can result in clefting. Two important regulators of this process are canonical Wnt signaling and the transcription factor Pax9, both of which contribute to normal palatal mesenchymal growth and patterning during early development. This paper first examines whether altered Dkk1/Wnt signaling contributes to the Pax9-null palate …

Comparing Gngt1 Expression In Eye Tissue Of Polymorphic Salamander Species Through Development, Fiona Coulbourne, Camila Cardozo, Macarena Machado, Ruben Tovar

Posters - 2026

The effect of the environment on organisms and their adaptations is widely studied. When exposed to different environmental niches, phenotypic adaptation is observed even within species. Animals that live in dark cave environments show a loss of their eyesight, since this sense is no longer useful to keep. Previous research has studied salamanders of the clade Eurycea and compared gene expression to subterranean and surface phenotypes1. E.pterophila is observed to express these two phenotypes depending on its environment, either Preserve Cave (subterranean) or Comal Springs (surface). Subterranean variant shows reduced eye volume and assumes to have decreased eyesight. Utilizing RNASeq …

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, …

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 …

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. …

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 …

Genomic Signatures Of Decline And Recovery In An Endangered Bat, Myotis Grisescens, Marxe Altman-Orbach

Graduate Theses/Dissertations

Tremendous population declines may result in the loss of genetic diversity, which can, in turn, lead to reduced adaptive potential, overexpression of deleterious phenotypes, and further population declines. In this way, genetic drift from a severe demographic decline may ultimately lead to an extinction vortex. However, populations that avoid the loss of genetic diversity may remain viable, despite demographic crashes. Therefore, understanding genetic diversity is vital for assessing the conservation status of species that have undergone declines, and can even reflect the effectiveness of management actions. I investigated signatures of genetic bottlenecks in the gray bat (Myotis grisescens), …

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 …