Genetics and Genomics Commons^™

Searching For Cause Of Unexplained Protein Interaction With Multiple Assembly Methods, Gavin Anderson

Master's Projects

Research into colistin adjuvants has identified interactions between a host of proteins and proteins found within certain strains of bacteria. BLAST, a widely adopted local sequence alignment tool, was used to create a database containing the genomes of relevant bacterial strains, which would then be used to query against the previously identified proteins. Many of these strains do not have publicly available assemblies, which makes database construction difficult. CATwalk, a new naïve fragment extender, is first described in this paper and used to extend fragments of interest. BLAST results first identified short fragments with sufficient similarity, which can then be …

Rapid Urbanization Reduces Genetic Diversity And Increases Genetic Differentiation Of A Lynx Spider Oxyopes Sertatus In Central Taiwan, Ying-Yuan Lo, Chi Wei, Wan-Jyun Chen, Chung-Ping Lin

Biological Sciences Faculty Publications

Urbanization is a dominant force driving destructive and irreversible changes of natural habitats in modern times. While the effects of urbanization on community composition and phenotypic responses are well-documented, its influence on genetic diversity and population structure remains understudied, particularly for invertebrates in subtropical regions. This study tested the hypothesis that urbanization reduces genetic diversity and increases population differentiation in the lynx spider Oxyopes sertatus, a common foliage-dwelling spider in Taiwan. We sampled 245 individuals from 17 sites distributed along an urban-rural gradient and quantified urbanization intensity using land-use composition at both landscape (4 km²) and local (0.25 km²) …

Microarray Analysis Of Human Abdominal Aortic Aneurysm With Emphasis On Cardiovascular Genes Revealed Differentially Expressed Genes, Song Lu, Li Ping Li, John V. White, Xiaoying Zhang, Ifeyinwa Nwaneshiudu, Adaobi Nwaneshiudu, Nectaria Ntaoula, John Gaughan, Dimitri S. Monos, Wan-Lu Lin, Charalambos C. Solomides, Emilia L. Oleszak, Chris D. Platsoucas

Biological Sciences Faculty Publications

Background/Aim: We examined gene expression profiles in abdominal aortic aneurysm (AAA) lesions vs. normal aortas by cDNA microarray and real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR).

Materials and Methods: Phosphorus (32P)-labeled cDNA from AAA specimens (mean AAA size 6.65 cm) and normal aortas were hybridized with a 588-gene microarray primarily of the cardiovascular system. The results were validated by qRT-PCR.

Results: A total of 35 out of the 588 genes were differentially expressed, with either log2 ratio of AAAs/controls ≥1 (upregulated; 20 genes) or ≤−1 (downregulated; 15 genes) in AAA lesions vs. normal aorta, and 25 of these were significantly …

Sex In Plants: Birth, Death, And Trying To Survive In Changing Climates, Elena M. Meyer

Theses and Dissertations

Plant mating systems are key determinants of fitness. Angiosperms exhibit a wide variety of reproductive strategies, including self-fertilization (or selfing), outcrossing, and mixed mating. It has been estimated that up to 43% of plant species are capable of selfing, and selfing has been hypothesized to provide reproductive assurance where opportunities for mating may be limited, such as in marginal environments. However, questions regarding the overall distribution of selfing rates across angiosperms, the maintenance of mixed mating in the face of inbreeding depression, and the impact of self-fertilization on diversification rates remain incompletely resolved. Here, we explore the dynamics of self-fertilization …

Epigenetic Modifications In Dedifferentiated Liver Cells To Restore Lost Liver Function, Shreya Sharma

Masters Theses

The goal of the study is to investigate whether the epigenetic modifications can enhance the restoration of liver gene expression in dedifferentiated hepatoma cells or not. For the study, we used dedifferentiated H11 hepatoma cell lines which overexpress one of a panel of introduced candidate liver-enriched transcription factors H11-HNF1a, H11-CREB3L3, H11-CREG1, H11- HHEX, H11-HNF6, and H11-IGFBP1. The cells were treated with the DNA methyltransferase inhibitor 5-azacytidine and the histone deacetylase inhibitor sodium butyrate, both individually and in combination. Gene expression analysis was determined by RT-qPCR, which revealed that while transcription factor overexpression alone produced limited activation, epigenetic modulation, particularly Histone …

A Complete Diploid Human Genome Benchmark For Personalized Genomics, Nancy F. Hansen, Nathan Dwarshuis, Hyun Joo Ji, Arang Rhie, Hailey Loucks, Glennis A. Logsdon, Mitchell R. Vallger, Jessica M. Storer, Juhyun Kim, Eleni Adam, Nicolas Alternose, Dmitry Antipov, Mobin Asri, Sofia Barreira, Stephanie C. Bohaczuk, Andrey V. Bzikadze, Sara A. Carioscia, Andrew Carroll, Kuan-Hao Chao, Yanan Chu, Arun Das, Peter Ebert, Adam English, Mark Fleharty, Laura E. Fleming, Giulio Formenti, Andrea Guarracino, Gabrielle A. Hartley, Katharine Jenike, Jenna Kalleberg, Yu Kang, Robert King, Josipa Lipovac, Mira Mastoras, Matthew W. Mitchell, Shloka Negi, Nathan D. Olson, Keisuke K. Oshima, Luis F. Paulin, Brandon D. Pickett, David Porubsky, Jane Ranchalis, Desh Ranjan, Mikko Rautiainen, Harold Riethman, Robert D. Schnabel, Fritz J. Sedlazeck, Kishwar Shafin, Mile Sikic, Steven J. Solar, Alexander P. Sweeten, Winston Timp, Justin Wagner, Dongahn Yoo, Ying Zhou, Erik Garrison, Evan E. Eichler, Michaeel C. Schatz, Andrew B. Stergachis, Rachel J. O'Neill, Karen H. Miga, Steven L. Salzberg, Sergey Koren, Justin M. Zook, Adam M. Phillippy

School of Medical Diagnostics & Translational Sciences Publications

Human genome sequencing typically relies on mapping reads to a reference genome to call variants, but this approach introduces technical biases, excluding duplicated and structurally polymorphic regions of the genome. To overcome this, we present a telomere-to-telomere genome benchmark with near-perfect accuracy across 99.4% of the diploid HG002 genome. This benchmark adds 701.4 Mb of autosomal sequence and both sex chromosomes (216.8 Mb), which were absent from prior benchmarks. We annotated genes and repeats on both haplotypes, including 19,956 protein-coding genes on the maternal haplotype and 19,190 on the paternal haplotype, and developed new methods to measure the accuracy of …

Identifying Rna Splicing Changes During Alcohol Withdrawal Using An Optimized Rna-Seq Analysis Pipeline, Yasaswi Veera, Luana Martins De Carvalho, Amy Lasek

UROP Posters

Alcohol use disorder (AUD) causes long-lasting changes in brain gene expression and RNA splicing, particularly in the ventral hippocampus. This study analyzes RNA-Seq data from rats exposed to chronic alcohol and withdrawal to identify transcript-level and splicing alterations. An optimized RNA-Seq pipeline using STAR, FeatureCounts, edgeR, and WGCNA improved efficiency by 25-40% while maintaining consistency across 25 datasets. Results reveal changes in neural signaling and stress-response pathways associated with withdrawal. This work provides both biological insight into AUD and a reproducible computational framework for transcriptomic analysis.

A Novel 3d Imaging Approach To Study Evolutionary Innovations In Solanaceae Inflorescences, Devin L. Jackson, Joonseog Kim, Wenheng Zhang Dr.

UROP Posters

Understanding the relatedness of angiosperms and the evolution of their inflorescence remains challenging, as these structures are highly modified and prone to convergent evolution. The current research describing inflorescence architecture, whether genetically or morphologically focused, typically relies on text based explanations, 2D images, or 3D based models created with CAD modeling software. This creates a disparity in the reader's understanding of these models since descriptions rely heavily on the author's interpretation of the inflorescence. The goal of our study is to bridge this disconnection by producing anatomically and color-correct 3D inflorescence models using Solanaceae flowers that readers can explore directly, …

Determining Genes Involved In Recovery From Chemotherapy In 4t1, Emt6, And Eo771 Breast Cancer Cells, Akash Jagdeesh, Joseph Landry Ph.D.

UROP Posters

Breast cancer is one of the most common types of cancer, and often has poor prognosis. Traditional treatments for breast cancer include chemotherapy, which involves a chemical attack on all growing cells within the body. However, these treatments are not 100% effective, and patients might experience recurrence in their cancer months or years after achieving remission. Cancer cells can evade chemotherapy through five mechanisms: senescence, quiescence, cytoprotective autophagy, and apoptosis/necroptosis suppression. Prior studies have conducted CRISPR screens and experiments involving inhibition of epigenetic regulators, to alter the regulation of genes that can contribute to breast cancer chemotherapy resistance. This study …

Dgamlss: An Exact, Distributed Algorithm To Fit Generalized Additive Models For Location, Scale, And Shape For Privacy-Preserving Population Reference Charts, Fengling Hu, Jiayi Tong, Margaret Gardner, Chris Adamson, Sophie Adler, Aaron F. Alexander-Bloch, Evdokia Anagnostou, Kevin M. Anderson, Ariosky Areces-Gonzalez, John Blangero

Human Genetics Publications

Motivation There is growing interest in estimating population reference ranges across age and sex to better identify atypical clinically-relevant measurements throughout the lifespan. For this task, the World Health Organization recommends using Generalized Additive Models for Location, Scale, and Shape (GAMLSS), which can model non-linear growth trajectories under complex distributions that address the heterogeneity in human populations. Fitting GAMLSS models requires large, generalizable sample sizes, especially for accurate estimation of extreme quantiles, but obtaining such multi-site data can be challenging due to privacy concerns and practical considerations. In settings where patient data cannot be shared, privacy-preserving distributed algorithms for federated …

Comparative Analysis Of Six New Chloroplast Genomes In Platanthera (Orchidaceae) Enhances Understanding Of Its Diversification, Lisa E. Wallace, Martin I. Batalla, Matthew Maisonave

Biological Sciences Faculty Publications

Platanthera is among the most diverse genera of orchids in north temperate regions, with high species diversity in Asia and North America. Despite many ecological studies in this group, little is known about its genomic diversity. Here, we report the newly annotated chloroplast genomes from six species in subgenus Limnorchis from North America and compare them with plastomes published for Platanthera species from Asia and Europe. We found that the plastomes of species in subg. Limnorchis are among the smallest reported for Platanthera thus far. While major structural differences were not detected in the newly sequenced species, ndh genes were …

Building A Cell Specific System For In Vivo Rna Imaging Of The Endogenous Actin Gene In C. Elegans, Jasmine A. Huerta Canete

Theses and Dissertations

Messenger RNA (mRNA) plays a crucial role in protein synthesis and cellular processes, important for the development of cells such as neurons. When dysregulation occurs, it can lead to outcomes such as aberrant translation, causing neurodegenerative conditions to arise. Unfortunately, the localization of mRNA in an in vivo cell specific manner is still not understood. To address this, we decided to develop a cell-specific system to image RNA in vivo, within the organism known as C. elegans with a focus on the actin gene. The Actin gene encodes for an important cytoskeleton protein expressed ubiquitously, vital for the cell …

The Disruption Of Gastrointestinal Hormonal Control Of Digestion In Nile Tilapia By Omeprazole, Rema Abutaha

Theses and Dissertations (Comprehensive)

Stomach acidity is a critical feature of the digestive system, facilitating the breakdown of protein through the activation of the protease pepsin. Gastric acid is secreted by H⁺/K⁺ ATPase, the gastric proton pump. A previous study on Nile tilapia (Oreochromis niloticus) showed that inhibiting the production of stomach acid using the proton pump inhibitor omeprazole (omz), reduced growth that correlated with an acceleration of the rate of gastric emptying. This contrasts with omz exposure studies in mammals in which there is a delay in gastric emptying and no impact on growth. To understand the mechanism …

Acute Fatty Liver Of Pregnancy And Fetal Fatty Acid Oxidation Disorders: A Systematic Review, Dante Varotsis, Sarah Araji, Rebecca Horgan, Jennifer E. Powel, Rodney Mclaren Jr., Brian Kirmse, Mona Makhamreh, Huda B. Al-Kouatly

Department of Obstetrics & Gynecology Faculty Publications

OBJECTIVE:

To evaluate the association between maternal acute fatty liver of pregnancy (AFLP) and fetal fatty acid oxidation (FAO) disorders and to define the clinical and genetic characteristics of mothers with AFLP and their fetuses affected by FAO disorders, we performed a systematic literature review of all reported cases of AFLP that underwent genetic testing for FAO disorders.

DATA SOURCES:

We searched PubMed, Ovid MEDLINE, Cochrane Library, CINAHL (EBSCO), Scopus, and ClinicalTrials.gov. Terms included were related to AFLP and FAO testing.

METHODS OF STUDY SELECTION:

We conducted a systematic literature review from inception through May 18, 2025, to evaluate the …

Physiologic Markers Of Mortality In Acute Valve Syndrome: An Ischemic Physiology Score Stratifies Patient Risk, Omar Saleh, Nicholas J. Valle, Israa Saleh, Raymond Benza, Deepak R. Talreja, Matthew R. Summers

Department of Medicine Faculty Publications

Background: Acute valve syndrome (AVS) represents a high-risk phenotype of advanced valvular disease with largely uncharacterized risk heterogeneity. We aimed to validate an expanded AVS definition and develop a physiology-dependent risk stratification tool using available clinical markers.

Methods: This retrospective study analyzed 2380 patients undergoing aortic valve replacement for severe aortic stenosis and classified them as AVS (n = 1556) or progressive valvular disease (n = 824). The primary outcome was 1-year all-cause mortality. An L2-regularized logistic regression model was developed to predict 1-year mortality using admission laboratory markers and comorbidity burden. Model performance was assessed using nested cross-validation with …

Cytonuclear Incompatibilities In Hybrid Systems: Oxidative Phosphorylation Capacity And Nuclear Marker Transmission Ratio Distortion In Hybrids Of An Introgressed Strain Of Parasitoid Wasp, Julie Kessler

College of Graduate Studies: Theses & Dissertations

Speciation is an evolutionary process resulting in the divergence of populations into reproductively isolated species, a key concept that supplies our planet with an abundance of biodiversity. Mechanisms for speciation center on obstacles to fertilization and include post-zygotic barriers, such as intrinsic deleterious interactions, that arise in hybrid systems where genetic variants are combined. Genes from separate parent lineages are often incompatible due to the co-evolution of paired genes within a singular species not matching their complement genes in another species, and the result is a reduction in fitness of the hybrid when these genes come together. The mitochondrial OXPHOS …

Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

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, …

Chromnet: A Multi-Task Learning Framework For Cross-Cell Type Prediction Of 3d Chromatin Interactions Using Epigenetic Signals, Bin Wang, Shaokai Wang, Liqing Ding, Hongdong Li, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

The 3D organization of chromatin plays a fundamental role in gene regulation, cellular function, and disease mechanisms. However, current experimental techniques, such as Hi-C, remain costly and labor-intensive, limiting their application in large-scale and disease-related studies. To address this challenge, ChromNet is presented, a multi-task learning framework that integrates epigenetic signals across diverse cell types to enable high-precision prediction of chromatin architecture. By incorporating noise perturbation and auxiliary classification tasks, ChromNet improves the identification of topologically associating domains (TADs) and cell-type-specific chromatin structures, demonstrating superior generalization performance. Notably, ChromNet accurately predicts chromatin interactions in acute myeloid leukemia (AML) samples by …

Explainable Convolutional Neural Network Model Provides An Alternative Genome-Wide Association Perspective On Mutations In Sars-Cov-2, Parisa C. Hatami, Richard Annan, Luis Miranda, Jane L. Gorman, Mengjun Xie, Letu Qingge, Hong Qin

Computer Science Faculty Publications

Identifying informative genomic features in SARS-CoV-2 can help clarify patterns of viral evolution. In this study, we developed an explainable convolutional neural network (CNN) model to classify SARS-CoV-2 genomic sequences into the WHO-designated Variants of Concern (VOCs), Alpha, Beta, Gamma, Delta, and Omicron. Using a balanced dataset of genomes, the classification CNN achieved 99.96% accuracy on the held-out test set. To interpret the model’s predictions, we applied SHapley Additive exPlanations (SHAP) to estimate the contribution of each nucleotide position to VOC-label prediction and compared aggregated attributions with a chi-square GWAS baseline applied to the same categorical labels. SHAP prioritized several …