Biomarker Identification For Breast Cancer Types Using Feature Selection And Explainable Ai Methods, 2023 University of Central Florida
Biomarker Identification For Breast Cancer Types Using Feature Selection And Explainable Ai Methods, David E. La Rosa Giraud
Honors Undergraduate Theses
This paper investigates the impact the LASSO, mRMR, SHAP, and Reinforcement Feature Selection techniques on random forest models for the breast cancer subtypes markers ER, HER2, PR, and TN as well as identifying a small subset of biomarkers that could potentially cause the disease and explain them using explainable AI techniques. This is important because in areas such as healthcare understanding why the model makes a specific decision is important it is a diagnostic of an individual which requires reliable AI. Another contribution is using feature selection methods to identify a small subset of biomarkers capable of predicting if a …
Statistical Methods For Gene Selection And Genetic Association Studies, 2023 Michigan Technological University
Statistical Methods For Gene Selection And Genetic Association Studies, Xuewei Cao
Dissertations, Master's Theses and Master's Reports
This dissertation includes five Chapters. A brief description of each chapter is organized as follows.
In Chapter One, we propose a signed bipartite genotype and phenotype network (GPN) by linking phenotypes and genotypes based on the statistical associations. It provides a new insight to investigate the genetic architecture among multiple correlated phenotypes and explore where phenotypes might be related at a higher level of cellular and organismal organization. We show that multiple phenotypes association studies by considering the proposed network are improved by incorporating the genetic information into the phenotype clustering.
In Chapter Two, we first illustrate the proposed GPN …
Association Of Interpersonal Trauma And Polygenic Risk Scores With Depressive Symptoms In College Students, 2023 Virginia Commonwealth University
Association Of Interpersonal Trauma And Polygenic Risk Scores With Depressive Symptoms In College Students, Rowan K. O'Hara
Theses and Dissertations
Major depression is considered a complex trait influenced by both polygenic risk factors and environmental exposures, such as childhood trauma. This study applied statistical genetic methods to calculate aggregate genetic risk for major depression to predict depressive symptoms scores in a college student sample. Data were from the Spit for Science (S4S) study in which college students from a large urban university self-reported interpersonal trauma (IPT) exposure prior to college and depressive symptoms from the past month (N = 7502; ancestry group: 20% African [AFR], 12% Admixed Americas [AMR], 10% East Asian [EAS], 49% European [EUR], 8% South Asian [SAS]). …
Statistical Methods For Gwas And The Impact Of Diabetic Medication Adherence On Healthcare Costs, 2023 Michigan Technological University
Statistical Methods For Gwas And The Impact Of Diabetic Medication Adherence On Healthcare Costs, Meida Wang
Dissertations, Master's Theses and Master's Reports
This dissertation includes three Chapters. In Chapter One, we develop a computationally efficient clustering linear combination approach to jointly analyze multiple phenotypes for GWAS. In this paper, based on the existing CLC method and ACAT strategy, we develop the ceCLC method to test association between multiple phenotypes and a genetic variant. In Chapter Two, we develop a novel method called sCLC for association studies of multiple phenotypes and a genetic variant based on GWAS summary statistics. Simulation results show that sCLC can control Type I error rates well and has the highest power in most scenarios. In Chapter Three, we …
The Effect Of Genetic Relatedness On Mate Selection And Spatial Distribution In The American Alligator, Alligator Mississippiensis, 2023 Georgia Southern University
The Effect Of Genetic Relatedness On Mate Selection And Spatial Distribution In The American Alligator, Alligator Mississippiensis, Mark Hoog
Electronic Theses and Dissertations
To date, most genetic studies on the American alligator (Alligator mississippiensis) have focused on population genetics and multiple paternity. There have not been any studies looking at how relatedness affects alligator behavior and movement. This study focused on three main questions: 1) what is the genetic diversity among alligators in this location? 2) can parentage be accurately defined among parents and offspring? and 3) how does individual relatedness affect their spatial distribution? We examined the relatedness of 174 unique individuals from the Okefenokee Swamp Park, in South Georgia, USA. In addition, we placed Telonics® satellite tags on …
Dna Methylation And The Response To Infection In Introduced House Sparrows, 2023 Georgia Southern University
Dna Methylation And The Response To Infection In Introduced House Sparrows, Melanie Gibson
Electronic Theses and Dissertations
Epigenetics is the study of molecular modification of a genome without changing its base pairs. The most studied type of epigenetic mechanism is DNA methylation, which is capable of turning a gene “on” or “off.” Epigenetic potential is the capacity to which an individual can have methylation on its genome. The more CpGs available, the greater the epigenetic potential. In invasive species, genetic variation has been observed to be paradoxical: not much of it exists on a genomic level, but epigenetically, phenotypic variation can occur. The focus on shift in gene expression in this study is on Toll-Like Receptor 4 …
Advancing Methods Of Diet Analysis: A Case Study Using Degraded Merlin (Falco Columbarius) Prey Remains, 2023 University of Montana
Advancing Methods Of Diet Analysis: A Case Study Using Degraded Merlin (Falco Columbarius) Prey Remains, Taylor A. Coon
Undergraduate Theses, Professional Papers, and Capstone Artifacts
Prey remains have long been used as a mechanism to approach diet analyses. As understanding diet is key to comprehending ecosystem dynamics, prey remains identification requires a unique methodological approach to determine diversity within a sample. With the advancement of technology, molecular protocols designed for species-specific identification have improved to incredible accuracy and precision. Yet, the visual identification method has remained a predominant technique within diet studies. With entry-level observers, we matched visual identifications with molecular-based methods to quantify the accuracy of the visual identification method. This study determined what fraction of visually identified prey remains could be correctly identified …
Knockout Of Endospanin 1 Via Crispr In Zebrafish, Danio Rerio, 2023 The University of Akron
Knockout Of Endospanin 1 Via Crispr In Zebrafish, Danio Rerio, Jared Kittinger
Williams Honors College, Honors Research Projects
I made endospanin 1 knockout (KO) zebrafish to examine its effects on lipid and bone metabolism. Endospanin 1, or leptin receptor overlapping transcript (leprot), is a cytosolic protein linked to the protein hormone leptin that influences the trafficking of leptin receptors to the plasma membrane of cells. Genes for endospanin and tyrosinase (a pigmentation enzyme) were targeted via a microinjection of guide RNAs and CRISPR Cas9 into zebrafish embryos at 2-4 cell stages. I was able to disrupt the endospanin 1 gene (based upon the disruption of tyrosinase), but very few mutant zebrafish fully developed into adults. Only low KO …
Intraspecific Hybrid Identification Of Black Walnuts Via Marker Assisted Selection, 2023 Missouri State University
Intraspecific Hybrid Identification Of Black Walnuts Via Marker Assisted Selection, Makenna B. Thompson
MSU Graduate Theses
The improvement of Eastern black walnut (Juglans nigra L.) cultivars could increase market expansion. Improved cultivars with superior qualities would increase profitability for both the seller and the buyer. Agronomically and economically important traits such as heavier nut weight, disease resistance, tree structure integrity, and yearly nut production can be efficiently improved by breeding black walnuts via marker-assisted selection. Microsatellite/simple sequence repeat markers were used in this research to determine potential intraspecific hybrids between ‘Football’ and ‘Sparrow’ cultivars. Intraspecific is defined as of the same genus and species. This quality makes it more difficult to identify hybrids because the parent …
Adjusting For Gene-Specific Covariates To Improve Rna-Seq Analysis, 2023 The Ohio State University
Adjusting For Gene-Specific Covariates To Improve Rna-Seq Analysis, Hyeongseon Jeon, Kyu-Sang Lim, Yet Nguyen, Dan Nettleton
Mathematics & Statistics Faculty Publications
Summary
This paper suggests a novel positive false discovery rate (pFDR) controlling method for testing gene-specific hypotheses using a gene-specific covariate variable, such as gene length. We suppose the null probability depends on the covariate variable. In this context, we propose a rejection rule that accounts for heterogeneity among tests by employing two distinct types of null probabilities. We establish a pFDR estimator for a given rejection rule by following Storey's q-value framework. A condition on a type 1 error posterior probability is provided that equivalently characterizes our rejection rule. We also present a suitable procedure for selecting a tuning …
Association Of The Bb Genotype Of The Abo Gene With The Risk Of Acute Myocardial Infarction In Hospital-Based Study, 2023 Aga Khan University
Association Of The Bb Genotype Of The Abo Gene With The Risk Of Acute Myocardial Infarction In Hospital-Based Study, Farzana Abubakar Yousuf, Iqbal Azam Syed, Asal Khan Tareen, Khawar A. Kazmi, Jibran Sualeh Muhammad, Mohammad Perwaiz Iqbal
Department of Biological & Biomedical Sciences
Objectives: The ABO gene locus has been identified to be associated with myocardial infarction in patients with coronary heart disease. The primary focus of this hospital-based study was to explore the relationship of ABO blood groups and ABO genotypes with acute myocardial infarction (AMI) in Karachi, Pakistan.
Methods: In a comparative cross-sectional study, an equal number of adult AMI patients and healthy controls (n=275 in each group; age range 30-70 years, both males and females) were recruited from the Aga Khan University and NICVD, Karachi, with informed consent. The blood samples were analyzed for ABO blood groups and other biomarkers. …
Cluster Homolog Of Immunoglobulin-Like Receptor Genes In Chicken Immune Responses, 2023 West Virginia University, Western University of Health Sciences
Cluster Homolog Of Immunoglobulin-Like Receptor Genes In Chicken Immune Responses, Brandi A. Sparling
Graduate Theses, Dissertations, and Problem Reports
This dissertation explores the identity and role of immunoglobulin-like (Ig-like) receptors in chickens, with focus on their implications in disease and disease progression. These receptors, wisely expressed across immune cells, interact with the major histocompatibility complex (MHC) class I molecules to modulate immune responses in mammals. Due to the insufficient representation of chicken Ig-like receptors in online databases, this study systematically annotates the chicken Cluster Homolog of Immunoglobulin-like Receptors (CHIR) genes using advanced bioinformatic techniques, aligning with the release of the 7th edition of the chicken genome assembly that comprises builds for a broiler and layer chicken. The analysis identifies …
The Role Of Cort And Anaphase Promoting Complex/Cyclosome (Apc/C) In Drosophila Sex Determination And Meiosis, 2023 University of Windsor
The Role Of Cort And Anaphase Promoting Complex/Cyclosome (Apc/C) In Drosophila Sex Determination And Meiosis, Abuzar Sikander Malik
Electronic Theses and Dissertations
The E3 ubiquitin ligase, APC/C, is essential for the completion cell cycle; along with its co-activators it allows mitotic exit and maintenance of G1. APC/C marks various substrates with ubiquitin chains; marked substrates are subsequently destroyed via the 26S proteasome pathway. Cort is a Drosophila female meiosis specific activator of APC/C. Cort works within meiosis in conjunction with Fzy to mediate Securin and cyclin destruction. A C-terminal IR-tail motif and a N-terminal C-box support Cort-APC/C interaction, whereas short motifs like D-box and KEN-box on the target protein impart substrate recognition to Cort. Cort expression is tightly controlled in the female …
Examining The Effectiveness Of Probiotic Therapy For Improving Growth Performance Of Triploid Chinook Salmon (Oncorhynchus Tshawytscha) In Aquaculture Using A Behavioural Genomics Approach, 2023 University of Windsor
Examining The Effectiveness Of Probiotic Therapy For Improving Growth Performance Of Triploid Chinook Salmon (Oncorhynchus Tshawytscha) In Aquaculture Using A Behavioural Genomics Approach, Chelsea Frank
Electronic Theses and Dissertations
With an increasing human population, there has been increased production of fish to meet nutritional needs. Commercial aquaculture accounts for a significant portion of seafood production with salmonids being the major farmed finfish in Canada. To obtain greater biomass from aquaculture with minimal drawbacks (e.g., compromised flesh quality), triploidization has been implemented, altering ploidy from 2N to 3N, to induce sterility and promote energy investment towards somatic growth. Triploid individuals experience transcriptional and behavioural changes resulting in disease, mortalities, and reduced growth. Probiotic therapies (live microorganisms) have been recommended to potentially overcome drawbacks of triploidy and improve mass due to …
Molecular Analysis Of Epigenetic Memory Of Stress Establishment And Long-Term Maintenance In A Perennial Woody Plant, 2023 University of Kentucky
Molecular Analysis Of Epigenetic Memory Of Stress Establishment And Long-Term Maintenance In A Perennial Woody Plant, Jia Wen Tan
Theses and Dissertations--Plant and Soil Sciences
Plants adapt to extreme environmental conditions through physiological adaptations, which are usually transient. Recent research has suggested that environmental conditions can activate a memory of stress that can result in a primed response to subsequent stress events. While the effect of priming has been observed in many plants, the underlying mechanisms are puzzling and seldom studied. A large body of research has been developed in the last decade linking response to stress, stress priming, and memory of stress with epigenetic mechanisms. This understanding of plant epigenetics has opened the door to the application of epigenetics to crop improvement, such as …
Executive Functioning Among The Karyotypes In Turner Syndrome And Implications For Interventions, 2023 Antioch University of New England
Executive Functioning Among The Karyotypes In Turner Syndrome And Implications For Interventions, Sara Scull
Antioch University Full-Text Dissertations & Theses
Turner syndrome (TS) is a genetic disorder seen in phenotypically female (pf) individuals who have either a complete or partial absence of the second sex (X) chromosome. TS includes different karyotypes, and it presents with a variety of phenotypic and genotypic features. In general, the neuropsychological profiles for individuals diagnosed suggest that TS can contribute to challenges in various aspects of daily life, including social and emotional functioning. With regard to academic performances, individuals with TS often present with relative strengths in a range of verbal abilities and relative weakness in visual-spatial/perceptual abilities, nonverbal memory, motor function, processing speed, executive …
Sequencing Antisense Transcriptome Of Populus Through Antisense/Sense Transcript Pair Enrichment, 2023 Michigan Technological University
Sequencing Antisense Transcriptome Of Populus Through Antisense/Sense Transcript Pair Enrichment, Emma V. Burke
Dissertations, Master's Theses and Master's Reports
Past transcriptome research on plants focused primarily on protein coding genes, and only recently researchers began looking into the non-protein coding regions that may play significant roles in gene regulation. Antisense RNA transcripts that are found naturally in the cell share complementary sequence with sense transcripts and have been shown to regulate expression of their sense counterparts. Since antisense RNA has been largely under-studied and difficult to sequence because of their low relative abundance, new methods are needed to target antisense RNA for efficient genome-wide profiling. To address this gap in methods to efficiently and cost effectively enrich antisense RNA …
Examining Genetically-Informed Etiologic Models Of Co-Occurring Posttraumatic Stress Disorder And Recreational Cannabis Use Among College Students, 2023 Virginia Commonwealth University
Examining Genetically-Informed Etiologic Models Of Co-Occurring Posttraumatic Stress Disorder And Recreational Cannabis Use Among College Students, Terrell A. Hicks
Theses and Dissertations
The college years encompass a period of increased risk recreational cannabis use (RCU), as well as a time of increased risk for trauma exposure and developing posttraumatic stress disorder (PTSD). Given the high co-occurrence between RCU and PTSD, and the potentially negative consequences of the two (e.g., worse academic outcomes), there is a need to understand the etiologic mechanisms of these commonly co-occurring conditions. Two primary phenotypic models exist: self-medication model (i.e., PTSD to RCU) and the high-risk model (i.e., RCU to PTSD). To date, there are two existing studies longitudinally examining the etiologic models proposed to explain co-occurring RCU …
Dissecting Interactions Across Gene Regulatory Layers In C. Elegans, 2022 Southern Methodist University
Dissecting Interactions Across Gene Regulatory Layers In C. Elegans, Morgan Taylor
Biological Sciences Theses and Dissertations
The nematode Caenorhabditis elegans is a powerful tool for studying nervous system genetics. Though relatively simple compared to mammals, C. elegans boasts a remarkably well-conserved neuronal genome and proteome, and its utility in the characterization of neuronal genes has been well-established. However, gene expression is often controlled by complex interactions between multiple genes, and teasing apart the functions of individual genes within such networks remains a challenge. Dissecting these interaction networks is crucial in determining the multifaceted functions of important, conserved regulatory genes. Here we explore interactions between gene regulatory layers in the C. elegans nervous system, employing a synthetic …
Bioinformatics And Cancer Genomics Approaches To Advance Precision Medicine And Elucidate Tumor Mutational Landscapes, 2022 Washington University in St. Louis
Bioinformatics And Cancer Genomics Approaches To Advance Precision Medicine And Elucidate Tumor Mutational Landscapes, Kelsy Cotto
Arts & Sciences Electronic Theses and Dissertations
Next-generation sequencing of DNA and RNA continues to be integrated into pre-clinical and clinical research. However, challenges still remain that impede the translation of findings into an improved understanding of human diseases or clinically actionable alterations. The projects described in this dissertation start with compiling efforts from experts who have identified druggable genes within the human genome, followed by in-depth analyses which characterize the pan-cancer landscape of splice-associated mutations and noncoding, regulatory mutations across multiple subtypes of breast cancer. In Chapters 2 and 3, substantial efforts were made to update the content and the user experience for the drug-gene interaction …