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Generative Ai And Student Engagement, Motivation, And Learning: Exploring The Use Of Generative Ai In Higher Education Online Courses, Jeffrey L. Simmons May 2026

Generative Ai And Student Engagement, Motivation, And Learning: Exploring The Use Of Generative Ai In Higher Education Online Courses, Jeffrey L. Simmons

Dissertations

ABSTRACT

The rapid emergence of Generative AI (GenAI) large language models (LLMs) such as ChatGPT in higher education has left many institutions unprepared to assess their potential benefits and risks. This mixed-methods study examined how ChatGPT and Google’s NotebookLM were integrated into online course development and delivery at a small private nonprofit university in California, and assessed their perceived impact on student engagement, motivation, and learning.

Data were collected from post-course Likert-scale surveys completed by students across three online master’s-level courses and from pre-course prediction surveys by instructors in the two NotebookLM courses. Quantitative analyses included one-sample t-tests against a …


Burning Out: A Narrative Exploration Of The Adaptive Challenge And Scaffolds Built Toward Sustenance Among Immigrant Rights Activists In San Diego County, Anna C. Runion May 2026

Burning Out: A Narrative Exploration Of The Adaptive Challenge And Scaffolds Built Toward Sustenance Among Immigrant Rights Activists In San Diego County, Anna C. Runion

Dissertations

Activist burnout has been identified as one of the greatest threats to social movement sustainability, and the lived experience of paid immigrant rights activists remains undertheorized. This narrative inquiry explored activist burnout among 10 San Diego County immigrant rights activists, revealing how this community understands burnout, what factors contribute to its production, and how activists sustain themselves within it. Using Clandinin and Connelly’s (2000) narrative inquiry methodology, the researcher conducted in-depth individual interviews with ten activists representing a range of intersectional identities and roles. Narrative profiles were analyzed through holistic narrative reading, narrative reporting, structural and emergent coding, and cross-narrative …


For My Oklahomies: Educators’ Perspectives On Policy, Public Discourse, And Professional Wellbeing, Cassandra Herndon May 2026

For My Oklahomies: Educators’ Perspectives On Policy, Public Discourse, And Professional Wellbeing, Cassandra Herndon

Dissertations

This critical qualitative study examines how ideologies rooted in ultra-conservative movements shape the professional lives of Oklahoma K–12 educators, and how they maneuver, resist, or accommodate ideological forces within a climate of surveillance and professional delegitimization. Grounded in critical social theory and drawing on Foucault (1977) and Leonardo (2003), the study applies a recontextualized model of transformational resistance (Hannegan-Martinez et al., 2024) to analyze educators’ acts of agency within a restrictive policy landscape.

Drawing on semi-structured interviews with eight Oklahoma K–12 teachers and administrators, this study employs critical narrative inquiry alongside reflexive thematic and critical policy analysis to ask: (1) …


Heat Shock Factor 1 Signaling: A Novel Pathway Implicated In Rett Syndrome Pathophysiology, Sonia Gonzalez May 2026

Heat Shock Factor 1 Signaling: A Novel Pathway Implicated In Rett Syndrome Pathophysiology, Sonia Gonzalez

Dissertations

Rett syndrome (RTT) is a severe neurodevelopmental disorder that is associated with loss-of-function mutations in the methyl-CPG binding protein 2 (MECP2) gene. There are limited therapeutic options to address the wide range of social, cognitive, motor, and respiratory symptoms that patients experience throughout their lifetime. To identify novel therapeutic targets, we leveraged a rare form of RTT known as MeCP2-mutation-negative or atypical RTT. Traditionally, RTT is first diagnosed clinically and then confirmed through the identification of mutations in the MECP2 gene. However, ~5% of RTT patients are found to be MeCP2-mutation-negative (atypical), despite sharing overlapping symptomology with typical RTT. We …


Lay Presidents In Jesuit Higher Education: How Ajcu Lay Presidents Learn About, Articulate, And Express Jesuit Mission And Identity, Carl Joseph Caceres May 2026

Lay Presidents In Jesuit Higher Education: How Ajcu Lay Presidents Learn About, Articulate, And Express Jesuit Mission And Identity, Carl Joseph Caceres

Dissertations

Since the year 2000, over the course of the past quarter century, lay presidents went from being an emerging phenomenon to becoming the majority of presidents in the Association of Jesuit Colleges and Universities (AJCU). Lay presidents are now the norm and no longer the exception, as 24 of the 28 institutions of the AJCU are now lay led. This qualitative research study intended to explore how lay presidents of the Association of Jesuit Colleges and Universities (AJCU) in the United States who have been at their current institution for at least three years, came to learn about Jesuit mission …


A Trinity Of Forces: A Critical Investigation Of The Intersection Of Lived Experience, Jesuit Secondary Education, And Corporate Curricula, Bernhard Bruno Walke May 2026

A Trinity Of Forces: A Critical Investigation Of The Intersection Of Lived Experience, Jesuit Secondary Education, And Corporate Curricula, Bernhard Bruno Walke

Dissertations

This dissertation examines how students' identities and personal experiences shape their encounters with both Jesuit Secondary Education and the Corporate Work Study Program (CWSP). Throughout this qualitative analysis, the researcher will examine how identity, secondary education, and corporate attitudes coexist, overlap, conflict, intersect, and compete with one another. By employing Gloria Ladsen-Billings’s Critical Race Theory (Ladson-Billings & Tate, 1995), Dolores Delgado Bernal and Daniel Solórzano’s contributions to Latinx Criticism (Lat Crit), (Solorzano & Bernal, 2001), Kimberlé Crenshaw’s Theory of Intersectionality (K. Crenshaw, 1989), and Tara Yosso’s Community Cultural Wealth Model (Yosso, 2005), the researcher will examine how students experience “non-linear …


The Effects Of Fluency Building On Undergraduate Student Performance, Lauren B. Shibley May 2026

The Effects Of Fluency Building On Undergraduate Student Performance, Lauren B. Shibley

Dissertations

Online learning has become integral to higher education, with enrollment steadily increasing over the past decade and accelerating during the COVID-19 pandemic. Research highlights the importance of flexibility, learner autonomy, and self-regulated learning skills in this environment, with studies demonstrating that strategies such as mastery-based, self-paced instruction, fluency training, and timely feedback support student engagement and academic success. Early work adapting personalized instruction for online use (Pear & Crone-Todd, 1999) and subsequent studies on fluency practice (Quigley et al., 2018; Urbina et al., 2019) emphasize how these supports can improve concept retention. Despite these advances, more quantitative research is needed …


The Impact Of Framing Effects And Moral Values On Prosocial Engagement, Olajuwon Olagbegi May 2026

The Impact Of Framing Effects And Moral Values On Prosocial Engagement, Olajuwon Olagbegi

Dissertations

Framing effects can shape perceptions, beliefs and behavior, particularly in prosocial contexts. The current study examined how language framing (social justice, social activism, volunteerism) and moral values influence interest in prosocial engagement across low- and high-cost helping scenarios. Participants (N = 219) were randomly assigned to one of three framing conditions and reported willingness to help in both low- and high-cost situations. They also completed the Moral Foundations Questionnaire. Replicating prior work (Olagbegi and colleagues, 2024), participants were more willing to engage in low- than high-cost helping. Across conditions, social justice framing elicited the greatest willingness to help. Higher fairness …


Intelligent Surveillance For Weapon Threat Detection: Transformer-Based Detection And Segmentation Using Thermal And Rgb Imagery, Akhila Kambhatla May 2026

Intelligent Surveillance For Weapon Threat Detection: Transformer-Based Detection And Segmentation Using Thermal And Rgb Imagery, Akhila Kambhatla

Dissertations

Proactive public-safety surveillance requires deep learning systems that can detect and segment weapons reliably under real-world conditions. This research develops and evaluates a progressive, multi-phase pipeline that moves (i) from RGB object detection to pixel-level semantic segmentation and (ii) from visible-spectrum cameras to thermal imagery to improve robustness under low-light, clutter, and occlusion. Early phases establish strong detection baselines using one-stage and two-stage detectors (YOLOv5 and Faster R-CNN) for multi-class weapon localization, followed by practical optimization through pruning and ensembling to reduce false positives and computational overhead while maintaining real-time feasibility. Building on the limitations of bounding-box localization, the methodology …


The Phylogenetic And Biogeographic History Of Cranes (Gruidae), Phillip Conrad Williams May 2026

The Phylogenetic And Biogeographic History Of Cranes (Gruidae), Phillip Conrad Williams

Dissertations

Cranes (Gruidae) are a globally distributed clade of large, wetland-associated birds. Prior phylogenetic analyses have shown there to be two major subfamilies, Balearicinae and Gruinae, and five consistently recovered clades within Gruinae. However, the relationships among those five clades has remained contentious. In addition, little has been done to reconstruct the biogeographic history of cranes. To that end, I first inferred phylogeny using a large, nuclear dataset sampled from all 15 extant crane species and two outgroup species. The phylogeny mostly agreed with previous analysis using whole mitochondrial genomes but differed in that the Anthropoides species group formed a sister …


Restorying The Reader: Adolescent Narratives Of Identity, Context, And Motivation, Jennifer R. Gardner May 2026

Restorying The Reader: Adolescent Narratives Of Identity, Context, And Motivation, Jennifer R. Gardner

Dissertations

This present study examined how adolescents narrate their reading experiences and what those narratives reveal about reading identity, motivation, and engagement. This study responds to a persistent problem in literacy education: adolescent reading is often framed through disengagement or reduced to isolated constructs, while students’ lived reading experiences across school, home, digital, linguistic, and social contexts remain underexamined. Guided by Self-Determination Theory, Intersectionality, and Reader Response Theory, this study centers on adolescent voices and treats these participants’ stories as the primary avenue of understanding how they experience and interpret their reading lives and selves. Data were collected through narrative interviews, …


Qualitative Phenomenography: Sustaining Motivations Of Black Women Principals In Pk-5 Title I Schools, Kahliah C. Rachel May 2026

Qualitative Phenomenography: Sustaining Motivations Of Black Women Principals In Pk-5 Title I Schools, Kahliah C. Rachel

Dissertations

Black women principals remain underrepresented in educational leadership, yet they are disproportionately assigned to PK-5 Title I schools, where complex academic, social, and political demands converge. Limited research examines what sustains these leaders over time, particularly in roles marked by intersecting oppressions of race and gender. Grounded in Black feminist thought and intersectionality, this qualitative phenomenographic study explored the sustaining motivations of six Black women who currently served or had served as principals in a PK-5 Title I school in Georgia. The purpose of this study was to describe the different ways these principals understood and experienced the internal and …


Vinicio Meza And The Bassoon: A Study Of The Costa Rican Composer’S Chamber Music And Episodios For Bassoon And Orchestra, Bryan Valderrama Vega May 2026

Vinicio Meza And The Bassoon: A Study Of The Costa Rican Composer’S Chamber Music And Episodios For Bassoon And Orchestra, Bryan Valderrama Vega

Dissertations

Vinicio Meza (b.1968) has had a significant impact on Costa Rican bassoon music, contributing over sixty chamber works featuring the instrument and a work for bassoon and orchestra. Despite his successful career and professional recognition, only a small number of his compositions have been the subject of academic study, offering a mere glimpse of the composer’s artistry. The present dissertation responds to this gap by utilizing Meza’s bassoon works as a vehicle to delve into his life and artistic production, following a qualitative approach to answer questions about his career and musical style, the historical and compositional particularities of his …


An Expertise-Based Approach To Training Decision-Making And Situational Awareness For Basketball Referees, Scott Warner Boatright May 2026

An Expertise-Based Approach To Training Decision-Making And Situational Awareness For Basketball Referees, Scott Warner Boatright

Dissertations

Expertise, rapid decision-making, and situational awareness are key components of high performance in many areas, including basketball officiating. Traditional methods of providing feedback on performance to basketball referees rely heavily on broadcast video and rule review, which does not adequately target the perceptual-cognitive skills associated with rapid and dynamic decision-making. The current study developed and evaluated a 360-degree video virtual reality (VR) Expertise-Based Training (XBT) program designed to accelerate expertise in intermediate-level basketball referees. Using think-aloud protocol, conducted with an expert basketball referee, expert judgments and rational were elicited and implemented as Expert-Model Feedback within the referee training program. Twelve …


The Use And Efficacy Of Non-Verbal Gestures In Applied Studio Voice Instruction And Vocal Coaching, Mark Eugene Lubas May 2026

The Use And Efficacy Of Non-Verbal Gestures In Applied Studio Voice Instruction And Vocal Coaching, Mark Eugene Lubas

Dissertations

Despite important innovations in the use of technology in vocal instruction, individualized, faceto- face communication remains the predominant delivery modality for applied voice lessons and vocal coaching. Applied voice instructors and vocal coaches consistently identify non-verbal, gestural communication as a significant dimension of these instructional interactions. Existing scholarship has examined the expressive use of gesture in musical performance, the role of gesture in facilitating pitch accuracy acquisition among young singers, and the neurological responses of singers to gestural input. However, systematic investigation of gesture as a pedagogical instrument from the perspective of the instructor remains underdeveloped in the literature. This …


Practices And Strategies Used In Classrooms For Children Who Are Deaf With Autism, Jennifer Anne Hills May 2026

Practices And Strategies Used In Classrooms For Children Who Are Deaf With Autism, Jennifer Anne Hills

Dissertations

Deaf education has a history spanning more than 200 years; however, there remain relatively few evidence-based practices specifically identified for use with children who are deaf or hard-of-hearing (DHH; Cawthon & Carrie, 2021). In contrast, autism as a diagnostic and educational category is a much more recent phenomenon. Just over 80 years ago, Donald Triplett, became the first person diagnosed with autism in the United States (Donovan & Zucker, 2016). The diagnosis and education of autism is a newer phenomenon with strong research underpinnings. Conversely, the field of deaf education has existed for over 200 years, yet few evidence-based practices …


Barriers To Climate Change And Sustainability Action: Nursing Education And Practice, Dawn Marie Smith May 2026

Barriers To Climate Change And Sustainability Action: Nursing Education And Practice, Dawn Marie Smith

Dissertations

Climate change is one of the most pressing public health emergencies of our time and nurses can have a great impact in their current practice and in the education of future nurses (The Alliance of Nurses for Healthy Environments, n.d.; American Nurses Association, 2023; Health Care without Harm, 2025). Deaths due to rising temperatures, vector-borne illness, and food insecurity related to drought and extreme weather are on the rise (WHO, 2024). It has been estimated that globally over 250,000 additional deaths will be attributed to climate related effects between 2030 and 2050 (Watts et al., 2020; WHO, 2023).

A primary …


Vital Environs: Ecologies Of Modernism And The Nature Tradition, Danielle Nasenbeny Jan 2026

Vital Environs: Ecologies Of Modernism And The Nature Tradition, Danielle Nasenbeny

Dissertations

Vital Environs: Ecologies of Modernism and the Nature Tradition is an investigation of late nineteenth and early twentieth century British literature that explores the space between the individual and the external world. The project begins by exploring the “mind-body problem,” which is a topic in philosophy that recognizes the difficulty in understanding how the mind emerges from physical matter. While this topic has been in discussion since at least Descartes, science is still making crucial discoveries that challenge our understanding of this connection. I argue that the environmental crisis we find ourselves in today is a mind-body problem of global …


Investigating Host Factors In Coronavirus Assembly And Egress, Surovi Binte Sharmin Mohona Jan 2026

Investigating Host Factors In Coronavirus Assembly And Egress, Surovi Binte Sharmin Mohona

Dissertations

Coronavirus (CoV) structural proteins congregate at the ER-Golgi intermediate compartments (ERGIC) prior to virus budding into the organelle lumen. Subsequent trafficking and fusion of virus-containing, ERGIC-derived vesicles then release nascent viruses from infected cells. Our findings in this dissertation illuminate mechanisms by which CoV structural proteins coalesce at the virus assembly and budding sites. The cytoplasmic tails of all CoV spike (S) glycoproteins contain variants of a consensus KxKxx coatomer-binding motif. Host coatomer complexes facilitate retrograde trafficking of client cargo proteins via recognition of such motifs. Utilizing reverse genetics methodologies, we introduced variations in the S coatomer motif in a …


Associating Emotional Intelligence, Cultural Intelligence, And Inclusive Leadership: A Correlational Study Of Seventh-Day Adventist Pastors And Church Leaders In Canada, Damson Anim Oppong Jan 2026

Associating Emotional Intelligence, Cultural Intelligence, And Inclusive Leadership: A Correlational Study Of Seventh-Day Adventist Pastors And Church Leaders In Canada, Damson Anim Oppong

Dissertations

Problem

In an increasingly polarized world, church leaders are expected to foster inclusion, belonging, and unity within diverse congregations. Inclusive leadership (IL), supported by emotional intelligence (EQ) and cultural intelligence (CQ), may offer a relational leadership posture well-suited to this challenge. Growing evidence suggests that relational qualities such as EQ and CQ help leaders develop inclusive communities, foster belonging, and bridge differences (Thomas & Inkson, 2017; Wise, 2022). Emotional and cultural intelligence are studied increasingly in organizational settings, but little is known about how they affect inclusive leadership in faith-based institutions, such as among pastors and church leaders in the …


Exploring Lessons In Research: A Survey On Parental Perceptions Of Reading Opportunities, Laura Kettlehut Jan 2026

Exploring Lessons In Research: A Survey On Parental Perceptions Of Reading Opportunities, Laura Kettlehut

Dissertations

Problem

This exploratory study examines how parents’ past reading experiences relate to their perceptions of their children’s current reading opportunities across home and school contexts. Grounded in longstanding literacy research, the study explores how parent‑led, educator‑led, and child‑initiated reading experiences collectively shape children’s literacy development.

Method

Two research questions guided the inquiry: (1) How do parents perceive their own past reading opportunities? and (2) How do they perceive their children’s reading opportunities at home and in school? To address these questions, a 41‑item survey was developed and administered to parents of children enrolled in K–8 schools. The instrument measured two …


A Ministry Manual For Supporting Pastoral Transitions: Addressing The Emotional And Spiritual Needs Of Clergy And Their Families, John Tucker Jan 2026

A Ministry Manual For Supporting Pastoral Transitions: Addressing The Emotional And Spiritual Needs Of Clergy And Their Families, John Tucker

Dissertations

Pastoral transitions represent spiritually significant yet often under-supported moments in the life of clergy, congregations, and ministry networks. While leadership change is frequently framed in theological language emphasizing divine calling and institutional continuity, insufficient attention is given to the emotional, relational, and familial dimensions of these transitions. This Doctor of Ministry project examines the spiritual and emotional impact of pastoral transitions within African American church contexts, with particular attention to clergy wellbeing and systems of care.

This study employed a mixed-methods research design integrating quantitative survey data with qualitative semi-structured interviews. Survey instruments were distributed to pastors affiliated with The …


Comprehending Levels Of Explainability And Ai Recommendations (Clear) Study Series, Virginia Sullivan Jan 2026

Comprehending Levels Of Explainability And Ai Recommendations (Clear) Study Series, Virginia Sullivan

Dissertations

AI systems can offer a great deal to improve decision-making through efficiency and predictive accuracy due to their unique ability to rapidly analyze large amounts of data relevant to the decision. Yet many AI systems remain opaque, limiting users’ ability to evaluate outputs and leading to issues of mistrust or over-reliance. This dissertation investigates how varying levels of AI explainability affect trust, perceived reliability, understanding, and confidence, and identifies perceptual and behavioral indicators of over-reliance behavior in AI-assisted decision making scenarios. This dissertation is organized as a three-study series. The CLEAR survey study uses a mixed design to examine the …


Role Of Mkp-2 In Pancreatic Beta Cell Function & Development Of Diabetes, Nabin Ghimire Jan 2026

Role Of Mkp-2 In Pancreatic Beta Cell Function & Development Of Diabetes, Nabin Ghimire

Dissertations

Diabetes mellitus is a chronic metabolic disease characterized by persistent hyperglycemia. Type 1 diabetes results from autoimmune destruction of β-cells, whereas Type 2 diabetes is associated with obesity and insulin resistance. Type 2 diabetes (T2D) and metabolic-associated fatty liver disease (MAFLD) are closely linked, as individuals with T2D are twice as likely to develop MAFLD. Previous work from our lab demonstrated that overexpression of MKP-2 in obesity promotes hepatic steatosis, diet-induced obesity, reduced insulin sensitivity, and increased body weight. However, the role of MKP-2 in the onset and progression of diabetes remains unclear. The objectives of this study were to …


Human Perceptions Of Social Intelligence In Large Language Models, Derek Koehl Jan 2026

Human Perceptions Of Social Intelligence In Large Language Models, Derek Koehl

Dissertations

This dissertation investigates how users form perceptions of social intelligence and trust when interacting with large language model chatbots. Three experimental studies manipulated chatbot agreeableness, goal orientation, and simulated short-term memory, measuring perceived social intelligence and trust. The primary finding is an asymmetric effect of personality: disagreeable chatbot behavior produced large reductions in perceived social intelligence and trust, whereas agreeable behavior produced negligible gains above a warm baseline, consistent with negativity bias in social cognition. Goal orientation did not independently enhance perceptions but functioned as a contextual moderator. Simulated memory produced medium-to-large increases in perceived social intelligence without reliably increasing …


Quantitative Metabolomics And ¹³C-Enrichment Analysis Of The Effects Of Fat10 Overexpression On Serum And Hepatocytes, Emily C. Hunt Jan 2026

Quantitative Metabolomics And ¹³C-Enrichment Analysis Of The Effects Of Fat10 Overexpression On Serum And Hepatocytes, Emily C. Hunt

Dissertations

Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease, is associated with obesity and type 2 diabetes, and as the prevalence of these conditions increases, the incidence of MASLD is expected to rise. However, the mechanisms that underlie the development of MASLD are complex and incompletely understood. Previous work from our group has indicated that the human leukocyte antigen-F adjacent transcript (Fat10) is overexpressed in the LEW.1WR1 rat model, which develops features of MASLD. The objective of this work was to quantify metabolites associated with MASLD in response to Fat10 overexpression. To achieve this end, we …


Called To Lead: Leadership Journeys And Workplace Experiences Of Women Presidents In Seventh-Day Adventist Institutions, Gary Thurber Jan 2026

Called To Lead: Leadership Journeys And Workplace Experiences Of Women Presidents In Seventh-Day Adventist Institutions, Gary Thurber

Dissertations

Problem

Although women constitute more than half of Seventh-day Adventist Church membership, they remain substantially underrepresented in senior leadership roles across North America. This disparity raises important questions about the historical, theological, organizational, and gender-related factors that shape women’s access to institutional leadership within the denomination. A growing body of scholarship has examined the life experiences of women clergy in the church; however, limited research has explored the experiences of women serving in presidential leadership roles within Seventh-day Adventist institutions.

Purpose

The purpose of this study was to understand and describe the experiences of women serving in presidential leadership roles …


Constructing Effectiveness: Culture, Legitimacy, And Strategic Planning In Zoos And Aquariums, Robin Keith Jan 2026

Constructing Effectiveness: Culture, Legitimacy, And Strategic Planning In Zoos And Aquariums, Robin Keith

Dissertations

Zoos and aquariums are complex organizations operating with multiple mandates—saving species, providing exceptional care to animals, connecting communities with nature, and inspiring environmental action—making “effectiveness” difficult to define. What counts as success depends on who is asked and which goals are foregrounded. This study investigated how stakeholders in Association of Zoos and Aquariums (AZA)–accredited organizations conceptualize and operationalize effectiveness within strategic planning processes. Prior research on nonprofit and mission-driven organizations has shown effectiveness is multidimensional and often defined differently by various stakeholders. However, little has been known about how these definitions are negotiated through the practice of strategic planning, …


Computational Design Of Nanoporous Materials For The Adsorption Of Per- And Polyfluoroalkyl Substances, Daniel D. Mottern Dec 2025

Computational Design Of Nanoporous Materials For The Adsorption Of Per- And Polyfluoroalkyl Substances, Daniel D. Mottern

Dissertations

Per- and polyfluoroalkyl substances (PFAS) are a large family of chemicals that have seen wide usage due to their fluorinated carbon backbone. The presence of strong C-F bonds in the backbone lends PFAS molecules high thermal and chemical stability, as well as strong hydrophobicity and lipophobicity. This combination of properties has led to heavy use of PFAS as surfactants, non-stick coatings, and aqueous foam forming films and flame retardants. However, these properties bring their own consequences. The high chemical and thermal stability of PFAS renders them persistent, with the C-F bonds resisting naturally occurring forms of degradation. Existing forms of …


Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren Dec 2025

Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren

Dissertations

Single-cell and multi-omic technologies have transformed the dissection of cellular heterogeneity and regulatory dynamics in health and disease. However, the high dimensionality, technical variability, and biological complexity of these datasets present significant challenges for integration, annotation, and interpretation. In this dissertation, a suite of computational approaches is introduced to address key problems in single-cell and multi-omic data analysis through model-based innovations and applied statistical frameworks.

First, a constrained deep learning framework for single-cell data integration, label transfer, and clustering is proposed. By incorporating biologically motivated constraints into the training process, robust performance is achieved across simulated and benchmark datasets spanning …