Reconstructing Gene Regulatory Networks From Time-Series Data In Knime,
2025
Randolph-Macon College
Reconstructing Gene Regulatory Networks From Time-Series Data In Knime, Raina Robeva
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
[Kadel] Robust Basins, Fragile Attractors: A New View On Boolean Network Dynamics,
2025
Illinois State University
[Kadel] Robust Basins, Fragile Attractors: A New View On Boolean Network Dynamics, Claus Kadelka
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
[Kadel] Understanding Aging In Worms Using Boolean Modeling,
2025
Southern Methodist University
[Kadel] Understanding Aging In Worms Using Boolean Modeling, Brandilyn Stigler
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
[Kadel] A Multilevel Extension Of Boolean Networks Captures Topologically-Stable Hybrid Attractors,
2025
Northeastern University
[Kadel] A Multilevel Extension Of Boolean Networks Captures Topologically-Stable Hybrid Attractors, Kishore Hari
Annual Symposium on Biomathematics and Ecology Education and Research
No abstract provided.
The Brain-Derived Neurotrophic Factor (Bdnf) And Its Importance To Organism Survival And Development,
2025
University of Connecticut
The Brain-Derived Neurotrophic Factor (Bdnf) And Its Importance To Organism Survival And Development, Christopher Monnett Smith
Holster Scholar Projects
Brain-Derived Neurotrophic Factor (BDNF) has been the subject of numerous studies regarding the functioning of the brain in relation to topics such as neural plasticity and neural survival. However, BDNF has also been implicated in the induction of changes not only in neural tissue but multiple other tissue types across the human body. The aim of this literature review is to provide a comprehensive, yet brief, overview of BDNF’s influence on the functioning of the nervous, cardiovascular, respiratory, muscular, and immune systems.
The Science Of Sound: Studying The Cognitive, Emotional, And Physiological Effects Of Frequency, Genre, And Music,
2025
Liberty University
The Science Of Sound: Studying The Cognitive, Emotional, And Physiological Effects Of Frequency, Genre, And Music, Jett Yarborough
Senior Honors Theses
Music influences emotion, physiology, and cognition, yet little is known about how the frequency it is tuned to affects these influences. Prior research has shown that music tuned to 432 Hz can reduce stress, lower blood pressure, and improve sleep. My colleagues and I conducted two studies to investigate this. Our research found that music tuned to 432 Hz promotes a significant increase in memory retention and induces a state of focus and relaxation. These results suggest that shifting from the standard tuning frequency of 440 Hz to 432 Hz could have a profoundly positive impact on our daily lives. …
Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions,
2025
Missouri University of Science and Technology
Ibi-Dt: A Novel Approach Combining Individualized Bayesian Inference And Decision Tree For Identifying Cancer Drivers And Their Interactions, Md Asad Rahman, Gregory F. Cooper, Jinying Zhao, Xinghua Lu, Jinling Liu
Engineering Management and Systems Engineering Faculty Research & Creative Works
Cancer is mainly caused by a relatively small portion of somatic genome alterations (SGAs), called cancer drivers. Despite success in identifying a good number of cancer drivers, many more remain to be discovered to explain various cancers. Moreover, limited tools are available to identify potential interactions among cancer drivers for a better understanding of oncogenesis. To tackle these challenges, we have developed a novel approach called individualized Bayesian inference using a decision tree (IBI-DT). IBI-DT recognizes the genetic heterogeneity among cancer patients, where different individuals or patient subgroups of distinct genomic makeup may have different drivers. IBI-DT works by constructing …
Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships,
2025
CUNY Graduate Center
Ai-Powered Multi-Omics Integration For Predictive Modeling Of Genotype-Environment-Phenotype Relationships, You Wu
Dissertations, Theses, and Capstone Projects
This dissertation presents a series of machine learning frameworks for modeling genotype–environment–phenotype relationships through integrative predictive modeling of multi-omics data. The work addresses three major axes of biological complexity: modeling biological information transmission cross-levels from genes to proteins to phenotypes, predicting molecular features cross-scale from cells to tissues to organisms, and translating phenotypes cross-species from model systems to humans. Each proposed method also tackles key machine learning (ML) challenges in the biomedical domain, including data scarcity, domain shift, out-of-distribution (OOD) generalization, and hierarchical modeling. Specifically, this dissertation introduces five novel deep learning algorithms: MultiDCP predicts drug-induced transcriptomic and viability responses …
Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops,
2025
Nova Southeastern University
Enhancing Cataract Surgery Outcomes: Optimal Use Of Pre- And Post-Operative Eye Drops, Keith Skolnick M.D., Anu Valiaveedu
Mako: NSU Undergraduate Student Journal
Many preoperative and postoperative cataract patients struggle with comprehending the use of prescription medication as directed. Language barriers and low health literacy levels are major factors contributing to improper use of prescriptions. To increase patients comprehension, the Fort Lauderdale Eye Institute employed an educational intervention consisting of a live presentation and an instructional video. Results found that 44% of patients were hesitant to ask questions to clinical staff, 32% felt overwhelmed, and nearly 70% lacked confidence in using their prescribed eye drops. Following the intervention, 91% of patients reported increased confidence in their medications, and most indicated that the video …
Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing,
2025
Swarthmore College
Statistical Analysis Of Multi-Endpoint Phenotypic Screening Increases Sensitivity Of Planarian Neurotoxicity Testing, Danielle Ireland, L. J. Word, Eva-Maria S. Collins
Biology Faculty Works
There is an urgent need for high-throughput screening (HTS) models to replace, refine, and/or reduce (“3Rs”) vertebrate toxicity testing. Replacing in vivo animal studies is challenging for neurotoxicity and developmental neurotoxicity (DNT), where the functional relevancy of adverse outcomes needs to be assessed on the whole organism. We previously screened the NTP 87-compound library (NTP87), consisting of known and suspected developmental neurotoxicants, and showed that planarian HTS can identify known (developmental) neurotoxicants. Because analysis methods can impact screening results, and our original analysis used the lowest-observed-effect-level (LOEL) only, we hypothesized that the use of state-of-the-art statistical analysis would increase the …
Variation In Phenotype, Genotype, And Somatic Diversity Among Asexual Schmidtea Mediterranea Planarians,
2025
Swarthmore College
Variation In Phenotype, Genotype, And Somatic Diversity Among Asexual Schmidtea Mediterranea Planarians, S. Kershenbaum, Danielle Ireland, Ziad Sabry , '20, Christina Rabeler, Vir Shetty , '22, A. Aboobaker, Eva-Maria S. Collins
Biology Faculty Works
Most multicellular life reproduces sexually, utilizing a single-celled stage that acts as a genetic bottleneck. This bottleneck limits the evolution of selfish cell adaptations by ensuring all cells descend from a single progenitor. We investigated an obligately asexual strain of Schmidtea mediterranea planarians that reproduces by self-bisection and lacks a single-cell bottleneck. Using 2.5 yearlong data on planarian reproductive behavior combined with genotyping, we revealed two previously undescribed genetically distinct substrains within the CIW4 strain. One substrain showed reduced fitness, which correlated with substantial losses of heterozygosity and increased somatic diversity. By genotyping consecutive head offspring over multiple generations, we …
Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates,
2025
Swarthmore College
Using Published Undergraduate Biomechanics Research On Hydra Mouth Opening To Train Undergraduates, Stephen Hackler, T. Goel, Jonah Pacis , '25, Eva-Maria S. Collins
Biology Faculty Works
Biophysics research is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysics laboratory module that teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer review. The module is accessible to students who are familiar with introductory statistics, cell biology, and differential calculus. We used published research on the biomechanics of Hydra mouth opening as a framework because it describes a stunning biological phenomenon: Hydra, a freshwater …
Computational Frameworks To Unravel The Immune Landscape,
2025
The University of Texas MD Anderson Cancer Center
Computational Frameworks To Unravel The Immune Landscape, Shan He
Dissertations and Theses (Open Access)
Recent advances in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, face challenges such as resistance and immune-related adverse events, partly due to our limited understanding of the immune signaling pathways. While high- throughput genomic data provide unprecedented resolution into these immune pathways, their full potential is limited by the lack of well-annotated, context-specific immune gene sets. To address this need, I developed a workflow to construct immune gene sets by integrating RNA- seq datasets and performing decomposition. Using this approach, I constructed 28 immune- specific gene sets from 83 bulk RNA-seq datasets and 12 Natural Killer (NK) …
Predicting Genetic Interactions Using Functional Interaction Networks,
2025
University of Texas Health Science Center at Houston
Predicting Genetic Interactions Using Functional Interaction Networks, Iulia Veronica Gheorghe
Dissertations and Theses (Open Access)
Mapping genetic interactions is central to understanding cellular systems and identifying therapeutic vulnerabilities, particularly in the context of cancer. Among these interactions, synthetic lethality, where simultaneous loss of two genes is lethal but loss of either alone is tolerated, offers a powerful framework for selectively targeting tumor-specific dependencies. In model organisms like S. cerevisiae, comprehensive double-knockout screens have revealed detailed genetic interaction maps, enabling systems-level insights into pathway structure, gene function, and cellular organization. Replicating this achievement in human cells, however, is complicated by the scale and complexity of the human genome. Recent advances in genome-wide CRISPR knockout screening have …
Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park,
2025
University of Nebraska-Lincoln
Catching A Fever: A Comparison Of Vachellia Xanthophloea Populations In The Limpopo And Luvuvhu River Floodplains Of The Makuleke Contractual Park, Kianie B. David
School of Natural Resources: Dissertations, Theses, and Student Research
This study investigates patterns of stand structure regeneration, growth characteristics, and coarse woody debris (CWD) patterns in Vachellia xanthophloea (fever tree) stands within the Makuleke Contractual Park (MCP), a semi-arid savanna system in northern Kruger National Park (KNP), South Africa. Fieldwork was conducted across two stand types: a monospecific fever tree stand in Rietbok Vlei and a mixed-species stand in the Western Nhlangaluwe Floodplain where fever tree is established with Faidherbia albida (ana tree). Data were collected from 20 total 1/4-acre (1,011 m2) circular plots between both stands in 2024 and 2025, including seedling root collar diameter (RCD), …
The Mayfly Newsletter,
2025
The Permanent Committee of the International Conferences on Ephemeroptera
The Mayfly Newsletter, Donna Giberson
The Mayfly Newsletter
The Mayfly Newsletter is the official newsletter of the Permanent Committee of the International Conferences on Ephemeroptera.
Network Analysis Of Antimicrobial Resistance In Staphylococcus Aureus: Characterization Of Hub Genes And Their Functional Implications,
2025
Texas A & M University - San Antonio
Network Analysis Of Antimicrobial Resistance In Staphylococcus Aureus: Characterization Of Hub Genes And Their Functional Implications, Md Imran Hasan, Davida Smyth, Jeong Yang, Ashley Teufel
Masters Theses (Archived)
Antimicrobial resistance is a major cause of morbidity and mortality in patients with S. aureus infections. In this study, we analyzed genes, molecular mechanisms, and pathways driving drug resistance in S. aureus using network analysis. Using whole-genome sequencing (WGS) data and systems biology approaches, we identified 229 AMR-associated genes and constructed a protein-protein interaction network among these genes. Through network topology and functional enrichment analyses, we not only confirmed their association with resistance, but also highlighted the central roles of these genes in resistance pathways, such as efflux, target replacement, and target protection, which are directly linked to multiple drug …
Identifying Novel Molecular Targets To Induce Ferroptosis In Drug-Tolerant Cancer Cells Through Computational Modeling,
2025
University of Arkansas, Fayetteville
Identifying Novel Molecular Targets To Induce Ferroptosis In Drug-Tolerant Cancer Cells Through Computational Modeling, Haris J. Rana
Biological Sciences Undergraduate Honors Theses
Ferroptosis is an iron-dependent, reactive oxygen species (ROS)-driven form of regulated cell death in which the cell membrane is degraded by lipid peroxidation. It is regulated by multiple enzymes, such as glutathione peroxidase 4 (GPX4), which prevents membrane degradation by reducing lipid peroxides and protecting cells from oxidative damage. When inhibitors like RSL3 target GPX4, lipid peroxides build up, and toxic ROS compromises membrane integrity. Traditional anticancer treatments, such as most chemotherapies, aim to eliminate tumor cells by damaging DNA and triggering apoptosis. However, resistance to apoptosis is a “hallmark of cancer,” often resulting in treatment failure. As a distinct …
A Genetic And Spatial Analysis Of The Last Megafaunal Species (Tapirus Terrestris) In The Paraguayan Dry Chaco Forest,
2025
University of New Orleans, New Orleans
A Genetic And Spatial Analysis Of The Last Megafaunal Species (Tapirus Terrestris) In The Paraguayan Dry Chaco Forest, Emily Bowers
LSU New Orleans Theses and Dissertations
No abstract provided.
Patterns Of Fire History And Vegetation Changes In The Last 5000 Years: A Paleoecological Study Of Iquitos,
2025
Florida Institute of Technology
Patterns Of Fire History And Vegetation Changes In The Last 5000 Years: A Paleoecological Study Of Iquitos, Annabel Zwarts
Theses and Dissertations
The vegetation of the Amazonian rainforest is hypothesized to have been shaped by pre-Columbian activities, such as burning and palm management to various extents. Management of palms is hypothesized to have caused some of the most useful species to become hyperdominant in Amazonia. This study investigated the extent to which human activities over the past 5000 years affected palm abundances in mature lowland rainforests near Iquitos, Peru. I used phytoliths and charcoal from soil cores to determine the history of local floras, and modern palm surveys to compare modern phytolith occurrence with modern vegetation. Because pre-Columbian activity clustered along the …
