Life Sciences Commons^™

Evaluating The Effectiveness Of The Genetic Cancer Prevention Clinic As A Tool For Managing Patients At Elevated Risk For Cancer, Sydney Marlene Price

Theses and Dissertations

People with an inherited cancer predisposition but have not been affected with cancer or tumors themselves are known as previvors. A previous study suggested the need for the establishment of a specialized management clinic for previvors in the Midlands of South Carolina. In 2022, the Genetic Cancer Prevention Clinic (GCPC) was established to serve this patient population. This study examined effectiveness of the GCPC in helping previvors manage their psychological and medical needs. A mixed methods design consisting of a chart review of patients enrolled in the GCPC (N=34) and a semi-structured phone interview (n=3) was …

Bias Effects Of Priming Towards Huntington’S Disease Among Second- Year Medical, Physician Assistant, And Genetic Counseling Students, Cameron Lynn Galley

Theses and Dissertations

Individuals with Huntington’s Disease (HD) have experienced bias in their interactions with the public and with health professionals. This study explored perceptions of HD and potential bias among students in interdisciplinary health professions. We hypothesized that the presence of symptoms in vignettes would reflect increased implicit bias, participants with exposure to HD would show less bias than those without, and genetic counseling students would exhibit lower bias towards HD than medical and physician assistant students.

Attitudes towards those with HD were assessed through one of four vignettes about a fictional character in which a presymptomatic diagnosis was present or absent, …

Parent & Provider Perspectives On Rehabilitative Therapies For Children With Mucopolysaccharidosis Type Iii, Laura Denise Ciccarelli

Theses and Dissertations

Mucopolysaccharidosis type III (MPS III) is a neurodegenerative lysosomal storage disorder characterized by autistic behaviors and skill regression. Although there is currently no cure for MPS III, various therapeutic approaches are recommended to manage the associated clinical manifestations. The aim of this exploratory study was to assess the perspectives of parents and providers on rehabilitative therapy for their children or patients with MPS III. Furthermore, it evaluated the potential benefit of an MPS III therapy resource developed by genetic counselors. Interview and survey responses were collected between September 2025 and January 2026. Eligible providers included certified speech, physical, occupational, and …

Evaluating Genetic Counseling Perspectives Around The Use Of Chat-Ai As A Standardized Patient, Mary Claire Sherman

Theses and Dissertations

Roleplays and standardized patients (SPs) are widely utilized and valued training tools in medical education. Artificial intelligence (AI) has emerged as a novel component of medical education, though its applications in genetic counseling remain underexplored. This study examined perceptions of genetic counseling students, recent graduates, and educators on chatbot artificial intelligence (chat-AI) as a SP in roleplay exercises. Eligible participants completed a survey requiring a roleplay interaction with ChatGPT. Standardized prompts included roleplay instructions and a framework based on the American Board of Genetic Counseling Practice-Based Competencies (PBCs) and the Reciprocal Engagement Model (REM) for chat-AI to provide feedback on …

Patient-Centered Insights Into The Triage And Diagnostic Experience Of Hypermobile Ehlers-Danlos Syndrome In Clinical Genetics Services., Rylan Makenzie Sweitzer

Theses and Dissertations

Hypermobile Ehlers-Danlos syndrome (hEDS) is the only form of Ehlers-Danlos syndrome (EDS) without a known genetic etiology. One of the criteria for diagnosing hEDS is the exclusion of other possible causes. This often leads to referrals for a clinical diagnosis with a medical geneticist or genetic testing for other forms of EDS. This study aimed to investigate the education that individuals diagnosed with or suspected to have hEDS are receiving and what genetic providers include in their appointments with these patients. This study included two original online surveys. The first was sent to patients through providers at Indiana University and …

Understanding P53 Regulation On Transposable Elements In Cancer, Xuan Qu

Arts & Sciences Graduate Student Theses and Dissertations

Transposable elements (TEs), traditionally known as “jumping genes”, are known to have the ability to move in the genome and alter the activation of transcriptions from nearby genes. Taking up nearly half of the human genome, TEs have evolved, and some have been selected to play important roles in biological processes. We found that in human diseases such as cancer, global hypomethylation resurrects many ordinarily silenced TEs. These TEs can often serve as alternative promoters for oncogenes and play functionally meaningful roles in driving disease processes. One of the top genetic mutation status that correlates with differential numbers of TE …

Dissecting The Etiology Of Alcohol Use Disorder By An Integrative Heritable Component Approach, Ivy Garrenton

Computer Science Theses & Dissertations

Alcohol Use Disorder (AUD) is a pervasive condition characterized by complex interplay among genetic, phenotypic, and environmental factors. Although previous studies have identi fied genetic loci associated with alcohol consumption, these efforts have not captured the genetic heterogeneity and gene-environment interactions underlying AUD pathogenesis. To address this critical gap, we developed a novel statistical methodology that integrates phenotypic, genotypic, and environmental data through an environmentally modified Genetic Relationship Matrix (GRM) to derive AUD-related traits with enhanced heritability.

This approach demonstrated superior performance in both simulated and real-world datasets. Traits derived using the environmentally modified GRM exhibited significantly higher estimated heritability …

A Randomized Study Of Digital Versus Genetic Counselor Return Of Actionable Genetic Research Results To Biobank Participants (Respect3 Study), Anuja Rajendra Godbole, Elisabeth Wood, Brian Egleston, Lily Hoffman-Andrews, Sarah Brown, Sarah Howe, Sanjana Shastri, Rajia Mim, Justin Feng, Anjali Owens, Susan Domchek, Reed Pyeritz, Bryson Katona, Staci Kallish, Giorgio Sirugo, Joellen Weaver, Linda Fleisher, Kuang-Yi Wen, Elena Elkin, Katherine Nathanson, Daniel Rader, Angela Bradbury

Department of Medical Oncology Faculty Papers

BACKGROUND: There is consensus that research participants should be informed about plans for return of genetic research results. However, best practices for return of results in large biobank and cohort studies do not exist currently, and how best to communicate actionable genetic research results remains unclear. While having genetic counselors disclose these results may be ideal to ensure understanding, minimize distress, and optimize medical follow-up, genetic counselor (GC) workforce shortages and costs are barriers. The RESPECT3 study evaluates whether digital delivery alternatives for pre-disclosure education and return of actionable genetic research results is non-inferior to remote telehealth disclosure by a …

Phenol–Chloroform Dna Extraction For Dna Amplification From Personal Items, Aditya Rahman Ernanto, Dinda Amaliyatul Khasanah, Yunita Aldirahayu, Rizki Setiyaningrum, Arya Iswara

Makara Journal of Science

This study examined the feasibility of extracting DNA from various personal items using the phenol–chloroform–isoamyl alcohol (PCIA) method. A towel, collared shirt, toothbrush, shower puff, comb, hair tie, and buccal swabs were analyzed. The quality of the DNA extraction, along with DNA concentration, purity, and suitability for multiplex PCR amplification, were evaluated. The shower puff exhibited the highest DNA concentration (68.35 ng/µL), whereas the collared shirt yielded the lowest (26.43 ng/µL). All samples exhibited good DNA purity (A260 nm/A280 nm ranging from 1.827 to 1.985), emphasizing the potential of this method for forensic analysis. Factors influencing DNA concentration included material …

Auditory Stimulation Rescues Cognitive Deficit In Fmr1-Ko Mice, Mohamed Ouardouz, Amanda E. Hernan, J. Matthew Mahoney, Rodney C. Scott

Department of Medicine Faculty Papers

Background/Objectives: Fragile X Syndrome (FXS) is a neurodevelopmental disorder caused by a triplet repeat expansion in the Fmr1 gene leading to the loss of Fragile X Messenger Ribonucleoprotein (Fmr1 protein). The loss of Fmr1 protein modulates many cell biological processes and leads to the emergence of intellectual disability and autism. FXS is modeled in Fmr1-KO mice that display features consistent with human FXS, including hypersensitivity, cognitive and learning deficits, hyperactivity and audiogenic seizures. Here, we investigated the effect of auditory stimulation during a range of developmental stages on recognition memory and sociability deficits in Fmr1-KO mice. Methods: Fmr1-KO mice were …

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) …

Multiplex Functional Assessment Of Variant Effect In The Retinal Transcription Factor Crx, James Lewis Shepherdson

Arts & Sciences Graduate Student Theses and Dissertations

The transcription factor Cone-Rod Homeobox (CRX) is a master regulator of photoreceptor cell fate. Sequence variants in CRX can cause Retinitis Pigmentosa, Cone-Rod Dystrophy, and Leber Congenital Amaurosis, all inherited causes of vision loss and blindness. CRX is the only gene implicated in the pathogenesis of all three of these diseases, which present with both rod- and cone-centric phenotypes of varying age of onset and severity. Several CRX variants have been reported to cause severe dominant disease through antimorphic genetic interactions with wild-type CRX, and yet these mutations are adjacent to variants which are benign or only cause mild, recessive …

Reproductive Performance And Its Association With Esr, Prlr, Fshb Genes In Indigenous “I” Pigs, Do Duc Luc, Phan Thi Tuoi, Nguyen Thai Anh, Do Thi Hue, Nguyen Hoang Thinh

The Thai Journal of Veterinary Medicine

Improving the reproductive performance of sows plays an important role in the pig industry, and it applies not only to commercial pigs but also to indigenous pigs. In this study, the polymorphisms of three genes, namely estrogen receptor (ESR), prolactin receptor (PRLR), and follicle-stimulating hormone beta subunit (FSHB) in the “I” pig population were investigated, and their associations with reproductive performance were evaluated. Ear tissue samples were collected from 151 fattening pigs and 126 sows across breeding farms in Vietnam for polymorphisms of the ESR, PRLR and FSHB genes. Three genotypes (AA, AB, and BB) were detected at the …

From Fair To Cure: Guidelines For Computational Models Of Biological Systems, Herbert M. Sauro, Eran Agmon, Michael L. Blinov, John H. Gennari, Joseph L. Hellerstein, Adel Heydarabadipour, Bartholomew E. Jardine, Elebeoba May, David P. Nickerson, Lucian P. Smith, Gary D. Bader, Frank T. Bergmann, Patrick M. Boyle, Andreas Dräger, James R. Faeder, Song Feng, Juliana Freire, Fabian Fröhlich, James A. Glazier, Thomas E. Gorochowski, Tomas Helikar, Henning Hermjakob, Stefan Hoops, Peter Hunter, Princess I. Imoukhuede, Sarah M. Keating, Matthias König, Reinhard Laubenbacher, Leslie M. Loew, Carlos F. Lopez, William W. Lytton, Rahuman S. Malik-Sheriff, Andrew Mcculloch, Pedro Mendes, Lealem Mulugeta, Chris J. Myers, Jerry G. Myers, Anna Niarakis, David D. Van Niekerk, Brett G. Olivier, Alexander A. Patrie, Ellen M. Quardokus, Nicole Radde, Johann M. Rohwer, Sven Sahle, James C. Schaff, Falk Schreiber, T. J. Sego, Janis Shin, Jacky L. Snoep, Rajanikanth Vadigepalli, H. Steven Wiley, Dagmar Waltemath, Ion I. Moraru

Computational Medicine Center Faculty Papers

Guidelines for managing scientific data have been established under the FAIR principles, requiring that data be Findable, Accessible, Interoperable, and Reusable. In many scientific disciplines, especially computational biology, both data and models are key to progress. For this reason, and recognizing that such models are a very special type of "data", we argue that computational models, especially mechanistic models prevalent in medicine, physiology and systems biology, deserve a complementary set of guidelines. We propose the CURE principles, emphasizing that models should be Credible, Understandable, Reproducible, and Extensible. We delve into each principle, discussing verification, validation, and uncertainty quantification for model …

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.

Genetic Variants And Molecular Components Associated With Metabolic Dysfunctional-Associated Steatotic Liver Disease And Depression: Shared Association Of Adamts7 And Thrap3, Eron G. Manusov, Vincent P. Diego, Marcio A. Almeida, Jacob A. Galan, Kathryn Herklotz, Edwardo Abrego Ii, Habiba Sultana, Luis A. Peña Marquez, Marco Arriaga, Marcelo Leandro, Juan M. Peralta, Ana C. Leandro, Tom Howard, Joanne Curran, Sandra Laston, John Blangero, Sarah Williams-Blangero

Human Genetics Publications

Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) and depression frequently occur together. Identifying the genes that influence both MASLD and depression may facilitate the discovery of biological pathways associated with disease risk.

Methods: We recruited 525 participants from Mexican American families living in the Rio Grande Valley of south Texas. We collected clinical data, biometric measurements, hepatic health assessments using Vibration-Controlled Transient Elastography (VCTE), and depression evaluations determined with the Beck Depression Inventory-II. We estimated the heritability (h2) of MASLD-related measures, depression status, aspartate aminotransferase (AST), alanine aminotransferase (ALT), the AST/ALT ratio, and Vibration-Controlled Transient Elastography measurements. For each gene, …

Structural Brain Analysis In Focal Upper Limb Dystonia, Danilo Donizete De Faria, Artur José Marques Paulo, Joselisa Péres Queiroz De Paiva, Anderson M. Winkler, Vanderci Borges, Sonia Maria Azevedo Silva, Henrique Ballalai Ferraz, Patricia De Carvalho Aguiar

Human Genetics Publications

Prior structural magnetic resonance imaging (MRI) studies that investigated structural alterations in focal dystonia have reported inconsistent findings, potentially due to methodological limitations or sample heterogeneity. This work investigates gray and white matter changes in patients with upper limb dystonia using T1-weighted images and diffusion tensor imaging (DTI). Imaging data collected with MRI at 3T from 28 right-handed individuals with right upper limb dystonia and 29 healthy controls were analyzed. T1-weighted images were analyzed using FreeSurfer to examine cortical thickness, volume and area. DTI data were assessed using tract-based spatial statistics, regions of interest (ROI) analysis and probabilistic tractography. ROI …

Genetic Testing Motivations Among Men With A History Of Prostate Cancer: A Judgment-Based Analysis, Maximilian Junge

USF Tampa Graduate Theses and Dissertations

Identifying individuals at increased hereditary cancer risk through genetic testing can improve early detection, inform treatment decisions, and enhance outcomes for patients and their families. While prior research has largely focused on women, less is known about factors that motivate men with prostate cancer to pursue genetic testing. This study examined components of visual messaging that may influence motivation to undergo genetic testing among men with a self-reported history of prostate cancer. Participants completed a survey in which they viewed eight visual messages that systematically varied across three components: image type (family-focused vs. individualized treatment-focused), written content (familial risk-focused vs. …

Assessing Capability, Opportunity, And Motivation In Relation To Guideline Adherence For Inherited Cancer Risk, Cecilia L. Delisanti

USF Tampa Graduate Theses and Dissertations

Introduction: Although National Comprehensive Cancer Network (NCCN) guidelines provide cancer screening or risk reduction recommendations for individuals with germline pathogenic and likely pathogenic variants (GPVs) in actionable hereditary cancer genes, guideline adherence remains inconsistent, and the behavioral contributors to this gap remain understudied. To identify behavioral factors related to adherence across inherited cancer risk genes, this study used the COM-B model, which posits that capability, opportunity, and motivation shape health behaviors.

Methods: IMPACT study participants, all with GPVs in a variety of actionable genes, completed surveys (N=575). Minimal adherence was based on gene-specific NCCN guidelines. COM-B constructs (capability, opportunity, motivation) …

Epigenetic Activation Of Ebv Bglf4 Determines Antiviral-Based Regimen Response In Ebv+Cns Lymphoproliferative Disease, Christoph Weigel, Haley Klimaszewski, Fode Tounkara, Selamawit Addissie, Sarah Schlotter, Betsy Pray, James Dugan, Bradley Haverkos, Lynda Villagomez, Mark Lustberg, Pierluigi Porcu, Timothy Voorhees, Richard Ambinder, Shannon Kenney, Joyce Fingeroth, Henri-Jacques Delecluse, Michael Caligiuri, Lapo Alinari, Ginny Bumgardner, Christopher Oakes, Robert Baiocchi

Kimmel Cancer Center Faculty Papers

Epstein-Barr virus (EBV)–associated primary central nervous system lymphoproliferative diseases (EBV+PCNSL) are aggressive conditions with poor prognoses. We previously reported durable responses in patients with PCNSL who were treated with the antivirals ganciclovir and azidothymidine, plus rituximab and dexamethasone (GARD). Responses were associated with the detection of the lytic viral protein kinases, BGLF4 and BXLF1. These antiviral activating kinases are associated with lytic EBV, however, the mechanism for expression in latently infected EBV+CNSL is unknown. Expanding on previous work, we provide long-term clinical outcome data (N = 24) and show that RNA expression analysis in CNSL tissue biopsies (n = 12) …

The Role Of The Virb Ligand Ctp In The Molecular Mechanism Of Transcriptional Anti-Silencing In Shigella Flexneri, Taylor M. Gerson, Monika M A Karney, Helen Wing

Life Sciences Faculty Research

In bacteria, nucleoid-structuring proteins bind and constrain DNA, often leading to transcriptional silencing. In Shigella spp., the histone-like nucleoid-structuring protein H-NS silences many genes on the large virulence plasmid. Upon a shift to human body temperature, VirB, a DNA-binding protein and key transcriptional regulator of the Shigella virulence cascade, is produced. VirB counteracts H-NS-mediated transcriptional silencing and belongs to a fast-evolving clade of the ParB superfamily. Like other ParB proteins, VirB binds the ligand CTP. While CTP is essential for the anti-silencing activity of VirB, the role of CTP in the mechanism of VirB-dependent anti-silencing has yet to be …

Could Gene Editing Increase Chicken Resistance To Avian Influenza?, Alta Crane

Research on Capitol Hill

Avian Influenza is a viral infection that causes outbreaks of "bird flu," greatly affecting avian health. Influenza A virus (IAV) relies on various host factors for efficient replication. Previous studies in human cells have identified four genes as critical host factors required for IAV infection. To investigate whether similar host– virus interactions exist in avian species, we utilized gene editing systems to generate knockout fibroblast cell lines targeting those four genes and then applied these techniques to germ cells.

Limitations Of Genetic Testing, Tony N. Jelsma

Faculty Work Comprehensive List

"Knowing about a pathogenic variant may sharpen our awareness of our mortality, but it should not fundamentally change our perspective on life."

Posting about the advantages and disadvantages of genetic screening from In All Things, an online hub that offers insight into maintaining and faithful and orthodox Reformed Christian worldview while fearlessly engaging in every aspect of contemporary life – until all is made new.

Limitations of Genetic Testing

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 …

Nanoencapsulation Of Tomentosin-Rich Pulicaria Crispa Fraction In Mil-53(Fe) Improves The Release Profile And In Vitro Anti-Colorectal Cancer Activity, Hamies Baher

Dentistry

No abstract provided.

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 …

Mutations Altering The Dna Binding Domains Of The Human Rad52 Protein Exert Distinct Effects On Homologous Recombination Repair In Saccharomyces Cerevisiae, Glenn M. Manthey, Elise W. Wolf, Jason Xu, M. Cristina Negritto, Renee A. Bouley, Ruben C. Petreaca, Adam M. Bailis

College of Health Professions Faculty Papers

RAD52 is a conserved member of the homologous recombination repair (HRR) apparatus from yeast to humans. Mutating conserved amino acids in the internal and external DNA binding domains of the human RAD52 protein (HsRAD52) has discrete effects in vitro. Previous studies have shown that HsRAD52 supports multiple mechanisms of HRR in budding yeast, suggesting the utility of this model system for exploring the correspondence between losses of HsRAD52 function in vitro and their impact in vivo. We report that disrupting the internal and external DNA binding domains of HsRAD52 produced distinct effects on the repair of genomic DNA double-strand breaks …

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 …

How To Measure, Analyze, And Interpret Age-Related Changes In Caenorhabditis Elegans: Lessons For Mechanistic And Evolutionary Theories Of Aging, Zuzana Kocsisova, Brian M. Egan, Andrea Scharf, Xavier Anderson, Franziska Pohl, Aaron Anderson, Kerry Kornfeld

Biological Sciences Faculty Research & Creative Works

Aging is characterized by progressive degenerative changes in tissue organization and function, some of which increase the probability of mortality. Major goals of aging research are to elucidate the series of events that cause degenerative changes, and to identify environmental, pharmacological, and genetic factors that influence these changes; this information might lead to new strategies to extend health span and lifespan. Mechanistic studies of aging depend on accurate and precise descriptions of age-related changes, since these descriptions define the aging phenotype. Here, we review studies that describe age-related changes in C. elegans, including measurements of integrated functions such as behavior …

Cellstaar: Incorporating Single-Cell-Sequencing-Based Functional Data To Boost Power In Rare Variant Association Testing Of Noncoding Regions, Eric Van Buren, Yi Zhang, Xihao Li, Margaret Sunitha Selvaraj, Zilin Li, Nicholette D. Palmer, Donna K. Arnett, John Blangero, Eric Boerwinkle, Joanne E. Curran, Ravi Duggirala

School of Medicine Publications

Understanding how rare genetic variants influence complex traits remains a major challenge, particularly when these variants lie in noncoding regions of the genome. The effects of variants within candidate cis-regulatory elements (cCREs) often depend on the cell type, making interpretation difficult. Here we introduce cellSTAAR, which integrates whole-genome sequencing data with single-cell assay for transposase-accessible chromatin using sequencing data to capture variability in chromatin accessibility across cell types via the construction of cell-type-specific functional annotations and regulatory elements. To reflect the uncertainty in cCRE–gene linking, cellSTAAR uses a comprehensive strategy to link cCREs to their target genes. We applied …