Digital Commons Network^™

Injuries In Children Undergoing Subspecialty Abuse Evaluations Because Of Intimate Partner Violence, M Katherine Henry, Gunjan Tiyyagura, Joanne N Wood, Jan Leonard, Kristine A Campbell, Daniel M Lindberg, Angela N Bachim, Farah W Brink, Lori D Frasier, Nancy S Harper, Claire Hickey, Natalie Laub, John D Melville, Hannah Sahud, Philip V Scribano

Faculty, Staff and Students Publications

Background and objectives: Intimate partner violence (IPV) and child physical abuse often co-occur, but the frequency and risk factors for abusive injuries in IPV-exposed children remain unknown. Our objectives were to (1) determine frequency of skeletal surveys (SSs) and neuroimaging use because of IPV and their diagnostic value in children aged less than 24 months evaluated by a child abuse pediatrics specialist (CAP) and (2) identify factors associated with performance of and findings on SS and neuroimaging.

Methods: We conducted a retrospective study of children aged less than 24 months undergoing CAP consultations because of IPV exposure from February 2021 …

Tracheobronchial Mucoepidermoid Carcinoma In Four Pediatric Patients, Kalen Hendra, Muhammad Ijlal Khan, Mitali Thanawala, Manuel Silva-Carmona, Eric D Zee

Faculty, Staff and Students Publications

Pediatric tracheobronchial mucoepidermoid carcinoma (MEC), also called pulmonary MEC, is a rare malignant primary lung neoplasm that is typically found in the large airways. Patients may present with symptoms such as cough, pneumonia, fever, hemoptysis, dyspnea, wheezing, chest pain, weight loss, and fatigue. These nonspecific symptoms (or lack of symptoms in some cases) often result in a delayed diagnosis. Chest CT typically demonstrates findings consistent with bronchial obstruction and diagnosis is made via histopathology. Surgical resection is the mainstay of treatment and children often have favorable outcomes. Here we present four cases of tracheobronchial MEC in children treated at three …

Prevalence Of Substance Use In Northwest Syria: A Cross-Sectional Study, Isabel Draper, Dania Albaba, Heba Mesbah, Huda Taktak, Nidhal Saadoun, Mohammad Alhusein, Elharit Alissa, Anas Barbour, Zaher Sahloul, Nidal Moukaddam

Faculty, Staff and Students Publications

Objectives: Syria has undergone significant socio-political turmoil since 2011 as internal conflict displaced portions of the population, destroyed infrastructure, and destabilized the economy. In the context of multilevel healthcare system disruptions, there have been increasing reports of substance use. This study seeks to evaluate patterns of substance use in Northwestern Syria.

Methods: Trained staff administered questionnaires to community members in Azaz, Syria. Questions focused on the substance use prevalence, societal and public health impacts, and perspectives on treatment availability.

Results: 480 individuals were surveyed (80·88% male, 19·12 % female; 43·39% were 18-25 yrs, 11·5% reported personal substance use). H-booz (amphetamines), …

Chemoradiation After Chemotherapy For Metastatic Cervical Cancer Can Provide Chemo-Free Time, Spoorthi Kamepalli, Ashley Chavana, Michelle Ludwig, Madeline Flanagan, Shelly Sharma, Tracilyn Hall, Anthony Costales, Jan Sunde, Claire Hoppenot

Faculty, Staff and Students Publications

Introduction: Stage IVB cervical cancer is treated with a life-prolonging and palliative intent with systemic chemotherapy and immunotherapy. The purpose of this study was to evaluate the number of these patients who had an adequate response to chemotherapy to be eligible for consolidative radiosensitizing chemotherapy and radiation (chemoradiation) and subsequent outcomes.

Materials and methods: This is a retrospective review of metastatic cervical cancer patients treated with chemotherapy and evaluated for treatment with consolidative pelvic chemoradiation at a single safety-net hospital system from 2016 to 2024. Demographic data and clinical information were collected from electronic medical records. Stata was used for …

Gender-Specific Behavior Reductions In Spontaneous Locomotive And Rearing In A Rat Model Of Paclitaxel-Induced Peripheral Neuropathy: A Pilot Study, Serena Jiyeon Kim, Kevin Cao, Patrick M Dougherty, Kathleen E Mcdonough, Saba Javed

Faculty, Staff and Students Publications

Introduction: Chemotherapy-induced peripheral neuropathy (CIPN) from agents like paclitaxel causes sensory loss and functional impairment, with limited treatment options. To better model patient-relevant outcomes, we used open field video tracking in rodents to assess gait, anxiety, and exploratory behavior. This approach provides a more comprehensive assessment of CIPN-related deficits beyond pain responses.

Methods and materials: Adult male and female Sprague Dawley rats were given paclitaxel (Taxol; 24 mg/kg cumulative dose) or a vehicle over 8 days. Their distance traveled, time spent in the center and outer zones of the OF test, and rearing behaviors were recorded using a PhenoTyper 4500 …

Phase 1 Trial Of Withania Somnifera Leaf Extract (Rh324) In Advanced Non-Small Cell Lung Cancer Including [18f]Fdg Pet/Ct As A Short-Term Metabolic Biomarker To Assess Efficacy: A Novel Model For Assessment Of Complimentary Therapies In Early Phase Human Clinical Trials, Jin Uk Heo, Santosh Rao, Herbert B Newton, Afshin Dowlati, Raymond F Muzic, Arash Kardan

Faculty, Staff and Students Publications

Background: Withania somnifera (WS), commonly known as ashwagandha, has been used in the traditional medical system of India. It has shown significant activity against numerous solid tumor varieties in pre-clinical in vitro and in vivo studies. This study focuses on RH324 (ReHeva Biosciences, Columbus, OH), a pharmaceutical-grade formulation derived from WS, which has received FDA allowance for clinical development as a botanical drug in the treatment of cancer.

Methods: A phase 1 open label dose ranging study of oral RH324 in advanced non-small cell lung cancer (NSCLC) was conducted. The primary endpoint of the study was assessment of short-term safety …

Beyond Drugs And Surgery: Superselective Adrenal Artery Embolization Redefines Primary Aldosteronism Management-A Systematic Review And Meta-Analysis, Kimia Darmiani, Mehrad Zare, Alisa Mohebbi, Mohammad Mirza-Aghazadeh-Attari, Mohammad Ghasemi Rad, Afshin Mohammadi

Faculty, Staff and Students Publications

Background: Primary aldosteronism (PA) is a leading cause of secondary hypertension associated with increased cardiovascular and cerebrovascular risk. Superselective adrenal artery embolization (SAAE) has emerged as a minimally invasive alternative to adrenalectomy and mineralocorticoid receptor antagonists (MRAs). This systematic review and meta-analysis evaluates the efficacy and safety of SAAE in PA management.

Methods: We searched PubMed, Web of Science, Embase, and Cochrane Library through June 2026 for studies enrolling patients with PA treated by SAAE. Outcomes of interest were changes in blood pressure (BP), biochemical markers (serum potassium, aldosterone, renin activity, and aldosterone-to-renin ratio), clinical and biochemical response rates, daily …

The All Of Us Evenings With Genetics Research Program, Stacy M Lloyd, Jasmine Baker, Carolina Jorgez, Julie Coleman, Laterrica Williams, April Adams, Ashley Butler, Elizabeth Atkinson, Shamika Ketkar, Steven Scherer, Kim Worley, Susan Fernbach, Keasia Daniels, Latanya Hammonds-Odie, Laura Rosales, Brendan Lee, Debra Murray

Faculty, Staff and Students Publications

The All of Us Evenings with Genetics (All of Us EwG) Research Program, funded in part by the National Institute of Health’s All of Us Research Program, engages researchers to utilize the All of Us Researcher Workbench to advance precision medicine. The All of Us EwG program has two core aims: (1) address barriers to research productivity for minorities, disadvantaged, and persons with disabilities aspiring to enter STEM fields; and (2) promote the use of the All of Us Researcher Workbench to develop research focused on health equity. To achieve these goals, the program implements three key activities: (1) …

Genome-Wide Association Study Identifies And Validates Genetic Variation In The Rig-I/Mavs Signaling Pathway Associated With Hiv-Related Kaposi Sarcoma In Children And Adults, Casey L Mcatee, Erin Peckham-Gregory, Pagna Sok, Melissa Richard, Luis Olivares, Deborah Marquez-Do, Grace Kisitu, Jeffrey Martin, Nader Kim El-Mallawany, Carl E Allen, Joseph Lubega, Michael E Scheurer

Faculty, Staff and Students Publications

Introduction: Immune deficiency and infection with human herpesvirus-8 (HHV-8) are established component causes of Kaposi sarcoma (KS), but they are insufficient to cause disease in most people at risk. Therefore, we hypothesized that genetic variation may contribute to KS risk in children and adults, as well as contribute to its unique epidemiology in sub-Saharan Africa.

Methods: To test this hypothesis, we conducted a two-phase genome-wide association study (GWAS): a discovery study in perinatally HIV-infected children (45 KS cases, 91 controls), followed by validation of significant results in a sample of adults living with HIV (215 cases, 262 controls). After standard …

Epigenetic Crosstalk In Neuroblastoma Development And Progression, Nathan Drolet, Amber Wolf, Joanna Yi, Eveline Barbieri

Faculty, Staff and Students Publications

Neuroblastoma (NB), a pediatric malignancy of the peripheral nervous system, accounts for 15% of pediatric cancer deaths and remains a major challenge for cancer therapy. NB originates from sympathoadrenal (SA) progenitors of the neural crest (NC) cell lineage, whose formation and differentiation are controlled by epigenetic mechanisms. Although signaling pathways and epigenetic factors implicated in NB tumorigenesis have been well-described, a holistic understanding of how development and epigenetics overlap to drive NB is lacking. By exploring vital interplays and co-dependencies between key pathways and their epigenetic control in NC development, we have gained novel insights into the mechanisms governing NB …

Surface Marker Identification To Capture Live Circulating Tumor Cells In Metastatic Triple-Negative Breast Cancer, Bree M Lege, Khushali J Patel, Brendan Panici, Ping Gong, Michael T Lewis, Matthew J Ellis, Chonghui Cheng

Faculty, Staff and Students Publications

Metastatic triple-negative breast cancer (TNBC) is highly aggressive and lacks targeted therapies. Circulating tumor cells (CTC) are invaluable for monitoring metastatic tumor progression and treatment response but are difficult to capture because of their rarity and heterogeneity. Surface-based staining for live CTCs is essential to preserve RNA quality in single cells, but current markers tend to perform poorly on more mesenchymal tumor cells such as TNBCs. To enhance live TNBC CTC detection, we developed a workflow for live CTC capture and single-cell RNA sequencing (scRNA-seq). Using a mouse model of metastatic TNBC, we identified four new CTC surface markers, AHNAK2, …

Amino Acids And Lean Mass Accretion In Preterm Neonates, Antonio C Ramos Dos Santos, Marta L Fiorotto, Teresa A Davis

Faculty, Staff and Students Publications

Purpose of review: This review evaluates recent evidence on how total protein and energy intake, amino acid composition, and nutrient delivery modality influence protein synthesis in preterm neonates, with the goal of informing nutritional strategies to support optimal lean mass accretion and growth.

Recent findings: Preterm neonates exhibit anabolic resistance to feeding due to impaired insulin and amino acid signaling in skeletal muscle. Enteral nutrition, especially fortified human milk, supports better lean mass accretion and neurodevelopment than parenteral nutrition. Intermittent bolus feeding and pulsatile leucine supplementation during continuous feeding further enhance mTORC1-dependent translation initiation signaling and protein synthesis efficiency in …

School-Level Gaps In Mmr Coverage As The Fuel For Measles Outbreaks, Meagan C Fitzpatrick, Chad R Wells, Abhishek Pandey, Lamia Ayaz, Peter J Hotez, Seyed M Moghadas, Alison P Galvani

Faculty, Staff and Students Publications

No abstract provided.

Priced Out Of Treatment: The Exorbitant Cost Of Antiparasitic Drugs In The United States, Cora Alperin, Nhi Nguyen, Megan Duffey, Eva H Clark

Faculty, Staff and Students Publications

Parasitic infections are often perceived as diseases of low-resource countries, yet they impose a significant and overlooked burden in the United States—especially among immigrants, low-income individuals, and other marginalized populations. This perspectives article examines the case of Mr. X, a landscaper in Houston diagnosed with neurocysticercosis, who faced unaffordable drug costs despite the availability of effective, off-patent treatments. Through his story, we explore the broader issue of pricing for commonly and not-so-commonly prescribed antiparasitic medications, highlighting the role of systemic market failures, regulatory hurdles, and restrictive assistance programs in limiting access to care. The consequences of incomplete treatment include long-term …

Clinical Factors And Diagnoses Associated With Inappropriate Urine Culture Ordering In Primary Care, Marissa Valentine-King, Barbara W Trautner, Michael A Hansen, Roger Zoorob, Lisa C K Danek, Kenneth Muldrew, Forrest Hudson, Robert L Atmar, Larissa Grigoryan

Faculty, Staff and Students Publications

Objective: Evaluate the prevalence and risk factors for inappropriately ordered urine cultures in primary care.

Design: Cross-sectional study using chart reviews.

Setting: Two primary care, safety-net clinics in Houston, Texas.

Patients: Non-pregnant adults without a urinary catheter who had a urine culture and a primary care visit between 11/2018 and 3/2020.

Methods: We classified patients lacking physician documentation of the following symptoms as having an inappropriately ordered urine culture: dysuria, frequency, urgency, hematuria, fever, chills, costovertebral angle tenderness, nephrolithiasis, and pain (suprapubic, pelvic, or flank). We extracted patient demographics, visit-related diagnostic codes, past medical history, and urine culture results. Diagnostic …

Tau In Alzheimer’S Disease: Shaping The Future Patient Journey, Catherine J Mummery, Christopher Chen Li-Hsian, Cristian A Lasagna-Reeves, Rik Ossenkoppele, Christopher C Rowe, Douglas W Scharre, Huali Wang, Simon Kyaga, Jeffrey L Cummings

Faculty, Staff and Students Publications

Alzheimer's disease is a complex and multifactorial disease characterized by two key pathological hallmarks: amyloid-beta plaques and tau neurofibrillary tangles. Recent progress has led to the development and approval of disease-targeted therapies for Alzheimer's disease in the form of anti-amyloid-beta monoclonal antibodies. However, findings suggest that amelioration of multiple pathological drivers may be required to maximize clinical effect. An increasing body of evidence suggests that tau is a critical player in Alzheimer's disease pathophysiology, contributing significantly to neurodegeneration and cognitive decline. There are now several tau-targeting drugs in clinical development. In this review, we build on research and advancements in …

Cerebellar Deep Brain Stimulation Rescues Purkinje Cell Mitochondrial Density In A Genetic Mouse Model Of Cerebellar Ataxia, Lauren N Miterko-Myers, Lauren E Peacoe, Lita Duraine, Zhongyuan Zuo, Roy V Sillitoe

Faculty, Staff and Students Publications

Deep brain stimulation (DBS) improves motor function in a growing list of movement diseases including Parkinson's disease, dystonia, and tremor. There is evidence that DBS may also be effective in ataxia. It is not known why DBS is effective, but modulating cell activity and conferring neuroprotection are hypothesized to underlie its benefits. Understanding the effects of DBS on neurons is paramount to extending its clinical use in the treatment of various motor and non-motor diseases. Here, we stimulated the cerebellum of Car8 waddles (Car8wdl) mice, given the cerebellum's important role in ataxia pathophysiology. Using transmission electron microscopy, we tested the …

Pd-L1-Centric Whole Blood-Based Immune Signature Profiles Of Tuberculosis Patients During Therapy, Johanna Eggeling, Martina Sester, Christoph Lange, Jan Heyckendorf, Barbara Kalsdorf, Anna M Mandalakas, Andrew R Dinardo, David Lewinsohn, Dagmar Schaub, Tina Schmidt, Eva Tolosa, Maja Reimann, Patricia M Sánchez Carballo

Faculty, Staff and Students Publications

This prospective study investigated whole blood-based immune cell biomarkers for pulmonary tuberculosis (TB) immunoprofiling. Blood samples from 34 healthy controls and 51 tuberculosis patients were analyzed at three timepoints: Prior to therapy (T0), after 14 days of therapy (T1), and at the end of treatment (Te). Using multiparameter flow cytometry, 386 immune cell populations were analyzed. Predictive models were developed using two machine learning algorithms. A TB5LF change score, which was based on five cell populations, effectively distinguished tuberculosis patients from controls (AUC = 0.89) and tuberculosis patients before and at the end of treatment (AUC = 0.92). Similarly, the …

A Year In Review On Tuberculosis And Non-Tuberculous Mycobacteria Disease: A 2026 Update For Clinicians And Scientists, Simone Tunesi, Graham Bothamley, Gunar Günther, Yousra Kherabi, Liga Kuksa, Berit Lange, Christoph Lange, Natalie Lorent, Francesca Saluzzo, Martina Sester, Xenia Emilie Sinding Iversen, Marc Tebruegge, Conor Tweed, Anca Vasiliu, Lorenzo Guglielmetti, Tuberculosis Network European Trials Group (Tbnet)

Faculty, Staff and Students Publications

Background: Tuberculosis (TB) remains a major cause of morbidity and mortality worldwide, while infections from non-tuberculous mycobacteria (NTM) represent a growing public health threat. In its 20th year of activity, the Tuberculosis Network European Trials group (TBnet; www.tbnet.eu) is one of the leading research networks in Europe. In this review, we summarize the main advances in TB and NTM that occurred in 2025.

Methods: We conducted a non-systematic review of articles published in 2025, with a strong emphasis on research with current or potential impact on clinical practice. We also selected the most impactful papers regarding the management of adult …

Use Of A Medication Management Algorithm In Depressed Youth Living With Hiv: Secondary Analysis Of A Multisite Randomized Controlled Trial, Graham J Emslie, Beth D Kennard, Kristin Baltrusaitis, Sophia M Jones, Jessica M Jones, Jaime G Deville, Kathleen Pitts, David E Shapiro, Allison Eliscu, Larry K Brown

Faculty, Staff and Students Publications

Objectives: Depression is a prevalent co-occurring condition in youth living with HIV. This report is a secondary analysis of a multisite cluster randomized trial evaluating the efficacy of a health and wellness cognitive behavioral therapy (CBT) combined with a medication management algorithm utilizing measure-based care (COMB-R) compared with enhanced standard of care (ESC). We describe and compare antidepressant prescribing strategies (i.e., antidepressant treatment, type of antidepressant) for youth living with HIV at COMB-R sites to those at ESC sites over the 24-week intervention. We also describe self-reported adherence to antidepressants.

Methods: Participants (12-24 years) were youth living with HIV diagnosed …

Updates In The Management Of Peanut Allergy, S Shahzad Mustafa, Aikaterini Anagnostou, Matthew Greenhawt

Faculty, Staff and Students Publications

Peanut allergy is a significant rising public health problem affecting both children and adults. Early peanut introduction has been adopted in multiple westernized nations as a preventative strategic measure to reduce the risk of developing peanut allergy, although implementation faces barriers. Multiple therapies to treat peanut allergy have been developed, including oral immunotherapy and omalizumab as approved treatments to provide protection against reactions from accidental exposure and reduce the risk of anaphylaxis, offering options beyond strict avoidance. Strategies in the developmental pipeline include epicutaneous immunotherapy and sublingual immunotherapy. The future is bright for individuals with peanut allergy, as these breakthroughs …

Layers To Leaves: A Suite Of Modular 3d Printed Hydroponics Components For Research And Education, Ethan A Shaw, Suraj K Chandramouli, Michael P Dzakovich

Faculty, Staff and Students Publications

Hydroponics is a widely utilized technique to precisely control the plant growing environment and maximize productivity. In some cases, hydroponics systems can be expensive and require specialized expertise to build and maintain. Here, we present a suite of 3D-printed devices that can be constructed into a single or double tower hydroponics system of variable height and composition. This system is easily scalable to fit the needs of a user and can be implemented in a variety of research and educational contexts. Components in this suite can be made from inexpensive plastic filament using household-grade 3D printers. The vertical design of …

Translating Evidence Into Action: Understanding How Community- Based Practitioners Make Intervention Implementation Decisions In Practice, Kristin C. Bennett

Dissertations and Theses (Open Access)

This study examined how community-based practitioners implement public health interventions in practice settings to identify gaps between existing implementation frameworks and real-world practice. Six farmers' markets in Southeast Texas served as cases to understand implementation decision-making by community-based practitioners addressing food access challenges. A qualitative case study approach was employed, using semi-structured interviews with program adopters and key stakeholders to examine how practitioners addressed food access problems, selected interventions, and navigated implementation decisions. This methodology captured the contextual nature of implementation decision-making in community settings. The findings revealed that program adopters recognized health problems through lived experience rather than formal …

Causal Functional Mediation Analysis With An Application To Functional Magnetic Resonance Imaging Data, Yi Zhao, Xi Luo, Michael E Sobel, Martin A Lindquist, Brian S Caffo

Faculty, Staff and Student Publications

A primary goal of task-based functional magnetic resonance imaging (fMRI) studies is to quantify the effective connectivity between brain regions when stimuli are presented. Assessing the dynamics of effective connectivity has attracted increasing attention. Causal mediation analysis serves as a widely implemented tool aiming to delineate the mechanism between task stimuli and brain activations. However, the case, where the treatment, mediator, and outcome are continuous functions, has not been studied. Causal mediation analysis for functional data is considered. Semiparametric functional linear structural equation models are introduced and causal assumptions are discussed. The proposed models allow for the estimation of individual …

Intrathoracic Manifestations Of Hematologic Malignancies: A Narrative Review, Kshama Bhyravabhotla, Gregory Gaskey, Jeremy R Walder, Diwakar D Balachandran, Sujith V Cherian, Bilal Zafar, Lara Bashoura, Ajay Sheshadri, Saadia A Faiz

Faculty, Staff and Student Publications

Background and objective: Although the global incidence of hematologic malignancies is decreasing, the risk of developing these cancers is increasing due to increased lifespan and modern treatments including targeted therapy, chemotherapy, and radiation. Intrathoracic manifestations of hematologic malignancies may be the presenting sign leading to diagnosis or result from various treatment toxicity. The most common respiratory manifestation of hematologic malignancies is infectious, but up to half of pulmonary findings are from non-infectious etiologies. We aim to summarize the current literature on non-infectious intrathoracic manifestations of hematologic malignancies and their treatment.

Methods: We performed a literature review using PubMed Central and …

Netrin-1 Promotes Pancreatic Tumorigenesis And Innervation Through Neo1, Hiroki Kobayashi, Yosuke Ochiai, Junya Arai, Masahiro Hata, Feijing Wu, Masaki Sunagawa, Tadashi Iida, Taisuke Baba, Ermanno Malagola, Takayuki Tanaka, Zhengyu Jiang, Ruth A White, Xiaofei Zhi, Jin Qian, Quin T Waterbury, Ruhong Tu, Biyun Zheng, Yi Zeng, Hualong Zheng, Puran Zhang, Shuang Li, Leah B Zamechek, Jonathan S Labella, Takahiro Sugie, Atsushi Enomoto, Holger K Eltzschig, Carmine F Palermo, Iok In Christine Chio, Kenneth P Olive, Timothy C Wang

Faculty, Staff and Student Publications

Nerves can regulate tumorigenesis and cancer progression. However, clarification of the role of axon guidance molecules in tumorigenesis, innervation, and metastasis is required to better understand the tumor-promoting functions of nerves. Using murine KrasG12D-mutant pancreatic organoids, we screened axon guidance molecules and identified netrin-1 upregulation. Netrin-1 was also upregulated in vivo during pancreatic tumorigenesis in humans and mice. Mutant KRAS and β-adrenergic signaling upregulated netrin-1 and its receptor NEO1 in epithelial cells in part through the MAPK pathway. Ex vivo culture of celiac ganglia showed that netrin-1 promoted the axonogenesis of sympathetic neurons through nerve NEO1. In the Pdx1-Cre;LSL-KrasG12D/+ model, …

Speeding Up Interval Estimation For R2-Based Mediation Effect Of High-Dimensional Mediators Via Cross-Fitting, Zhichao Xu, Chunlin Li, Sunyi Chi, Tianzhong Yang, Peng Wei

Faculty, Staff and Student Publications

Mediation analysis is a useful tool in investigating how molecular phenotypes such as gene expression mediate the effect of exposure on health outcomes. However, commonly used mean-based total mediation effect measures may suffer from cancellation of component-wise mediation effects in opposite directions in the presence of high-dimensional omics mediators. To overcome this limitation, we recently proposed a variance-based R-squared total mediation effect measure that relies on the computationally intensive nonparametric bootstrap for confidence interval estimation. In the work described herein, we formulated a more efficient two-stage, cross-fitted estimation procedure for the R2 measure. To avoid potential bias, we performed …

Nutrition Support Adequacy In Children With Biliary Atresia After Liver Transplant, Nicole Knebusch, Manpreet Virk, Moreshwar S Desai, Marwa Mansour, Stacey Beer, Brittany Pearo, Kelby Fuller, Krupa Mysore, John Goss, Thomas Fogarty, Fernando Stein, Jorge A Coss-Bu

Faculty, Staff and Students Publications

No abstract provided.

An Integrated Platform For Concurrent Structural And Single-Nucleotide Variants Improves Copy-Number Detection And Reveals Pathogenic Alleles In Undiagnosed Mendelian Families, Haowei Du, Ming Yin Lun, Lidiia Gagarina, Jesse D Bengtsson, Christopher M Grochowski, Michele G Mehaffey, James Paul Hwang, Shalini N Jhangiani, Sravya V Bhamidipati, Donna M Muzny, M Cecilia Poli, Sebastian Ochoa, Ivan K Chinn, Anna Lindstrand, Jennifer E Posey, Richard A Gibbs, Pengfei Liu, James R Lupski, Claudia M B Carvalho

Faculty, Staff and Students Publications

Background: Copy number variation (CNV) is a class of genomic structural variation (SV) that contributes to genomic disorders and can significantly impact health. Short-read genome sequencing (sr-GS) enables genome-wide SV calling which has been shown to increase diagnosis in unsolved rare disease families. The growing number of large sequencing cohort projects with sr-GS data available requires open free analytical tools that provide visualization of CNV and SV integrated calls associated with gene annotation, proband-parent trio analysis to enable prioritization of de novo variants, B-allele frequency (BAF) plots to support CNV calls, parent of origin assessment and mosaicism detection.

Methods: To …

Gut Microbiome Metagenomics In Clinical Practice: Bridging The Gap Between Research And Precision Medicine, Henok Ayalew Tegegne, Tor C Savidge

Faculty, Staff and Students Publications

Gut microbiome metagenomics is emerging as a cornerstone of precision medicine, offering exceptional opportunities for improved diagnostics, risk stratification, and therapeutic development. Advances in high-throughput sequencing have uncovered robust microbial signatures linked to infectious, inflammatory, metabolic, and neoplastic diseases. Clinical applications now include pathogen detection, antimicrobial resistance profiling, microbiota-based therapies, and enterotype-guided patient stratification. However, translation into routine care is hindered by significant barriers including methodological variability, limited functional annotation, lack of bioinformatics standardization, and underrepresentation of global populations. This review synthesizes current translational strategies, emphasizing the need for hypothesis-driven designs, multi-omic integration, longitudinal and multi-center cohorts, and mechanistic validation. …