Featured Publications
Get to know some of the latest publications by our faculties.
Analysis of metagenomic data
September 7, 2025
Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth’s diverse ecosystems.
Locus-specific HERV expression associated with hepatocellular carcinoma
September 7, 2025
Human endogenous retroviruses (HERVs) harbor accessory proteins that influence cellular processes and have been linked to a wide variety of diseases, including cancer. This study investigates locus-specific HERV expression and its association with gene dysregulation in hepatocellular carcinoma (HCC), a highly prevalent and deadly form of liver cancer worldwide.
Estimating rare disease prevalence and costs in the USA: a cohort study approach using the Healthcare Cost Institute claims data
September 7, 2025
Estimating rare disease prevalence and costs in the USA: a cohort study approach using the Healthcare Cost Institute claims data
Orienting Ordered Scaffolds: Complexity and Algorithms
September 7, 2025
We address the problem of orientating ordered scaffolds as an optimization problem based on given weighted orientations of scaffolds and their pairs.
Integrated relationship of nasopharyngeal airway host response and microbiome associates with bronchiolitis severity
September 7, 2025
Bronchiolitis is a leading cause of infant hospitalizations but its immunopathology remains poorly understood.
Metabolite, protein, and tissue dysfunction associated with COVID‑19 disease severity
September 7, 2025
Proteins are direct products of the genome and metabolites are functional products of interactions between the host and other factors.
High-sensitivity pattern discovery in large, paired multiomic datasets
September 7, 2025
We present a novel framework which integrates hierarchical hypothesis testing with FDR correction to reveal linear and non-linear relationships among data.
Association of Early Aspirin Use With In-Hospital Mortality in Patients With Moderate COVID-19
September 7, 2025
Prior studies suggest aspirin may be associated with reduced mortality in high-risk patients with COVID-19, but patients with moderate COVID-19 are not studied.
546 Therapeutic beta-lactam dosages and broad-spectrum antibiotics are associated with short-term reductions in microbial richness and beta-diversity
September 7, 2025
People with cystic fibrosis have morbid pulmonary exacerbations. Antibiotics are common, yet the beta-lactam doses administered are less than half the time.
Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions
September 7, 2025
Host evolutionary history is a key factor shaping the earthworm cast microbiome, although its effect can be shadowed by the earthworm’s diet.
Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice
September 7, 2025
To understand the host-tropism phenomena of bovine-tropic mastitis microbiomes, we developed a cow-to-mouse mastitis model.
Differential expression of single-cell RNA-seq data using Tweedie models
September 7, 2025
To model the technological variability in cross-platform scRNA-seq data, here we propose to use Tweedie generalized linear models.