Publications

Click on the articles below. More publications by Dr. Chapkin and the Chapkin Lab Team can be found on PubMed.

• Pesco-vegetarian food components promote colonocyte ferroptosis in preclinical mouse models and a randomized crossover trial in healthy human adults
  December 29, 2025 by Yang-Yi Fan
  CONCLUSIONS: Our findings demonstrate that dietary fish oil and fermentable fiber combination induces ferroptosis exclusively in colonocytes.
• Quantum Generative Modeling of Single-Cell transcriptomes: Capturing Gene-Gene and Cell-Cell Interactions
  November 24, 2025 by Selim Romero
  Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the […]
• BAYESIAN DIFFERENTIAL CAUSAL DIRECTED ACYCLIC GRAPHS FOR OBSERVATIONAL ZERO-INFLATED COUNTS WITH AN APPLICATION TO TWO-SAMPLE SINGLE-CELL DATA
  September 2, 2025 by Junsouk Choi
  Observational zero-inflated count data arise in a wide range of areas such as genomics. One of the common research questions […]
• Quantum Annealing for Enhanced Feature Selection in Single-Cell RNA Sequencing Data Analysis
  August 20, 2025 by Selim Romero
  Feature selection is a machine learning technique for identifying relevant variables in classification and regression models. In single-cell RNA sequencing […]
• Gut microbial community and host intestinal gene expression with combined fish oil and soluble corn fiber compared with corn oil and maltodextrin: A randomized crossover trial in healthy older individuals
  August 3, 2025 by Darya Moosavi
  CONCLUSIONS: Thirty-day supplementation of SCF + FO compared with MD + CO showed significant shifts in intestinal cell pathways relevant […]
• Targeting plasma membrane cholesterol as a novel anticancer therapy
  June 20, 2025 by Alfredo Erazo-Oliveras
  An effective therapeutic strategy to treat oncogenic Wnt signaling in the context of colorectal cancer (CRC) remains elusive. A new […]
• Expression of Prooncogenic Nuclear Receptor 4A (NR4A)-Regulated Genes β1-Integrin and G9a Inhibited by Dual NR4A1/2 Ligands
  May 7, 2025 by Lei Zhang
  Bis-indole-derived compounds including 1,1-bis(3'-indolyl)-1-(3,5-disubstitutedphenyl)methane (DIM-3,5) analogs bind both orphan nuclear receptors 4A1 (NR4A1) and NR4A2, and DIM-3,5 compounds act as […]
• Single-cell transcriptomics reveals that human milk feeding shapes neonatal immune cell interleukin signaling pathways in a nonrandomized clinical trial
  April 28, 2025 by Michael L Salinas
  CONCLUSIONS: These findings suggest that human milk downregulates peripheral immune cell cytokine transcriptional signatures linked to allergic inflammation and infection […]
• A Chalcone Synthase-like Bacterial Protein Catalyzes Heterocyclic C-Ring Cleavage of Naringenin to Alter Bioactivity Against Nuclear Receptors in Colonic Epithelial Cells
  March 26, 2025 by Ebru Ece Gülşan
  Gut microbial metabolism of dietary flavonoids leads to a diverse array of bioactive products that are closely associated with human […]
• Targeting polyunsaturated fatty acids desaturase FADS1 inhibits renal cancer growth via ATF3-mediated ER stress response
  March 23, 2025 by Gioia Heravi
  CONCLUSION: Our findings suggest that PUFA desaturation is crucial for rescuing cancer cells from persistent ER stress, supporting FADS1 as […]
• Exploring cell-to-cell variability and functional insights through differentially variable gene analysis
  March 21, 2025 by Victoria Gatlin
  Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular variability by capturing gene expression profiles of individual cells. The […]
• Perfluorooctane Sulfonate (PFOS) and Related Compounds Induce Nuclear Receptor 4A1 (NR4A1)-Dependent Carcinogenesis
  March 11, 2025 by Amanuel Hailemariam
  Polyfluoroalkyl substances (PFAS) are widely used industrial compounds that have been identified as contaminants in almost every component of the […]
• Diet therapy abates mutant APC and KRas effects by reshaping plasma membrane cholesterol nanodomains
  December 22, 2024 by Eunjoo Kim
  Cholesterol-enriched plasma membrane domains are known to serve as signaling platforms in a diverse array of cellular processes. However, the […]
• Graphical Dirichlet Process for Clustering Non-Exchangeable Grouped Data
  December 18, 2024 by Arhit Chakrabarti
  We consider the problem of clustering grouped data with possibly non-exchangeable groups whose dependencies can be characterized by a known […]
• 1,4-dihydroxy-2-naphthoic acid prevents 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced motor function deficits
  December 11, 2024 by Caitlin A Madison
  Parkinson's disease (PD), characterized by death of dopaminergic neurons in the substantia nigra, is the second most prevalent progressive neurodegenerative […]