Kellie Nicole Smith

replicateFest uses negative binomial models for replicated and Fisher's exact tests for unreplicated FEST TCR-seq to call antigen-expanded clonotypes, recovering all nine published HIV-1 responders.

This study shows that tissue injury accelerates tumor growth and reduces response to immunotherapy in mice, but biomaterials that enhance wound healing can improve outcomes and ICB response.

This study shows immune checkpoint inhibitors enhance type 2 immunity and regeneration in ECM-treated wounds by promoting Treg/TH2 plasticity and pro-regenerative macrophages.

The paper identifies riboflavin-auxotrophic Enterococcus spp. that synergize with metabolites to boost MR1 expression and activate MAIT cells in the tumor microenvironment.

This study examines how dual checkpoint blockade with Anti-PD-1 and Anti-LAG-3 affects T cell clones in glioblastoma, showing increased clonal expansion and differentiation into effector T cells.

The paper develops a spatial biomarker, DONUTS, to predict treatment response in lung cancer by analyzing the niche surrounding CD8+FoxP3+ T-cells.

This study analyzes the TCR repertoire in UC patients over time, finding most do not share persistent clones, while a subset has persistent clones linked to more active disease.

The paper introduces BigMHC, a deep learning model that predicts MHC-I epitopes and immunogenic neoepitopes with high accuracy, outperforming existing methods.