Cenk Celik

This paper shows that E. faecalis uses lactic acid to suppress macrophage activation, enabling persistent and polymicrobial wound infections.

This study identifies E. faecalis extracellular electron transport as a source of ROS that triggers the UPR in epithelial cells, impairing wound healing.

The paper introduces a framework combining graph neural networks and geostatistics to predict and explain cell state variation in spatial transcriptomics data, showing mesenchymal states are stabilized by genetic and environmental factors while hybrid states remain plastic.

EnrichMap improves spatial coherence in gene set enrichment analysis for spatial transcriptomics by integrating batch correction, smoothing, and spatial confounder adjustment.

The paper quantifies G0 arrest and proliferation in breast cancer using single-cell and spatial data, identifying a prolonged G0 state and its spatial organization within an immunosuppressive niche.

This study evaluates single-cell foundation models for modeling cellular plasticity, finding they can improve state resolution but are limited by domain shifts and complexity.

This study develops a zebrafish injury model to study heterotopic ossification, identifies differentially regulated genes, and shows that Kcnk5b and Il11ra influence bone formation after injury.

This study uses scRNA-seq to analyze infected and uninfected wounds in mice, revealing transcriptional and metabolic changes linked to E. faecalis infection and its impact on wound healing.